Biology subjects

Li, Y.

Publications and source records attributed to Li, Y..

At least 163 records · Page 9Linked to original sources

bioRxiv2026

Defining the genetic landscape of acid and oxidative stress tolerance in Streptococcus mutans by pooled CRISPR interference screening

Bacterial stress tolerance is a fundamental ecological adaptation that enables survival, competitive fitness, and persistent colonization under fluctuating environmental conditions. Dental caries remains a major global health burden. As an etiologic agent in caries, Streptococcus mutans (S. mutans) has the ability to adapt to sudden and substantial acid and oxidative stress. Nevertheless, the genome-wide genetic programs that support these stress tolerances remain incompletely defined. Herein, we established a xylose-inducible, genome-wide pooled CRISPR interference (CRISPRi) platform in S. mutans and performed parallel functional screens under acidic conditions (pH 5.0) and low-dose hydrogen peroxide (H{square}O{square}) stress. Using predefined screening thresholds, we identified 422 genes whose repression reduced fitness during acid challenge and 337 genes whose repression reduced fitness during H{square}O{square} exposure. Functional and network analyses revealed that stress tolerance is strongly constrained by core physiological processes, including RNA (particularly transfer RNA) metabolism, macromolecule maintenance, and damage repair. Comparative analyses further indicated that growth-associated pathways displayed opposite trends between the two stresses, consistent with a stress-dependent allocation trade-off. These two complementary findings redefine the dual-stress adaptation paradigm of S. mutans: stress resistance is not determined merely by canonical stress signaling, but requires intact core physiological modules, and bacteria tune resource allocation dynamically to adapt to divergent stress microenvironments. Collectively, the present study provides a comparative, genome-scale functional map of acid- and oxidative-stress tolerance in a key oral pathogen and identifies genetic determinants for mechanistic studies and anti-caries interventions.

microbiology↗

bioRxiv2026

The S1B-Targeting PEDV Neutralizing Antibody C62 Prematurely Activates S-trimer and Mimics Receptor Function

Porcine epidemic diarrhea virus (PEDV) causes devastating enteric disease in piglets, yet the mechanistic basis of antibody-mediated neutralization remains poorly understood. Here, we determined the structure of PEDV HNXX-strain spike domain B (S1B) simultaneously bound by C62, a neutralizing porcine monoclonal antibody against PEDV G2 strains, and N34, a non-neutralizing porcine PEDV antibody. The structure reveals that C62 targets a conserved, cryptic epitope that is accessible only when S1B adopts an "up" conformation. Functionally, we showed that C62 has substantially stronger activity than N34 in triggering S-trimer disassembly and inducing the formation of proteinase K-resistant, post-fusion-like S2 structures. Despite the weaker triggering activity of N34, both C62 and N34 can function as artificial receptors. Notably, although the C62 epitope is conserved across both G1 and G2 strains, C62 exhibits G2-strain-biased neutralizing activity. We further showed that differences in cell-surface membrane fusion activity among PEDV spikes correlate with distinct viral entry pathways and are jointly determined by the S1A and S1B sequences. Together, our findings identify a strain-specific vulnerable site on the PEDV S-trimer and provide insight into how cell-surface membrane fusion activity may influence viral entry pathway selection and antibody neutralization efficacy.

microbiology↗

bioRxiv2026

MEGA-ODE: Learning Biologically Structured and Navigable Continuous Perturbation Dynamics from Sparse Omics

Perturbation-omics experiments usually measure only a subset of molecular feature, intervention and time space, leaving many response trajectories, perturbation effects and disease- or differentiation-associated transitions unobserved. Here we present MEGA-ODE, a graph-constrained continuous-time framework for reconstructing sparse dynamic omics landscapes, predicting unmeasured molecular states and prioritizing virtual perturbations toward defined biological endpoints. MEGA-ODE integrates molecular-network priors, graph neural ordinary differential equations and context-adaptive mixture-of-experts routing. In L1000 transcriptomic perturbations and CPPA proteomic drug-response data, MEGA-ODE improved held-out-feature and unseen-perturbation prediction over baseline methods, and in SARS-CoV-2 infection time-series data it remained competitive for future-time-point forecasting. In a COVID-19 patient cohort, predicted intermediate profiles improved retrospective disease-stage stratification relative to observed profiles alone, while expert programs highlighted immune and inflammatory signals associated with severity. Across the MAPK drug-response and stem-cell differentiation case studies, graph- and expert-level attributions prioritized perturbation-associated MAPK edges, developmental regulators and TF-target relationships supported by independent promoter-proximal ChIP-seq overlap. In hESC-to-definitive-endoderm differentiation, MEGA-ODE prioritized candidate transcription-factor perturbations predicted to shift 12-36 h profiles toward 96 h definitive-endoderm marker signatures, framing trajectory navigation as a concrete hypothesis-generation task. Together, these results support biologically structured continuous-time modeling for prediction, interpretation and virtual-perturbation prioritization from sparse temporal omics data.

bioinformatics↗

bioRxiv2026

Joint modeling of multi-timepoint spatial observations for time-resolved spatial-unit-specific gene regulatory network inference

BackgroundHow gene regulatory programs reorganize across space and time is central to development and disease, but current methods infer regulatory structure from single snapshots. The emergence of spatiotemporal transcriptomics calls for methods that resolve regulation along both axes. ResultsWe introduce SpaTemGRN, which jointly models observations from multi-timepoint slides in spatiotemporal transcriptomics to infer time-resolved spatial-unit-specific putative GRNs. Compared with existing methods, SpaTemGRN allows later-stage units to borrow statistical strength from spatially proximate and temporally preceding units. In the AppNL-G-F mouse model of Alzheimers disease, SpaTemGRN revealed region- and age-dependent strengthening of complement-glia regulatory coupling. An early, broadly distributed complement signature precedes later, spatially focal coupling with astrocytic and microglial responses. In the developing mouse embryonic brain, SpaTemGRN identified progressively sharpening and spatially segregated regulatory programs as the early neural tube regionalizes. Across simulated datasets, SpaTemGRN recovered regulatory edges more robustly than four existing methods and maintained the most stable performance across stages. ConclusionsSpaTemGRN provides a flexible hypothesis-generating framework for investigating how spatially localized gene-gene dependencies are remodeled across biological stages. All source code for SpaTemGRN is available at https://github.com/yibingjiang/SpaTemGRN.

bioinformatics↗

bioRxiv2026

Enhancing Recombinant Vector Assembly Efficiency: A Novel Methodological Approach

With the rapid development of modern biotechnology, DNA vectors have become fundamental tools for inserting, transferring, and expressing specific gene sequences in various fields such as gene cloning, gene expression, gene editing, and gene therapy. However, when dealing with complex structured DNA sequences, traditional vector construction methods face challenges with low connection efficiency. This study proposes a new method for constructing recombinant vectors by employing a strategy of high-temperature treatment followed immediately by placement on ice, effectively reducing the complexity of DNA structures and enhancing the efficiency of PCR product-vector connection, thereby improving the construction efficiency of recombinant vectors. This paper describes the technical details of the method, experimental validation, and applications in gene cloning, gene recombination editing, and the preparation of gene therapy drugs, providing a new efficient tool for molecular biology experiments.

biochemistry↗

bioRxiv2026

Adult Clock Neuron Somatic Neuropeptide Release and Cytonemes Regulate Sleep

Drosophila s-LNv clock neurons promote nighttime sleep by releasing the neuropeptide sNPF to activate sNPF receptors (sNPF-Rs) on l-LNv clock neurons. Behavior is controlled by synaptic transmission, but s-LNv and l-LNv neurons are not connected directly by chemical synapses. To investigate the basis of sNPF/sNPF-R communication between LNv neurons, the spread of sNPF was imaged in the adult brain. We report the daily midmorning burst of sNPF released from s-LNv terminals does not reach l-LNv neurons or s-LNv somata. Instead, sNPF released by the s-LNv soma late at night in response to sleep-promoting IP3 signaling reaches l-LNv somata, but not their terminals. In addition to communication by neuropeptide diffusion, analysis of fly connectomes revealed that adult s-LNv and l-LNv neurons form non-synaptic direct contacts mediated by cytonemes. Remarkably, genetically perturbing LNv neuron cytonemes alters sleep latency, but not nighttime sleep, the target of somatic sNPF release, or circadian behavior, which depends on PDF neuropeptide released by LNv terminals. Therefore, three distinct aspects of adult rhythmic behavior are produced by terminals, the soma and cytonemes, with the latter possibly acting via contacts that are not currently annotated in the connectome.

neuroscience↗

bioRxiv2026

Deciphering the Effect of Melittin on Murine Cervical Cancer Cells Based on Transcriptomic Investigation

Melittin, a highly active natural antimicrobial peptide derived from honeybee venom, holds immense pharmacological potential against solid tumors. However, its specific anti-tumor efficacy and transcriptomic dynamics in cervical carcinoma remain to be systematically characterized. This study evaluated the anti-cancer properties of melittin on murine U14 cervical cancer cells following by transcriptomic investigation of the underlying mechanism. Phenotypic evaluations revealed that melittin potently inhibited U14 cell viability, while wound healing assays demonstrated a profound, dose-dependent suppression of cellular migration, culminating in near-complete migratory arrest at high concentrations. Furthermore, flow cytometry quantified a dramatic, dose-dependent surge predominantly in late apoptotic cell populations. These apoptotic events were structurally corroborated by scanning electron microscopy (SEM), which revealed severe plasma membrane perforation and morphological exhaustion. Enrichment analyses indicated that the physical membrane disruption inflicted by melittin translated into a severe metabolic crisis, marked by a global suppression of ribosomal biogenesis and mitochondrial oxidative phosphorylation. Furthermore, melittin profoundly repressed the Tie2-mediated angiogenic pathway (Etv2 down-regulation) while triggering the lethal hyperactivation of the AP-1 transcriptional stress complex (Jun, Fos, Fosb). Collectively, these findings elucidate the pharmacological networks underlying melittins cytotoxicity, providing solid molecular evidence for its development as a natural therapeutic agent against cervical cancer.

cancer biology↗

bioRxiv2026

A hierarchical activation threshold shapes RSV F antibody repertoires from toddler vulnerability to adult protection

Respiratory syncytial virus (RSV) causes severe infant morbidity, yet the mechanisms underlying their suboptimal immunity and the failure of prefusion F-stabilized adult vaccines in infants remain unclear. Here we integrate deep mutational scanning of 761 preF-binding antibodies, repertoire profiling of 102 repeatedly exposed pediatricians and 61 RSV-experienced toddlers, structural analysis, and >40,000 viral genomes to decode RSV F immunity. We resolved 12 immunologically distinct functional antibody subclasses and uncovered a hierarchical activation threshold: apical epitope-targeting antibodies with superior neutralizing potency demand extensive somatic hypermutation and cooperative CDR networks, whereas central-to-basal epitope-directed, marginal or non-neutralizing antibodies engage germline-encoded antibodies through minimal mutations (e.g., S31G). Toddler repertoires are confined to low-threshold, non-productive sites; adult repertoires enrich for apical elite neutralizers whose immune pressure drives contemporary RSV-B evolution. These reframe pediatric RSV vulnerability as a threshold-gated repertoire deficit and prescribe vaccine strategies that actively redirect immunodominance from permissive epitopes toward high-barrier apical targets.

immunology↗

bioRxiv2026

Structural characterization of stochastic detailed balance in chemical reaction networks

The global potential of a chemical reaction network has many applications and is closely related to the stochastic detailed balance. However, many fundamental questions concerning stochastic detailed balance remain unresolved, such as whether it depends on the system volume and how to construct new systems that satisfy it. In this paper, we show that stochastic detailed balance may depend on the system volume. We therefore introduce four types of stochastic detailed balance according to their dependence on volume and rate constants, and systematically investigate the relationships among them. Our results distinguish detailed balance arising from particular choices of volume and parameters from that enforced by network structure, and identify conditions under which detailed balance at one volume extends to all volumes. We further obtain a class of networks satisfying stochastic detailed balance for every volume and every positive choice of rate constants, and construct new systems whose global potentials exhibit double-well structures.

systems biology↗

bioRxiv2026

Transcriptomic datasets of melittin- and un-treated murine cervical carcinoma U14 cells

Melittin, a potent amphipathic cationic peptide derived from bee venom, exhibits broad-spectrum antineoplastic efficacy, notably against cervical carcinoma. Despite its established therapeutic potential, the global transcriptional reprogramming orchestrating its acute multi-pathway cytotoxicity remains incompletely understood. To bridge this knowledge gap, we generated the first comprehensive, untargeted RNA-seq dataset profiling the acute phase of melittin-induced cell death in murine cervical carcinoma U14 cells (exposed to 4 g/mL melittin for 20 minutes) alongside untreated controls. Utilizing deep sequencing and rigorous bioinformatics workflows, we quantified genome-wide mRNA abundances and mapped a distinct transcriptomic shift, identifying 254 significantly differentially expressed genes, comprising 158 up- and 96 down-regulated transcripts. Validated by stringent quality control metrics, exceptional genomic mapping rates, and comprehensive functional annotations via the GO and KEGG databases, this high-resolution transcriptomic resource provides a systems-level map of early molecular alterations. All raw and processed sequencing data are publicly available. This transcriptomic resource provides a valuable foundation for elucidating the acute regulatory networks underlying melittin-induced anti-cervical cancer effects. DatasetThe dataset can be accessed through the NGDC website by searching with the BioProject accession number PRJCA068439. Reviewers may use this link for anonymous access during the review process. Direct URL to data: Genome Sequence Archive-CNCB-NGDC

genomics↗

bioRxiv2026

Hologenomics of xylotrophic bivalves reveals a minimalist, remote-acting evolutionary strategy of wood digestion

Wood constitutes the largest reservoir of biogenic carbon on Earth, yet remarkably few animals can exploit it. While terrestrial wood-feeders like termites rely on highly diverse gut microbiomes, xylotrophic marine bivalves have evolved a fundamentally different approach: a spatially segregated system where intracellular gill symbionts produce enzymes that act remotely within a nearly sterile cecum. However, the genetic and evolutionary basis of this unique symbiosis remains largely elusive. Here, we integrate hologenomics, transcriptomics, and biochemistry of a shallow-water shipworm (Teredo navalis) and a deep-sea borer (Xyloredo sp.). We find that despite diverging approximately 147 million years ago and occupying drastically different habitats, these bivalves maintain a strictly conserved ancestral karyotype and a shared genomic architecture for wood digestion. Our models reveal a clear host-symbiont division of labor. The host genome is specialized for lignin modification and targeted enzyme transport, whereas a highly streamlined symbiont community is responsible for core polysaccharide degradation. Central to this minimalist strategy is a lineage-specific GH5-GH6 dual-catalytic enzyme. By sharing amino acids across proximal binding pockets, this fusion protein unites endo- and exo-cellulase activities, enabling highly synergistic cellulose cleavage without the need for complex microbial communities. Ultimately, our comparative analysis with terrestrial models demonstrates that these marine invertebrates achieve efficient biomass degradation not through microbial expansion, but through extreme functional streamlining and molecular innovation, offering a distinct evolutionary paradigm for marine carbon cycling.

evolutionary 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

A GSK3-dependent phosphorylation switch licenses BNIP3-mediated mitophagy

The turnover of mitochondria through mitophagy is essential for maintaining mitochondrial function and matching mitochondrial content to cellular demand. In many cells, this process is mediated by the paralogous mitochondrial receptors BNIP3 and BNIP3L, which recruit WIPI-family autophagy effectors to initiate mitophagosome formation. However, the mechanisms that activate BNIP3/L remain poorly understood. Here, we show that the kinase GSK3 directly phosphorylates BNIP3, licensing receptor activity and activating mitophagy. Phosphorylation promotes BNIP3 recruitment of WIPI proteins, thereby initiating mitophagosome formation. We identify the critical phosphorylation sites required for this regulation and demonstrate that disruption of these sites abolishes BNIP3-dependent mitophagy. Together, our findings identify phosphorylation as a molecular switch controlling BNIP3/L activity and suggest that receptor phosphorylation may temporally and spatially license mitophagosome formation and mitochondrial clearance.

cell biology↗

bioRxiv2026

Time-Resolved Profiling: Metabolic Adaptation & Morphology-Specific Drug Response in MCF-7 spheroids

Three-dimensional (3D) tumor models exhibit drug responses that differ from conventional 2D cultures. However, how cellular metabolism dynamically evolves across culture models and during drug treatment remains poorly understood. We compared the responses of MCF-7 cells in 2D and 3D environments to 5-fluorouracil (5-FU), combining {superscript 1}H NMR cellular metabolomics with viable cell counts, the GLUT1-positive population, gene expression, ATP activity, and morphology. Principal component analysis revealed that culture dimensionality, rather than 5-FU treatment, was the primary driver of metabolic flux variation. 3D spheroids exhibited higher glycolytic flux at 72h. Importantly, this elevated glycolysis reflected a higher per-cell flux in larger spheroids rather than an increased cell number. We further observed a higher proportion of GLUT1-positive cells and increased HK2 expression in 3D culture, together with an epithelial phenotype characterized by increased CDH1 and decreased VIM expression. Functionally, 3D displayed maintaining higher cell viability, ATP activity following treatment. Together, these findings suggest that 3D architecture promotes a metabolically defensive phenotype and cellular metabolic behaviors is associated with morphology, which may inform future drug screening model selection. BlurbTime-resolved NMR metabolomics reveals that 3D culture architecture, rather than 5-FU treatment, defines the metabolic phenotype of MCF-7 cells, linking spheroid morphology with per-cell glycolytic activity, ATP preservation, and reduced chemotherapy sensitivity. Synopsis O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/740505v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@15cfa5corg.highwire.dtl.DTLVardef@138ca69org.highwire.dtl.DTLVardef@170d0d8org.highwire.dtl.DTLVardef@19f3572_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical abstract -- Time-resolved metabolic and phenotypic responses of 2D and 3D MCF-7 cultures to 5-fluorouracil. Bullet pointsO_LITime-resolved {superscript 1}H NMR cellular metabolomics combined with multilevel phenotypic readouts reveals that culture dimensionality, rather than 5-FU chemotherapy, is the dominant determinant of metabolic phenotype in MCF-7 breast cancer cells. C_LIO_LI3D spheroids develop a glycolysis-dominant metabolic state with markedly elevated GLUT1 populations and HK2 transcript, accompanied by substantially reduced sensitivity to 5-FU compared with 2D monolayers. C_LIO_LISpheroid morphology correlates with cellular metabolic flux: larger and more elongated spheroids exhibit higher glycolytic activity on a per cell, independent of spheroid cell number. C_LIO_LIThe 3D-defined metabolic state buffers ATP under 5-FU stress and reinforces an epithelial transcriptional program (CDH1{uparrow}, VIM{downarrow}), arguing that culture architecture must be considered when interpreting preclinical drug responses. C_LI

cancer biology↗

bioRxiv2026

Integrative AI-Enabled Virtual Cell Modeling Reveals a Clinically Relevant Latent Effector State of Human CD8 T Cells Undetectable by Conventional Analyses

Understanding how immune checkpoint inhibitors (ICIs) reshape human T-cell responses requires models that move beyond static transcriptomic snapshots and discrete cell-state classifications. Here, we present an integrative AI-enabled virtual cell framework that represents human CD8 T-cell responses as dynamic and computable systems during ICI therapy. By integrating single-cell RNA sequencing with paired T-cell receptor sequencing within the C2S-scale foundation model, we construct a virtual representation of individual T cells, in which each cell is encoded by a unique functional identity that captures its transcriptional, signaling, and clonal characteristics. Using this framework, we identify a previously unrecognized dynamic latent effector state of CD8 T cells characterized by intermediate expression of effector genes, distinct signaling activity, and ongoing clonal expansion. Across independent patient cohorts, the virtual cell model consistently indicates that ICI therapy mainly acts by unmasking pre-existing effector potential rather than inducing de novo effector differentiation. Notably, this latent effector population remains transcriptionally restrained despite active signaling and clonal expansion, revealing a hidden reservoir of antitumor immune capacity. More broadly, our study demonstrates how AI-enabled virtual cell modeling can reconstruct latent cellular states and their dynamic transitions from multidimensional single-cell data. By incorporating functional identity into virtual cell model, this framework uncovers biologically meaningful yet non-obvious T-cell effector program during cancer immunotherapy and provides a generalizable approach for studying immune dynamics in human disease.

immunology↗

bioRxiv2026

Effect of nuclear electrostatic potential on the nucleoplasmic distribution of histones and nucleosome stability

Differences in the density of heterochromatic and euchromatic regions are often assumed to play an important role in determining the transcriptional state of chromatin by influencing its accessibility to transcription factors. Yet, experiments show that even the most densely packed chromatin domains are readily accessible to transcription factors. Thus, the molecular mechanisms underlying differences in the transcriptional states of hetero- and euchromatin remain poorly understood. In this study, using electrically charged mEGFP probes, we demonstrated that heterochromatin and euchromatin differ not only in density but also in the magnitude of the local electrostatic potential. Furthermore, the nucleoplasmic distribution of electrically charged proteins, such as histone-chaperone complexes, was found to correlate with the local electrostatic potential. Estimates based on experimental data have also shown that the difference in electrostatic potentials between heterochromatic and euchromatic regions could lead to unequal nucleosome stability in them, which was successfully confirmed experimentally. Subsequent theoretical calculations showed that this could shift the balance in the DNA-binding competition between transcription factors and nucleosomes, thereby explaining experimental observations that heterochromatin is less transcriptionally active than euchromatin. Overall, our study suggests the existence of a nuclear electrostatic potential-mediated pathway that may be involved in the regulation of gene transcription.

biophysics↗

bioRxiv2026

Evaluation of phage activity against diverse Enterococcus faecalis from infective endocarditis

Enterococcus faecalis is a leading cause of infective endocarditis, particularly in older and hospitalized patients. Treatment is challenging due to the intrinsic resistance of E. faecalis to many clinically important antibiotics and the increasing prevalence of multidrug-resistant strains. Bacteriophage (phage)-based therapies, including phage cocktails and phage-antibiotic combinations, offer a promising approach for treating resistant bacterial infections. In this study, we isolated ten novel phages from wastewater by screening on E. faecalis clinical isolates and tested phage activity both individually and in phage-phage and phage-antibiotic combinations against 18 E. faecalis clinical isolates collected from patients with infective endocarditis. We found that 15/18 (83%) isolates were susceptible to at least one phage tested, and that the same proportion of isolates were susceptible to a cocktail of three phages with complementary activities. We also observed improved bacterial growth inhibition and increased killing when phages were combined with ampicillin or daptomycin, two antibiotics commonly used to treat E. faecalis infections. Finally, we found that treatment with the three-phage cocktail improved the survival of Galleria mellonella infected with a pathogenic E. faecalis endocarditis isolate. Overall, these findings suggest that phages could be a helpful addition to the therapeutic repertoire for treating E. faecalis infective endocarditis. ImportanceNew approaches are needed for treating infective endocarditis, a life-threatening heart infection. Here we focus on Enterococcus faecalis, a resilient bacterium that is increasingly resistant to standard-of care antibiotic regimens, and explore the use of phage therapy for treating E. faecalis endocarditis. We found that combining phages together in a cocktail or pairing them with existing antibiotics can effectively kill E. faecalis clinical isolates from patients with infective endocarditis, and that treatment of infected waxworm moth larvae with a phage cocktail improved their survival. The results of this study contribute to the development of phage-based therapeutic approaches for E. faecalis endocarditis, which could ultimately lead to improved outcomes for patients facing this severe infection.

microbiology↗

bioRxiv2026

An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid

The retinal pigment epithelium and choroid are critical for supporting the function and maintaining the homeostasis of the outer retina, and their dysfunction underlies a range of inherited and complex ocular diseases. To comprehensively characterize the cellular, transcriptomic, and epigenomic heterogeneity and dynamics within these tissues, we assembled an integrated multi-omics reference atlas comprising 719,813 single-cell/single-nucleus transcriptomes and 234,007 snATAC-seq profiles from 102 ancestrally diverse donors spanning 0 to 99 years of age, including cells from both the macula and periphery. This atlas resolves 48 distinct cell types or states and catalogs 448,567 open chromatin regions. Specifically, we resolved five distinct RPE subpopulations organized along a central-to-peripheral spatial axis, alongside two distinct stress/senescence states. We reconstructed the transcriptomic and epigenetic zonation of endothelial cells and expanded choroidal stromal heterogeneity by characterizing 11 fibroblast and two pericyte types. Age-associated compositional analysis revealed a significant fractional depletion of melanocytes, PI16+ fibroblasts, and venule endothelial cells with age, alongside a modest relative loss of central RPE and a corresponding increase in far-peripheral RPE. Cell-type-specific aging transcriptomics uncovered shared pathways related to inflammatory responses alongside distinct cell-type-specific signatures. Notably, significant age-associated epigenetic changes concentrated in the macula during the transition from early-to-middle adulthood and remained stable into old age, with transcription factors from the AP-1/bZIP family emerging as the dominant enriched motifs. Finally, integrating this atlas with AMD GWAS data provides novel variant-to-gene evidence implicating LIPG and COL4A3 in AMD pathogenesis. Together, this multi-omics atlas serves as both an invaluable community reference and a powerful discovery engine that translates genetic risk signals into localized target cells and candidate mechanisms, laying a foundation for understanding RPE/choroid biology in health and disease.

genomics↗