Biology subjects

Li, H.

Publications and source records attributed to Li, H..

At least 307 records · Page 17Linked to original sources

bioRxiv2025

Isoflurane and Surgical Stress Disrupt Fatty Acid and Carbon Metabolism Leading to Cardiomyopathy

Aging alters cardiac resilience to anesthetic and surgical stress, yet the molecular basis of these effects remains poorly understood. To define age-dependent cardiac transcriptional responses to isoflurane exposure and operative (ISO/OP) stress, we analyzed gene expression profiles across young adult (3m), late middle-aged (17m), and geriatric mice (27m) following short-term 2 h ISO/OP exposure. At 24 h after cessation, all age groups exhibited distinct cardiac transcriptional signatures separating ISO/OP from sham controls. In young adult hearts, transcriptional alterations 24 hours after cessation of ISO/OP were characterized by dysregulation of small molecule catabolic processes, fatty acid metabolism, disruptions to protein processing in endoplasmic reticulum and cytoskeletal organization. Late middle-aged mice displayed amplified perturbations in lipid metabolism alongside suppression of muscle system and calcium signaling pathways, while old mice showed robust activation of PPAR and AMPK signaling and downregulation of genes governing contractility and morphogenesis. In contrast, geriatric mice showed upregulation of fatty acid metabolic pathways, robust activation of PPAR and AMPK signaling, coupled with suppression of muscle differentiation and actin organization following ISO exposure, indicating a maladaptive metabolic reprogramming. Overlapping DEGs across all age groups converged on pathways regulating oxidative stress, Ca2+ handling, hypertrophy, and energy metabolism, suggesting a conserved but age-intensified cardiac stress response. Longitudinal profiling in aged mice revealed persistent transcriptomic remodeling five weeks after stress. Crucially, this remodeling was observed even after ISO exposure alone, indicating that general anesthesia is a primary driver of this long-term effect. This persistent signature was marked by mitochondrial dysfunction and dysregulation of genes associated with diabetic cardiomyopathy, extracellular matrix integrity, and neurodegenerative signaling. Together, these findings identify isoflurane exposure as a potent inducer of persistent, age-dependent metabolic and structural reprogramming in the heart, implicating impaired lipid utilization and mitochondrial homeostasis as central mechanisms linking the perioperative period, and specifically anesthetic exposure, to long-term cardiovascular vulnerability.

pharmacology and toxicology↗

bioRxiv2025

Dynamic ecological interactions of two quarantine-concern Ralstonia strains in river water and plants

Plant pathogenic Ralstonia belonging to the IIB-1 ("race 3 biovar 2") and I-33 (rose) subgroups are emerging quarantine and biosecurity threats. Both strains have been introduced to Europe, where they persist in weedy plants and surface water and cause occasional costly disease outbreaks. We combined in planta, in vitro, and environmental water microcosm experiments to determine if these two concerning strains are likely to co-exist in environments where they have become established or if one might be expected to displace the other. Using a representative strain from each subgroup we investigated the dynamics and fitness of these two Ralstonia pathogens across ecologically relevant environments. Interactions between the strains were context dependent: the presence of a competing strain had little impact on bacterial survival in river water microcosms, but the I-33 strain had a fitness advantage in wilt susceptible tomato plants. We found no evidence of direct growth inhibition by either strain in vitro. The IIB-1 strain persisted longer than I-33 in cool temperature river water microcosms. Warmer temperatures extended the culturability of both strains, which may be important as climate change warms surface water globally. Additionally, Ralstonia strains persisting in 20{degrees}C water microcosms for 6 months were still able to cause disease in tomato plants. Together, our results provide useful insight into the dynamics of these two strains in environments where they are currently established, which may inform management practices moving forward.

microbiology↗

bioRxiv2025

ATR promotes genome instability via CENP-A eviction from centromeres under replication stress

Replication stress leads to genome instability in part by promoting missegregation of chromosomes lacking centromeres. Yet the molecular mechanism linking replication stress to centromere dysfunction has remained elusive. Here, we show that sustained replication stress induces eviction of the histone H3 variant CENP-A. Displaced CENP-A relocalizes to nucleoli. This process is dependent on the DNA damage response kinase, ATR, and occurs in both human and mouse cells. We show that ATR promotes CENP-A eviction by recruiting the AAA+ ATPase VCP to centromeres, destabilizing CENP-A-containing nucleosomes. The canonical CENP-A chaperone, HJURP, but not H3 histone chaperones DAXX or ATRX, is necessary for nucleolar CENP-A localization. Importantly, ATR-dependent CENP-A eviction endures after cell-cycle re-entry and correlates with the emergence of acentric chromosomes, linking replication stress directly to segregation defects. Our findings reveal an undiscovered role for ATR in regulating centromere identity under stress and uncover a mechanistic pathway that drives genome instability.

cell biology↗

bioRxiv2025

Tryptoline Stereoprobe Elaboration Identifies Inhibitors of the GRPEL1-HSPA9 Chaperone Complex

Activity-based protein profiling has identified hundreds of proteins from diverse classes that react at specific cysteine residues with stereochemically defined electrophilic compounds (stereoprobes) in human cells. The structure-activity relationships underlying these stereoprobe-protein interactions, however, remain poorly understood. Here we show that the protein interaction landscape of tryptoline acrylamide stereoprobes can be profoundly altered by structural modifications distal to the acrylamide reactive group. The majority of stereoprobe liganding events occurred at non-orthosteric sites and mostly evaded assignment by the machine learning-based co-folding model Boltz-2, which instead tended to misplace the stereoprobes in orthosteric pockets (an outcome we term "orthostery burnout"). We found that stereoprobes reacting with C124 in the nucleotide exchange factor GRPEL1 disrupt interactions with the mitochondrial HSP70 chaperone HSPA9/mortalin, leading to impairments in mitochondrial protein import and induction of mitophagy. Our results highlight tryptoline acrylamides as a versatile source of covalent ligands targeting non-orthosteric sites on proteins, including tool compounds that perturb the mitochondrial HSP70 chaperone system.

biochemistry↗

bioRxiv2025

Targeted α-Synuclein mRNA Degradation by PMO-Based RNA-Degrading Chimeras

-Synucleinopathies are devastating neurodegenerative diseases characterized by pathological accumulation of a neuronal protein, -synuclein (Syn). Lowering soluble Syn levels is a promising therapeutic strategy to limit aggregation and neurotoxicity, but directly targeting this protein is hindered by its intrinsically disordered structure and other factors, such as its conformational heterogeneity and intracellular drug delivery barriers. Consequently, increasing attention has been directed toward targeting the SNCA transcript, which encodes Syn. Here, we developed phosphorodiamidate morpholino oligonucleotide (PMO)-based RNA-degrading chimeras (RDCs) that selectively bind the 5' untranslated region of SNCA mRNA and recruit RNase L for targeted RNA degradation. Through the systematic evaluation of 10 RDCs, we identified and optimized 4-D1, which effectively reduced SNCA mRNA and Syn protein expression in HEK293T cells in an RNase L-dependent manner. 4-D1 lowered SNCA transcript and Syn protein levels in both primary cortical neurons from humanized SNCA mice and in human induced pluripotent stem cell-derived cortical neurons. This reduction prevented prion-like seeding induced by patient-derived Syn fibrils and protected neurons from fibril-induced cytotoxicity. Finally, in vivo studies confirmed the efficacy of 4-D1 in reducing Syn mRNA expression in humanized SNCA mice. These findings indicate that PMO-based RDCs may represent a promising therapeutic modality for -synucleinopathies. Significance StatementAbnormal aggregation of the neuronal protein -synuclein is central to Parkinsons disease and related disorders, yet therapeutic candidates that directly target this protein have yet to demonstrate efficacy. in clinical trials. We developed a new strategy that lowers -synuclein production at the RNA level using phosphorodiamidate morpholino oligonucleotide (PMO)-based RNA-degrading chimeras (RDCs). These molecules recruit a natural RNA-degrading enzyme to selectively destroy the RNA transcript encoding -synuclein. Our lead RDC reduced -synuclein levels in cultured cells, humanized mouse and human neurons, blocked -synuclein pathological aggregation, and protected neurons from toxicity. This study establishes RDCs as a promising therapeutic platform for Parkinsons disease and other neurodegenerative diseases driven by -synuclein.

biochemistry↗

bioRxiv2025

A newly identified Duck orbivirus as the etiological agent of egg-production decline in Chinese breeder ducks

The genus Orbivirus comprises double-stranded RNA viruses, many of which are transmitted by arthropods and cause febrile, hemorrhagic, or reproductive diseases in animals. In recent years, unexplained outbreaks characterized by marked egg-production decline have occurred in breeder duck flocks in China. To identify the causative agent, samples were collected from affected farms in multiple regions across China between 2022 and 2025. Representative samples were analyzed by high-throughput sequencing, followed by phylogenetic analysis, transmission electron microscopy, host cell infection assays, and animal challenge experiments. A previously unreported Orbivirus, designated Duck orbivirus (DORV), was identified. Epidemiological investigation indicated that outbreaks mainly affected breeder ducks during the peak laying period (21-55 weeks of age), with higher incidence in summer and autumn. The DORV genome contains ten double-stranded RNA segments encoding seven structural and five nonstructural proteins. Phylogenetic analysis showed that DORV is closely related to Parrys Lagoon virus (PLV) and Corriparta virus (CORV). Electron microscopy revealed icosahedral particles 30-40 nm in diameter. DORV replicated efficiently in DEF, DEL and C6/36 cells but not in MDCK and LMH cells, suggesting a restricted host range with potential arthropod-borne features. Infection of breeder ducks with DORV-SD01 reduced egg production by 30-40% and caused lesions in the ovary, liver, and spleen. This study describes a novel duck-origin Orbivirus linked to egg-production decline, offering new etiological insights and extending the host spectrum of Orbivirus. The results provide a foundation for future surveillance and prevention of emerging waterfowl diseases.

microbiology↗

bioRxiv2025

Ptf1a robustly drives the gliogenic switch in the rodent embryonic cortex in a dosage-dependent manner by activating pro-glial gene expression programs

It is widely believed that the gliogenic switch during rodent embryonic development is governed by the orchestrated crosstalk between a cohort of genes and extracellular cues. Here we report that ectopic expression of the single bHLH factor, pancreas transcription factor 1 (PTF1A), is sufficient to drive radial glial progenitors (RGPs)-regardless of progenitor heterogeneity and developmental stage-to differentiate into glial cells. Ptf1a- expressing RGPs exhibit progenitor behaviors indicative of a neurogenic-to-gliogenic fate transition, resembling endogenous progenitors at the late stages of embryonic development, and preferentially produce OLIG2+ oligodendrocytes in vivo, some of which are positive for PDGFR or CC1. This robust gliogenic competency depends on the dosage of stable Ptf1a expression in RGPs. RNAseq reveals the glial transcriptome, including upregulated expression of several notch signaling components and the endothelin receptors in Ptf1a RGPs. We further identify Ednrb as one of the downstream targets of Ptf1a that directs RGPs toward gliogenesis via the ERK1/2 signaling pathway. In summary, our study uncovers a novel and robust role for Ptf1a in glial fate specification, offering a potential strategy for generating human oligodendrocytes in vitro.

neuroscience↗

bioRxiv2025

Genetically Engineered Cell Membrane-Coated Nanodrug for Targeted Treatment of Thyroid Cancer

Thyroid cancer is the most common endocrine malignancy, particularly in patients with radioactive iodine-refractory differentiated thyroid cancer (RAIR-DTC), who have limited treatment options and poor clinical prognosis. In this study, doxorubicin (DOX) and sorafenib (SOR) were loaded into the photothermal conversion agent mesoporous polydopamine (mPDA), forming mPDS. Tumor cell membrane coating engineering resulted in the formation of mPDS@CAR-M, significantly improving tumor targeting. After internalization by tumor cells, the loaded drugs are rapidly released under near-infrared (NIR) laser irradiation. mPDS@CAR-M effectively inhibits tumor cell proliferation by enhancing oxidative stress, suppressing the PI3K-AKT-mTOR signaling pathway, and inducing cytotoxic autophagy. By activating harmful autophagy, mPDS@CAR-M further inhibits the epithelial-mesenchymal transition (EMT) process, reducing tumor cell migration capacity. In vivo experiments showed that mPDS@CAR-M significantly reduced tumor volume, with its therapeutic efficacy closely related to the expression level of the targeted surface antigen. Therefore, mPDS@CAR-M demonstrates significant potential in the treatment of RAIR-DTC, providing a novel direction for further clinical exploration.

cancer biology↗

bioRxiv2025

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

bioRxiv2025

The complete genome of a songbird

Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding [~]90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.

genomics↗

bioRxiv2025

Machine learning-based definition of cellular senescence reveals pro-senescence potential implication in lung adenocarcinoma

Despite growing evidence implicating cellular senescence in tumor progression, methodological challenges in objectively quantifying senescent cell burden across cancer types continue to limit mechanistic studies and clinical translation. To address this, we developed the Predictive Cellular Senescence Model (PreCSenM), a machine learning-based tool that assigns a CS score by integrating senescence-associated features across 888 samples. Benchmarking analyses confirmed that PreCSenM markedly outperforms existing methodologies in reliably predicting senescent states within both normal and cancerous transcriptomic datasets. In lung adenocarcinoma (LUAD), PreCSenM identified the CS score as a robust predictor of clinical outcomes. Multi-omics analyses further revealed that lower CS levels correlate with decreased genomic stability and enhanced immune responses, aligning with clinical observations. Notably, drug discovery using PreCSenM identified histone deacetylase inhibitors (HDACis) as potent inducers of CS in LUAD. Transcriptional and epigenetic profiling of HDACi-treated cells pinpointed FOSB as a core transcription factor driving CS, and FOSB knockdown blocked HDACi-induced senescence. Overall, our study establishes PreCSenM as a multidimensional senescence quantification tool, bridging computational prediction with clinical relevance and mechanistic validation to enable senescence-directed therapies in precision oncology.

bioinformatics↗

bioRxiv2025

Agro-STARR-seq enables in planta genome-wide enhancer discovery and AI-empowerd enhancer design

Comprehensive enhancer screening is essential for dissecting gene regulatory networks. However, methods for such screening remain limited in plants. We present Agro-STARR-seq, an in planta enhancer screening platform using Agrobacterium-mediated delivery of STARR-seq libraries into Nicotiana benthamiana leaves. In the Arabidopsis genome, we identified 14,715 sequences with enhancer activity, of which 91.59% were located outside of open chromatin regions. This largest in planta enhancer dataset to date enabled AI-assisted design of highly active synthetic enhancers. For the large N. benthamiana genome, we pre-processed the genomic DNA with an Assay for Transposase Accessible Chromatin (ATAC) procedure before the Agro-STARR-seq protocol,and found that only one-third of open chromatin exhibited enhancer activity, 76.00% of which showed no canonical H3K27ac histone marks. Footprinting analysis further enables systematic linkage of transcription factor (TF) binding to enhancer function. Overall, Agro-STARR-seq provides a novel platform for dissecting and engineering plant enhancers.

genomics↗

bioRxiv2025

Fluid-Squid: DIY Multiplexed Imaging of Cells and Tissues

Recent advances in multiplexed single-cell characterization have revolutionized our insight into cell biology, but many available technologies remain limited by high costs or a lack of customizability. To address these challenges, we developed Fluid-Squid, a cost-effective, quantitative imaging platform that integrates automated fluidics to support customizable, do-it-yourself multiplexed imaging workflows. Using Fluid-Squid, we successfully imaged fresh frozen human intestinal tissues with a 36-plex oligonucleotide-barcoded antibody panel and further demonstrated the feasibility of lyophilizing such multiplexed panels. We also adapted existing multiplexed imaging workflows to characterize individual cells to identify immune cell populations, phenotype, and antigen-specific cells from mouse splenocytes and human peripheral blood mononuclear cells (PBMCs) with a 39-antibody panel. To further expand its utility, we developed a barcoding strategy that allows for the pooling and simultaneous staining of multiple samples, reducing time, costs, and batch effects in single-cell experiments. This approach facilitated rapid titration to optimize antibody concentrations and assess the impact of various blood preparation methods on cell type retention. Overall, our work provides a new open-source framework for automated fluidics and microscopy in a flexible, cost-effective platform, empowering adaptable multiplexed characterization of both single cells and tissues.

bioengineering↗

bioRxiv2025

Notch canonical activity in a subset of glial cells regulates short-term memory in Drosophila

Notch is a transmembrane receptor expressed at the cell surface that mediates transcriptional responses upon binding to its ligands, in a variety of contexts. Evolutionarily conserved, Notch plays a key role in numerous cell fate decisions during development and is also required in post-mitotic brain neurons for the consolidation of long-term memory and long-term habituation. Notch signaling is highly expressed in glial cells, where it plays a key role in regulating their development and proliferation. More recently, a Notch-dependent neuroglial pathway has been implicated in modulating the susceptibility of short-term memory to sleep deprivation in Drosophila. In this study, we demonstrate that canonical Notch signaling in glia-- mediated by the Delta ligand and the transcription factor Suppressor of Hairless--is activated in a subset of cortex and ensheathing glial cells. This signaling is essential for the formation of short-term memory in the aversive phototaxic suppression assay, which is sensitive to sleep deprivation. Dopaminergic transmission is known to be required for this type of learning and is negatively impacted by sleep deprivation, suggesting a possible interaction between Notch and dopamine pathways. Supporting this idea, we find that modulating dopaminergic transmission downregulates canonical Notch activity in glial cells. Conversely, activating Notch signaling in glia near dopaminergic neurons prevents the learning impairments typically caused by sleep deprivation. Notably, Notch signaling itself does not appear to alter dopamine levels in the brain. Together, these findings indicate that canonical Notch signaling in a specific subset of glial cells is essential for short-term memory formation and is modulated by dopaminergic signaling. This suggests that sleep loss-induced disruption of dopaminergic transmission impairs learning by downregulating canonical Notch signaling. Since Notch homologs are highly expressed in mammalian glia, this pathway may be conserved and functionally relevant in other species, including humans.

neuroscience↗

bioRxiv2025

EPAS1 regulates host antibacterial defense in response to bacterial quorum sensing

Hypoxia-inducible factors (HIFs) are a family of transcription factors that function as sensors of hypoxia. However, it remains unclear whether and how HIFs modulate host immunity by responding to other ligands. Here, we describe an immune regulatory function of HIF-2 (also known as EPAS1) in response to cis-2-dodecenoic acid (BDSF), a quorum sensing (QS) signal, secreted by Burkholderia cenocepacia. Upon ligand binding, EPAS1 activation leads to the production of inflammatory cytokines and the initiation of antibacterial defense. Inoculation with diffusible BDSF or liposome-encapsulated BDSF improves survival in mice infected with B. cenocepacia or Acinetobacter baumannii by preconditioning the immune system. Our findings reveal a previously unidentified role of EPAS1 as an intracellular pattern recognition receptor (PRR) for bacterial QS signal to control host antibacterial defense.

microbiology↗

bioRxiv2025

An antifungal with a novel mechanism of action discovered via resistance gene-guided genome mining

Invasive fungal infections claim over two million lives annually, a problem exacerbated by rising resistance to current antifungal treatments and an increasing population of immunocompromised individuals. Despite this, antifungal drug development has stagnated, with few novel agents and fewer novel targets explored in recent decades. Here, we validate acetolactate synthase (ALS), an enzyme critical for branched-chain amino acid biosynthesis and absent in humans, as a promising target for new therapeutics. Using resistance gene-guided genome mining, we discovered a biosynthetic gene cluster in Aspergillus terreus encoding HB-35018 (1), a novel spiro-cis-decalin tetramic acid that potently inhibits ALS. Biochemical and antifungal assays demonstrate that 1 surpasses existing ALS inhibitors in efficacy against Aspergillus fumigatus and other pathogenic fungi. Structural studies via cryo-electron microscopy reveal a unique covalent binding interaction between compound 1 and ALS, distinct from known inhibitors and finally, we demonstrate that ALS is essential for the virulence in a mouse model of invasive aspergillosis. These findings position ALS as a promising target for antifungal development and demonstrate the potential of resistance gene-guided genome mining for antifungal discovery.

bioengineering↗

bioRxiv2025

Multi-platform framework for mapping somatic retrotransposition in human tissues

Mobile element insertions (MEI) shape the human genome in both germline and somatic tissues. While inherited MEIs are well characterized, mapping somatic MEIs (sMEI) in non-cancer tissues remains challenging due to their low allelic fraction and repetitive nature. We established an integrative framework for sMEI analysis leveraging modern sequencing technologies and analytical innovations. We first benchmarked sMEI detection and demonstrated advantages of long-read and MEI-targeted sequencing for ultra-low-frequency events using a mixture of well-established cell lines. We then showed that haplotype phasing and donor-specific assemblies refine sMEI detection, effectively distinguishing from germline and false signals in in-silico tumor-normal mixtures. We further developed a source-tracing strategy based on internal sequence variation, expanding the catalogue of active source elements beyond traditional transduction-based methods. Applying this framework to donor tissues, we identified 18 rare somatic L1 insertions, revealing structural and source diversity. Our work provides a foundational framework and biological insight into sMEIs.

genomics↗

bioRxiv2025

Consistent Induction of Broadly Neutralizing HIV Antibodies by a Novel Two-Step Mechanism Informs Immunogen Design

A major obstacle confronting HIV-1 vaccine and cure research is the lack of an outbred animal model for rapid and consistent induction of broadly neutralizing antibodies (bNAbs). We designed an epitope-focused simian-human immunodeficiency virus (SHIV.5MUT) that elicited broad and potent V3-glycan-targeted antibodies within a year of infection in 14 of 22 macaques compared with 0 of 14 control animals. SHIV.5MUT elicited bNAbs by a novel two-step mechanism, inducing an initial wave of V1-directed antibodies that selected for Envs with shortened, hypoglycosylated V1 loops, which in turn primed V3-glycan bNAb precursors. Rhesus bNAbs were immunogenetically and structurally diverse, closely resembling human V3-glycan bNAbs. Env-bNAb coevolution revealed a diverse repertoire of bNAb precursors and the Env variants that matured them, yielding a molecular blueprint for vaccine design.

immunology↗