Biology subjects

Lee, Y. J.

Publications and source records attributed to Lee, Y. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Signal peptidase complexes set species-specific rules for signal peptide cleavage

Protein secretion is essential for cell function and begins when signal peptides direct nascent proteins into the secretory pathway, where they are cleaved by the signal peptidase complex (SPC). Although this pathway is highly conserved, signal peptides do not always function efficiently across species, and the molecular basis for this incompatibility remains unclear. Here, we show that human signal peptides with longer hydrophobic cores efficiently target and translocate nascent proteins in both yeast and human but are frequently left uncleaved in yeast, identifying signal peptide cleavage as a major barrier to cross-species compatibility. Molecular dynamics (MD) simulations reveal that, despite their highly conserved architectures, yeast and human SPCs generate distinct membrane-thinning profiles near the signal peptide-binding region. Our results support a model in which SPC-lipid interactions tune the local membrane environment to accommodate signal peptides of distinct hydrophobic core length, providing a biophysical mechanism for species-specific signal peptide recognition. These findings offer a mechanistic framework for understanding and potentially engineering protein secretion across diverse expression hosts.

cell biology↗

bioRxiv2026

Stress granule fusion is a mitochondria-coordinated process for stress adaptation

Stress granules are cytoplasmic membraneless organelles assembled during stress to maintain cellular homeostasis. Although fusion is a hallmark of liquid-like behavior of these condensates, whether this process carries functional significance beyond its physical coalescence remains unclear. Here, we show that stress granule fusion is facilitated by mitochondrial dynamics and membrane potential. Intact mitochondria actively associate with stress granules, facilitating fusion and maturation. In contrast, loss of mitochondrial membrane potential, along with disrupted mitochondrial structure or motility, weakens these interactions and reduces fusion frequency. We find that impaired fusion leads to the accumulation of immature granules that retain fewer sequestered components, which correlates with premature cell death. Remarkably, restoring mitochondrial membrane potential rescues granule fusion and enlargement, and is accompanied by increased cell viability and a corresponding increase in granule-associated apoptotic factors. These results demonstrate that stress granule fusion is actively coordinated by mitochondria rather than driven solely by passive coalescence, reshaping how condensate dynamics are understood to integrate with organelle function during cellular stress response.

cell biology↗

bioRxiv2026

A Rapidly Excretable, ROS-Scavenging Ionizable Lipid Decouples mRNA Delivery Potency from Toxicity

The broader clinical application of mRNA therapeutics remains constrained by dose-limiting toxicities, vector-associated immunogenicity, and prolonged tissue retention of lipid nanoparticles (LNPs) in vivo. Here, we report a class of ionizable lipids incorporating a sulfur-bearing hexyl 2-hydroxyethyl sulfide (HHES) motif that decouples mRNA delivery potency from these safety liabilities through dual functionality: the sulfur moiety acts as an intrinsic reactive oxygen species scavenger to suppress oxidative stress, while undergoing oxidative conversion into hydrophilic metabolites to promote rapid systemic clearance. HHES-based LNPs demonstrated a 3.3-fold shorter hepatic half-life and 29-fold lower total hepatic exposure than MC3, while maintaining robust protein expression including functional monoclonal antibody production in vivo. Repeated dosing in non-human primates confirmed negligible systemic, hepatic, or hematological toxicity. Leveraging this safety profile, subretinal HHES LNP delivery achieved up to 57% genome editing efficiency in retinal pigment epithelium, suppressing choroidal neovascularization by [~]65% in a wet age-related macular degeneration model without structural damage or microglial activation. This dual-function design provides a generalizable framework for safe, transient, non-accumulative mRNA nanomedicines.

bioengineering↗

bioRxiv2026

cGAS-mediated IFN-I signaling contributes to disease progression in drug-refractory epilepsy

Epilepsy is a prevalent neurological disease with a third of patients becoming non-responsive to antiepileptic drugs and developing drug-refractory epilepsy (DRE). Here we report that DRE disease progression is contributed by overactive cyclic GMP-AMP synthase (cGAS), a double-stranded DNA sensor that induces type I interferon (IFN-I) signaling. In human DRE microglia, we observe a robust IFN-I signature and the activation of upstream cGAS-STING signaling. Further, in mouse models of Dravet syndrome, a genetic form of DRE, we observe the activation of the cGAS pathway. We show that microglial cGAS can be activated by DNA released from hyperexcitable neurons. Genetic reduction and pharmacological inhibition of cGAS reduces epileptic phenotypes, glial inflammatory signatures, and neuronal transcriptomic changes, underscoring the therapeutic potential of targeting cGAS for DRE treatment.

neuroscience↗

bioRxiv2025

SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data

Cell-cell communication and gene regulatory programs jointly coordinate cellular behaviors during development, regeneration, and disease. Recent advances in spatial transcriptomics enable measurement of gene expression with spatial context across developmental trajectories, providing new opportunities to study dynamic signaling and regulatory processes. However, most existing methods analyze either ligand-receptor (LR) signaling or gene regulatory networks (GRNs) separately, rely on curated interaction databases, and often assume steady-state gene expression, limiting their ability to capture temporal regulatory dynamics and discover novel interactions. We present SpaTRACE, a spatiotemporal recurrent autoencoder framework for joint inference of intercellular signaling and gene regulatory networks from spatial transcriptomics data. SpaTRACE models time-lagged dependencies along pseudotime-sampled cellular trajectories using an attention-based encoder-decoder architecture that predicts future target gene expression from upstream intra- and intercellular signals. The learned attention structure enables simultaneous reconstruction of transcription factor-target gene (TF-TG) regulatory interactions, ligand-receptor-target gene (LR-TG) signaling pathways, and ligand-receptor binding relationships without requiring predefined LR databases. Across synthetic benchmarks, SpaTRACE accurately recovers both GRN and signaling interactions and outperforms existing GRN and cell-cell communication inference methods. Applications to mouse midbrain development reveal transcriptional regulators and signaling programs associated with neuronal differentiation, while analysis of axolotl brain regeneration identifies stage-specific signaling dynamics and candidate interactions involved in tissue repair. Availability: Source code and documentation are available at https://github.com/VariaanZhou/SpaTRACE.

bioinformatics↗

bioRxiv2025

Enhanced liver regeneration via targeted mRNA delivery for partial in vivo reprogramming

Recent studies suggest that injury-induced dedifferentiation, which leads to the formation of injury-responsive cells, contributes significantly to tissue repair across various organs, including the liver. Utilizing Yamanaka factors (Oct4, Sox2, Klf4, and c-Myc: OSKM) for in vivo partial reprogramming generates injury-responsive cells in the intestine, mirroring those derived from injury-induced dedifferentiation. Thus, the transgene induction of OSKM or viral delivery of Oct4, Sox2, and Klf4 shows promise in facilitating tissue regeneration in the intestine, liver, skeletal muscle, and retina. Herein, we demonstrated that transient OSKM induction produces two distinct liver progenitor-like cell populations. One of these populations resembles liver progenitor-like cells (LPLCs) generated by acute acetaminophen (APAP) injury without triggering immune responses. To explore in vivo reprogramming as a viable strategy for tissue regeneration, we employed lipid nanoparticles (LNP) carrying OSKM mRNA (OSKM mRNA-LNP) to stimulate LPLCs formation. Notably, the production of Sox9+ LPLCs, and OSKM-induced dedifferentiation, was closely correlated with successful tissue regeneration in the liver post APAP injury. Thus, the OSKM mRNA-LNP approach represents a promising therapeutic intervention for the repair of acute liver injuries.

physiology↗

bioRxiv2025

TDP-43 loss of function drives aberrant splicing in Parkinson's disease

Introductory paragraphWhile mRNA splicing dysregulation is a well-established contributor to neurodegeneration in disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), its role in Parkinsons disease (PD) remains underexplored. Here, we analyse transcriptomic data from >500 post-mortem human brain samples from individuals with and without PD to show that splicing alterations are frequently detected. Differentially spliced genes were significantly more enriched for those causally-implicated in both PD and ALS than genes that were differentially expressed. Furthermore, we observed a strong association between these splicing alterations and dysfunction of the RNA-binding protein (RBP), TAR DNA-binding protein 43 (TDP-43). Strikingly, genes and exon junctions affected by TDP-43 knockdown overlapped significantly with those dysregulated across brain regions in PD. In brains from individuals with the LRRK2 c.6055G>A (p.G2019S) mutation, the most common genetic cause of PD, we also observed significant enrichment of TDP-43-dependent splicing changes. This finding was corroborated in human pluripotent stem cell-derived midbrain dopaminergic neurons and a LRRK2 p.G2019S knock-in mouse model, where reduced nuclear TDP-43 levels evidenced the well-recognised loss-of-function mechanism contributing to splicing dysregulation. By leveraging our RNA-based analyses we predicted TDP-43-dependent novel peptide sequences and validated their existence within human LRRK2 mutation mDNs, while also demonstrating an overall loss of protein and mRNA expression in mis-spliced genes. Collectively, our findings reveal that PD is marked by extensive splicing dysregulation dependent on TDP-43, making TDP-43 a promising new therapeutic target in PD.

neuroscience↗

bioRxiv2025

RESCUE: recovery of idiosyncratic expression patterns in spatial transcriptomics

Spatial transcriptomics (ST) enables gene expression profiling while preserving the spatial architecture of intact tissue. Analyzing ST data often proceeds by first extracting cell-level information, typically through cell segmentation or cell-type deconvolution. However, a critical oversight has been that a substantial portion of molecular expression is systematically lost or unannotated by these methods. This lost expression can arise from diverse and biologically important sources like fragile or underrepresented cell types, subcellular structures like neurites, and extracellular expression. These omissions can result in biased analyses and incorrect or incomplete biological interpretations. We describe a new computational method, RESCUE, that can recover the unattributed spatial expression patterns missed by existing ST analysis methods and enable robust inference even when reference is incomplete. We validate RESCUE using MERFISH data from the honey bee brain and apply it to multiple ST datasets to demonstrate how it can reveal novel insights into complex tissue biology.

bioinformatics↗

bioRxiv2025

Cytoplasmic Abundant Heat-Soluble Proteins from Tardigrades Protect Synthetic Cells Under Stress

Cytoplasmic abundant heat-soluble (CAHS) proteins, a stress-responsive intrinsically disordered protein from tardigrades, have been discovered to form gel-like networks providing structural support during dehydration, thus enabling anhydrobiosis. However, the mechanism by which CAHS proteins protect the dehydrating cellular membrane remains enigmatic. Using giant unilamellar vesicles (GUVs) as a model membrane system, we show that encapsulated CAHS12 undergoes a reversible structural transformation that reinforces membrane integrity and preserves encapsulated components, mimicking natural anhydrobiosis. CAHS12-containing GUVs demonstrated stability for weeks and mechanical robustness under dehydration, elevated temperature, and osmotic stresses. Molecular simulations suggest that CAHS12 forms a filamentous network within the vesicle lumen that mitigates membrane collapse and preserves compartmental architecture. Synthetic cells with cell-free transcription-translation capabilities withstand desiccation and recover biochemical activities, akin to the tun state of the tardigrade. This discovery opens up synthetic cell applications in bioengineering, cold-chain-independent biomanufacturing, and adaptive biointerfaces.

synthetic biology↗

bioRxiv2025

An artificial nervous system for communication between wearable and implantable therapeutics

Bioelectronics have transformed our capacity to monitor and treat diseases; however, a lack of micrometer-scale, energy efficient communication options limit these devices from forming integrated networks that enable full-body, sensor driven, physiological control. Inspired by our nervous systems ability to transmit information via ionic conduction, we engineered a Smart Wireless Artificial Nervous System (SWANS) that utilizes the bodys own tissue to transmit signals between wearables and implantables. When SWANS emits signals, it generates voltage gradients throughout the body that selectively turn on implanted transistor switches when exceeding their gate threshold voltages. SWANS implantable communication components maintain syringe-injectable footprints and >15x greater power efficiencies than Bluetooth and Near Field Communication. In vivo studies in rats demonstrate SWANS ability to wirelessly regulate dual hind leg motor control by connecting electronic-skin sensors to implantable neural interfaces via ionic signaling as well as coordinate bioelectronics throughout the epidermal, subcutaneous, intraperitoneal, and gastrointestinal spaces.

bioengineering↗

bioRxiv2024

Ustilago maydis disrupts carbohydrate signaling networks to induce hypertrophy in host cells

Ustilago maydis is a biotrophic fungus infecting maize, secreting effector proteins to manipulate host cellular processes and create nutrient-rich environments for its growth. Three effectors, Hap1-3 (hypertrophy-associated proteins), were identified as virulence factors promoting hypertrophic mesophyll tumor cells (HTT). Immunoprecipitation and mass spectrometry revealed interactions among Hap effectors, suggesting potential effector complex formation. CRISPR-Cas9 triple knockout of hap1-3 demonstrated Hap1s role in HTT formation. Infection assays identified Hap1 as a key virulence factor interacting with maize Snf1-related kinase 1 (SnRK1), a central energy regulator. RNA-seq analysis showed that Hap1 promotes cell cycle and starch biosynthesis genes, while CR-hap1 induced defense-related WRKY transcription factors. Phosphoproteomics revealed increased phosphorylation of SnRK1 and metabolic enzymes during SG200 infection. Our findings support a model where U. maydis induces hypertrophy through Hap1, targeting the SnRK1 subunit to prevent SnRK1 inhibition by high trehalose-6-phosphate (T6P), disrupting the antagonistic relationship between T6P and SnRK1. This reprograms host transcription to enhance starch metabolism and induce endoreduplication, leading to hypertrophy induction, while suppressing sugar-induced immune signaling.

plant biology↗

bioRxiv2024

Controlled release of microorganisms from engineered living materials

Probiotics offer therapeutic benefits by modulating the local microbiome, the host immune response, and the proliferation of pathogens. Probiotics have the potential to treat complex diseases, but their persistence or colonization is required at the target site for effective treatment. Although probiotic persistence can be achieved by repeated delivery, no biomaterial that releases clinically relevant doses of metabolically active probiotics in a sustained manner has been previously described. Here, we encapsulate stiff probiotic microorganisms within relatively less stiff hydrogels and show a generic mechanism where these microorganisms proliferate and induce hydrogel fracture, resulting in microbial release. Importantly, this fracture-based mechanism leads to microorganism release with zero-order release kinetics. Using this mechanism, small ([~]1 L) engineered living materials (ELMs) release >108 colony-forming-units (CFUs) of E. coli in 2 h. This release is sustained for at least 10 days. Cell release can be varied by more than three orders of magnitude by varying initial cell loading and modulating the mechanical properties of encapsulating matrix. As the governing mechanism of microbial release is entirely mechanical, we demonstrate controlled release of model Gram-negative, Gram-positive, and fungal probiotics from multiple hydrogel matrices. SIGNIFICANCEProbiotics offer therapeutic benefits and have the potential to treat complex diseases, but their persistence at the target site is often required for effective treatment. Although probiotic persistence can be achieved by repeated delivery, no biomaterial that releases metabolically active probiotics in a sustained manner has been developed yet. This work demonstrates a generic mechanism where stiff probiotics encapsulated within relatively less stiff hydrogels proliferate and induce hydrogel fracture. This allows a zero-order release of probiotics which can be easily controlled by adjusting the properties of the encapsulating matrices. This generic mechanism is applicable for a wide range of probiotics with different synthetic matrices and has the potential to be used in the treatment of a broad range of diseases.

bioengineering↗

bioRxiv2024

Identification of genes conferring individual-level variation responsible for metabolic dysfunction-associated steatohepatitis using single-cell eQTL analysis

Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly recognized for its medical and socioeconomic impacts, driven by diverse genetic and environmental factors. To address the urgent need for individually tailored therapies, we performed single-cell expression quantitative trait loci (sc-eQTL) analysis on liver biopsies from 25 MASLD patients and 23 controls. This approach identified over 3,500 sc-eQTLs across major liver cell types and cell state-interacting eQTLs (ieQTLs) with significant enrichment for disease heritability (for MASLD trait, ieQTL enrichment odds ratio = 10.27). We integrated transcription factors (TFs) as upstream regulators of ieQTLs, revealing 601 functional units ("quartets") composed of TFs, cell states, ieSNPs, and ieGenes. From these results, we pinpoint the loss of an eQTL in EFHD1 during hepatocyte maladaptation associated with genotype-specific regulation by FOXO1, further contributing to the risk of MASLD. Our approach underscores the role of eQTL analysis in capturing crucial genetic variations that influence gene expression and clinical outcomes in complex diseases.

genetics↗

bioRxiv2024

SLIRP mediates nuclear-mitochondrial communication during antiviral signaling to promote robust interferon response

The abnormal innate immune response is a prominent feature underlying autoimmune diseases. One emerging factor that can trigger dysregulated immune activation is cytosolic mitochondrial double-stranded RNAs (mt-dsRNAs). However, the mechanism by which mt-dsRNAs stimulate immune responses remains poorly understood. Here, we discover SRA stem-loop interacting RNA binding protein (SLIRP) as a key amplifier of mt-dsRNA-triggered antiviral signals. In autoimmune diseases, SLIRP is commonly upregulated, and targeted knockdown of SLIRP dampens the interferon response. We find that the activation of melanoma differentiation-associated gene 5 (MDA5) by exogenous dsRNAs upregulates SLIRP, which then stabilizes mt-dsRNAs and promotes their cytosolic release to activate MDA5 further, augmenting the interferon response. Furthermore, the downregulation of SLIRP partially rescues the abnormal interferon-stimulated gene expression in autoimmune patients primary cells and makes cells vulnerable to certain viral infections. Our study unveils SLIRP as a pivotal mediator of interferon response through positive feedback amplification of antiviral signaling.

molecular biology↗

bioRxiv2024

Comparison of Alternative pre-mRNA Splicing and Gene Expression Patterns in Midbrain Lineage Cells Carrying Familial Parkinson's Disease Mutations

Parkinsons disease (PD) arises from genetic and environmental factors. Human genetics has identified mutations in [~]20 inherited familial genes linked to monogenic forms of PD. To investigate the effects of individual familial PD mutations, human pluripotent embryonic stem cells (hPSCs) carrying 12 distinct familial PD mutations were differentiated into midbrain lineage cells, including dopaminergic (mDA) neurons. Global gene expression and pre-mRNA splicing patterns were analyzed in midbrain cultures carrying pathogenic PD mutations in the PRKN, SNCA, LRRK2, PINK1, DNAJC6, FBXO7, SYNJ1, DJ1, VPS13C, ATP13A2 and GBA1 genes. We have grouped the analysis of these familial PD mutations to genes expressed in mDA neurons and whose pre-mRNA splicing changes are linked to known PD defects in transport, cytoskeleton, lysosomes and mitochondria. Importantly, we have also shown that subsets of these splicing changes overlap with changes found in PD patient postmortem brains. Mutation-specific pre-mRNA isoforms may function as both diagnostic biomarkers for familial PD-associated genotypes and promising therapeutic targets.

neuroscience↗

bioRxiv2023

scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics

Many popular spatial transcriptomics techniques lack single-cell resolution. Instead, these methods measure the collective gene expression for each location from a mixture of cells, potentially containing multiple cell types. Here, we developed scResolve, a method for recovering single-cell expression profiles from spatial transcriptomics measurements at multi-cellular resolution. scResolve accurately restores expression profiles of individual cells at their locations, which is unattainable from cell type deconvolution. Applications of scResolve on human breast cancer data and human lung disease data demonstrate that scResolve enables cell type-specific differential gene expression analysis between different tissue contexts and accurate identification of rare cell populations. The spatially resolved cellular-level expression profiles obtained through scResolve facilitate more flexible and precise spatial analysis that complements raw multi-cellular level analysis.

bioinformatics↗

bioRxiv2023

Seasonally increasing parasite load is associated with microbiome dysbiosis in wild bumblebees

The microbiome is increasingly recognized for its complex relationship with host fitness. Bumblebees are host to a characteristic gut microbiome community that is derived and reinforced through social contact between individuals. The bumblebee microbiome is species-poor, and primarily composed from a small number of core taxa that are associated with the greater tribe of corbiculate bees. Experimental findings support a role for the core bumblebee microbiome in resistance to severe infections by a common trypanosomal parasite, Crithidia bombi. However, most studies have been small in scale, often considering just one or two bumblebee species, or making use of commercially-reared bees. To better understand the microbiome diversity of wild populations, we have deeply sampled field populations of ten sympatric species found throughout central and down east Maine in a three-year microbiome field survey. We have used 16S amplicon sequencing to produce microbiome community profiles, and qPCR to screen samples for infections by Crithidia bombi. The breadth of our dataset has enabled us to test for seasonal and interspecific trends in the microbiome community. Controlling for these external sources of variation, we have identified microbial factors associated with infection and parasite load that support the role of the core microbiome in resistance to severe infection.

microbiology↗

bioRxiv2022

Bystander memory-phenotype conventional CD4+ T cells exacerbating autoimmune neuroinflammation

Memory-phenotype (MP) CD4+ T cells are a substantial population of conventional T cells that exist in steady-state mice, and their immunologic functions in autoimmune disease have not yet been studied. In this work, we unveil a unique phenotype of MP CD4+ T cells by analyzing single-cell transcriptomics and T cell receptor (TCR) repertoires. We found that steady-state MP CD4+ T cells exist regardless of germ and food-antigen which are composed of heterogenous effector subpopulations. Distinct subpopulations of MP CD4+ T cells are specifically activated by IL-1 family cytokines and STAT activators, revealing that the cells have TCR-independent effector functions. Especially, CCR6high MP CD4+ T cells are major responders to IL-1{beta} and IL-23 without MOG35-55 antigen reactivity, which gives them pathogenic-Th17 characteristics and allows them to contribute to autoimmune encephalomyelitis. We identified Bhlhe40 in CCR6high MP CD4+ T cells drives the expression of GM-CSF, contributing to CNS pathology in experimental autoimmune encephalomyelitis. Collectively, our findings reveal heterogeneity of MP CD4+ T cells that can contribute to autoimmune neuroinflammation in bystander manner synergistically with antigen-specific T cells.

immunology↗