Biology subjects

Li, C.

Publications and source records attributed to Li, C..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

Nephrobase Cell+: Multimodal Single-Cell Foundation Model for Decoding Kidney Biology

BackgroundLarge foundation models have revolutionized single-cell analysis, yet no kidney-specific model currently exists, and it remains unclear whether organ-focused models can outperform generalized models. The kidneys complex cellular architecture and dynamic microenvironments further complicate integration of large-scale single-cell and spatial omics data, where current frameworks trained on limited datasets struggle to correct batch effects, capture cross-modality variation, and generalize across species. MethodsWe developed Nephrobase Cell+, the first kidney-focused large foundation model, pretrained on ~100 billion tokens from ~39.5 million single-cell and single-nucleus profiles across 4,319 samples, four mammalian species (human, mouse, rat, pig), and multiple assay modalities (scRNA-seq, snRNA-seq, snATAC-seq, spatial transcriptomics). Nephrobase Cell+ uses a transformer-based encoder-decoder architecture with gene-token cross-attention and a mixture-of-experts module for scalable representation learning. ResultsNephrobase Cell+ sets a new benchmark for kidney single-cell analysis. It produces tightly clustered, biologically coherent embeddings in human and mouse kidneys, far surpassing previous foundation models such as Geneformer, scGPT, and UCE, as well as traditional methods such as PCA and autoencoders. It achieves the highest cluster concordance and batch-mixing scores, effectively removing donor/assay batch effects while preserving cell-type structure. Cross-species evaluation shows superior alignment of homologous cell types and >90% zero-shot annotation accuracy for major kidney lineages in both human and mouse. Even its 1B-parameter and 500M variants consistently outperform all existing models. ConclusionsWith organ-scale multimodal pretraining and a specialized transformer architecture, Nephrobase Cell+ delivers a unified, high-fidelity representation of kidney biology that is robust, cross-species transferable, and unmatched by current single-cell foundation models, offering a powerful resource for kidney genomics and disease research.

genetics↗

bioRxiv2025

A Low-dimensional Manifold Representation of the Human Brain Aging Continuum

Brain aging involves complex structural changes that challenge traditional analytical methods and hinder personalized assessment of brain health. Integrating regional brain alterations into a unified, interpretable representation is difficult due to the high dimensionality of neuroimaging data. Here, we projected regional brain volumes from the Human Connectome Project Aging Dataset onto a low-dimensional manifold that reflects underlying neuroanatomical constraints. We then built a transparent framework on the manifold to estimate brain age and identify key regional drivers of the estimate. By analyzing local neighborhoods on the manifold, we identified distinct structural aging trajectories, including pronounced frontal atrophy occurring predominantly in males. This approach provides a biologically interpretable means of characterizing individual brain-aging patterns, reveals heterogeneous aging pathways, and supports more personalized assessments and insights into the aging process. TeaserA manifold representation can map brain aging patterns across regions and reveal distinct trajectories

bioengineering↗

bioRxiv2025

Genomic and Epigenetic Interplay Drives Adaptive Fusion via Reproduction Trade-Off

Investment in sexual reproduction has long been seen as a fitness cost for asexual proliferation, raising the question of how cells evolve to accommodate cyclical demands of sexual and asexual cycles. We addressed this question by evolving Schizosaccharomyces pombe lacking the critical fusion gene Prm1 through 18 cycles of alternating meiosis and mitosis. Initially, transcriptional tweaks offered a fragile means to fuse despite Prm1s absence. However, a telomeric 1% genome deletion that epigenetically silenced Clr5 ultimately locked in a latent, Prm1-independent fusion pathway involving the mating regulator Ste11 and the pheromone-MAPK scaffold Sms1. This adaptation, though efficient at restoring sexual reproduction, came at the cost of mitotic growth. By contrast, rationally constructing mutations in a "synthetic evolution" approach bypassed the trade-off, enabling simultaneous high fusion efficiency and near-wild-type proliferation. Our findings illustrate how epigenetic de-repression and genetic assimilation converge to create innovative solutions under cyclical selection pressures with trade-offs.

evolutionary biology↗

bioRxiv2025

Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input

Accurate identification of small molecule binders to RNA is critical for chemical probes and therapeutics. Computational approaches offer a cost-effective strategy to identify small molecules targeting RNA but are often limited by poor predictive accuracy and high computational demands. Here, we introduce Small Molecule Approaches to RNA Targeting Binder Discovery (SMARTBind), a structure-agnostic ligand discovery framework that combines an RNA large language model with contrastive learning and a ligand-specific decoy enhancement strategy. The RNA language model, pre-trained on millions of RNA sequences, together with the decoy enhancement strategy, addresses data scarcity and improves model generalizability. SMARTBind uses only RNA primary sequence to identify small molecule binders and their binding sites accurately. Across multiple benchmarks and case studies, SMARTBind outperforms existing data-driven and docking-based methods while significantly reducing computational cost. In a real- world application, SMARTBind identified novel small molecules targeting the precursor of oncogenic microRNA-21, validated by in vitro and cellular assays. These results highlight SMARTBinds potential as a scalable, accurate, and structure-independent platform for RNA-targeted small molecule discovery.

bioinformatics↗

bioRxiv2025

A New Aneurysm Rupture-Prone Marfan Mouse Model with FBN1Q2467X Nonsense Mutation Reveals Adventitial Inflammation

Marfan syndrome (MFS) is a genetic disorder caused by mutations in fibrillin-1(FBN1), which encodes FBN1, a key structural component of the extracellular matrix. Mutations in FBN1 influence the severity of aortic disease and therapeutic responses, with aortic aneurysm being the leading cause of mortality in patients with MFS. To investigate the mechanisms driving aneurysm progression, we generated a mouse model (Fbn1Q2469X/+) carrying the FBN1Q2467X nonsense mutation identified in MFS patients. This mutation results in FBN1 deficiency. Although Fbn1Q2469X/+ mice appear normal, showing only mild, nonprogressive dilation of the aortic root and ascending aorta with minor reductions in blood pressure, homozygous Fbn1Q2469X/Q2469X mice develop spontaneous thoracic aortic aneurysms (TAA) that progress to rupture between 10 and 25 days of age, with 100% penetrance. Histopathology shows progressive vessel wall degeneration characterized by disorganized vascular smooth muscle cells, collagen loss, and elastic fiber fragmentation from early to late stages. RNA-seq analysis identifies inflammation as the dominant process in late-stage aneurysms. Immunofluorescence assay reveals inflammatory cells prominently localized to the adventitia near rupture sites, linking adventitial inflammation to aneurysm progression. This genetically modified Fbn1Q2469X/Q2469X mouse model consistently develops progressive aortic aneurysms and provides a reliable, cost-effective platform to investigate the molecular mechanisms of aneurysm progression and to evaluate therapeutic strategies in aneurysm diseases, including Marfan syndrome and related disorders.

genetics↗

bioRxiv2025

Deciphering acquired resistance mechanisms to sustained auxin-inducible protein degradation in cells and mice

Targeted protein degradation is a favorable strategy for studying the immediate downstream effects of protein loss-of-function. An appealing platform among these technologies is the auxin-inducible degron (AID) system. Although this system has been applied extensively to cell and animal models, degradation resistance to long-term auxin treatment has not been studied. With the advent of the new AID2 system, cellular toxicity due to the high concentrations of auxin required in the original AID1 system is no longer a concern, making it possible to study protein degradation over extended periods. In this study, we derived multiple miniAID-tagged knock-in human cell lines and a Ctcf-miniAID knock-in mouse strain to investigate mechanisms of degradation resistance. We revealed four independent resistance mechanisms, including a nonsense mutation in the CTCF coding sequence that removed the miniAID peptide, a missense point mutation in the miniAID coding region that disrupted ubiquitin complex targeting, and silencing of the OsTIR1 adaptor protein. Resistance to auxin degradation was also acquired in mouse primary CtcfminiAID/miniAID knock-in B-ALL cells through missense mutations of the OsTIR1(F74G) protein in vivo and ex vivo. In summary, our innovative study expands our understanding of the AID system and cautions careful consideration of design for future applications in mammalian system.

cell biology↗

bioRxiv2025

Illuminating the Virosphere's Dark Matter using Hierarchical Deep Learning

Systematic discovery of novel viruses is essential for pandemic preparedness, understanding tumor-associated viruses, developing viral delivery systems, and advancing biomedical applications. Yet, the majority of sequences in metagenomic datasets lack close relatives in existing references, representing a vast viral "dark matter" whose biology and evolution remain largely unknown. The central task is threefold: 1) to determine whether a genome is viral or non-viral, 2) to correctly assign viral genomes to known lineages when possible, and, critically, 3) to recognize when no existing lineage applies and thereby identify candidates for entirely novel viral groups. Existing approaches, which depend on sequence homology or narrow markers, struggle to capture this uncharted viral space. Here we present DeepVirus, a hierarchical transformer-based framework that models viral genomes as structured sequences of protein-coding genes. By combining protein-level embeddings from a foundation model with genome-aware representations, DeepVirus not only achieves accurate classification across deep taxonomic hierarchies, but also extends beyond conventional classification to detect and organize candidate novel viral lineages through open-set recognition. Applied to large-scale metagenomic resources, DeepVirus uncovered extensive viral diversity, including previously uncharacterized RNA-dependent RNA polymerases (RdRps), thereby expanding the known evolutionary space of RNA viruses. DeepVirus integrates deep learning with genome-aware open-set discovery to illuminate viral dark matter, providing a foundation for systematic viral taxonomy and advancing exploration of the global virosphere, with broad implications for safeguarding human health.

bioinformatics↗

bioRxiv2025

Synthesis and In Vitro Characterization of OGA-2506 as a High Affinity Radioligand for O-GlcNAcase

O-GlcNAcase (OGA) is a glycoside hydrolase that regulates protein O-GlcNAcylation, a dynamic post-translational modification implicated in numerous cellular processes. Dysregulation of OGA alters cellular O-GlcNAc homeostasis and has been linked to neurodegenerative and other chronic diseases. The development of radioligands targeting OGA, particularly those derived from well-characterized tool compounds, could substantially advance drug discovery in this area. Herein, we report the radiosynthesis of a novel tritium (3H)-labeled radioligand 7 (code name [3H]OGA-2506) derived from a chiral piperidine scaffold, and its preliminary in vitro binding evaluation. Starting from iodine precursor 8, palladium-catalyzed tritiation afforded [3H]7 with excellent molar activity (1822 GBq/mmol) and high radiochemical purity (>99%). Saturation binding studies revealed that [3H]7 binds OGA with high affinity to rat striatum homogenates (Kd = 3.56 nM; Bmax = 42.62 nM). Competition assays yielded an IC50 of 5.55 nM, and preliminary autoradiography demonstrated heterogeneous regional distribution in the brain with specific binding. These findings highlight [3H]7 as a valuable tool for OGA binding studies and provide a foundation for the future development of novel positron emission tomography (PET) ligands to probe O-GlcNAc signaling in the brain.

pharmacology and toxicology↗

bioRxiv2025

Per- and Polyfluoroalkyl Substances Induces Salt-Sensitive Hypertension by Upregulating Epithelial Sodium Channel - The First Experimental Evidence Supporting Causality

Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals found in the plasma of 98% of Americans. Epidemiological studies associate PFAS exposure with hypertension and kidney dysfunction, but causality and mechanisms remain unclear. We examined the effects of a mixture of 4 PFAS commonly detected in humans, including PFOA, PFOS, PFHxS, and PFNA, on blood pressure, salt sensitivity, and renal injury in 129S6 mice. Exposure to a lower dose for 3 weeks produced plasma PFAS levels in mice resembling occupational and regional environmental exposures; while a upper dose achieved levels similar to PFAS production workers. PFAS induced dose-dependent pressor effects in male but not female mice on a 0.4% low salt diet. During 4% high salt feeding, PFAS induced greater salt-sensitive hypertension in male mice, accompanied by glomerulopathy, interstitial fibrosis, and a trend towards increased albuminuria. Pressor effects were independent of plasma norepinephrine. Single-cell RNA sequencing of kidneys revealed most transcriptional changes in proximal tubule, thick ascending limb, and collecting duct, with enrichment of pathways in cholesterol synthesis, mitochondria respiration, ATP production, and transmembrane transporter activity. PFAS markedly increased the mRNA and protein of the pore-forming subunit of epithelial sodium channel (ENaC), with no change in {beta}ENaC and a slight reduction in {gamma}ENaC protein. Elevated ENaC coincided with a 30% decrease in Nedd4-2 phosphorylation (Ser448), suggesting reduced ENaC ubiquitination and degradation. However, protein expression of 1 Na+-K+-ATPase and serum- and glucocorticoid-regulated kinase 1 (SGK1) as well as SGK1 phosphorylation (Ser78) were unaltered. Amiloride abolished salt-induced hypertension in lower-dose mice but only partially corrected hypertension in the upper dose group. Taken together, our results provide causal evidence that PFAS exposure promotes hypertension, salt sensitivity, and kidney injury via renal epithelial mechanisms, supporting and extending human epidemiologic observations. Translational StatementOur findings establish four PFAS as causal drivers of salt-sensitive hypertension and kidney injury through convergent effects on ENaC and other tubular sodium transporters. These results not only provide a mechanistic explanation for epidemiologic associations but also identify PFAS as environmental amplifiers of dietary sodium risk. Given the ubiquity of human exposure, reducing PFAS burden alongside salt reduction may represent a complementary strategy to curb the global epidemic of hypertension and kidney disease.

physiology↗

bioRxiv2025

Endothelial CEPT1 Regulates Hepatic MTTP-Mediated Lipid Metabolism and Impacts Aortic Atherosclerosis

BackgroundThe regulation of hepatic lipid metabolism by vascular endothelial factors remains poorly characterized, despite its relevance to atherosclerosis and steatosis. Microsomal triglyceride transfer protein (MTTP) is essential for hepatic lipid metabolism, but its regulation by endothelial cells has not been previously investigated. ObjectiveThis study examined whether endothelial choline ethanolamine phosphotransferase 1 (CEPT1) modulates hepatic MTTP activity, impacting systemic lipid homeostasis and aortic plaque formation. Methods and ResultsHuman steatotic liver samples exhibited reduced CEPT1 and MTTP protein levels, correlating with diminished lipid exports. In mice, endothelial-specific Cept1 knockdown decreased hepatic MTTP expression, reduced serum triglyceride and cholesterol levels, and markedly attenuated aortic atherosclerosis without evidence of fat malabsorption. In vitro, endothelial CEPT1 silencing suppressed MTTP activity in co-cultured hepatocytes via a paracrine mechanism involving peroxisome proliferator-activated receptor (PPAR) signaling, which was rescued by fenofibrate treatment. Aortic histology confirmed reduced plaque burden and macrophage infiltration in CEPT1-deficient mice. ConclusionsEndothelial CEPT1 critically regulates hepatic MTTP through a paracrine axis, influencing lipid metabolism and atherogenesis. Targeting endothelial CEPT1 may represent a novel therapeutic approach to reduce steatosis and vascular atherosclerosis.

molecular biology↗

bioRxiv2025

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones

Sea anemones occupy the full depth of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades. Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families-- including the complete circadian toolkit--were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, Rad21, Mlh3), indicating a shift towards asexual reproduction. Despite this extensive genomic erosion, deep-sea anemones exhibit sophisticated molecular tuning: specific amino-acid substitutions enhance protein stability and activity under deep-sea conditions, while selective expansions of gene families related to neural excitability, membrane systems, etc., likely mitigate the suppressive environmental effects on vital physiological processes. Enzyme activity assays in the yeast system confirm that the deep-sea variants exhibit superior activity and enhanced growth at 4{degrees}C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

evolutionary biology↗

bioRxiv2025

Molecular architecture of OXGR1 reveals evolutionary conserved mechanisms for metabolite surveillance

The ability of cells to sense and respond to metabolic signals is fundamental to life, yet the molecular mechanisms underlying metabolite surveillance remain incompletely understood. Here, we elucidate the structural basis of metabolite recognition by OXGR1, a GPCR that monitors key intermediates in the tricarboxylic acid cycle (TCA). Using cryo-electron microscopy, we determined four cryo-EM structures of OXGR1 bound to -ketoglutarate (AKG), itaconate (ITA), and structural related succinate (SUC) and maleate (MA). These structures reveal a positively charged binding pocket and an extensive hydrogen-bond network critical for OXGR1 recognizing dicarboxylic acids. In addition, we identify a distinct arrangement of hydrophobic residues that modulates ligand potency and selectivity. Mutational analysis and molecular dynamics simulations further demonstrate that non-canonical micro-switch motifs, including FRY and NLxxY, are essential for ligand recognition and receptor activation. Comparative structural and evolutionary analyses indicate that these mechanisms are conserved across species, underscoring the critical role of OXGR1 in maintaining metabolic homeostasis. Together, our findings provide a mechanistic framework for metabolite sensing via OXGR1 and suggest potential strategies for therapeutic modulation of metabolic and inflammatory diseases.

molecular biology↗

bioRxiv2025

Genome Sequencing of Rice Landraces from the Yuanyang Terraces Uncovers Ancient and Diverse Lineages of Indica Rice

High-yielding elite rice cultivars exhibit limited genetic variability, raising concerns about our capacity to sustain productivity in the face of changing biotic and abiotic threats. Meeting the challenges that lie ahead largely depends on our ability to make use of novel sources of genetic variation and re-engineer agrosystems. Here, we report on the evolutionary history and population genetic structure of 353 accessions representing 91 landraces from Chinas centuries-old Yuanyang terraces of rice paddies (YYT). We found that the indica YYT landrace population is genetically structured and exhibits high standard variation. Analysis of natural selection reveals that innate immunity genes have a marked difference in coevolutionary dynamics between modern and traditional rice, characterized by a stronger influence of directional selection, which reduces diversity, in modern varieties. Our study highlights the importance of preserving landraces and the need for targeted efforts to integrate the standing variation in landraces into new varieties.

evolutionary biology↗

bioRxiv2025

The 'Iceberg region of the Grapevine leafroll-associated virus 3 replicase polyprotein contains signals for mitochondrial targeting and outer membrane association

Positive-sense single-stranded (+ss) RNA viruses such as Grapevine leafroll-associated virus 3 (GLRaV3) replicate their genomes within membrane-bound viral replication complexes (VRCs). The biogenesis of such VRCs is driven by viral "replicase" polyproteins containing several replication-related domains. Past electron microscopy evidence suggests that GLRaV3 forms VRCs from the outer mitochondrial membrane of host grapevine plants. Here, we report the subcellular localization of the replicase polyprotein encoded by GLRaV3 ORF1a (PP1a) towards understanding its putative role in VRC formation. Through confocal laser scanning microscopy analysis of distinct EGFP-tagged PP1a domains, interdomain regions and truncations expressed in model plants, we report the molecular signals responsible for the targeting and association of PP1a to the mitochondria. This signal, located in the "Iceberg" region downstream from the methyltransferase-guanylyltransferase (M/GTase) domain, comprises an amphipathic -helix and a downstream transmembrane domain (TMD). Mutagenesis studies suggest that the polar face of the amphipathic -helix functions as the targeting signal, whereas the non-polar face, together with the TMD, act in membrane-anchoring. Microscopy observations are confirmed through mitochondrial isolation via gradient centrifugation and Western blotting. Structure prediction of the GLRaV3 M/GTase domain and its downstream TMD suggests a putative dodecameric oligomeric state. This dodecamer may gate the neck of GLRaV3 VRCs and contribute to their biogenesis, a hypothesis to be tested in follow-up studies. SIGNIFICANCE STATEMENTPositive-sense RNA viruses such as GLRaV3 form specialized membrane-bound viral replication complexes (VRCs) within host cells to sequester viral genome replication. Past evidence suggests that GLRaV3 targets the outer mitochondrial membrane (OMM) of grapevine host cells for VRC formation, however the viral protein responsible remained unknown. Here, we report a newly identified amphipathic -helix and a downstream transmembrane domain in the replicase polyprotein encoded by GLRaV3 ORF1a that are crucial for OMM targeting and membrane association. Since OMM targeting mechanisms in plants are poorly understood, our findings not only shed light on how GLRaV3 assembles VRCs, but also provides insight into OMM targeting more broadly. This work lays the foundation towards elucidating the molecular mechanisms of GLRaV3 replication and host-pathogen interactions.

plant biology↗

bioRxiv2025

Albumin-STING Nanocomplex Reprograms HSPCs to Antitumor Neutrophils with Enhanced MHC I Antigen Presentation for Cancer Immunotherapy

Tumor-associated immunosuppressive neutrophils, termed myeloid-derived suppressor cells (MDSCs), compromise cancer immunotherapy. They can be pathologically programmed as early the hematopoietic stem and progenitor cell (HSPC) stage by suppressing interferon signaling. Reprogramming HSPCs toward antitumor neutrophils through the stimulator of interferon genes (STING) activation offers a promising therapeutic strategy. Here, we demonstrate that an albumin-STING nanoagonist (Nano ZSA-51D) reprograms HSPCs to generate antitumor neutrophils, enhancing MHC I-mediated CD8 T cell immunity. Nano ZSA-51D activates STING-interferon signaling in HSPCs, promoting their expansion and differentiation toward granulocyte-monocyte progenitors via STING-NF-{kappa}B-IL-6 signaling. It further reprograms neutrophils into CD14ICAM-1+ subset through STING-NF-{kappa}B-TNF- signaling, enhancing tumor infiltration. These neutrophils upregulate interferon signaling and MHC I antigen presentation, boosting tumor-specific CD8 T cell responses. Adoptive transfer of Nano ZSA-51D-reprogrammed neutrophils with -PD1 therapy achieves complete colon tumor remission. Our findings provide a novel strategy to reprogram HSPCs toward antitumor neutrophils and highlight the potential of early interventions at HSPC stage to rewire neutrophil fate for cancer immunotherapy.

immunology↗

bioRxiv2025

RNA helicase Ddx21 safeguards fetal HSPC expansion by recruiting Kdm5a to epigenetically sustain ribosomal and hematopoietic gene transcription

Fetal hematopoietic stem and progenitor cells (HSPCs) require active ribosome biogenesis to sustain their rapid proliferation, yet how non-structural ribosomal factors regulate this process remains unclear. Here, we identify the RNA helicase Ddx21 as a critical determinant of fetal hematopoiesis through its epigenetic role in maintaining active ribosomal transcription. Conditional knockout of Ddx21 in murine fetal hematopoietic cells resulted in severe anemia, fetal liver hypoplasia, and depletion of HSPCs, accompanied by erythroid maturation arrest. Mechanistically, Ddx21 deficiency disrupted ribosomal and hematopoietic gene expressions, impaired translational capacity, and activated p53 pathway, triggering cell cycle arrest and apoptosis. While p53 inhibition partially rescued proliferation defects, it failed to restore rRNA transcription, pointing to p53-independent mechanisms. Multi-omics profiling revealed that Ddx21 interacts with the histone demethylase Kdm5a, co-occupying active promoters marked by H3K4me3. Loss of Ddx21 diminished H3K4me3 levels at ribosomal DNA (rDNA) and hematopoietic genes such as cKit and Gata1, downregulating their transcription. Strikingly, Kdm5a inhibition restored rRNA expression and protein translation in Ddx21-deficient cells, and combined inhibition of Kdm5a and p53 cooperatively rescued HSPC function. These findings demonstrate a paradigm wherein Ddx21 couples ribosome biogenesis to epigenetic regulation by sequestering Kdm5a at active chromatin, thereby preserving transcriptional output essential for fetal hematopoietic expansion.

cell biology↗

bioRxiv2025

Guess till correct: Gungnir codec enabling high error-tolerance and low-redundancy DNA storage through substantial computing power

DNA has emerged as a compelling archival storage medium, offering unprecedented information density and millennia-scale durability. Despite its promise, DNA-based data storage faces critical challenges due to error-prone processes during DNA synthesis, storage, and sequencing. In this study, we introduce Gungnir, a codec system using the proof-of-work idea to address substitution, insertion, and deletion errors in a sequence. With a hash signature for each data fragment, Gungnir corrects the errors by testing the educated guesses until the hash signature is matched. For practicality, especially when sequenced with nanopore long-read, Gungnir also considers biochemical constraints including GC-content, homopolymers, and error-prone motifs during encoding. In silico benchmarking demonstrates its outperforming error resilience capacity against the state-of-art methods and achieving complete binary data recovery from a single sequence copy containing 20% erroneous bases. Gungnir requires neither keeping many redundant sequence copies to address storage degradation, nor high-coverage sequencing to address sequencing error, reducing the overall cost of using DNA for storage.

bioinformatics↗

bioRxiv2025

WSB-1 regulates DNA repair and the response to DNA damage response inhibitors in breast cancer

Tumour hypoxia is a poor prognostic factor and linked with metastatic spread and treatment resistance in most solid tumours, including breast cancer. We previously showed hypoxia-regulated E3 ligase WSB-1s association with poor prognosis in breast cancer. Here, we evaluated the role of WSB-1 in DNA repair regulation in breast cancer, and whether these phenotypes can be exploited therapeutically. WSB-1 knockdown led to transcriptome-wide DNA repair factor upregulation, including homologous recombination (HR) factors BRCA1and RAD51. Reciprocally, WSB-1 overexpression led to downregulation of these repair factors and decreased DNA repair capacity. Patient gene expression datasets analyses also showed an inverse correlation between WSB1 expression vs DNA repair and HR pathways. HR-deficient cancers, including BRCA1/2-deficient breast cancers, are extremely sensitive to PARP inhibitors, a phenotype described as BRCAness. We therefore hypothesised if high WSB-1 expression could be similarly exploited therapeutically. WSB-1 overexpression alone radiosensitised cells and led to increased Olaparib (PARP inhibitor) and Berzosertib (ATR inhibitor) sensitivity in vitro. Our study indicates that WSB-1 expression in breast cancer is associated with modulation of HR factor expression, and we propose that elevated WSB-1 expression could be considered as a potential BRCAness biomarker and promote increased sensitivity to DNA repair targeted therapy in these patients.

cancer biology↗