Biology subjects

Li, S.

Publications and source records attributed to Li, S..

At least 289 records · Page 16Linked to original sources

bioRxiv2025

Nucleosome stability safeguards cell identity, stress resilience and healthy aging

Nucleosomes are the minimal repeating units of chromatin. Their dynamic assembly and disassembly underpins chromatin organization and genome regulation. However, it remains unclear how intrinsic nucleosome stability contributes to higher-level yet fundamental cellular and organismal properties--such as preservation of cell identity, lineage specification, stress resilience and ultimately healthy aging. To address this, we tested the impact of decreased intrinsic nucleosome stability across multiple cell, tissue and organismal models by introducing histone mutants that weaken histone-histone interactions. While nucleosome instability did not broadly alter global chromatin accessibility, DNA damage, cell proliferation or viability, it impaired lineage-specific gene expression programs, altered lineage specification and activated intrinsic inflammatory and stress pathways in a manner reminiscent of aging in mouse tissues and human cells. Consistently, nucleosome instability accelerated the onset of age-associated transcriptional alterations and functional decline in Caenorhabditis elegans and Drosophila melanogaster, and reduced cellular resilience to exogenous perturbations-- including environmental, epigenetic and mitotic stress--in human cells and Saccharomyces cerevisiae. These cross-species findings identify nucleosome stability as an evolutionarily conserved epigenetic safeguard that preserves cell identity and stress resilience and supports organismal function and healthy aging.

genomics↗

bioRxiv2025

DNA Data Storage Architecture via Ligation of Dynamic DNA Bytes

The explosive growth of digital data is overwhelming conventional storage media, creating an urgent need for more efficient solutions. DNA offers immense potential for digital data storage, yet most systems remain static and archival. Here, we present a modular DNA storage architecture based on dynamic DNA bytes (DynaBytes)-- pre-fabricated DNA segments that can be ligated into reconfigurable information units. Utilizing core, functional and control DynaBytes, we stored 210,776 bits (26,347 bytes) of digital information organized within a file-system, and demonstrated CRUD (Create-Read-Update-Delete)-like operations, hierarchical access and nanopore-based realtime retrieval. Robust data recovery was achieved under [~]100x error-prone sequencing using streamlined error correction and fuzzy decoding. By relying on in vitro ligation of standardized components, DynaBytes reduces cost, scales efficiently, and allows interactive, rewritable storage. These features advance DNA storage beyond passive archiving toward a reconfigurable framework, opening new possibilities for dynamic, practical and large-scale DNA-based data systems.

synthetic biology↗

bioRxiv2025

stk32a links sleep homeostasis to suppression of sensory and motor systems

Sleep is regulated by a homeostatic process and associated with an increased arousal threshold, but the genetic and neuronal mechanisms that implement these essential features of sleep remain poorly understood. To address these fundamental questions, we performed a zebrafish genetic screen informed by human genome-wide association studies. We found that mutation of serine/threonine kinase 32a (stk32a) results in increased sleep and impaired sleep homeostasis in both zebrafish and mice, and that stk32a acts downstream of neurotensin signaling and the serotonergic raphe in zebrafish. stk32a mutation reduces phosphorylation of neurofilament proteins, which are co-expressed with stk32a in neurons that regulate motor activity and in lateral line hair cells that detect environmental stimuli, and ablating these cells phenocopies stk32a mutation. Neurotensin signaling inhibits specific sensory and motor populations, and blocks stimulus-evoked responses of neurons that relay sensory information from hair cells to the brain. Our work thus shows that stk32a is an evolutionarily conserved sleep regulator that links neuropeptidergic and neuromodulatory systems to homeostatic sleep drive and changes in arousal threshold, which are implemented through suppression of specific sensory and motor systems.

neuroscience↗

bioRxiv2025

SLFN11 restricts escape from telomere crisis to prevent alternative lengthening of telomeres

The tRNA nuclease SLFN11 is epigenetically silenced in [~]50% of treatment-naive tumours and is the strongest predictor of chemoresistance but why it is frequently inactivated in cancer is unknown. To acquire immortality, cancer cells can activate alternative lengthening of telomeres (ALT), typically accompanied by ATRX loss. Here, we implicate SLFN11 in sensing telomere replication stress, triggering eradication of ATRX deficient cells prior to ALT establishment. Whereas progressive telomere shortening of cells lacking telomerase and ATRX leads to telomere crisis and cell death, SLFN11 loss confers tolerance to PML-BLM dependent ALT intermediates, permitting emergence of ALT survivors. We propose that during tumorigenesis SLFN11 inactivation is selected as means to tolerate endogenous replication stress following telomere crisis, leading to the development of therapy resistant tumours before treatment.

molecular biology↗

bioRxiv2025

Crosslinking of Lipid Nanoparticles Enhances the Delivery Efficiency and Efficacy of mRNA Vaccines

Lipid nanoparticles (LNPs) have enabled the effective delivery of RNA therapeutics and mRNA vaccines. However, their broader applications are limited by the suboptimal stability and endosomal escape efficiency. Here, we present an easy-to-adopt post-assembly crosslinking approach to enhance the structural and functional stability of mRNA LNPs. By leveraging a series of cholesterol derivatives and crosslinking methods, we induce crosslinks of the lipid components following mRNA LNP assembly to form the crosslinked LNPs (cLNPs). We systematically evaluated crosslinking parameters and identified optimal conditions that enhance both the physical stability and transfection efficiency of cLNPs. Our findings demonstrate that cLNPs exhibit improved structural integrity under storage and lyophilization conditions, as well as increased extracellular stability and endosomal escape efficiency, resulting in improved performance of mRNA LNPs both in vitro and in vivo. This crosslinking strategy represents a critical advance in LNP engineering, enabling more resilient LNPs and broadening the applicability of LNP-based therapies for gene therapy and vaccine delivery. Our work lays the foundation for developing next-generation LNPs with superior stability and delivery efficiency, broadening the impact of RNA therapeutics and vaccines.

bioengineering↗

bioRxiv2025

Epstein-Barr Virus Latent Membrane Protein 1 targets cIAP1, cIAP2 and TRAF2 for Proteasomal Degradation to Activate the Non-canonical NF-κB Pathway

The Epstein-Barr virus oncoprotein Latent Membrane Protein 1 (LMP1) is expressed in multiple malignancies and is critical for B-cell immortalization. LMP1 constitutively activates NF-{kappa}B signaling pathways, which are essential for EBV-mediated B cell transformation and for transformed B cell survival. Reverse genetic analysis revealed two LMP1 regions critical for primary human B cell immortalization, termed transformation effector site (TES) 1 and 2, which activate multiple host growth and survival pathways, in particular NF-{kappa}B. Of these, only TES1 signaling is required for B-cell transformation within the first several weeks of infection. TES1 signaling is also critical for EBV-transformed lymphoblastoid B-cell survival. However, precisely how TES1 initiates NF-{kappa}B signaling has remained incompletely understood. Here, we provide multiple lines of evidence that TES1 associates with cellular inhibitor of apoptosis protein 1 and 2 (cIAP1/2) in a tumor necrosis factor associated factor 3 (TRAF3) dependent manner. TES1 signaling drives cIAP1 autoubiquitination and targets TRAF2, cIAP1 and 2 for proteasomal degradation in a TRAF3 dependent manner. Overexpression of either cIAP1 or 2 impaired LMP1 TES1-mediated non-canonical NF-{kappa}B activation. Collectively, these studies suggest that LMP1 TES1 initiates non-canonical NF-{kappa}B signaling distinctly from CD40 and other host immunoreceptors, thereby highlighting a therapeutic target.

microbiology↗

bioRxiv2025

Uncovering directionally and temporally variable genes with STAVAG

Spatially variable genes (SVGs) are crucial for understanding spatial heterogeneity in spatial transcriptomics. Yet, SVGs are challenging to align with established biological axes and lack straightforward mechanistic interpretation, thereby limiting their ability to inform downstream experiments or clinical applications. Here, we introduce the concept of directionally variable genes (DVGs) and temporally variable genes (TVGs). Also, we propose a unified framework, STAVAG, that models spatial or temporal information to identify DVGs and TVGs. STAVAG effectively identifies biologically meaningful DVGs for uncovering prognostically relevant gene modules that align with the malignant-immune-stroma structure in the tumor microenvironment, identifying marker genes in three-dimensional brain data, and detecting 12 polarization genes regulating planarian regeneration. Furthermore, by tracking the progression of myocardial infarction and tissue development, STAVAG reveals critical TVGs that can serve as diagnostic biomarkers for the ultra-acute phase of myocardial infarction. STAVAG also identifies both global and local gene modules involved in mouse placentation, as well as tissue-specific and interactive TVG modules that dynamically evolve during mouse embryonic development.

bioinformatics↗

bioRxiv2025

HIF-1α and RhoA Drive Enhanced Motility and Aerotaxis of Polyaneuploid Prostate Cancer Cells in Hypoxia

Most cancer deaths result from metastasis, yet only a rare subset of tumor cells can complete this process. Among these, polyaneuploid cancer cells (PACCs), which arise via endoreplication under stressors such as hypoxia, are implicated as metastatic drivers, but how they acquire this potential is poorly understood. Here, we show that prostate cancer-derived PACCs exhibit features predictive of invasion and intravasation. Time-lapse fluorescence microscopy and single-cell tracking under hypoxia revealed that PACCs migrated significantly farther than Non-PACCs, consistent with local invasion. PACC trajectories showed a strong tendency to migrate toward oxygen, consistent with aerotaxis and predictive of intravasation. siRNA-mediated knockdown demonstrated that the enhanced motility and aerotaxis of hypoxic PACCs require both HIF-1and RhoA, with RhoA expression suppressed upon HIF-1 inhibition. Altogether, we propose a HIF-1[->] RhoA [->] motility/aerotaxis mechanism enabling PACCs to escape hypoxic cores, invade tissue, and access vasculature, highlighting them as a uniquely invasive subpopulation with implications for anti-metastatic therapies.

cancer biology↗

bioRxiv2025

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

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

bioinformatics↗

bioRxiv2025

Hormetic nutrient stress promotes longevity by orchestrating histone acetylation on key lipid catabolism and antioxidant defense genes

Exposure to low levels of environmental challenges, known as hormetic stress, such as nutrient deprivation and heat shock, fosters subsequent stress resistance and promotes healthy aging in later life. However, specific mechanisms governing transcriptional reprogramming upon hormetic nutrient stress remain elusive. In this study, we identified histone H3 lysine 27 acetylation (H3K27ac) as a crucial driver of transcriptomic adaptation to hormetic fasting. Beyond its immediate function of enhancing lipid catabolism for alternative energy sources, stress-induced H3K27ac activates lifelong antioxidant defenses, thereby reducing reactive oxygen species (ROS) produced by stress-induced fatty acid oxidation and their accumulation during aging. The increase in H3K27ac, mediated by pioneer factor PHA-4/FOXA and cooperating transcription factor NHR-49/HNF4, is crucial for lifespan extension under hermetic nutrient stress in Caenorhabditis elegans. Our findings establish H3K27ac as a key transcriptional switch that bridges nutrient status with transcriptomic reprogramming, underpinning the pro-longevity effects of hormetic fasting through orchestrating lipid catabolism and antioxidative defenses.

molecular biology↗

bioRxiv2025

Lineage-Specific Epigenomic Mapping of Proximal and Distal Fallopian Tube Epithelium Reveals Mesenchymal/Wnt-Driven Tumor Phenotype Diversification

High-grade serous ovarian cancer (HGSC) typically originates from the distal fallopian tube epithelium (disFTE), while the proximal epithelium (proFTE) remains less explored. Here, Using isogenic murine organoid models with common oncogenic drivers (Tp53-/-; Krasmut; Pten-/-), we show that disFTE and proFTE generate distinct tumor subtypes driven by region-specific transcriptional programs. Unlike disFTE, proFTE demonstrates continuous activation of epithelial-mesenchymal transition (EMT) across wild-type, mutant organoids, and derived tumors. Additionally, mutated proFTE organoids and their tumors exhibit persistent WNT signaling activation and grow independently of WNT signals. Chromatin profiling shows that mutant proFTE maintains a distinctive epigenetic profile with promoters associated with EMT and WNT pathways. Human proFTE with BRCAmut also shows epigenetic activation of EMT- and WNT-related genes. Tumors near the uterotubal junction (UTJ)--anatomically akin to proFTE--exhibit a pronounced EMT signature, increased Vimentin+E-cadherin+ and nuclear {beta}-catenin expression. These findings suggest proFTE-derived tumors may occupy a unique niche in gynecological malignancies, with regional identity shaping tumor phenotypes.

cancer biology↗

bioRxiv2025

Post-inhibitory rebound firing drives hypothalamic activation for male mating

Many behaviorally relevant limbic circuits are dominated by inhibitory connections, raising the question of how neuronal activation arises in such contexts. In male mating, both activation of mPOA and its inhibitory inputs are essential--a paradox previously ascribed to disinhibition. Here, we show that the mPOA largely lacks local inhibitory circuits, arguing against disinhibition. Instead, in vivo recordings reveal that mount-active mPOA neurons are suppressed prior to behavioral onset, and this inhibition negatively correlates with subsequent activation, consistent with post- inhibitory rebound firing (PIR). A biologically plausible conductance-based model demonstrates that synaptic inhibition interacts with T-type Ca{superscript 2} currents -- the ionic basis of PIR -- to promote mPOA neuron firing. Experimentally, bidirectional manipulations of mPOA T-type Ca{superscript 2} channels confirm this mechanism: knockdown reduces PIR and impairs male mating, while overexpression enhances mating. Together, these results identify PIR as a critical mechanism by which inhibition promotes activation in limbic circuits to drive male mating.

neuroscience↗

bioRxiv2025

Structural insights and engineering of deep-sea halophilic PET hydrolytic enzymes

Pervasive use of polyethylene terephthalate (PET) poses tremendous challenges for global waste management and environmental sustainability, fueling growing interests in enzymatic degradation as an eco-friendly solution. While PET hydrolases hold significant promise, their industrial deployment is hindered by insufficient performance, particularly under high-salinity conditions raised from high substrate loads. Building on our previous discovery of three deep-sea PET hydrolases (dsPETase01, dsPETase05 and dsPETase06) with exceptional halophilicity and PET-degrading activity, we here present their three-dimensional structures and mechanistic characterization. Structural comparison, site-directed mutagenesis, and domain swapping reveal key structural features and the essential role of C-terminal acidic residues in salt tolerance. Integrating semi-rational protein design, Transformer-based modeling, and disulfide bond engineering, we synergistically enhance the thermostability and catalytic efficiency of dsPETase05. These findings elucidate the unique structural features and salt adaptation mechanisms of deep-sea halophilic PET hydrolases, and inform the future engineering of biocatalysts for application in harsh industrial environments.

molecular biology↗

bioRxiv2025

Plasma membrane accessible cholesterol is regulated by ACC1 and lipid droplets

Accessible cholesterol, the pool of membrane cholesterol with high chemical activity, regulates vital processes including vertebrate development and pathogen evasion. The mechanisms that govern plasma membrane (PM) cholesterol accessibility are incompletely understood. Using a genome-wide screen we find that acetyl-CoA carboxylase alpha (ACC1) loss causes a ~10-fold increase in PM accessible cholesterol in cells and a male mouse model. We demonstrate that reduced fatty acyl-CoA levels, achieved by targeting metabolic enzymes including ACC1, fatty acid synthase (FASN) or acyl-CoA synthetases long chain (ACSL1, 3 and 4), results in the activation of adipose triacylglycerol lipase (ATGL). ATGL activation elevates polyunsaturated diacylglycerols even in triacylglycerol-deficient backgrounds, suggesting that ATGL acts independently of triacylglycerol hydrolysis. These diacylglycerol species are utilized to generate polyunsaturated phosphatidylcholine and phosphatidylethanolamine, which raises PM fluidity and cholesterol accessibility. Conversely, ATGL inhibition rigidifies the PM, reducing PM accessible cholesterol. Increased PM fluidity impairs cholesterol transport, triggering SREBP2 activation. This study reveals a surprising link between fatty acid metabolism and cholesterol homeostasis, demonstrating how ATGL-dependent lipid remodeling tunes membrane fluidity to regulate intracellular cholesterol signaling.

cell biology↗

bioRxiv2025

Identification and quantification of alternative polyadenylation sites in single cell RNA-seq data using scPAISO

AbstractsAlternative polyadenylation (APA) is a critical posttranscriptional mechanism that generates transcriptomic diversity through the production of mRNA isoforms with distinct 3 UTRs or coding sequences. Current APA analysis based on single-cell RNA sequencing (scRNA-seq) for establishing cell type-specific APA landscapes primarily rely on Read2 data, which lacks precise cleavage site (CS) information. This limitation restricts their ability to achieve precise de novo mapping of polyadenylation sites (PASs). Here, we present single-cell PolyAdenylation ISOform quantification (scPAISO), a computational pipeline designed for de novo identification of PAS and quantification of PAS isoforms in scRNA-seq data, by leveraging the often-discarded Read1 from 3 tag-based scRNA-seq protocols. Unlike existing tools, scPAISO directly captures mRNA 3 end cleavage sites, enabling superior performance in motif enrichment (stronger AAUAAA signal) and peak precision (sharper PAS peaks). Moreover, the smaller peak widths enhance the spatial resolution, enabling more accurate detection of closely spaced PASs in the genome. By integrating Read1 and Read2 data, scPAISO achieves isoform-level quantification with an assignment accuracy exceeding 95%. We demonstrate the robustness of scPAISO in identifying PASs and quantifying APA events across diverse biological contexts, including hematopoiesis, systemic sclerosis (SSc), and mouse tissues. We identified stage-specific 3 UTR lengthening in hematopoietic progenitors, global 3 UTR remodeling in SSc and tissue-specific polyadenylation (PA) preference along with RNA-binding proteins in mice. Overall, scPAISO represents a significant advancement in the analysis of APA at single-cell resolution and provides a powerful tool for exploring the regulatory landscape of APA, offering new insights into transcriptome complexity and gene regulation in both health and disease.

bioinformatics↗

bioRxiv2025

IRE1α-XBP1s axis is required for BCG-induced trained immunity against viral infection by inhibiting AHR signaling

Although Bacille Calmette-Guerin (BCG) has been proved to be suitable in inducing trained immunity, mechanism-related issues have not yet been fully resolved. In this study, we found that in vitro BCG training protects both BCG harboring and bystander macrophages against DNA virus and RNA virus infection and demonstrated that BCG harboring cells protect bystanders partly by type I interferon (IFN). We determined aryl hydrocarbon receptor (AHR) as a negative regulator in BCG-induced trained immunity on defense against viral infection in vitro and in vivo and blockade of type I IFN signaling partially impaired the enhanced antiviral effect of AHR deficiency in BCG training. Furthermore, we revealed IRE1-XBP1s signaling as a critical pathway in BCG-induced trained immunity against viral infection in vitro and in mice. Mechanistically, we demonstrated that IRE1-XBP1s pathway influenced BCG-induced trained immunity by limiting AHR mRNA expression and the translocation of AHR protein into the nucleus.

immunology↗

bioRxiv2025

C9orf72/SMCR8 complex maintains microglial homeostasis via RAB8A-ESCRT-mediated lysosomal repair

Microglia are critical regulators of neuroinflammation and neurodegeneration. Haploinsufficiency of C9orf72, the most common genetic cause of ALS and FTD, has been mainly linked to autophagy-lysosomal pathway defects, but its precise role in microglial lysosomal function remains unclear. Here we identify the C9orf72/SMCR8 complex as a key regulator of microglial homeostasis through lysosomal repair. Loss of C9orf72 and SMCR8 in mice causes age-dependent neuroinflammation and microgliosis, with microglia adopting a disease-associated state. In aged CNS tissue, microglia display lysosomal damage, marked by galectin-3 upregulation and its accumulation on lysosomes. To model this process, we applied the lysosomotropic agent LLOMe to microglia, which recapitulated lysosomal damage and revealed defective recruitment of phosphorylated RAB8A and the ESCRT machinery in C9orf72/SMCR8-deficient cells. Notably, mutant microglia accumulate GTP-bound RAB8A, which becomes aberrantly hyperphosphorylated and mislocalized to non-lysosomal vesicles. We further show that the GAP activity of the C9orf72/SMCR8 complex is essential for lysosomal repair. These findings uncover a previously unrecognized role for the C9orf72/SMCR8 complex in coordinating RAB8A-ESCRT-mediated lysosomal repair, thereby safeguarding microglial homeostasis and limiting neuroinflammation.

cell biology↗

bioRxiv2025

Establishment of a Systemic Lupus Erythematosus Mouse Model in Humanized CD3/CD19 Mice and Evaluation of the Efficacy of a Human Bispecific Antibody

Systemic Lupus Erythematosus (SLE) is a complex autoimmune disease affecting multiple organ systems and is considered one of the most severe autoimmune diseases worldwide, significantly impacting womens health. B cells play a crucial role in disease pathogenesis by becoming abnormally activated and producing autoantibodies that attack the bodys normal tissues, leading to inflammation and organ damage. Therefore, targeting the human B cell receptor has emerged as a promising strategy for therapeutic intervention. In this study, we established an SLE animal model using double-humanized CD3/CD19 mice, in which human CD3 and CD19 genes replaced their murine counterparts. The phenotype was confirmed by ELISA and flow cytometry. hCD3/hCD19 mice induced by a combination of pristine x 2, imiquimod (IMQ) and nephrectomy exhibited several key features of SLE, including anti-dsDNA antibody production, proteinuria, increased immune cell populations, and kidney lesions. Furthermore, treatment of these humanized mice with anti-human CD3/CD19 bispecific antibodies significantly inhibited these pathological indicators. Thus, pristine x 2, IMQ and nephrectomy induced hCD3/hCD19 mice provide a validated preclinical model for investigating novel therapeutic agents targeting B cells in SLE. Graphical abstractThis study explores the effects of different modeling strategies on agent induction, with a particular emphasis on the link between the induced agents and their corresponding clinical manifestations. Through an extensive literature review and experimental validation, a novel approach for inducing systemic lupus erythematosus (SLE) has been established. By employing gene editing techniques, mouse CD3 and CD19 antibody recognition sites were substituted with their human equivalents. This humanized mouse model enables the direct assessment of humanized bispecific antibodies in the context of SLE induction. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/668572v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@652c83org.highwire.dtl.DTLVardef@4d6233org.highwire.dtl.DTLVardef@6a2f8forg.highwire.dtl.DTLVardef@1587652_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗