Biology subjects

Chen, S.

Publications and source records attributed to Chen, S..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

Preclinical CRX augmentation therapies for CRX-associated autosomal dominant cone-rod dystrophies

Cone-rod dystrophies (CoRD) are inherited retinal diseases (IRDs) with variable ages of onset, characterized by the progressive loss of cones, followed by secondary degeneration of rods. Cone-rod homeobox (CRX) is a transcription factor that regulates gene expression essential for photoreceptor development and maintenance. Mutations in CRX gene, including CRXE168d2 and CRXE80A, are implicated in autosomal dominant CoRDs. Although these mutations show distinct pathogenic mechanisms, published studies in knock-in mouse models have suggested a common treatment strategy: increasing WT CRX expression to reduce the detrimental activities of mutant proteins. This study employs two independent strategies of CRX augmentation to evaluate their therapeutic potential in CrxE168d2/+ and CrxE80A/+ mouse models. The Tet-On-hCRX transgenic system, a platform of proof-of-principle gene therapy, induces consistent and pan-photoreceptor expression of CRX augmentation in diseased retinae, allowing for the faithful assessment of functional and behavioral recovery. AAV-mediated CRX augmentation confirms the biosafety, delivery efficiency and efficacy of viral transduction in diseased retinae. Both strategies have achieved significant treatment outcomes in cone photoreceptor survival and overall photoreceptor functions in young adulthood. Treated cones survive past the age point of complete cone loss in untreated controls of both models. Treated rods show functional improvement and long-term survival through later adulthood. This preclinical study establishes valuable treatment regimens and benchmarks for CRX augmentation in the treatment of CRX-associated IRDs, and offers new insights into the mechanisms for photoreceptor development and survival.

neuroscience↗

bioRxiv2026

Super-resolution single-cell spatial atlas of plant de novo regeneration

Plant de novo regeneration, a capacity absent in animals, relies on stem-cell-niche formation rather than pre-existing reservoirs. Growth hormones such as auxin and cytokinin, together with numerous genetic regulators, participate in regeneration, but the architectural principles coordinating extensive cellular reprogramming at the individual-cell scale remain elusive. Using super-resolution multimodal spatial transcriptomics to 1.16 million cells, we tracked tomato regeneration across temporal intervals from wounding to organogenesis. Datasets are available at http://www.single-cell-spatial.com.

cell biology↗

bioRxiv2026

Atomic structure and plasticity of the MthK-CTX complex investigated by cryo-EM, NMR, and MD simulations

Scorpion toxins block potassium channels, disrupting cellular excitability and causing symptoms such as pain, muscle spasms, or paralysis. Here, we use an integrated structural biology approach to uncover the binding mode of the scorpion toxin charybdotoxin (CTX) to the MthK channel, a model system for human large-conductance potassium (BK) channels. Cryo-EM defines the overall architecture of the MthK-CTX complex, while complementary solution- and solid-state NMR experiments identify key binding residues and show that toxin engagement alters the selectivity filter (SF) ion configuration without rearranging the filter itself. NMR and MD simulations further reveal an anchoring lysine residue stably inserted into the SF, while other contacts undergo fast NMR timescale dynamics. Together, these findings explain how CTX-like toxins maintain exceptionally high affinity while tolerating binding across multiple K+ channel subtypes, paving the way for site-specific extracellular modulation.

molecular biology↗

bioRxiv2026

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

bioRxiv2026

Pragmatic analysis with knowledge-guided for unraveling peptide-protein pairwise non-covalent mechanisms

Understanding peptide-protein interactions is vital for decoding cellular signaling and developing targeted therapies. However, the complexity of multi-molecular associations and diverse non-covalent interactions make accurate prediction and site-specific annotation challenging. Here, we propose KGIPA, a knowledge-guided pragmatic analysis framework that incorporates pragmatic concepts from natural language into life science, capturing the influence of biological environments on non-covalent interactions. KGIPA integrates intra- and extra-linguistic contextual information to combine multimodal single-molecule features and build residue-level interaction maps. It also uses biological prior knowledge to coordinate various non-covalent interaction types. Benchmark tests demonstrate KGIPA outperforms the state-of-the-art methods in evaluating molecular binding, including protein and peptide binding residues and residue-pair interactions. Furthermore, KGIPA demonstrates strong performance in peptide-protein binding affinity prediction and peptide virtual screening. Wet-lab experiments validate its reliability, revealing high consistency between predicted and experimentally measured binding behaviors. These results highlight KGIPAs potential to accelerate peptide drug discovery and establish pragmatic analysis as an effective paradigm for decoding the molecular language of interactions.

bioinformatics↗

bioRxiv2026

Large-scale quantum computing framework enhances drug discovery in multiple stages

Coherent Ising machines (CIMs) excel at solving large-scale combinational optimization problems (COPs), but their insufficient long-term stability has hindered their applications in compute-intensive tasks like computer-aided drug discovery (CADD). By improving fiber vibration isolation and temperature control system, we have implemented a 2000-node CIM named QBoson-CPQC-3Gen achieving stable solutions over one hour on large-scale COPs. Graph-based encoding schemes were further introduced to realize a CIM-based CADD workflow including allosteric site detection, protein-peptide docking and intermolecular similarity calculation. CIM-based methods demonstrated superior speed and accuracy than heuristic algorithms. Especially, QBoson-CPQC-3Gen identified 2 novel druggable sites and bioactive compounds for 6 targets, which were further validated in vitro, in-cell and by crystal structures. Our contributions established a quantum-computing framework for multi-stage drug discovery, representing a significant advancement in both quantum computing applications and pharmaceutical research.

bioinformatics↗

bioRxiv2026

ATLAS: Population-Level Disease Locus Discovery via Differential Attention in Genomic Language Models

Identifying disease-associated genetic variants remains a key challenge in genomics, especially in small cohorts or for rare and complex mutation types where genome-wide association studies (GWAS) often fall short. We introduce ATLAS, a population-level framework that leverages attention signals from pretrained genomic language models (gLMs) to detect disease-associated genes and loci directly from raw sequences--without requiring explicit variant calls or supervised training. ATLAS first performs gene-level differential attention analysis to prioritize candidate genes, followed by base-level analysis to localize disease-associated regions at single-haplotype resolution. We validate ATLAS on synthetic and {beta}-thalassemia datasets, demonstrating robust performance across diverse allele frequencies (down to 10%), cohort sizes (below 200 individuals per group), and genomic scales. Compared to GWAS, ATLAS achieves higher recall of known loci and captures haplotype-specific signals missed by traditional methods. Cross-model benchmarking further shows that precise localization depends on both model size and pretraining on diverse human genomes. In summary, ATLAS offers a scalable, sequence-native alternative to traditional statistical genetics.

genetics↗

bioRxiv2026

IFN gamma-induced IRF1 synergizes with TLR7 signals to tune the IRF4-IRF8 axis and drive pathogenic effector B cell fate

Interferon regulatory factor 1 (IRF1), a transcription factor encoded within the 5q31 locus harboring systemic lupus erythematosus (SLE) associated variants, promotes inflammatory responses by T and myeloid cells. Although IFN{gamma}-activated B cells also express IRF1, its role in B cell biology and SLE is unclear. Here, we use a mouse SLE model, single-cell multiomics, and human B cells to show that IRF1 intrinsically regulates Irf4 gene chromatin accessibility and expression in B cells to control the balance between the antibody secreting cell (ASC) lineage commitment factor, IRF4, and the B cell identity factor, IRF8. We demonstrate that IRF1, through its integration of IFN{gamma} and TLR7 induced transcriptional programs, tips B cells toward a terminal effector inflammatory AC fate at the expense of preserving more stem-like, resting and regulatory B cells that do not elicit autoantibody-associated pathology in SLE. Thus, IRF1 serves as a central node controlling B cell-driven autoimmune disease.

immunology↗

bioRxiv2026

A genome-wide CRISPR screen reveals cancer-specific regulators of hyaluronan binding and cellular invasion

Metastatic spread of cancer cells is driven by binding between the cell-surface receptor CD44 and hyaluronan (HA) in the extracellular matrix. The specific oncogenes that drive increased CD44-HA binding in cancer remain poorly defined. Using a fluorescently labeled hyaluronan probe, we performed a genome-wide CRISPR screen to identify genes whose knockdown disrupts HA binding in breast cancer cells. We subsequently developed a bioinformatic analysis pipeline that enabled stratification and prioritization of cancer-specific regulators. This work provides a first-in-class resource for the identification of druggable targets to inhibit HA binding. We further validate RAB4A, a top hit from our screen, as a novel regulator of this process. Mechanistically, RAB4A KO dramatically reduces CD44 expression and inhibits the invasion of breast cancer cells through HA-rich matrices. This study validates a novel strategy for identifying regulators of cancer cell invasion and identifies immediate actionable targets for anti-metastatic therapy.

cancer biology↗

bioRxiv2026

Functional characterization and molecular engineering of a O-methyltransferase involved in bis-benzylisoquinoline alkaloids biosynthesis from Nelumbo nucifera

Nelumbo nucifera (lotus), a traditional aquatic plant in Asia, is valued for its nutritional and therapeutic properties. Benzylisoquinoline alkaloids (BIAs) are its major bioactive components, with significant bioactivities and pharmacological values. O-methyltransferases (OMTs) play a crucial role in shaping the structural and functional diversity of BIAs. Herein, we characterized a specific OMT, designated Nn7OMT, which exhibits a novel catalytic function: methylating the C7 position of the bisbenzylisoquinoline (bisBIA) skeleton. Nn7OMT also displayed substrate promiscuity, catalyzing O-methylation at the C7 position of bisBIAs, C6/C7 positions of 1-benzylisoquinolines, C7 position of aporphines, and C9 position of protoberberines, with isoliensinine as its preferred substrate. The expression profile of Nn7OMT correlates with bisBIA accumulation in planta, supporting its involvement in bisBIA biosynthesis in N. nucifera. Protein engineering guided by molecular docking and molecular dynamics simulations identified key residues critical for Nn7OMT activity. Mutants M158A and V306A retained catalytic activity toward isoliensinine while showing nearly undetectable activity against 1-benzylisoquinoline alkaloids, thereby significantly improving Nn7OMTs substrate specificity. These findings advance our understanding of BIAs biosynthesis in lotus and provide valuable biocatalysts with enhanced specificity. SIGNIFICANCEIn this study, we report the innovative discovery and characterization of Nn7OMT, the first O-methyltransferase isolated from Nelumbo nucifera that harbors a novel catalytic activity toward the bisbenzylisoquinoline alkaloid (bisBIA) backbone. Nn7OMT displayed substrate promiscuity, catalyzing methylation at the C7 position of the bisbenzylisoquinoline skeleton (isoliensinine), C6/C7 positions of the 1-benzylisoquinoline skeleton (norcoclaurine, coclaurine, N-methylcoclaurine), C7 position of the aporphine skeleton (lirinidine), and C9 position of the protoberberine skeleton (scoulerine)--with isoliensinine as its most preferred substrate. Innovatively, the catalysis of isoliensinine by Nn7OMT was a novel function and the first O-methyltransferase identified to catalyze the bisbenzylisoquinoline backbone, which may be involved in the biosynthesis of neferine. Nn7OMTs expression profile correlated with bisBIA accumulation in planta, further supporting its role in bisBIA biosynthesis in N. nucifera. We further engineered Nn7OMT using molecular docking and MD simulation-guided strategies. Mutants M158A and V306A retained catalytic activity for isoliensinine while showing nearly undetectable activity against 1-benzylisoquinoline alkaloid substrates. This targeted engineering significantly improved the specificity of Nn7OMT, rendering it highly suitable for methylated isoliensinine biosynthesis by reducing by-product accumulation and simplifying purification processes. Our work deepens understanding of the unique BIA metabolic pathway in N. nucifera through the identification of the first bisBIA-catalyzing O-methyltransferase, and provides valuable biocatalysts with enhanced substrate specificity.

molecular biology↗

bioRxiv2026

Disease diagnosis via sperm motility variations induced by body fluids in bioassay

Precise diagnosis of high-risk conditions such as cardiovascular and cerebrovascular diseases still remains a challenge. We previously developed a microfluidic chip for sperm selection and observed that sperm motility is highly sensitive to environmental changes. Building on this finding, we hypothesized that motility traits of sperm could be differentially modulated by body fluids from healthy versus diseased individuals, thereby serving as potential biomarkers for disease diagnosis. To test this hypothesis, we designed a diagnostic system in which mouse sperm were co-incubated with serum samples from patients with myocardial infarction, cerebral infarction, and pancreatitis, along with matched healthy controls. Key kinematic parameters--including motility rate (MR), curvilinear velocity (VCL), straight-line velocity (VSL), linearity (LIN), and amplitude of lateral head displacement (ALH)--were analyzed using a multiparameter sperm quality analysis system. The results revealed that disease-specific serum induced distinct and reproducible changes in sperm motility patterns, enabling accurate discrimination between healthy and pathological conditions. Evaluation of these motility parameters demonstrated high diagnostic performance, with area under the receiver operating characteristic curve (AUC) values ranging from 0.719 to 0.888. This sperm-based bioassay offers a non-invasive, rapid, and cost-effective platform for disease detection and personalized health assessment, with the potential to complement existing diagnostic approaches.

bioengineering↗

bioRxiv2026

CellCov: gene-body coverage profiling for single-cell RNA-seq

MotivationGene-body coverage bias differs across scRNA-seq protocols and can influence downstream analyses, yet coverage is often assessed using bulk-level summaries that obscure cell-to-cell variability. ResultsCellCov provides gene-body coverage profiling at single-cell resolution, enabling exploration of coverage heterogeneity across both cells and features. The accompanying workflow supports flexible grouping and robust aggregation of profiles by user-provided annotations, allowing principled comparison of coverage bias across sequencing protocols. We demonstrate its use on public datasets from several full-length scRNA-seq chemistries. AvailabilityCellCov source code and documentation are available at https://github.com/ziegenhain-lab/CellCov Contactchristoph.ziegenhain@ki.se Supplementary informationSupplementary data are available at Bioinformatics online

bioinformatics↗

bioRxiv2026

Bacteroides intestinalis-Driven Arabinoxylan Fermentation Mitigates Inflammatory and Metabolic Dysfunction

Insufficient dietary fiber intake is closely linked to gut microbiome dysfunction and increased risk of noncommunicable diseases. Synergistic synbiotics, pairing defined microbes with their dietary substrates, offer a precise strategy to restore microbiome function. Here, we show that pairing the human colonic commensal Bacteroides intestinalis with insoluble wheat arabinoxylan (inWAX) yields pronounced metabolic and anti-inflammatory benefits. Using mono-associated gnotobiotic mice and high-fat diet-induced obese mice, we demonstrate that this synbiotic enhances resistance to intestinal inflammation and improves glucose homeostasis. Mechanistically, this synbiotic increases production of 6-hydroxylated bile acids with anti-diabetic and anti-steatotic effects. It also promotes microbial transformation of phenolic compounds and redirects protein metabolism toward neuroactive metabolites. These metabolic shifts are accompanied by transcriptional remodeling in the colon, spleen and liver, involving induction of genes essential for circadian rhythm, lipid metabolism, immune defense, and bile acid 6-hydroxylation. Notably, Y chromosome-linked genes associated with epigenetic regulation and protein turnover are also induced, suggesting a potential sex-specific response to synbiotics. Together, our findings establish a mechanistic framework for targeted synbiotic interventions to combat inflammatory and metabolic disorders.

microbiology↗

bioRxiv2026

Cancer-associated synonymous mutations reveal stress signal-dependent mRNA folding that selectively modulates protein function.

Recent technical advances have facilitated studies on changes in mRNA structures in response to signaling pathways. However, if mRNA structures can affect the function of the encoded protein remains poorly understood. In-cell RNA structural probing (SHAPE-MaP) demonstrates how two cancer-associated synonymous mutations (CASMs) at proline codon 34 (c.102 C>A and c.102 C>G) prevent DNA damage-induced TP53 mRNA folding, whereas the non-cancer-associated c.102C>U mutation does not. Transcript and chromatin immunoprecipitation (ChIP) analysis reveal that p53 expressed from CASM34 has reduced promoter binding and reduced induction of p53 downstream target genes PUMA and 14-3-3-{sigma}, but not p21CDKN1A. Transcriptome analysis reveals a CASM34-mediated global attenuation of DNA damage-responsive gene expression. Together, the results demonstrate that CASM34 interferes with signal-induced p53 mRNA folding during DNA damage, leading to selective modulation of protein activity. More broadly, our findings highlight a general concept by which cancer-associated synonymous mutations target signal-induced mRNA structures that influence the encoded protein. Significance statementRecent studies have revealed that synonymous mutations can target RNA metabolism and are associated with numerous diseases; however, how these mutations affect the function of the encoded protein remain unclear. Using in-cell RNA structural probing, we show that two cancer-associated synonymous mutations in TP53 disrupt DNA damage-induced folding of p53 mRNA. These mutations selectively impair p53 promoter binding and transcriptional activation of specific downstream target genes. Our results demonstrate that disruption of signal-induced mRNA folding by synonymous mutations can modulate the activity of the encoded protein. More broadly, this work identifies signal-responsive mRNA structures as functional targets of cancer-associated synonymous mutations.

molecular biology↗

bioRxiv2026

Systematic Identification of Germ Granule Proteins Reveals Specialized Roles in RNAi and Small RNA Inheritance

Biomolecular condensates, such as germ granules, organize RNAi pathways critical for fertility and genome regulation. Yet, the protein composition and functional contributions of these condensates remain poorly defined. Here, we applied TurboID proximity labeling to the Caenorhabditis elegans germ granule protein SIMR-1, integrating mass spectrometry with genetic screening, CRISPR-based tagging, and small RNA sequencing. This systematic approach identified several previously uncharacterized germ granule proteins that contribute to fertility, germline immortality, exogenous RNAi, and transgenerational inheritance. Small RNA sequencing of 21 mutants revealed broad and class-specific defects in siRNA and miRNA biogenesis, with distinct factors associated with defects in WAGO-class 22G-RNAs, CSR-class 22G-RNAs, or histone-directed small RNAs. Among these, we identified PINT-1, a highly disordered protein that directly interacts with and is recruited to germ granules by the PIWI Argonaute PRG-1. PINT-1 is required for piRNA-dependent and -independent secondary siRNA biogenesis and germline development. Comparative genomics revealed that PINT-1 has co-evolved with PRG-1 across clade V nematodes, with a conserved structured N-terminus and a rapidly diverging repeat-rich intrinsically disordered region. Together, our findings expand the germ granule proteome and reveal how distinct condensate components contribute to specialized functions within the small RNA pathways, while highlighting an evolutionarily co-adapted PIWI interactor critical for siRNA biogenesis.

genetics↗

bioRxiv2026

Telomere-to-telomere gap-free and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres

Common tobacco (Nicotiana tabacum) is an economically important crop worldwide whose allotetraploid genome sequence remains incompletely assembled. We report a 4.2Gb telomere-to-telomere gap-free N. tabacum reference genome phased into two subgenomes (subS/subT) , revealing differential evolutionary trajectories between two subgenomes marked by a rapid divergence in paternal T-genome, especially for heterochromatic centromeric regions. To understand the evolutionary dynamics of tobacco centromeres following polyploidization, we characterize the centromere architecture in tetraploid N. tabacum and its diploid progenitors, demonstrating clear subgenomic diversification and repositioning of centromeres during speciation and allopolyploidization. These findings enrich our knowledge on centromere paradox in polyploid genomes.

genomics↗

bioRxiv2026

Evolutionary genomics of local adaptation, climate vulnerability, and linarin metabolism in Opisthopappus longilobus

Global climate change and human activities are posing substantial threats to biodiversity. The genus Opisthopappus (O. taihangensis and O. longilobus), endemic to Chinas Taihang Mountains, possesses great ecological, ornamental and medicinal value. However, it is confronted with the pressures of habitat fragmentation and climate change. Here, we present the first haplotype-resolved, chromosome-scale genome assembly of O. longilobus ([~]2.95 Gb) and re-sequence 115 individuals across its range. Comparative analyses show Opisthopappus is sister to Artemisia-Chrysanthemum, with Opisthopappus and Chrysanthemum diverging at 5.15-5.18 million years ago. A profound genetic divergence is evident between O. taihangensis and O. longilobus, resulting in two distinct lineages within each species, driven by geography and climate. Our analyses indicate restricted gene flow, low diversity, and recurrent demographic bottlenecks collectively contribute to their endangerment. By integrating population genomics and environmental variables, we identified 4,437 core adaptive genes linked to water deprivation, and metabolism. Genomic offset predicts higher maladaptation risk in populations under drastic climate change. Furthermore, diverged promoters of two O-methyltransferase genes, OMT250 and OMT310, likely underlie the differential acacetin/linarin accumulation between C. morifolium and O. longilobus. These findings advance understanding of Opisthopappus evolution and climate vulnerability, offering a model for genomics-guided biodiversity conservation.

plant biology↗

bioRxiv2026

Optimizing broadly neutralizing antibodies via all-atom interaction modeling and pre-trained language models

Antibody optimization is a fundamental challenge, and the identification of antibody-antigen interactions is crucial in the optimization process. However, current methods cannot accurately predict antibody-antigen interactions, providing limited functional guidance to improve the time-consuming and costly traditional optimization techniques. Here, we present InterAb and InterAb-Opt, a unified computational framework that integrates all-atom modeling with antibody language models to predict antibody-antigen interactions and enable antibody optimization. Leveraging the proposed all-atom modeling approach, AtomInter, and pre-trained antibody language models, InterAb outperforms existing methods in predicting antibody specificity and antibody-antigen binding affinity. InterAb successfully identified influenza A virus-binding antibodies from an antibody library and accurately detected high-affinity antibodies in the AIntibody competition. Empowered by the robust functional insights from InterAb, InterAb-Opt was developed to optimize broadly neutralizing antibodies. For R1-32 antibody, biolayer interferometry results reveal that 85%, 80%, 90%, and 67.5% of the 40 InterAb-Opt-optimized antibodies exhibit enhanced binding affinities to wild-type SARS-CoV-2, Lambda, BQ.1.1, and EG.5.1, respectively, with a maximum improvement of up to 96-fold. For the newly emerging BA.2.86 and KP.3, 55% and 52.5% of the optimized antibodies notably transition from non-binding to binding. Neutralization assays demonstrated that the optimized antibodies exhibited enhanced neutralization activity across multiple targets, highlighting the capability of InterAb-Opt in engineering broadly neutralizing antibodies. This technology enables precise analysis of antibody-antigen interactions and optimization of broadly neutralizing antibodies, holding promise for addressing challenges in immune evasion and vaccine design.

bioinformatics↗