Biology subjects

Duan, C.

Publications and source records attributed to Duan, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Synthetic inhibitors of pregnancy-associated plasma protein-A regulate IGF-1 signaling in vitro and in vivo

Dysregulation of insulin-like growth factor (IGF) signaling contributes to diverse human diseases. Therapeutic strategies have largely targeted the IGF-1 receptor, but the complexity of the IGF system has limited their clinical efficacy. Pregnancy-associated plasma protein-A (PAPP-A) is a secreted metalloproteinase that regulates local IGF signaling through proteolytic cleavage of IGF-binding proteins (IGFBPs) and represents an attractive therapeutic target. Here, we report the first synthetic PAPP-A inhibitors designed to target the enzyme active site using an IGFBP-5-derived anchor sequence. Replacing the scissile bond with phosphinate or phosphonate moieties yielded potent and selective PAPP-A inhibitors. Cryo-electron microscopy revealed the molecular basis of inhibition and key active-site interactions. The compounds inhibited cleavage of IGFBP-4 and IGFBP-5, two physiological PAPP-A substrates. They suppressed IGF-1 signaling in A549 lung cancer cells, with efficacy comparable to the endogenous PAPP-A inhibitor stanniocalcin-1. They also inhibited Papp-aa-dependent IGF signaling and cell proliferation in wild-type and stc1a-/- mutant zebrafish in vivo in a dose-dependent manner. Together, these findings establish the first class of synthetic, selective PAPP-A inhibitors capable of modulating IGF signaling. They provide new chemical tools for studying and modulating pathological IGF signaling and offer new directions for developing PAPP-A-targeted therapeutic strategies.

biochemistry↗

bioRxiv2026

Genetic regulation of circulating metabolome in cattle

The circulating metabolome is a vital intermediate layer linking genetics to complex phenotypes, yet existing genome-wide studies-even in humans-rarely capture dynamic physiological contexts or cellular regulatory mechanisms. Here, we present the Cattle Metabolome Atlas (https://cattlema.farmgtex.org/), a comprehensive resource of 3,436 plasma metabolites and 4,851 serum metabolites from 4,651 animals with matched sequence-level genotypes across highly dynamic parity and lactation stages. We mapped 728 plasma and 622 serum metabolite quantitative trait loci (mQTL), revealing widespread context-dependent regulatory architectures. Integrating these mQTL with the multi-tissue expression quantitative trait loci (eQTL) and single-cell atlas of 59 tissues demonstrates that 74-79% of mQTL colocalize with eQTL across 29 tissues, prioritizing the liver as the primary systemic hub and resolving metabolic programs at single-cell resolution. Furthermore, we charted 538 causal gene-tissue-metabolite-trait cascades across 11 complex traits in cattle. Finally, cross-species analyses demonstrate partial evolutionary conservation of genetic metabolism between cattle and humans, establishing this atlas as a powerful asset for cattle genetics and genomics, selective breeding, and comparative biology.

genetics↗

bioRxiv2026

Multi-parametric NIR-II fluorescence perfusion imaging towards quantitative stroke evaluation

Preclinical stroke research is severely hampered by the lack of high-throughput, quantitative perfusion imaging tools capable of bridging the gap between functional hemodynamics and structural injury. The emerging second near-infrared (NIR-II) fluorescence imaging offers superior spatial resolution and tissue penetration, but its utility remains restricted by a lack of standardized analysis protocols and inability to resolve in-depth infarct regions. Here, we introduce FIMPA, an integrated analytical framework for standardized, multi-parametric stroke evaluation based on NIR-II fluorescence perfusion imaging. FIMPA systematically processes the image sequence through motion correction and atlas registration to generate an anatomically aligned library of 125 vascular and hemodynamic parameters. Statistical screening identifies 67 stroke-correlated features, enabling objective, data-driven quantification of perfusion deficits. To resolve spatial infarct boundaries, we developed FIMPA-SI (FIMPA Stroke Index), a deep learning-based index utilizing a ViT-UNETR framework. By leveraging self-supervised pre-training with MRI data, FIMPA-SI suppresses dominant vascular signals to translate multi-parametric dynamics into anatomically precise stroke severity maps. Validated in tMCAO mice, FIMPA-SI achieves high spatial concordance with MRI and significantly outperforms conventional laser speckle contrast imaging and single-parameter metrics. FIMPA provides a robust solution for accelerating preclinical therapeutics and advancing optical neuroimaging.

bioengineering↗

bioRxiv2026

Promoter architecture decodes response regulator phosphorylation into distinct transcriptional logics in Pseudomonas aeruginosa

Two-component systems convert environmental signals into transcriptional responses, but how one response-regulator phosphorylation state produces different outputs at different promoters remains unclear. Here we show that promoter architecture determines how the ParR response regulator in Pseudomonas aeruginosa interprets phosphorylation. Phenotypic, transcriptomic, biochemical and promoter-engineering analyses showed that phosphorylation of the conserved ParR receiver residue Asp57 lowered DNA-occupancy thresholds across target promoters. Individual promoters, however, converted this shared increase in binding into activation, repression or phosphorylation-dependent sign switching. Chromosomally D57 ParR variants reproduced these behaviours at endogenous loci and altered antibiotic susceptibility, biofilm formation and virulence-associated phenotypes. Mapping and engineering of representative promoters identified a two-tier cis-regulatory code: half-site sequence compatibility determines productive ParR engagement, whereas spacer length determines regulatory sign and magnitude. Spacer swaps were sufficient to reprogram promoter logic between regulatory modes. These findings separate regulator state from promoter decoding and show how bacterial promoter architecture can diversify the outputs of a shared phosphorylation signal. ImportancePseudomonas aeruginosa is an opportunistic pathogen that survives antimicrobial treatment and adapts to diverse host environments by rapidly changing gene expression. How a single sensory pathway generates different, and sometimes opposing, responses across many genes has remained unclear. We show that the regulatory protein ParR does not impose one fixed transcriptional program. Instead, the DNA architecture of each target promoter determines whether the same phosphorylation signal activates, represses, or reverses gene expression. The sequence and spacing of ParR recognition sites form a compact regulatory code, and changing spacer length alone can reprogram promoter behavior. Different ParR states were also associated with changes in antibiotic susceptibility, biofilm formation, and virulence-associated phenotypes. Our findings explain how one bacterial signaling pathway can generate diverse physiological outcomes without additional regulators and provide a framework for understanding regulatory flexibility in Pseudomonas aeruginosa and for engineering genetic circuits with multiple outputs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/740031v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1b6ec28org.highwire.dtl.DTLVardef@4a3f2eorg.highwire.dtl.DTLVardef@79e528org.highwire.dtl.DTLVardef@b3aa77_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Promoter architecture diversifies ParR-dependent transcription in Pseudomonas aeruginosa

Two-component systems convert environmental signals into transcriptional responses, but how one response-regulator phosphorylation state produces different outputs at different promoters remains unclear. Here we show that promoter architecture determines how the ParR response regulator in Pseudomonas aeruginosa interprets phosphorylation. Phenotypic, transcriptomic, biochemical and promoter-engineering analyses showed that phosphorylation of the conserved ParR receiver residue Asp57 lowered DNA-occupancy thresholds across target promoters. Individual promoters, however, converted this shared increase in binding into activation, repression or phosphorylation-dependent sign switching. Chromosomally D57 ParR variants reproduced these behaviours at endogenous loci and altered antibiotic susceptibility, biofilm formation and virulence-associated phenotypes. Mapping and engineering of representative promoters identified a two-tier cis-regulatory code: half-site sequence compatibility determines productive ParR engagement, whereas spacer length determines regulatory sign and magnitude. Spacer swaps were sufficient to reprogram promoter logic between regulatory modes. These findings separate regulator state from promoter decoding and show how bacterial promoter architecture can diversify the outputs of a shared phosphorylation signal. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/738673v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1a0a26forg.highwire.dtl.DTLVardef@10836a8org.highwire.dtl.DTLVardef@3c6cd8org.highwire.dtl.DTLVardef@10dfefb_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsParR coordinates antibiotic resistance, biofilm formation and virulence-linked phenotypes in P. aeruginosa. Promoters convert ParR phosphorylation into activation, repression or sign switching. Half-site compatibility and spacer length form a cis-regulatory code for ParR output.

biochemistry↗

bioRxiv2026

A Pro-Regenerative Petroleum Jelly-Based, Copper-Doped Bioactive Glass Ointment for Impaired Wound Healing in Metabolic Syndrome

Chronic wound healing is often impaired in conditions such as metabolic syndrome, requiring effective therapeutic interventions to promote tissue regeneration and repair. In this study, we evaluated the wound healing potential of petroleum jelly (P Jelly)-based bioactive glass ointments (PBGCu) with varying copper concentrations (0, 1, and 3 wt%) in both in vitro and in vivo models of wound healing. PBGCu formulations demonstrated high biocompatibility with human dermal fibroblasts (HDF) and human umbilical vein endothelial cells (HUVEC). Additionally, PBGCu ointments exhibited strong antibacterial activity against Staphylococcus aureus, suggesting their utility for the care of chronic wounds. In both metabolic syndrome mouse and pig models, PBGCu3-treated wounds showed significantly faster wound closure, enhanced epithelial regeneration, and increased dermal thickness compared to saline and P Jelly controls. Histological analysis also revealed 50% increased vascularization (p < 0.0001) and a 90% reduction in scar formation (p < 0.0001) in PBGCu3-treated wounds. These findings show that PBGCu formulations, especially at 3 wt% copper concentration, significantly improve wound healing by promoting epithelial regeneration, dermal tissue formation, and vascularization, while also offering antibacterial protection. The sustained Cu2+ ions release from PBGCu ointments provides long-term support for tissue regeneration, positioning this ointment composition as a promising therapeutic tool for chronic wound management. Future studies will focus on elucidating the underlying mechanisms and evaluating the therapeutic efficacy of PBGCu formulations in infected wounds. HighlightsO_LIDeveloped a Petroleum Jelly-based copper-doped bioactive glass ointment (PBGCu) enabling sustained and controlled Cu{superscript 2} ion release. C_LIO_LIPBGCu significantly accelerated wound closure and improved epithelial and dermal tissue regeneration. C_LIO_LIPBGCu enhanced hair follicle regeneration and tissue remodeling in full-thickness wounds. C_LIO_LIValidated therapeutic efficacy in both mouse and pig models that support translational relevance. C_LIO_LIOffers a simple, low-cost, and clinically adaptable topical formulation for metabolic syndrome-related wound complications. C_LI

bioengineering↗

bioRxiv2026

Ultrasensitive, Low-Input Detection of Avocado Sunblotch Viroid via RPA-CRISPR and Nanopore-Array Single-Bead Fluorescence Readout

Rapid and sensitive detection of plant pathogens, such as the Avocado Sunblotch Viroid (ASBVd), is essential for early disease management and agricultural biosecurity. Yet, most current diagnostic methods not only require relatively large sample inputs but also often lack the ultrasensitivity required for reliable detection with scarce or minimally collected plant material. Here, we report a novel low-input but ultrasensitive diagnostic platform that integrates isothermal recombinase polymerase amplification (RPA), CRISPR-Cas12a detection, and a solid-state nanopore array for the detection of ASBVd. The system leverages CRISPR-Cas12a collateral cleavage activity to generate single-bead fluorescent signals, which are captured by a nanopore array through pressure-driven blockage. Our platform achieves a detection limit down to 1.68 copies/L while using only 40 nL of bead-fluorophore mixture per readout, which is over 100-fold less than conventional assays based on fluorescent readout using an imaging reader, enabling detection from minimal avocado sample collection. We demonstrate robust binary classification of ASBVd-positive and -negative samples from multiple avocado tissue types and orchards in California. The assay requires just 60 minutes and operates entirely under isothermal conditions, avoiding the need for bulky PCR instruments and supporting on-site deployment with minimal equipment. This method provides a promising platform for field-deployable, ultrasensitive, and low-input diagnostics of viroids and other low-titer pathogens in plant or clinical settings.

bioengineering↗

bioRxiv2025

Sugar ABC transporter repertoires predict ecological dynamics in gut microbiome communities

The gut microbiome plays a central role in human health, but modern diets and lifestyles alter its composition. The microbial genomic traits that drive these ecological shifts, particularly in response to dietary sugars, remain poorly characterized. Here, we integrate a large dataset of longitudinal human diet-microbiome records and comparative genomics of human and murine gut isolates with in vitro and in vivo experiments to identify sugar ABC (ATP-binding cassette) transporters as key predictors of bacterial fitness and microbial community responses to dietary sugars. Strains encoding these transporters exhibit enhanced growth and consistently outcompete others in both monocultures and complex consortia across contexts. In gnotobiotic mice, dietary sugar supplementation selectively increases the expansion of sugar ABC transporter-positive bacteria, including the model gut pathobiont Escherichia coli. Systematic deletion of sugar transporter genes in E. coli revealed that a specific sugar ABC transporter gene was required to invade a model gut consortium, highlighting its importance in microbial competition. Together, these findings establish sugar ABC transporters as genomic predictors of microbial community dynamics in response to dietary sugars.

microbiology↗

bioRxiv2025

Stc2a inhibits IGF-stimulated somatic growth in favor of organismal survival under hypoxia

In response to hypoxia, animals reduce somatic growth to shift energy resources toward the maintenance of vital functions and survival. Although this phenomenon is widespread in the animal kingdom, the factors and mechanisms involved remain poorly understood. Here we report that hypoxia causes major changes in zebrafish transcriptomic landscapes with hormonal activity or hormonal signaling identified as most prominently up-regulated GO term and KEGG pathway. Among the top in this group is Stanniocalcin 2a (Stc2a), a secreted glycoprotein that inhibits insulin-like growth factor (IGF) signaling by binding to pappalysin metalloproteinases and inhibiting their activities. The hypoxic induction of stc2a expression is attenuated in Hif2-deficient fish. Genetic deletion of Stc2a increased the developmental speed and growth rate, resulting in enlarged adult organ and body size. Under hypoxia, stc2a-/- fish grew faster than wild-type fish but showed reduced survival rate. These phenotypes were reversed by inhibiting pappalysin activity or blocking IGF signaling. These findings suggest that Stc2a limits IGF-mediated growth in favor of survival and that the induction of Stc2a is part of a conserved mechanism regulating the trade-off between somatic growth and survival under hypoxic stress.

physiology↗

bioRxiv2025

Gut Delivery of Pentameric GLP-1 Using Genetically Engineered Bacillus subtilis for Diabetes and Obesity Treatment

Glucagon-like peptide-1 (GLP-1) receptor agonists and GLP-1 analogs are widely used for type 2 diabetes and weight management, but current approaches can be limited by manufacturing complexity, cost, formulation requirements, and the need for repeated administration. Living microbial delivery systems offer a potential strategy for sustained gastrointestinal production of therapeutic peptides, yet achieving stable expression, intestinal survival, and biologically relevant systemic exposure remains challenging. Here, we developed an engineered Bacillus subtilis (B. subtilis) spore-based platform for gastrointestinal delivery of pentameric GLP-1. By leveraging the stress resistance, storage stability, and genetic tractability of B. subtilis, we generated a chromosomally integrated strain that secretes a multimeric GLP-1 construct, which is processed in the intestine to release active GLP-1 monomers. Oral administration of engineered spores resulted in detectable serum GLP-1-related peptide signals in mice, accompanied by preliminary glucose-lowering activity in a fasting-refeeding test. In a longer-term study, engineered spore administration was associated with reduced body weight and adiposity in diet-induced obese mice, with semaglutide included as a positive pharmacologic benchmark. To improve translational suitability, we further generated a marker-free strain, which retained probiotic-relevant features of the parental strain, including gastrointestinal stress tolerance, epithelial cell adhesion, and antibiotic susceptibility. These findings establish proof-of-concept evidence that engineered spore-forming bacteria may serve as a scalable gastrointestinal peptide-delivery platform and support further evaluation of this approach in disease-relevant models of metabolic dysfunction.

bioengineering↗

bioRxiv2025

The Cumulative Distribution Function Based Method for Random Drift Model

We propose a numerical method to uniformly handle the random genetic drift model for pure drift with or without natural selection and mutation. For pure drift and natural selection case, the Dirac {delta} singularity will develop at two boundary ends and the mass lumped at the two ends stands for the fixation probability. For the one-way mutation case, known as Mullers ratchet, the accumulation of deleterious mutations leads to the loss of the fittest gene, the Dirac {delta} singularity will spike only at one boundary end, which stands for the fixation of the deleterious gene and loss of the fittest one. For two-way mutation case, the singularity with negative power law may emerge near boundary points. We first rewrite the original model on the probability density function (PDF) to one with respect to the cumulative distribution function (CDF). Dirac {delta} singularity of the PDF becomes the discontinuity of the CDF. Then we establish a revised finite difference method(rFDM), which keeps the total probability, is positivity-preserving and unconditionally stable. For pure drift, the scheme also keeps the conservation of expectation. It can catch the discontinuous jump of the CDF, then predicts accurately the fixation probability for pure drift with or without natural selection and one-way mutation. For two-way mutation case, it can catch the power law of the singularity. The numerical results show the effectiveness of the scheme. We also compare rFDM with a standard finite difference method(sFDM). We find that, for pure drift problem, sFDM fails to keeps the conservation of expectation and can not predict the fixation probability, because there is artificial mutation introduced near two boundary ends.

genetics↗

bioRxiv2025

Resolving the estrogen paradox in hereditary retinal degeneration: Esr1 activation suppresses Tnf-α signaling as a photoreceptor self-protection mechanism

Retinitis pigmentosa (RP) is an inherited retinal degenerative disorder characterized by progressive photoreceptor loss and irreversible blindness. Increasing evidence implicates neuroinflammation as a contributor to photoreceptor degeneration extending beyond the initial genetic insult. Although estrogen has been reported to exert anti-inflammatory effects in the central nervous system, its role in RP remains controversial, with some studies suggesting a paradoxical exacerbation of retinal pathology. To address this discrepancy, we identify estrogen receptor alpha (Esr1) as a central immunoregulatory hub in RP. Transcriptomic analyses of rd1 and rd10 revealed upregulation of estrogen-responsive and inflammatory pathways, with Esr1 expression markedly elevated during degeneration. TUNEL assays demonstrated that systemic estradiol (E2) exerted divergent effects, protective in rd1 yet deleterious in rd10, whereas selective pharmacological activation of Esr1 with propyl pyrazole triol (PPT) consistently reduced photoreceptor death, preserved dark-adapted ERG responses, and downregulated inflammatory mediators including Tnf-, Cx3cl1/Cx3cr1, Cd68, and Iba1. Mechanistically, Esr1 activation repressed microglial Tnf transcription and disrupted a self-sustaining Cx3cl1/Cx3cr1-Tnf- signaling loop driving microglial recruitment, activation and neurotoxicity in the outer nuclear layer (ONL). Targeted interventions confirmed tumor necrosis factor receptor 1 (Tnfr1) as the principal mediator of Tnf-induced photoreceptor death: selective inhibition with R7050 conferred superior protection compared with broad-spectrum Tnf- inhibitors (etanercept, infliximab). Cx3cr1 blockade likewise suppressed microglial activation and improved visual outcomes. Collectively, our findings establish Esr1 activation as not merely an external intervention but the amplification of an intrinsic self-protective program, positioning Esr1, Tnfr1, and Cx3cr1 as actionable therapeutic targets to suppress neuroinflammation and preserve vision in RP and related retinal disorders.

neuroscience↗

bioRxiv2025

Advancing Target Discovery Through Disease-Specific Integration of Multi-Modal Target Identification Models and Comprehensive Target Benchmarking System

Target identification is crucial for drug development. AI-driven approaches leveraging multi-omics and computational modeling can accelerate this process. However, integrating multi-modal data for disease-specific target identification and predicting translational potential remains challenging. Moreover, the absence of a systematic evaluation framework for model performance limits confidence in target reliability. We present a unified platform combining machine learning-based target identification with comprehensive benchmarking. As a testbed, we developed Target Identification Pro (TargetPro), a disease-specific model spanning 38 diseases across oncology, metabolic, immune, fibrotic, and neurological categories. TargetPro shows strong predictive performance for clinical-stage targets and reveals disease-specific patterns, underscoring the need for tailored target detection models. We next created Target Identification Benchmark (TargetBench 1.0) to rigorously assess target identification systems, including large language models, based on their ability to recover established targets and find high-quality novel candidates. This integrated approach offers a streamlined strategy to evaluate target discovery models, ultimately improving drug development efficiency.

bioinformatics↗

bioRxiv2025

Reading specific memories from human neurons before and after sleep

The ability to retrieve a single episode encountered just once is a hallmark of human intelligence and episodic memory[1]. Yet, decoding a specific memory from neuronal activity in the human brain remains a formidable challenge. Here, we develop a transformer neural network model[2, 3] trained on neuronal spikes from intracranial microelectrodes recorded during a single viewing of an audiovisual episode. Combining spikes throughout the brain via cross-channel attention[4], capable of discovering neural patterns spread across brain regions and timescales, individual participant models predict vocalization of specific concepts such as persons or places during out-of-distribution memory recall. Brain regions differentially contribute to memory decoding before and after sleep. Models trained using only medial temporal lobe (MTL) spikes significantly decode concepts before but not after sleep, while models trained using only frontal cortex (FC) spikes decode concepts after but not before sleep, with better FC decoding relating to increased non-REM sleep. These findings suggest a system-wide distribution of information across neural populations that transforms over wake/sleep cycles[5]. Such decoding of internally generated memories suggests a path towards brain-computer interfaces to treat episodic memory disorders through enhancement or muting of specific memories.

neuroscience↗

bioRxiv2025

The Volume of Mitochondria Inherited Impacts mtDNA Homeostasis in Budding Yeast

Most eukaryotic cells maintain mitochondria in well-distributed, reticular networks. The size of the mitochondrial network and copy number of its genome scale with cell size. However, while the size scaling features of mitochondria and their genome are interrelated, the fitness consequences of this interdependence are not well understood. We exploit the asymmetric cell division of budding yeast to test the hypothesis that mitochondrial scaling with cell size impacts mitochondrial DNA (mtDNA) function. We find that the volume of mitochondria inherited by daughter cells affects the ability of cells to maintain functional mtDNA; daughter cells that inherit a significantly reduced volume of mitochondria have an increased frequency of losing respiratory competence. In cells with such mitochondrial inheritance defects, mtDNA integrity can be maintained by upregulating mtDNA copy number. Collectively, these data support a bet-hedging model whereby the faithful inheritance of an adequate volume of mitochondria ensures enough mtDNA copies are transmitted to daughter cells to counteract pre-existing and/or inevitable mtDNA mutations. SummaryRay et al. demonstrate that the volume of mitochondria inherited impacts mtDNA homeostasis in the model system budding yeast. They propose a model by which inheritance of an adequate mitochondrial volume results in the transmission of sufficient mtDNA copies to counteract existing and/or inevitable mutations.

cell biology↗

bioRxiv2025

A novel method for detection of Cas9 gRNAs using a fluorophore-labeled DNA oligo

Clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9) has become one of the most important gene editing tools. CRISPR guide RNA (gRNA) serves as an important component in guiding Cas proteins to a target site in gene editing processes. For effective gene editing or site specific gene integration, levels of gRNA present in a target cell are critical. Especially, for prime editing, even the ratio of different gRNAs present in target cells has a major effect on gene editing efficiency. Therefore, having a convenient, highly sensitive method for direct detection of gRNAs can improve editing design and optimize targeting efficiency. Here, we have developed a convenient, highly sensitive method for direct detection of gRNAs, which may be used to improve editing design and optimize targeting efficiency.

molecular biology↗

bioRxiv2025

A method for inducing a senescence trend in mesenchymal stem cells using D-galactose

The aging of the body is accompanied by a decline in tissue function, and this decline mainly stems from the aging of tissue stem cells. Therefore, they play a crucial role in the aging of the body.This study explores the biological characteristics of senescent hUCMSCs by establishing a replicative senescence model of hUCMSCs and a rapid senescence model induced by D - galactose (D-Gal), and analyzing the proliferative capacity, cell viability, cell cycle, pluripotency, and reactive oxygen species (ROS) levels of senescent hUCMSCs.

cell biology↗

bioRxiv2024

One-Size-Fits-Many: Antisense oligonucleotides for rescuing splicing mutations in hotspot exons

Mutations that impact splicing play a significant role in disease etiology but are not fully understood. To characterize the impact of exonic variants on splicing in 71 clinically-actionable disease genes in asymptomatic people, we analyzed 32,112 exonic mutations from ClinVar and Geisinger MyCode using a minigene reporter assay. We identify 1,733 splice-disrupting mutations, of which the most extreme 1-2% of variants are likely to be deleterious. We report that these variants are not distributed evenly across exons but are mostly concentrated in the [~]8% of exons that are most susceptible to splicing mutations (i.e. hotspot exons). We demonstrate that splicing defects in these exons can be reverted by ASOs targeting the splice sites of either their upstream or downstream flanking exons. This finding supports the feasibility of developing single therapeutic ASOs that could revert all splice-altering variants localized to a particular exon.

molecular biology↗