Biology subjects

Li, H.

Publications and source records attributed to Li, H..

At least 163 records · Page 9Linked to original sources

bioRxiv2026

Arrestin-3 promotes locomotor sensitization to psychostimulants via JNK signaling in nucleus accumbens

Arrestins play key role in desensitization of G protein-coupled receptors. Direct signaling role of arrestins has also been documented. Two ubiquitously expressed arrestin isoforms, arrestin-2 and -3 (Arr3), perform similarly in receptor desensitization and share many signaling functions, enabling them to substitute for one another. However, certain signaling roles are specific to each isoform. Mice lacking Arr3 (A3KO) show blunted acute responsiveness to the locomotor stimulatory effect of amphetamine (AMPH). Here we demonstrate that AMPH- and cocaine-induced locomotion of A3KO mice is significantly reduced. This loss-of-function phenotype suggests that Arr3-mediated signaling contributes to the effect. Virus-driven expression of Arr3 in caudate-putamen of A3KO and wild type mice suppressed AMPH-induced locomotion. In contrast, restoration of Arr3 in nucleus accumbens rescued locomotor response. Thus, in caudate-putamen Arr3 participates in the desensitization of dopamine receptors, whereas Arr3-dependent signaling in nucleus accumbens underlies the molecular mechanism of the locomotor response and sensitization. Using monofunctional Arr3-derived peptides, we showed that in the nucleus accumbens Arr3 promoted drug-induced locomotor responses via facilitation of JNK3 activation.

neuroscience↗

bioRxiv2026

Microtubule stability modulates Schlemm's canal cell mechanobiology and outflow facility in glaucoma

PurposeThe inner wall of Schlemms canal (SC) is a mechanosensitive endothelial monolayer that provides resistance to conventional aqueous humor drainage, a process dependent on pore formation. This study examined how microtubule (MT) stability affects SC cell mechanobiology, transcellular pore formation, and aqueous humor outflow dynamics. MethodsMT stability in cultured SC cells from normal and glaucomatous human donors was manipulated pharmacologically. Changes in MT acetylation, phosphorylated myosin light chain, and F-actin were assessed by immunofluorescence and immunoblotting. GEF-H1 was knocked down using siRNA. Cellular stiffness was measured by atomic force microscopy. Transcellular pore formation was quantified using an established pore formation assay. Outflow facility was measured in enucleated mouse eyes using the iPerfusion system. ResultsMT stabilization in normal SC cells decreased actomyosin contractility and cellular stiffness, whereas MT destabilization increased contractility and stiffness; these effects involved the MT-associated Rho guanine nucleotide exchange factor GEF-H1. MT stability was also mechano-responsive to substrate stiffness. Furthermore, SC cells derived from glaucomatous donors exhibited reduced MT stability compared with normal SC cells. MT stabilization increased transcellular pore formation in both normal and glaucomatous SC cells. In ex vivo mouse eyes, paclitaxel perfusion to stabilize MTs significantly increased outflow facility relative to contralateral control eyes. ConclusionsOur data suggest that MT stability influences SC cell contractility, stiffness, and transcellular pore formation and can alter aqueous humor outflow facility. These findings identify MT-dependent cytoskeletal remodeling as an important contributor to the biomechanics of the conventional outflow pathway and suggest that MT-associated pathways may represent potential targets for improving outflow function in glaucoma.

cell biology↗

bioRxiv2026

Development of Potent and Cell Active 5-Azaindole-Based Tau Tubulin Kinase Inhibitors

We have developed and characterized a potent and cell active tau tubulin kinase 1 and 2 (TTBK1 and TTBK2) inhibitor, 13. Compound 13 demonstrates in-cell, kinome-wide selectivity, and potently inhibits both TTBK1 and TTBK2. As part of our medicinal chemistry campaign, we also identified a structurally similar negative control, compound 5, which lacks in-cell affinity for TTBK1 and TTBK2. Based on their substrates, which include TDP-43, tau, and tubulin, TTBK1 and TTBK2 inhibition has been pursued as a therapeutic approach for Alzheimers disease, frontotemporal lobe dementia, and amyotrophic lateral sclerosis. TTBK2 is also an effector of ciliogenesis, acting in concert with CEP164, CP110, and CEP83 to initiate the biogenesis of primary cilia. The development of selective chemical tools for these kinases facilitates investigation into TTBK1/2-mediated pathways and potential disease-altering ramifications linked to their pharmacological perturbation.

cell biology↗

bioRxiv2026

Protein structure-informed deep learning enables species-specific codon optimization

Codon usage bias is highly species-specific, posing a major challenge for heterologous protein expression. Existing deep learning approaches to codon optimization rely primarily on DNA or protein sequence information and largely neglect constraints imposed by protein structure and folding. Here, we present Protein structure-Informed Species-specific Codon Optimization (PISCO), a Geometric Vector Perceptron (GVP)-based model that integrates protein sequence, three-dimensional protein structure, and host codon usage statistics to generate optimal, host-specific codon sequences. Compared with protein-structure-agnostic models, PISCO improves codon recovery by 6% and substantially increases similarity to natural coding sequences, reducing divergence by at least 42% in Codon Similarity Index (CSI), 50% in Codon Frequency Distribution (CFD), and 14% in Dynamic Time Warping (DTW) metrics. Ablation analyses demonstrate that incorporating protein folding kinetics and host-specific information is critical to these gains. Moreover, by leveraging host codon usage statistics, PISCO generalizes to optimize codon sequences for species absent from the training data. An autoregressive variant of PISCO further enhances concordance with natural codon usage patterns, at the cost of a modest reduction in codon recovery rate. Wet-lab validation confirms that PISCO-optimized sequences significantly enhance protein solubility and functional expression. Together, these results establish protein structure as a key determinant of species-specific codon optimization and provide a transferable framework for structure-aware gene design.

molecular biology↗

bioRxiv2026

Identification of AAV Capsids with Enhanced Intravitreal Transduction and Favorable Safety Profile in Non-Human Primates

We report the discovery of novel adeno-associated virus (AAV) capsid variants engineered for superior intravitreal (IVT) gene delivery to the primate retina. Utilizing the REACH platform, we constructed a diverse AAV variant library and employed a multi-stage screening strategy involving in vitro selection on human retinal pigment cells followed by direct in vivo screening in non-human primates (NHPs). Following IVT administration in NHPS of a barcoded variant pool, next-generation sequencing analysis of retinal tissues identified lead candidates (e.g., E52, E54, and E57) that achieved transduction levels in the neural retina and RPE 5-10 fold higher than the benchmark R100. Concurrently, these high-potency variants exhibited an exceptional ocular confinement profile, with minimal to undetectable vector genome distribution in systemic organs. This combination of markedly enhanced retinal transduction and stringent local tropism establishes these engineered capsids as promising next-generation vectors for the treatment of inherited and acquired retinal diseases via a minimally invasive IVT route.

bioengineering↗

bioRxiv2026

Chromosomal markerless integration of anthelmintic Cry proteins into the Bacillus thuringiensis genome

Bacillus thuringiensis (Bt) is a Gram-positive bacterium that during sporulation produces insecticidal Crystal (Cry) proteins, which play a major role in insect control today. Some Bt Cry proteins, e.g., Cry5Ba, target nematodes and, when given orally, can cure animals of gastrointestinal nematode (GIN) parasites. To eliminate concerns about treating humans and animals with spores and live bacteria, we developed an asporogenous system for scalable and safe Cry protein delivery called IBaCC (Inactivated Bacteria with Cytosolic Crystal(s)), which results in production of a bioactive crystal and a dead bacterium. However, to date, IBaCC involves expression of Cry proteins from antibiotic-selectable plasmids to ensure maintenance. Here, we develop and validate tools for markerless and stable integration and expression of Cry proteins in Bt. We markerlessly integrate an expression construct for Cry5Ba into either the spo0A or the sigK locus and demonstrate robust Cry5Ba expression. We also integrate our Cry5Ba expression construct into both loci simultaneously, increasing expression further. We demonstrate that an expression construct for a second anthelmintic Cry protein, Cry21Aa, can be integrated either alone or in combination with Cry5Ba in a single Bt strain. We furthermore show that these markerless integrants are stable in the absence of a selectable marker. These integrated strains, processed to IBaCC, demonstrate excellent ex vivo nematicidal bioactivity toward the larval stages of the sheep GIN parasite Haemonchus contortus and adult stages of the human hookworm GIN parasite Ancylostoma ceylanicum. This study demonstrates the successful markerless integration of 1-2 identical or dissimilar Cry proteins into Bt. These Cry integrants, in which genes essential to sporulation are deleted or replaced, provide robust Cry expression, stability, and bioactivity. These studies represent an important advance in Bt genetics and toward a safe, deployable, and cost-effective anthelmintic therapy to treat GIN parasitic infections in humans and animals.

microbiology↗

bioRxiv2026

A new species of Rana from Anhui, China (Anura, Ranidae)

The diversity of the brown frog genus Rana may be underestimated as the high similarity of morphological characters. A new species belonging to the genus Rana is delineated based on eight specimens obtained from the Tianma National Nature Reserve, Jinzhai County, Luan City, Anhui Province, China. The phylogenetic analysis based on three mitochondrial genes (12S, ND2, and Cyt b) and one nuclear gene (BDNF) showed that the new species formed an independent clade closely related to R. culainensis and received strong support. In addition, morphological differentiation confirmed the phylogenetic results, and both supported the validity of a new species (Rana tianmaensis sp. nov.) in the R. japonica species group. The discovery of this new species enhances peoples understanding of the biodiversity of Rana and can provide important foundational data for scientific decision-making on protected area construction, ecological conservation, and species diversity. With the inclusion of newly described species in this study, the distribution of Rana genus in China now includes 31 recognized species.

zoology↗

bioRxiv2026

Amyloid plaques drive long-range circuit reorganization in a mouse model of Alzheimer's disease

Amyloid plaques are a pathological hallmark of Alzheimers disease, but how they drive widespread neuronal dysfunction remains unclear. While studies in anesthetized animals show that plaques drive local hyperactivity1,2, it is unknown how this pathology shapes functional hippocampal maps in freely behaving animals. We combined chronic 1-photon calcium imaging, local field potential recordings, and post hoc 2-photon plaque imaging in freely behaving APP/PS1 mice across behavior and sleep to correlate real-time hippocampal activity and place coding with precise plaque topography. Here we show that plaques exert nonlocal, long-range effects on hippocampal activity that depend on plaque size, laminar position, and the animals behavioral state. Place cells, which encode spatial position and are normally uniformly distributed, are preferentially enriched near plaques, revealing an aberrant reorganization of plaque-adjacent neurons into the hippocampal map of space. In longitudinal experiments, pre-existing place cell locations do not predict future plaque sites, whereas hyperactivity during slow-wave sleep weakly predicts future amyloid deposition. These findings identify a mechanism by which amyloid pathology reorganizes brain circuits, degrading the functional architecture of the hippocampus and contributing to widespread dysfunction and cognitive impairment in Alzheimers disease.

neuroscience↗

bioRxiv2026

Therapeutic Potential of Hypoxia-Preconditioned hiPSC-Epicardial Cell-Derived Exosomes in Mice with Myocardial Infarction

BackgroundIt has been demonstrated that stem cell transplantation promotes healing of the infarcted heart through paracrine effects. However, the therapeutic potential of exosomes secreted by hiPSC-derived epicardial cells (hEP-Exos) for treating infarcted hearts remains unclear. Myocardial infarction (MI) can trigger EP activation, increasing EP paracrine function. Therefore, this study aims to determine and compare the cardioprotective effects of exosomes secreted by hEPs under normoxic (Exo-N) and hypoxic (Exo-H) conditions in MI mice and to explore the underlying mechanisms. MethodsTwo types of exosomes were collected by ultracentrifugation and delivered via intramyocardial injection in a murine MI model. The protective effects of Exo-N and Exo-H on the infarcted heart were assessed using echocardiography, histological examination, and immunofluorescence analysis. Additionally, microRNA sequencing, luciferase activity assays, and miRNA gain-and loss-of-function experiments were performed to identify enriched miRNAs and investigate their roles in different exosome populations. ResultsIn vitro, both Exo-N and Exo-H enhanced the migration and tube-formation capacities in human umbilical vein endothelial cells (HUVECs) and reduced the apoptosis in hiPSC-derived cardiomyocytes (hCMs) under oxygen-glucose deprivation (OGD), with Exo-H exhibiting a stronger effect. In vivo, both Exo-N and Exo-H significantly improved contractile function, reduced infarct size, and mitigated adverse remodeling in mouse hearts with MI, accompanied by increased cardiomyocyte survival and angiogenesis, with Exo-H showing superior efficacy. Mechanistically, miRNA sequencing revealed distinct cargo profiles between Exo-N and Exo-H. miR-214-3p was identified as a key mediator of the enhanced therapeutic potency of Exo-H. miR-214-3p promoted EC angiogenesis by suppressing vasohibin-1 and attenuated cardiomyocyte mitochondrial fission and apoptosis by suppressing mitochondrial elongation factor 2 (MIEF2). ConclusionsThis study demonstrates that administration of hEP-Exos, particularly Exo-H, provides robust cardioprotection by enhancing cardiomyocyte survival and angiogenesis, potentially mediated by miR-214-3p. These findings suggest that conditioned hEP-Exos could be a promising and effective acellular therapeutic option for treating MI.

cell biology↗

bioRxiv2026

Delineating the Transcriptional and Phenotypic Impact from Biotherapeutic Glycoengineering

Glycosylation is critical to biopharmaceutical activity, stability, and pharmacokinetics. While production cells can be engineered to produce better protein glycoforms, glycans decorate thousands of host cell proteins, and it remains unclear how glycoengineering impacts the host cell. To decipher the cell response to glycoengineering, we studied a library of 166 glycoengineered CHO-K1 cell clones representing 54 different glycosyltransferase modifications. Through integrated analysis of glycomics, RNA-Seq, and phenotypic data, we discovered that glycoengineered mutants clustered into three distinct groups (wild-type-like, Moderate, and Substantial) based on their glycosylation patterns. Different glycosyltransferase families exhibited distinct phenotypic signatures: St3gal modifications increased growth rate and cell density, B4galt knockouts affected cell size, and Mgat knockouts enhanced cell viability. Notably, we found specific cellular reprogramming associated with each glycosyltransferase family, including alterations in energy metabolism, stress responses, and DNA repair mechanisms. These findings were validated in an independent set of 30 glycoengineered CHO-S cell lines, expressing a panel of 10 recombinant proteins. Our extensive analysis reveals phenotypic changes resulting from glycoengineering, identifies their molecular bases, and provides crucial insights for controlling glycosylation during therapeutic protein production.

synthetic biology↗

bioRxiv2026

Reveal Principles of Codon Optimization via Machine Learning

High level of protein expression is usually welcomed in industry and research, and codon optimization is widely used to achieve high expression. Methods of implementing codon optimization can be divided into two branches, one is classical methods which develop cost functions based on empirical law, another is AI methods which learn the codon choice principles from endogenous genes with neural networks. Here we develop two codon optimization tools based on two branches respectively, namely OptimWiz 2.1 and OptimWiz 3.0. Results of fusion protein fluorescence detection indicate that both OptimWiz 2.1 and OptimWiz 3.0 are superior to all the other commercially available codon optimization tools. Principles of codon optimization are revealed in the process of machine learning on both tools.

bioinformatics↗

bioRxiv2026

Germline-mediated ubiquitous recombination in ScxCre male mice: implications for tendon research

Scleraxis (Scx), a basic helix-loop-helix (bHLH) transcription factor, is a primary marker for tendon and ligament lineages. Consequently, mouse models utilizing Cre recombinase under the control of the Scx locus represents a powerful tool for control of gene expression in tendon. The constitutive ScxCre mouse line is widely used for tendon-specific genetic manipulation. In this study, we demonstrate that ScxCre exhibits undesired significant off-target activity in the male germline, leading to ubiquitous recombination of floxed alleles in all tissues of the resulting offspring. This inheritance of recombined LoxP alleles occurs independently of Cre inheritance, indicating that ScxCre-induces recombination occurs prior to meiosis in diploid germ cells. This off-target activity is not observed in female germline. These findings highlight a critical need for stringent parental sex selection when using ScxCre lines to ensure tissue-specific targeting and avoid unintentional global gene deletion or transgene activation.

genetics↗

bioRxiv2026

Robust causal gene network estimation for large-scale single-cell perturbation screens using reduced control function

Single-cell CRISPR perturbation screens provide a foundation for causal discovery in gene regulatory networks, but existing methods struggle with latent confounding, count-valued expression data, and high-multiplicity-of-infection (high-MOI) designs. We introduce RICE, a unified framework that addresses all three challenges. At its core is a reformulated control function tailored to the network-estimation setting, which restores robustness to exclusion-restriction violations that are pervasive in real CRISPR screens and that cause standard control function approaches to fail. RICE pairs this estimator with a constrained negative binomial model and a differentiable acyclicity penalty, accommodating hard and soft interventions and natively supporting high-MOI designs within a single, GPU-scalable model. Across extensive synthetic benchmarks, RICE consistently outperforms existing methods and remains stable under strong confounding, exclusion violations, and high-MOI conditions. Applied to CRISPRi screens, RICE achieves stronger causal-discovery performance on held-out data. RICE further reconstructs the canonical interferon (IFN)-{gamma} signaling pathway in melanoma cells upon immune stimulation, and nominates stable regulatory candidates that conventional significance tests may overlook due to limited statistical power. Together, these results establish RICE as a robust and scalable framework for causal discovery in single-cell perturbation genomics.

bioinformatics↗

bioRxiv2026

Relative Index of Chimeric Expression (RICE) Analysis: A Quantitative Approach for Chimeric RNAs Using FusionBlaster

Chimeric RNA molecules, which contain nucleotide sequences originating from multiple genes, are generated by chromosomal rearrangements, transcriptional read-throughs, or trans-splicing between separate parental transcripts. Chimeric RNAs have been functionally validated in both pathological and normal healthy physiological contexts indicating the biological significance of chimeric RNA expression. There is, however, currently no standard for computationally quantifying chimeric RNA expression and only limited benchmarking data available for the few chimeric RNA detection software that attempt to measure the abundance of the predicted chimeras. Here, we develop the relative index of chimeric expression, RICE, that is calculated based on the relative expression of chimeric transcripts compared to the respective parental WT transcripts. We evaluate three different methods for generating this measurement from simulated RNA sequencing data with known transcript abundances. Our BLAST-based approach outperforms STAR and Kallisto based approaches when considering both accuracy and consistency between simulated data of different read lengths and sequencing depths. We further demonstrate that RICE values can be validated using qPCR and are sensitive to dynamic conditions using siRNA targeting chimeric RNA expression. Finally, we apply our RICE analysis pipeline to clinical prostate cancer data. We quantify over 1200 chimeric RNAs in primary prostate cancer, metastatic prostate cancer, and non-cancer tissue samples from GTEx. Our differential RICE analysis revealed a clustering of prostate cancer tissue samples from three different sequencing cohorts distinct from their associated tissue type noncancer GTEx clusters. Our pipeline is publicly available on github and can be run on a personal laptop with computational resources and processing time dependent on the number of quantified chimeras.

bioinformatics↗

bioRxiv2026

Combination of engineered cell type-specific promoters and a high-efficiency AAV capsid restores hearing in adult DFNB1 mice model with demonstrated safety in nonhuman primate

A major challenge in gene therapy for GJB2-related hearing loss (DFNB1)--the most common form of hereditary deafness--is achieving efficient and precise connexin 26 delivery. Herein, we engineered two cell type-specific promoters (GJB2-1 and WFS1-2274) and developed an AAV capsid, AAV-MAS012, with enhanced transduction efficiency in mature cochlear cells. Our AAV-mediated gene therapy systems restored hearing of low-to-mid-frequencies in newborn Gjb2 cKO mice to wild-type levels and maintained for 45 weeks. Additionally, our therapeutic systems restored low-to-mid-frequencies hearing function to wild-type levels in adult Gjb2 cKO mice. A humanized version of the therapy, AAV-MAS012-WFS1-2274-hGJB2, rescued hearing function in two distinct Gjb2-deficient mouse models, and demonstrated a favorable safety profile in nonhuman primates. This study represents the first successful hearing restoration in adult Gjb2-deficient mice. The significant therapeutic efficacy of the humanized gene therapy system shows great potential for clinical translation in DFNB1 patients.

genetics↗

bioRxiv2026

Ultra-sensitive FLORA-seq links cell-type-specific tRNAome dynamics to differentiation trajectories guiding therapeutic suppressor tRNA candidate selection

Mammalian genomes encode hundreds of tRNA genes, but the role of individual tRNAs in development and cell identity remains unclear. Here, we introduce FLORA-seq, a method for simultaneous, low-input profiling of tRNAs, tRNA-derived RNAs (tdRs) and their modifications from as few as 5-20 cells. Applying FLORA-seq to mouse hematopoiesis revealed 50 high-variance isodecoders whose expression profiles recapitulate known hematopoietic cell types and correlate with differentiation trajectories. At the isoacceptor level, tRNA pools are largely stable within hematopoietic stem and progenitor cells (HSPCs), showing only subtle, specific variations, but become both distinct from HSPCs and internally stable within each terminally differentiated lineage. We further detected dynamic changes in tdR ratios and modification patterns, underscoring precise tRNA regulation during differentiation. Crucially, analysis of 54 endogenous tRNA isodecoders and their engineered suppressor counterparts showed that efficient premature termination codon readthrough preferentially arises from highly expressed cognate isodecoders. This correlation provides a rational framework for prioritizing suppressor tRNA candidates and implies non-redundant functions for individual isodecoders.

molecular biology↗

bioRxiv2026

SpaceExpander: Automated Drafting and Evaluation of Markush Claims for Chemical Space Expansion

Drafting Markush claims for chemical patents remains difficult because manual claim writing is slow, error prone, and often fails to capture related chemical space in a systematic manner. We developed SpaceExpander, a computational method that converts disclosed compounds into generalized Markush claims by extracting core scaffolds, defining variable positions, decomposing complex substituents, and expanding substituent space through fragment matching. We evaluated the method on 24 publicly available chemical patents and compared its performance with IntelliPatent. SpaceExpander achieved a mean atom level scaffold accuracy of 0.92 and exactly recovered the reference scaffold in 19 of 24 patents. By contrast, IntelliPatent could process only 2 patents from the same set, indicating more limited applicability to structurally diverse cases. We further examined practical claim coverage in a case study based on the Osimertinib patent. Using representative disclosed compounds as input, SpaceExpander drafted a Markush claim that covered 5 of 7 additional approved third-generation EGFR inhibitors beyond Osimertinib. These results show that SpaceExpander is a validated method for automated Markush claim drafting and chemical space expansion.

bioinformatics↗

bioRxiv2026

Single-cell lineage tracing maps clonal and transcriptional dynamics in melanoma metastasis

Melanoma metastasis is driven by extensive intratumoral heterogeneity and phenotypic plasticity, yet how clonal identity relates to transcriptional programs during metastasis remains unclear. Here, we applied MeRLin, a single-cell lineage tracing platform, to dissect the clonal and transcriptional heterogeneity of metastatic melanoma in a patient-derived spontaneous metastasis model. Clonal analyses revealed hierarchical structures during tumor progression, with a subset of lineages from primary tumors consistently enriched across metastatic sites, supporting a model of polyclonal seeding followed by selective expansion of pre-existing highly metastatic subpopulations. Single-cell transcriptomic profiling identified two major metastatic subpopulations of distinct transcriptional programs, characterized by neural crest stem cell-like and lipid metabolism signatures. Both programs were enriched for invasion-associated genes and maintained across organs through distinct regulatory networks. Spatial mapping by barcode RNA-FISH linked these transcriptional states to their tissue context and showed that OLFML3 expression partially co-localized with a dominant subpopulation at the tumor-liver interface, marking the invasive fronts of metastatic growth. Together, these findings establish a framework in which clonal identity, transcriptional state, and spatial organization jointly shape metastatic melanoma progression.

cancer biology↗