Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 379 records · Page 21Linked to original sources

bioRxiv2025

Longevity in plants impacts phylogenetic and population dynamics

Many long-lived plant species exhibit notable patterns in phylogenies, such as short molecular branch lengths and high gene-tree conflict. However, it is not clear what biological properties of long-lived plant species or concomitant processes acting within these lineages generate these patterns. To explore this mystery, we implemented an agent-based model and conducted simulations to investigate how longevity affects molecular evolution and population dynamics. Through these simulations, we demonstrated that the patterns exhibited in empirical datasets for long-lived species can be explained by their lifespan and overlapping generations. We also show that somatic mutations can exacerbate these patterns, although evidence for substantive rates in empirical systems high enough to impact phylogenetic patterns is scarce. We discuss several empirical datasets containing life history shifts that exhibit diverse phylogenomic patterns. The variation produced through different parameterizations of our simulations reflects the diversity of patterns found in empirical datasets. Our results have broad implications for phylogenomic patterns and population genetics in general, as well as for specifically explaining patterns of evolution in long-lived lineages.

evolutionary biology↗

bioRxiv2025

High-throughput Single-cell Proteomics Enabled by an Integrated Hyperplexing and Automatic Labelling Approach without Fractionation

Single-cell proteomics (scProteomics) enables comprehensive analysis of protein composition, expression and functions at the single-cell level. While label-free techniques have generated promising results, achieving high-throughput scProteomics remains a substantial challenge. In this study, we present an approach that increases scProteomics throughput by approximately 30-fold through the true integration of isobaric tags (IBT) with tandem mass tags (TMT), a method we term Integral-Hyperplex. Due to remarkable differences in signal response between TMT16 and IBT16 reporter ions, we implemented two normalization strategies to ensure accurate and integrated quantification: (1) the inclusion of a normalization channel in both IBT and TMT groups to serve as internal standards; and (2) the generation of protein-specific conversion factors between IBT16 and TMT16 signals. We validated the quantification accuracy of the Integral-Hyperplex method by labeling HeLa digests at varying ratios. Furthermore, we demonstrated fully automated labeling on the active-matrix digital microfluidics chip, consuming only 12 nL of labeling reagent per single cell and with a reaction volume as low as 20 nL. Our approach was validated through proof-of-principle quantification experiments across three types of single cells. Approximately 2,000 protein groups were quantified per cell, and the three cell types can be well clustered, confirming the reliability of the Integral-Hyperplex approach. Approximately 300 samples can be analyzed per day due to insufficient resolution of timsTOF SCP. Throughput can be further enhanced using TMT32, additional labeling reagents, and more advanced mass spectrometers such as Orbitrap Astral and timsTOF Ultra 2, and our approach is theoretically capable of analyzing up to [~]2,000 single cells per day.

biochemistry↗

bioRxiv2025

BiGER: Bayesian Rank Aggregation in Genomics with Extended Ranking Schemes

With the rise of large-scale genomic studies, large gene lists targeting important diseases are increasingly common. While evaluating each study individually gives valuable insights on specific samples and study designs, the wealth of available evidence in the literature calls for robust and efficient meta-analytic methods. Crucially, the diverse assumptions and experimental protocols underlying different studies require a flexible but rigorous method for aggregation. To address these issues, we propose BiGER, a fast and accurate Bayesian rank aggregation method for the inference of latent global rankings. Unlike existing methods in the field, BiGER accommodates mixed gene lists with top-ranked and top-unranked genes as well as bottom-tied and missing genes, by design. Using a Bayesian hierarchical framework combined with variational inference, BiGER efficiently aggregates large-scale gene lists with high accuracy, while providing valuable insights into source-specific reliability for researchers. Through both simulated and real datasets, we show that BiGER is a useful tool for reliable meta-analysis in genomic studies.

genomics↗

bioRxiv2025

Dynamic growth trajectories distinguish bacteriostatic and bactericidal antibiotics at subinhibitory concentrations

Subinhibitory antibiotic exposures are common in clinical and environmental contexts, yet their effects on bacterial growth dynamics remain incompletely understood. We studied the temporal response of Escherichia coli to a panel of bactericidal ("cidal") and bacteriostatic ("static") antibiotics at sub-minimum inhibitory concentrations (sub-MIC). We uncover a sharp dynamical distinction between the two classes. Bacteriostatic antibiotics reduce the initial growth rate in a dose-dependent manner, similar to a nutrient starvation response. In contrast, bactericidal antibiotics do not alter initial growth rates - cells continue to grow as fast as untreated cells - until an abrupt slowdown in growth rate. The onset of slowdown occurs earlier with increasing dose, suggesting a damage accumulation mechanism leading to a lethal threshold. Cidals also show a steeper dose-response curve. We propose that bacteria respond to cidal antibiotics with a "grow-fast-then-crash" strategy that is adaptive for transient lethal threats, whereas static antibiotics trigger stress adaptation and slower growth. While clinical outcomes of statics and cidals may be similar at full inhibitory doses, these sub-MIC dynamical signatures could influence resistance evolution and treatment outcomes in biofilms or partially resistant strains. Our findings offer a dynamic framework for antibiotic classification and raise new questions about how bacteria respond to sublethal antibiotic stress.

systems biology↗

bioRxiv2025

Bacteriophage diversity declines with COPD severity in the respiratory microbiome

Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterised the lung virome by re-analysing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. Whilst viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Phages infecting anaerobic oral bacteria showed disproportionately lower abundance--Porphyromonas phages were 40-fold less abundant despite only 4-fold lower bacterial abundance--whilst pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonised patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognised feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.

microbiology↗

bioRxiv2025

Treating Myotonic Dystrophy with artificial RNA endonucleases to specifically degrade toxic RNA expansions

Myotonic dystrophy type 1 (DM1), the most common autosomal dominant muscular disorder, is driven by expanded CUG repeats in the 3' UTR of DMPK gene, which sequester RNA-binding proteins and cause aberrant alternative splicing. Despite extensive study, no effective treatment exists, and current care remains limited to symptomatic management. Using a customized dual-color reporter carrying RNA repeats in different lengths, we engineered a new class of programmable artificial enzymes (artificial RNA cleavers, or ARCs) that preferentially degrade the pathogenic repeats both in cells and in a mouse model. We further examined the in vivo efficacy of ARCs by systematically delivering ARCs into the DM1 mouse model with muscle-specific adeno-associated viruses, and validated that ARCs can rescue the muscular pathology and movement ability. The treatment by ARCs showed sustained efficacy, low immunogenicity, and minimal off-target effects in animal model, which are key concerns in clinical translation of gene therapies. Collectively, these findings establish ARCs as a potent and precise RNA-targeting platform with strong clinical potential for the treatment of DM1 and other repeat expansion disorders.

synthetic biology↗

bioRxiv2025

Deciphering the microbial landscape of lower respiratory tract in health and respiratory diseases

The microbiota plays an important role in maintaining lung homeostasis and the development of respiratory diseases. However, there have not been detailed characteristics of lung microbiome in health and respiratory diseases. Bronchoalveolar lavage fluid of 43 healthy individuals, 23 COVID patients, and 28 non-small cell lung cancer patients was conducted to characterize microbial diversity and function by metagenomic sequencing. We identified 196 species in health lung after removing low abnudance species. The most abundant species were Staphylococcus aureus, Salmonella enterica, and Klebsiella pneumoniae. Keystone species were identified through co-network analysis, such as Granulicatella adiacens and Mogibacterium diversum. To further explore the microbial function in the healthy lung, we obtained 56 non-redundant metagenome-assembled genomes (MAGs) and subsequently classified them into nine phyla. Metabolism and genetic information processing exhibit high abundance, including bacterial secretion systems, protein export, and Staphylococcus aureus infection, indicating a close correlation between microbiota and the host. Furthermore, the microbiome pairwise distances of non-small cell lung cancer (NSCLC) participants were more similar to those of the healthy group than those of individuals with COVID-19. Rothia dentocariosa, Corynebacterium kefirresidentii, Sphingobium yanoikuyae were enriched in the healthy group, while Schaalia odontolytica, Actinomyces graevenitzii, and Rothia mucilaginosa was enriched in the NSCLC group. Overall, this study provides a comprehensive overview of the diversity and gene function of the lung microbiome, which will facilitate future studies of microbiota associated with respiratory diseases in humans.

microbiology↗

bioRxiv2025

Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine

The mammalian intestine regenerates rapidly after damage, yet the clonal dynamics and species-specific regulation of different populations remain poorly understood. Here we used synthetic or naturally occurring DNA alterations to reconstruct clonal histories of the mouse and human intestinal epithelium at single-cell resolution. In mice, we uncovered the clonal architecture of different cell types and their roles in regeneration, supporting a hierarchical regenerative response model. We identified a rare embryonic precursor population that persisted in the adult and was crucial for regeneration after irradiation. This population was marked by Tob2, which is required for nuclear transport of Ascl2. A parallel clonal analysis of 65 human colonic biopsies revealed secretory lineage bias and an age-associated decline in clonal diversity in the distal colon. Unlike highly proliferative murine Lgr5+ stem cells, human LGR5+ cells were found largely quiescent, revealing species-specific difference in clonal potency, and suggesting a distinct regulation of intestinal stemness.

genomics↗

bioRxiv2025

Hyperpolarization activated cation channel mediated intrinsic plasticity changes underlie the malleability of with-in cell-type electrophysiological heterogeneity

Within cell-type neuronal electrophysiological, morphological, and transcriptomic heterogeneity is the norm in the brain. Although generally considered a fixed property within cell-types, this heterogeneity is malleable and declines in regions of the human brain that generate seizures. Building off this foundational work we hypothesize that such plasticity of cell-type heterogeneity, specifically its decline, arises from the shared history of neuronal activity that drive intrinsic plasticity mechanisms in a concerted fashion. To explore this hypothesis we study neuronal activity in two model systems: human cortical slice cultures from patients with epilepsy as well as slices from the medial prefrontal cortex (mPFC) and subiculum of rodent kainic acid (KA) model of temporal lobe epilepsy. Biophysical properties and spiking dynamics were characterized using whole-cell patch clamp recordings of layer 2 and layer 3 (L2&3) pyramidal neurons in human slice culture as well as deep layer subicular neurons and layer 5 (L5) mPFC of KA mice. We found a significant decline in biophysical heterogeneity and a reduction in information coding in both the KA and slice culture models. In both these models we found a consistent increase in hyperpolarization-activated cation current (HCN) dependent electrophysiological properties, the blockade of which restored electrophysiological heterogeneity and information coding. Our findings demonstrate that within cell-type heterogeneity is malleable, and despite being a complex distributed network property, can be tuned by a single ionic current. These findings emphasize the plasticity of within cell-type heterogeneity, suggesting the potential for targeted interventions to restore neuronal heterogeneity changes that accompany epilepsy and potentially other neurological and neuropsychiatric diseases.

neuroscience↗

bioRxiv2025

Phytoene synthase modulates seed longevity via the action of β-carotene derived metabolites

Seed longevity, the seeds ability to stay viable over time, is an important trait in agriculture. Despite extensive research, seed longevity remains one of the fundamental topics in plant biology. Here, we discovered the novel role of carotenoid metabolites in prolonging seed lifespan. We found that phytoene synthase (PSY), the gene encoding a major rate-limiting enzyme in carotenoid biosynthesis, modulated seed storability in Arabidopsis under both natural and artificial aging conditions. Seeds from the PSY overexpression (OE) lines exhibited significantly enhanced lifespan with low levels of reactive oxygen species (ROS), a major factor affecting longevity, whereas those from the psy mutants had decreased viability with high ROS levels. While lutein and {beta}-carotene were detected in seeds, only {beta}-carotene and its derived apocarotenoids, i.e. {beta}-cyclocitral and {beta}-ionone, were found to improve seed lifespan. Notably, the carotenoid cleavage dioxygenase 1 and 4 (ccd1 ccd4) double mutant and PSY ccd1 ccd4 seeds showed significantly reduced seed longevity, indicating that {beta}-carotene cleavage is necessary for or it is apocarotenoids playing the role in preserving seed lifespan. Comparative proteomic analysis identified TIP2;2, an aquaporin protein, which showed differential abundances in seeds of PSY OE and psy mutant vs wild type. The mutant tip2;2 had reduced seed longevity, and its promoter was transactivated by apocarotenoids. Collectively, this study uncovers a novel role of apocarotenoids in protecting seed longevity and highlights the importance of seed carotenoid production in strengthening agriculture. One Sentence SummaryPhytoene synthase, the gene encoding a major rate-limiting enzyme in carotenoid biosynthesis, modulates seed longevity via {beta}-carotene derived apocarotenoids and an aquaporin protein TIP2;2 identified is a new player that responds to apocarotenoid signaling and influences seed longevity.

plant biology↗

bioRxiv2025

Effect and Mechanism Analysis of Melittin on Promoting Muscle Differentiation of Adipose Stem Cells

PurposeMelittin is the main peptide component of melittin venom, with anti-allergic, anti-inflammatory, anti-arthritis, anti-cancer, and neuroprotective effects. Melittin has been confirmed to have anti-inflammatory effects in immune and liver cells and is widely used in treating arthritis and rheumatic diseases. At the same time, related studies have shown that melittin can enhance the expression of muscle differentiation related factors in mice. However, whether the melittin can improve the expression of stem cells into muscle differentiation and use it to treat Skeletal muscle atrophy, it has not yet been clarified.As "seed cells," stem cells have been widely concerned in the field of regenerative medicine research, such as embryonic stem cells, induced pluripotent stem cells, mesenchymal stem cells, etc., among which adipose mesenchymal stem cells (ADSCs) have excellent application potential in the treatment of Skeletal muscle atrophy because of their quantitative advantages, easy access, and inherent good differentiation potential and self-renewal ability. To investigate whether melittin can stimulate ADSCs MYOGenic differentiation and whether combined with ADSCs can treat Skeletal muscle atrophy. MethodsO_LIFour concentration ranges of melittin were set, namely Group A (20 mg/L, 40 mg/L, 80 mg/L, 160 mg/L, 320 mg/L), Group B (2 mg/L, 4 mg/L, 8 mg/L, 16 mg/L, 32 mg/L), Group C (0.2 mg/L, 0.4 mg/L, 0.8 mg/L, 1.6 mg/L, 3.2 mg/L), and Group D (0.02 mg/L, 0.04 mg/L, 0.08 mg/L, 0.16 mg/L, 0.32 mg/L), Intervention of adipose stem cells with different concentrations of melittin for 48 hours, followed by measurement of relative cell viability using the CCK-8 method. C_LIO_LIMelittin after 48 hours of intervention with ADSCs, Western blot was used to detect the expression levels of MYOGenic differentiation related factors. C_LIO_LIThe control group (C), melittin group (M), dexamethasone group (D), and Dexamethasone+Melittin group (D+M) were set separately. After 12 hours of intervention with dexamethasone (10umol/L), the ADSCs were added with melittin for 48 hours. Western blot was used to detect MYOGenic differentiation related factors MYOGenic(MYOG), MYF5, MYOD, MYH4 p38 and p-p38 protein. In order to observe the process of melittin repairing cell atrophy, detected MYOD and MYOG using immunofluorescence. C_LIO_LIRandomly divided into control group (C), damage group (T), stem cell therapy group (SC), melittin combined with ADSCs therapy group (SC+M). Group C does not do any treatment. Group T, SC, and SC+M set up a mouse shoulder sleeve injury model, all from the left gang of the rats, and the suture is marked with surgical sutures. On the first day of surgery, The SC group of the muscle injecting ADSCs(1x106)in the SC group, and the ADSCs after the melittin intervention of the SC+M mouse is repeatedly treated every seven days. On the left, the tendon is extracted, and the muscles are extracted to perform related tissue-related testing such as Su Mu Jing-Yi Hong dyed (H&E dyed), immunohistochemistry, muscle fiber weight and diameter. C_LI ResultsO_LICCK-8 Experiment shows that the suitable concentration of Melittin has no significant toxic effect on ADSCs. C_LIO_LIWestern blot experiment shows that the appropriate concentration of Melittin can enhance the expression of muscle differentiation related factors in ADSCs. C_LIO_LIWestern blot and immunofluorescence staining results show that the expression related factors of the D+M group are better than that of group D, and the expression related factors of forming muscle differentiation in group M is also better than group C. C_LIO_LIMelittin can promote ADSCs muscle differentiation through the p38-MAPK signaling pathway. C_LIO_LIAnimal experiments have shown that the expression related factors of the SC+M treatment groups muscle differentiation related factors is significantly higher than that of the SC therapy group, and the expression related factors of the two groups of rats of SC+M and SC groups are better than the T group Rat. Organic research has confirmed that rats who have been treated with ADSCs treated with melittin have significantly improved in muscle weight, muscle fiber diameter, and muscle fiber cross-sectional area. At the same time, the result of immunohistochemicals shows that the expression of MYOD and MYOG in the SC+M group is better than the SC group. C_LI ConclusionThe results of this study indicate that melittin can promote MYOGenic differentiation of ADSCs and increase the expression of MYOGenic differentiation related factors in atrophic ADSCs.Secondly, melittin can activate the p38-MAPK signaling pathway and promote the MYOGenic differentiation of ADSCs. Stem cells treated with melittin intervention can improve the recovery of muscle mass, muscle fiber diameter, and muscle fiber cross-sectional area in rats with skeletal muscle injury compared to rats treated with stem cells alone. Therefore, the above results provide insights into MYOGenic differentiation and may provide a potential alternative strategy for related diseases such as skeletal muscle atrophy.

cell biology↗

bioRxiv2025

Discovery of excited state proton transfer in flavin-based fluorescent protein with large Stokes shift

Flavin-binding proteins (flavoproteins) are widespread in nature, revealing versatile oxidation-reduction reactions and photochemistry. Flavoproteins derived from LOV domains are used for engineering of ligh-tresponsive tools in optogenetics, as well as fluorescent markers and photogenerators of reactive oxygen species. Despite extensiev efforts, all currently used LOV-derived proteins have similar absorption spectra with maxima around 275, 35-0375, and 450-485 nm. Here, we describe the discovery of a large Stokes shift flavi-nbased fluorescent protein, LSSFbFP, which can be obtainedin vivo and in vitro, with absorption maxima at 340-350 and 395-405 nm. Fluorescence emission of LSSFbFP mirrors that of classical FbFPs with the maximum at ~500 nm. We sho that the protein binds lumichrome as the chromophore and use low temperature and time-resolved spectroscopy, X-ray crystallography and modeling to prove that the apparent Stokes shift of LSSFbFP occurs due to excited state proton phenomena observed in flavoproteni s and pave the way for engineering of new flavin-based molecular instruments.

biochemistry↗

bioRxiv2025

Examining the Role of Extrachromosomal DNA in 1,216 Lung Cancers

The role of extrachromosomal DNA (ecDNA) in lung cancer, particularly in subjects who never smoked (LCINS), remains unclear. Examination of over 1200 whole-genome-sequenced lung cancers identified ecDNA in 18.9% of patients. Recurrent amplification of MDM2 and other oncogenes via ecDNA possibly drives a LCINS subset. Tumors harboring ecDNA showed worse overall survival than tumors harboring other focal amplifications. A strong association with whole-genome doubling suggests most ecDNA reflects genomic instability in treatment-naive lung cancer.

bioinformatics↗

bioRxiv2025

Global profiling of the proteome and acetylome in mice with abdominal aortic aneurysms

BackgroundAbdominal Aortic Aneurysm (AAA) is a life-threatening vascular condition characterized by a progressive dilation of the abdominal aorta and a high risk of rupture. Currently, no effective pharmacological therapies are available, and treatment relies mainly on surgical intervention. The lack of drug targets is largely due to limited understanding of the molecular mechanisms underlying AAA development. This study aims to identify potential therapeutic targets by performing comprehensive proteomic and acetylomic analyses in a mouse model of AAA. MethodsWe conducted global proteomic and acetylomic profiling on abdominal aortic tissues collected from an AAA mouse model. A total of 7,858 proteins and 1,790 acetylated proteins encompassing 4,581 acetylation sites were quantified. Bioinformatics analyses were performed to investigate the regulatory networks and biological pathways associated with these proteins and post-translational modifications. ResultsIntegrated analysis revealed that histone-related proteins were significantly enriched in pathways co-regulated by the proteome and acetylome. These pathways are influenced by histone acetyltransferases and deacetylases, implicating histone acetylation in AAA-related inflammatory and immune processes. Notably, the deacetylases Sirt2 and Sirt5 were identified as potential regulators of neutrophil extracellular trap (NET) formation through suppression of histone acetylation. ConclusionsThis study provides the first comprehensive proteomic and acetylomic dataset for abdominal aortic tissues in a mouse model of AAA, substantially expanding the mouse acetylation database. The results highlight the central role of histone modifications in immune dysregulation and inflammation, and propose Sirt2 and Sirt5 as candidate therapeutic targets that may inhibit NET formation and slow AAA progression. These findings suggest new avenues for drug development targeting the sirtuin family, although further experimental validation and cross-species studies are needed to confirm translational relevance. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/657536v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1c397a3org.highwire.dtl.DTLVardef@188180org.highwire.dtl.DTLVardef@de1a59org.highwire.dtl.DTLVardef@193e740_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Gene therapies alleviate absence epilepsy associated with Scn2a deficiency in DBA/2J mice

Mutations in the voltage-gated sodium channel gene SCN2A, which encodes the NaV1.2 channel, cause severe epileptic seizures. Patients with SCN2A loss-of-function (LoF) mutations, such as protein-truncating mutations, often experience later-onset and drug-resistant epilepsy, highlighting an urgent unmet clinical need for new therapies. We previously developed a gene-trap Scn2a (Scn2agt/gt) mouse model with a global NaV1.2 reduction in the widely used C57BL/6N (B6) strain. Although these mice display multiple behavioral abnormalities, EEG recordings indicated only mild epileptiform discharges, possibly attributable to the seizure-resistant characteristics associated with the B6 strain. To enhance the epileptic phenotype, we derived congenic Scn2agt/gt mice in the seizure-susceptible DBA/2J (D2J) strain. Notably, we found that these mice exhibit prominent spontaneous absence seizures, marked by both short and long spike-wave discharges (SWDs). Restoring NaV1.2 expression in adult mice substantially reduced their SWDs, suggesting the possibility of SCN2A gene replacement therapy during adulthood. RNA sequencing revealed significant alterations in gene expression in the Scn2agt/gt mice, in particular a broad downregulation of voltage-gated potassium channel (KV) genes, including KV1.1. The reduction of KV1.1 expression was further validated in human cerebral organoids with SCN2A deficiency, highlighting KV1.1 as a promising therapeutic target for refractory seizures associated with SCN2A dysfunction. Importantly, delivery of exogenous human KV1.1 expression via adeno-associated virus (AAV) in D2J Scn2agt/gt mice substantially reduced absence seizures. Together, these findings underscore the influence of mouse strain on seizure severity and highlight the potential of targeted gene therapies for treating SCN2A deficiency-related epilepsies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/657652v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@35374eorg.highwire.dtl.DTLVardef@1c22197org.highwire.dtl.DTLVardef@2b4582org.highwire.dtl.DTLVardef@e06e68_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefScn2a deficiency leads to absence seizures in D2J mice and neuronal hyperexcitability with compensatory KV reduction; restoring NaV1.2 or introducing human KV1.1 reduces seizure burden. HighlightsO_LIScn2a deficiency induces robust absence seizures in the DBA/2J but not the C57BL/6N strain. C_LIO_LICortical neurons in adult DBA/2J mice with Scn2a deficiency exhibit intrinsic hyperexcitability. C_LIO_LISevere Scn2a deficiency leads to downregulation of multiple potassium channel genes. C_LIO_LIGenetic restoration of NaV1.2 expression alleviates spike-wave discharges (SWDs). C_LIO_LIAAV-mediated human KV1.1 delivery substantially reduced absence seizures, demonstrating the therapeutic potential of targeted gene therapy. C_LI

neuroscience↗

bioRxiv2025

In silico design and validation of high-affinity RNA aptamers for SARS-CoV-2 comparable to neutralizing antibodies

Nucleic acid aptamers hold promise for clinical applications, yet understanding their molecular binding mechanisms to target proteins and efficiently optimizing their binding affinities remain challenging. Here, we present CAAMO (Computer-Aided Aptamer Modeling and Optimization), which integrates in silico aptamer design with experimental validation to accelerate the development of aptamer-based RNA therapeutics. Starting from the sequence information of a reported RNA aptamer, Ta, for the SARS-CoV-2 spike protein, our CAAMO method first determines its binding mode with the spike proteins receptor binding domain (RBD) through a multi-strategy computational approach. We then optimize its binding affinity via structure-based rational design. Among the six designed candidates, five were experimentally verified and exhibited enhanced binding affinities compared to the original Ta sequence. Furthermore, we directly compared the binding properties of the RNA aptamers to neutralizing antibodies, and found that the designed aptamer TaG34C demonstrated a comparable binding affinity to the RBD compared to the representative neutralizing antibodies analyzed in this study. This highlights its potential as an alternative to existing COVID-19 antibodies. Our work provides a robust approach for the efficient design of a relatively large number of high-affinity aptamers with complicated topologies. This approach paves the way for the development of aptamer-based RNA diagnostics and therapeutics.

biophysics↗

bioRxiv2025

Contrastive Learning-Enhanced Drug Metabolite Prediction Drives the Discovery of an Orally Bioavailable RSK4 Inhibitor for Esophageal Cancer

Drug metabolism liabilities are a major bottleneck in drug development, necessitating accurate metabolite prediction tools. While AI-driven methods have advanced, challenges remain in achieving high-precision, robustness, broad reaction coverage and seamless integration into the drug development workflow. To address this, we first constructed the most comprehensive human-specific drug metabolism database to date, encompassing 11,665 human metabolic reactions and 2,497 high-quality rules. Leveraging this resource, we developed ConMeter (Contrastive learning and feature interaction based Metabolic Reaction prediction), a novel model integrating chemical feature interaction and contrastive learning. ConMeter demonstrates significant improvements, achieving [~]80% accuracy in identifying at least one metabolite within the top 5 predictions and showing an average 25% relative enhancement in ranking true positives compared to state-of-the-art methods. The comprehensive database also expands the range of predictable metabolic reactions. To demonstrate the utility of ConMeter, we integrated it into a metabolite prediction-guided drug design strategy aimed at addressing the low oral bioavailability of a metabolically vulnerable RSK4 lead compound -- a pervasive issue among known RSK inhibitors. This strategy successfully yielded R636, a novel RSK4 inhibitor exhibiting remarkably improved bioavailability (a 63-fold increase, reaching 63% absolute bioavailability) while maintaining its potent activity. Notably, R636 showed favorable safety profile and significant anti-tumor efficacy against esophageal squamous cell carcinoma (ESCC) in vitro and in two distinct patient-derived xenograft (PDX) mouse models. This work introduces ConMeter as a powerful and practical tool for high-accuracy metabolite prediction, demonstrating its potential to accelerate lead optimization, exemplified by the discovery of R636 as a promising orally bioavailable candidate for ESCC.

cancer biology↗

bioRxiv2025

Towards Unmanned Proteomics Data Generation: A Fully Automated Sample-to-Data System for Proteomic Experiments

The {pi}-HuB project requires proteomic measurements of millions of low-input samples that are challenging with current technology. Here, we introduce a pilot {pi}-HuB data factory that features a fully automated sample-to-data system to enable high-throughput digitization of human samples. Our platform, as a proof-of-concept towards unmanned proteomics, was demonstrated to show longitudinal robustness and applied for spatial proteomics and the profiling of plasma and cell lines, thereby serving as the workhorse to drive {pi}-HuB.

biochemistry↗