Biology subjects

Lee, S.

Publications and source records attributed to Lee, S..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

Chimeric Antigen Receptors Discriminate Between Tau and Distinct Amyloid-Beta Species

Abstract/SummaryThe lack of a definitive cure for Alzheimers disease (AD) is fueling the search for innovative therapeutic strategies. Having revolutionized cancer immunotherapy, immune cell engineering with chimeric antigen receptors (CAR) is being explored to target AD. Whether CARs can recognize distinct amyloid-{beta} (A{beta}) species and tau neurofibrillary tangles (NFTs)--hallmark pathologies of AD--remains unclear. To investigate this, we engineered CARs based on AD antibodies targeting tau (E2814), A{beta} (Lecanemab and Aducanumab), and truncated pyroglutamate form of A{beta} (A{beta}p3-42; Donanemab and Remternetug). To evaluate CAR function, we established the murine DO11.10 hybridoma T-cell line as a practical and scalable testing platform. Our findings demonstrate that CARs can detect and discriminate between tau preformed fibrils (PFFs), A{beta}1-42, and A{beta}p3-42 aggregates. This highlights the potential of repurposing AD antibodies for CAR-based therapies to selectively target tau NFTs and distinct forms of A{beta} senile plaques.

synthetic biology↗

bioRxiv2025

A Human Neuron Alzheimer's Disease Model Reveals Barriers to Senolytic Translatability

Therapeutic successes in mouse models of Alzheimers disease (AD) largely fail to translate into clinical trials, with experimental drugs rarely validated in human models before being administered to humans. To address this, we developed an accessible method for long-term culture of commercially available primary human neurons and astrocytes, along with an amyloid-beta 1-42 (A{beta})-based in vitro AD model. Using this system, we evaluated two senolytic regimens previously shown to be effective in AD mouse models--Navitoclax and Dasatinib plus Quercetin (DQ)--and the natural killer cell line NK92 for emerging immune-mediated senescent cell ablation therapies. NK92 cells preferentially--but not exclusively--targeted A{beta}-treated neurons and astrocytes with senescent-like phenotypes. DQ demonstrated a safe profile for human neurons, but Navitoclax exhibited non-selective neurotoxicity. These findings highlight risks of Navitoclax and NK-based interventions and underscore the critical need for human-relevant models in the AD drug-development pipeline to improve safety and clinical translatability.

neuroscience↗

bioRxiv2025

Perilysosomal Ca2+ overload impairs autophagic degradation in β-cell lipotoxicity

Saturated fatty acids impose lipotoxic stress on pancreatic {beta}-cells, leading to {beta}-cell failure and diabetes. In this study, we investigate the critical role of organellar Ca2+ disturbance on defective autophagy and {beta}-cell lipotoxicity. Palmitate, a saturated fatty acid, induced perilysosomal Ca2+ elevation, sustained mTORC1 activation on the lysosomal membrane, suppression of the lysosomal transient receptor potential mucolipin 1 (TRPML1) channel, and accumulation of undigested autophagosomes in {beta}-cells. These Ca2+ aberrations with autophagy defects by palmitate were prevented by a mTORC1 inhibitor or a mitochondrial superoxide scavenger. To alleviate perilysosomal Ca2+ overload, strategies such as lowering extracellular Ca2+, employing voltage-gated Ca2+ channel blocker or ATP-sensitive K+ channel opener effectively abrogated mTORC1 activation and preserved autophagy. Furthermore, redirecting perilysosomal Ca2+ into the endoplasmic reticulum (ER) with an ER Ca2+ ATPase activator, restores TRPML1 activity, promotes autophagic flux, and improves survival of {beta}-cells exposed to palmitate-induced lipotoxicity. Our findings suggest oxidative stress-Ca2+ overload-mTORC1 pathway involves in TRPML1 suppression and defective autophagy during {beta}-cell lipotoxicity. Restoring perilysosomal Ca2+ homeostasis emerges as a promising therapeutic strategy for metabolic diseases.

physiology↗

bioRxiv2025

From Local Interactions to Global Patterns: An Analysis of Silk Density in Spider Webs

This study explores the structural complexity of spider webs through information-theoretic and harmonicity-based frameworks to quantify spatial patterns in silk density across different web regions and reveal the underlying resource allocation strategies. Currently, there is no normalized approach for describing web structure and complexity, particularly for sheet-webs, and this methodology allows for non-destructive scanning and quantification of web characteristics. By analyzing the entropy of silk density distributions, a single scalar that captures the heterogeneity of material investment across the entire web, we observed that the entropy values follow a normal distribution with a mean of 1.24 {+/-} 0.22 bits when using 10 quantization levels. In the second part of the paper, by measuring the harmonicity of the silk density, we reveal that the silk density at a given point can be inferred from its neighbors, with an average harmonicity value of 0.0039 {+/-} 0.0017 (fraction of total points in point cloud data). The harmonic behavior is notable for its maximum principle, suggesting that the strongest parts of the web appear at the boundaries, aligning with existing knowledge of spider web construction. These findings provide a new technique for quantifying web-building strategies and offer new insights into spider behavior and evolution.

animal behavior and cognition↗

bioRxiv2025

Lambda N as a model substrate for studying the mechanism of Escherichia coli ATP-dependent protease Lon as a regulatory enzyme.

As an ATP-dependent protease, the quality control functions of Lon have been extensively studied and reviewed in the literature. By contrast, very little research has been conducted to investigate Lons physiological functions and its mechanism as a regulatory protease. In this manuscript, we provided a survey of literature and data to convey that the lambda N ({lambda}N) protein is a suitable Escherichia coli Lon (ELon) substrate for studying the role played by Lon in regulating an RNA transcription process. For proof of principle, we demonstrated that the minimal component of the RNA transcription complex containing RNA polymerase (RNAP) and the {sigma} factor can inhibit {lambda}N degradation by ELon through SDS-PAGE, and the carboxyl-terminal of {lambda}N is important for Lon competing with RNAP interaction. Using negative stain electron microscopy, we obtained structural evidence to show that {lambda}N lacking the carboxyl-terminal flanked by residues 99-107 interacted with ELon differently than full-length {lambda}N. Taken together, the activity and EM data provide a starting point for performing a physiological enzymology study on the contribution of ELon toward RNA transcription.

biochemistry↗

bioRxiv2025

Dual Probe Ligation In Situ Hybridization with Rolling-Circle Amplification for High-Plex Spatial Transcriptomics

New biological insights are increasingly dependent upon a deeper understanding of tissue architectures. Critical to such studies are spatial transcriptomics technologies, especially those amenable to analysis of the most widely available human tissue type, formalin-fixed and paraffin-embedded (FFPE) clinical specimens. Here we build on our previous oligonucleotide probe ligation-based approach to accurately analyze FFPE mRNA, which suffers from variable levels of degradation. Ligation In Situ Hybridization followed by rolling circle amplification (LISH-LocknRoll or LISH-LnR), provides a streamlined method to detect the spatial location of specific mRNA isoforms within FFPE tissue architectures. Iterative fluorescent probe hybridization and imaging enables highly multiplexed spatial transcriptomic studies, as demonstrated herein for fixed specimens from inclusion body myositis patients and pediatric rhabdomyosarcoma patients. We additionally demonstrate a system of molecular rheostats that can be used to fine tune the performance of the LISH-LnR assay. Combined with LISH-seq and LISH-QC, the LISH-LnR methodology provides a powerful approach to spatial transcriptomics.

molecular biology↗

bioRxiv2025

Autism-Associated Genes and Neighboring lncRNAs Converge on Key Gene Regulatory Networks

Autism spectrum disorder (ASD) is highly heritable, and mutations in hundreds of genes have been implicated as individually rare causes of ASD1-3. Understanding how disruptions to these functionally diverse genes lead to the core features of ASD remains a major challenge4. Moreover, ASD is three- to four-fold more common in males than females5, and autistic females tend to carry more autosomal risk alleles for ASD compared to autistic males6,7, but the biological basis of this "female protective effect" (FPE) is unknown8,9. Here we show that individual perturbations of 18 ASD genes in human neural progenitor cells converge on shared effects on gene expression, including widespread downregulation of other ASD genes. De novo reconstruction of a gene regulatory network (GRN) enabled the identification of central transcriptional regulators, including the prominent ASD gene CHD8 as well as novel candidates such as REST, that drive this transcriptomic convergence. Furthermore, the X-linked transcription factor ZFX, which is expressed from both the active and the inactive X chromosomes in females10, emerged as a key activator of many ASD genes: we propose that the higher ZFX expression level observed in female brain can buffer damaging mutations in diverse ASD genes, contributing to the FPE. Together, these results reveal how key GRNs can become broadly and similarly dysregulated upon disruption of individual ASD genes and provide molecular insight into the female protective effect in ASD.

genetics↗

bioRxiv2025

Structural basis for the evolution of a domesticated group II intron-like reverse transcriptase to function in host cell DNA repair

A previous study found that a domesticated bacterial group II intron-like reverse transcriptase (G2L4 RT) functions in double-strand break repair (DSBR) via microhomology-mediated end joining (MMEJ) and that a mobile group II intron-encoded RT has a basal DSBR activity that uses conserved structural features of non-LTR-retroelement RTs. Here, we determined G2L4 RT apoenzyme and snap-back DNA synthesis structures revealing novel structural adaptations that optimized its cellular function in DSBR. These included a unique RT3a structure that stabilizes the apoenzyme in an inactive conformation until encountering an appropriate substrate; a longer N-terminal extension/RT0-loop with conserved residues that together with a modified active site favors strand annealing; and a conserved dimer interface that localizes G2L4 RT homodimers to DSBR sites with both monomers positioned for MMEJ. Our findings reveal how a non-LTR-retroelement RT evolved a dedicated cellular function and suggest new ways of optimizing these RTs for genome engineering applications.

molecular biology↗

bioRxiv2025

Contrastive Learning for Omics-guided Whole-slide Visual Embedding Representation

While computational pathology has transformed cancer diagnosis and prognosis prediction, existing computational methods remain limited in their ability to decipher the complex molecular characteristics within tumors. We present CLOVER (Contrastive Learning for Omics-guided whole-slide Visual Embedding Representation), a novel deep learning framework that leverages self-supervised contrastive learning to integrate multi-omics data (genomics, epigenomics, and transcriptomics) with slide representations, connecting the morphological and molecular features of tumors. Using the breast cancer cohorts comprising diagnostic slides and multi-omics paired data from 610 breast cancer patients, we validated CLOVERs excellence by demonstrating its ability to generate effective slide-level representations that consider molecular states of cancer. CLOVER outperforms existing methods in few-shot learning scenarios, particularly in cancer subtype classification and clinical biomarker prediction tasks (ER, PR, and HER2 status). Through comprehensive interpretability analysis, we identified tumor microenvironment components within slides and revealed molecular features associated with breast cancer. Our results demonstrate that CLOVER enables detailed molecular characterization from single slide analysis, suggesting its potential for effective utilization in future cancer diagnosis and prognosis prediction studies.

pathology↗

bioRxiv2025

Omics-based insights into human liver reveal GTPase-driven mechanisms of MASLD progression in obesity

Metabolic dysfunction-associated steatotic liver disease (MASLD) is often asymptomatic early on but can progress to irreversible conditions like cirrhosis. Due to limited access to human liver biopsies, systematic and integrative molecular resources remain scarce. In this study, we performed transcriptomic analyses on liver and metabolomic analyses on liver and plasma samples from morbidly obese individuals without liver pathology or at early-stage MASLD. While, the plasma metabolomic profile did not fully mirror liver histological features, dual-omics integration of liver samples revealed significantly remodeled lipid and amino acid metabolism pathways. Integrative network analysis uncoupled metabolic remodeling and gene expression as independent features of hepatic steatosis and fibrosis progression, respectively. Notably, GTPases and their regulators emerged as a novel class of genes linked to early liver fibrosis. This study offers a detailed molecular landscape of early MASLD in obesity and highlights potential targets of obesity-linked liver fibrosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/632747v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1188eborg.highwire.dtl.DTLVardef@1340070org.highwire.dtl.DTLVardef@108d560org.highwire.dtl.DTLVardef@f0adda_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Psilocybin induces sex- and context-specific recruitment of the stress axis

Psychedelics have reemerged as potential treatments for mental health disorders, yet their impact on stress-related brain regions remains poorly understood. Here, we provide the first real-time, in vivo evidence of psilocybin-induced neuronal activation, specifically in hypothalamic corticotropin-releasing hormone neurons. Notably, psilocybin elicited more pronounced responses in female mice and produced context-related alterations in threat assessment. Our findings provide valuable insight into the impact of psychedelics on a key stress center in the brain.

neuroscience↗

bioRxiv2024

Evolutionary conserved reciprocal senescence and tumor suppressor signals limit lifetime cancer

Cellular senescence features a durable exit from the cell cycle triggered by stress or carcinogens. The INK4 locus is inactivated in various cancers, yet in senescence, p16Ink4a is activated. Whether senescence is tumor-suppressing or -promoting remains a conundrum. We discovered an evolutionally-conserved Vertebrata INK4-homolog. This ink4ab triggers senescence upon oxidative- and/or carcinogenic-stress. Adult Ink4ab-deficient animals failed to activate senescence and developed spontaneous cancers. Combined Ink4ab and Tp53 deficiency revealed a reciprocal senescence and apoptosis regulation, controlling tumorigenesis, including retinoblastoma. INK4-hematopoietic-deficient mice exhibited p19Arf-dependent enhanced senescence-like phenotypes, uncontrolled cell proliferation, defective stem cell differentiation, and splenomegaly, with single-splenocytes spatially-enriched in senescence-associated secretory profiles. Our studies reveal the evolutionary origin of paradigms co-regulating senescence and tumor suppression and offer strategies to exploit these reciprocal pathways for cancer prevention and therapy.

cancer biology↗

bioRxiv2024

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE)/choroid. We identified 420,824 unique candidate regulatory elements and characterized their chromatin states in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells further revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina and relevant diseases.

genomics↗

bioRxiv2024

PAX2 is Transcriptionally Silenced by a Distinct Mechanism of Epigenetic Reprogramming to Initiate Endometrial Carcinogenesis

In most cancers, including endometrial cancer, tumor suppressor genes harboring inactivating mutations have been systematically cataloged. However, locus-specific epigenetic alterations contributing to cancer initiation and progression remain only partly described, creating knowledge gaps about functionally significant tumor suppressors and underlying mechanisms associated with their inactivation. Here, we show that PAX2 is an endometrial tumor suppressor recurrently inactivated by a distinct epigenetic reprogramming event not associated with promoter hypermethylation. PAX2 is expressed throughout normal endometrial glands; however, microscopic clones with PAX2 protein loss arise spontaneously in adulthood and progress to endometrial precancers and cancers. Here we show that PAX2 protein loss occurs via transcriptional silencing in 80% of endometrial cancers. Mechanistically, transcriptomic, epigenomic, 3D genomic, and machine learning analyses showed that silencing is associated with replacement of open/active chromatin features (H3K27ac/H3K4me3) with inaccessible/repressive features (H3K27me3). The spread of the H3K27me3 signal is restrained by cohesin loops, preventing transcriptional dysregulation of neighboring genes. Functionally, PAX2 loss promoted endometrial carcinogenesis by rewiring the transcriptional landscape via global enhancer reprogramming. Genetically engineered mouse models together with organoid and human cell line studies established Pax2 as an in vivo endometrial tumor suppressor that cooperates with Pten to produce lethal cancers. Our discovery of a specific and recurring epigenetic alteration that transcriptionally silences PAX2 to initiate most endometrial cancers opens new lines of investigation into the origins of endometrial cancer with diverse implications for its diagnosis and treatment. One Sentence SummaryWe demonstrate that PAX2 is silenced by a highly recurrent epigenetic mechanism to initiate most endometrial cancers, establishing a novel mechanism of tumor suppressor inactivation.

cancer biology↗

bioRxiv2024

APOE4 alters the lipid droplet proteome and modulates droplet dynamics

Excess lipid droplet (LD) accumulation is associated with several pathological states, including Alzheimers disease (AD). However, the mechanism(s) by which changes in LD composition and dynamics contribute to pathophysiology of these disorders remains unclear. Apolipoprotein E (ApoE) is a droplet associated protein with a common risk variant (E4) that confers the largest increase in genetic risk for late-onset AD. E4 is associated with both increased neuroinflammation and excess LD accumulation. In the current study, we sought to quantitatively profile the lipid and protein composition of LDs between the neutral E3 and risk variant E4, to gain insight into potential LD-driven contributions to AD pathogenesis. Targeted replacement mice expressing human E3 or E4 were injected with saline or lipopolysaccharide (LPS), and after 24 hours, hepatic lipid droplets were isolated for proteomic and lipidomic analyses. Lipidomics revealed a shift in the distribution of glycerophospholipids in E4 LDs with a concomitant increase in phosphatidylcholine species, and overall, the baseline profile of E4 LDs resembled that of the LPS-treated groups. Quantitative proteomics showed that LDs from E4 mice are enriched for proteins involved in protein/vesicle transport but have decreased levels of proteins involved in fatty acid {beta}-oxidation. Interestingly, proteins associated with LDs showed substantial overlap with previously published lists of AD postmortem tissue and microglia omics studies, suggesting a potential role for LDs in modulating AD risk or progression. Given this, we exposed primary microglia from the same E3 or E4 mice to exogenous lipid, inflammatory stimulation, necroptotic N2A cells (nN2A), or a combination of treatments to evaluate LD formation and its impact on the cells immune state. Microglia from E4 mice accumulated more LDs in every condition tested - at baseline and following addition of fatty acids, LPS stimulation, or nN2As. E4 microglia also secreted significantly more cytokines (TNF, IL-1{beta}, IL-10) than E3 microglia in the control, oleic acid, and nN2A treatment conditions, yet showed a blunted response to LPS. In sum, these results suggest that E4 microglia accumulate more LDs compared to E3 microglia and that E4 is associated with a basal LD composition that resembles a pro-inflammatory cell. Together with the high overlap of the LD proteome with established AD-associated datasets, these data further support the idea that alterations in LD dynamics, particularly within microglia, may contribute to the increased risk for AD associated with APOE4.

physiology↗

bioRxiv2024

HIV-SEQ REVEALS GLOBAL HOST GENE EXPRESSION DIFFERENCES BETWEEN HIV-TRANSCRIBING CELLS FROM VIREMIC AND SUPPRESSED PEOPLE WITH HIV

"Active" reservoir cells transcribing HIV can perpetuate chronic inflammation in virally suppressed people with HIV (PWH) and likely contribute to viral rebound after antiretroviral therapy (ART) interruption, so they represent an important target for new therapies. These cells, however, are difficult to study using single-cell RNA-seq (scRNA-seq) due to their low frequency and low levels of HIV transcripts, which are usually not polyadenylated. Here, we developed "HIV-seq" to enable more efficient capture of HIV transcripts - including non-polyadenylated ones - for scRNA-seq analysis of cells from PWH. By spiking in a set of custom-designed capture sequences targeting conserved regions of the HIV genome during scRNA-seq, we increased our ability to find HIV RNA+ cells from PWH by up to 44%. Implementing HIV-seq in conjunction with surface phenotyping by CITE-seq on paired blood specimens from PWH before vs. after ART suppression, we found that HIV RNA+ cells were enriched among T effector memory (Tem) cells during both viremia and ART suppression, but exhibited a cytotoxic signature during viremia only. By contrast, HIV RNA+ cells from the ART-suppressed timepoints exhibited a distinct anti-inflammatory signature involving elevated TGF-{beta} and diminished IFN signaling. Overall, these findings demonstrate that active reservoir cells exhibit transcriptional features distinct from HIV RNA+ cells during viremia, and underscore HIV-seq as a useful tool to better understand the mechanisms by which HIV-transcribing cells can persist during ART.

immunology↗

bioRxiv2024

A real-time forecasting framework for emerging infectious diseases affecting animal populations

Infectious disease forecasting has become increasingly important in public health, as demonstrated during the COVID-19 pandemic. However, forecasting tools for emergency animal diseases, particularly those offering real-time decision support when parameters governing disease dynamics are unknown, remain limited. We introduce a generalised modelling framework for near-real-time forecasting of the temporal and spatial spread of infectious livestock diseases using data from the early stages of an outbreak. We applied the framework to the 2007 equine influenza outbreak in Australia, generating prediction targets at three timepoints across four regional clusters. Our targets included future daily case counts, outbreak size, peak timing and duration, and spatial distributions of future spread. We evaluated how well the forecasts predicted daily cases and the spatial distribution of case counts, using skill scores as a benchmark for future model improvements. Forecast accuracy, certainty, and skill improved significantly after the outbreaks peak, while early predictions were more variable, suggesting that pre-peak forecasts should be interpreted with caution. Spatial forecasts maintained positive skill throughout the outbreak, supporting their use in guiding response priorities. This framework provides a tool for real-time decision-making during livestock disease outbreaks and establishes a foundation for future refinements and applications to other animal diseases.

bioinformatics↗

bioRxiv2024

Multi-omics analysis and genome-scale metabolic reconstruction of cattle Bos taurus for optimal production of cultured meat

With the growing urgency of addressing climate change, cultured meat has gained significant attention as a sustainable alternative to conventional meat production. Bos taurus, a key cattle species, is considered as a potential source of cultured meat. However, much remains to be understood about the biology of B. taurus muscle cells. In this study, bovine satellite cells (BSCs) derived from the semimembranosus muscle of Korean Hanwoo cattle were subjected to multi-omics profiling and genome-scale metabolic reconstruction. First, differential gene expression and gene set enrichment analyses, based on RNA-seq data, identified key pathways associated with muscle cell proliferation (e.g., Cell cycle and RNA polymerase) and differentiation (e.g., Cytoskeleton in muscle cells and Tryptophan metabolism). Next, using the human1 GEM as a template, we constructed the first B. taurus-specific genome-scale metabolic model (GEM), named BtaSBML2986, which comprises 2,986 genes, 13,278 reactions, and 8,652 metabolites. Muscle cells were cultured under six distinct conditions, and biomass predictions generated using BtaSBML2986 were validated against experimental growth rates. This integrated approach also provided insights into core pathways such as glycolysis and the TCA cycle. BtaSBML2986 represents a significant step forward in understanding B. taurus muscle metabolism and will serve as a valuable tool for advancing cultured meat research and optimizing culture processes.

systems biology↗