Biology subjects

Lee, B. S.

Publications and source records attributed to Lee, B. S..

12 recordsLinked to original sources

bioRxiv2026

AI-Informed neoantigen prioritization enables a multi-epitope mRNA/LNP vaccine with antigen-specific immunogenicity and antitumor activity

Personalized neoantigen vaccines are an emerging strategy for cancer immunotherapy, but their effectiveness depends on selecting tumor-specific antigens capable of inducing functional T-cell responses. The VACINUS AI-informed neoantigen prioritization framework previously identified and peptide-validated three immunogenic Tier 1 neoantigens in the B16F10 melanoma model. In this study, we extended that framework by translating these validated neoantigens into a multi-epitope messenger RNA vaccine formulated with lipid nanoparticles and evaluating its preclinical immunogenicity and antitumor activity. The three VACINUS-prioritized B16F10 neoantigens were encoded within a single multi-epitope construct, BF-V1_27-Ser, and formulated to generate BF-RNA-P. In B16F10 tumor-bearing mice, BF-RNA-P induced neoantigen-specific CD8+T-cell responses, with the strongest response directed against the B16F10-1-4 epitope. Combination with anti-PD-1 further enhanced vaccine-induced CD44+IFN-{gamma}+ CD8+ T-cell activation, whereas anti-PD-1 alone did not induce detectable peptide-specific responses. BF-RNA-P also suppressed tumor growth in vivo, and combination treatment produced the strongest antitumor effect, reflected by reduced tumor volume and lower endpoint tumor burden. Together, these findings demonstrate that VACINUS-prioritized and peptide-validated neoantigens can be reformatted into a multi-epitope messenger RNA/lipid nanoparticle vaccine while retaining antigen-specific immunogenicity and antitumor activity. This study provides preclinical proof-of-concept for integrating AI-informed, TCR-aware neoantigen prioritization with messenger RNA/lipid nanoparticle delivery as a translational strategy for personalized cancer vaccine development.

immunology↗

bioRxiv2026

From Metabolomics to Function: Ranking Plant Stem Cell Metabolomes for Use in Health and Cosmetics

BackgroundPlants produce diverse metabolites with potential benefits for human health. However, the metabolomes of plant callus cultures--cell cultures analogous to stem cells--remain poorly characterized in terms of their functional relevance. MethodsWe profiled the metabolomes of six plant calli: Acacia concinna (Shikakai), Daucus carota (carrot), Hibiscus sabdariffa (hibiscus), Linum usitatissimum (flax), Ocimum sanctum (tulsi), and the Nicotiana tabacum Bright-Yellow 2 (BY-2) cell line. To facilitate functional interpretation, we developed Metabolite2Function (M2F), a pipeline that annotates metabolites with biological functions using scientific literature and large language modeling. ResultsUntargeted metabolomics identified 177 metabolites, revealing clustering patterns independent of genetic relationships, culture age, or growth rate. Tulsi and carrot calli exhibited enrichment in metabolites relative to the tobacco reference line, whereas flax and hibiscus were comparatively depleted. Most metabolites varied across at least four calli, and 10% were unique to a single species. Using M2F, we annotated 87 metabolites with beneficial activities, including antioxidant, anti-glycation, anti-inflammatory, and anti-senescence functions, as well as skin-related effects such as collagen production and brightening. Notably, antioxidant and anti-senescence metabolite levels correlated with corresponding biological activities in human cells. ConclusionsPlant callus cultures generate distinct and functionally diverse bioactive metabolomes. M2F provides a scalable framework for systematic functional annotation relevant to human health and cosmetic applications.

biochemistry↗

bioRxiv2026

Yeast-Plant-Derived Consortia Factors Exhibit A Distinct And Enriched Beneficial Metabolome For Health And Beauty

Cells secrete metabolites and other factors into the extracellular medium, collectively referred to as the secretome. The effect of co-culturing cells from different species on their combined secretome remains poorly understood. Here, we investigated the effect of co-culturing plant and yeast cells to produce a unique set of secretory factors collectively termed Consortia Factors (CFx). Specifically, a yeast suspension of Ustilago cynodontis (Ustilago) was co-cultured with plant cells derived from Ocimum sanctum (Tulsi). The metabolome of the Ustilago-Tulsi CFx (termed CFx-1) was then profiled and compared with that of the individual cultures. Statistical clustering analyses revealed that the CFx-1 metabolome was substantially different from either culture grown alone and was enriched in metabolites relative to single cultures. Notably, significant enrichment was observed among metabolites mutually upregulated in CFx compared with both single cultures, with approximately one-third absent from either culture alone. Using an algorithm designed to identify scientifically validated antioxidant metabolites, the CFx-1 was found to be enriched in antioxidants relative to the single cultures, including vitamin C. Accordingly, the CFx-1 exhibited stronger antioxidant activity than either of the single-culture secretomes, and even than the combination of the two single-culture secretomes. These findings suggest that consortia factors derived from co-culturing yeast and plant cells can generate a unique and more potent secretome that is enriched in bioactive metabolites beneficial for human health.

cell biology↗

bioRxiv2025

A functional amyloid matrix underpins the PDIM-architected corded superstructure of the Mycobacterium tuberculosis biofilm

Bacterial biofilms generate collective properties that cannot be explained by individual cells alone. Yet the structural principles that organize these communities and their relationship to drug tolerance remain poorly understood, including in major human pathogens such as Mycobacterium tuberculosis (Mtb). Here we show that submerged Mtb biofilms form organized multicellular architectures in which bacterial cords are integrated with a composite extracellular matrix. The virulence lipid phthiocerol dimycocerosate (PDIM) governs the higher-order organization of cords, proteinaceous matrix interactions support cohesion and attachment, an amyloid-like component contributes to biofilm integrity and establishment, and the ESX-1 secretion system increases matrix biochemical complexity. Biofilm growth conferred antibiotic tolerance across genetic backgrounds, while PDIM-dependent organization provided additional protection against first-line anti-tuberculosis drugs, most clearly isoniazid. Targeting amyloid assembly with epigallocatechin gallate impaired biofilm establishment without inhibiting planktonic growth. Together, these findings establish a cording-centred framework linking bacterial surface composition, cellular organization and extracellular matrix assembly to antibiotic tolerance, and show how resolving higher-order biofilm architecture can reveal processes amenable to chemical perturbation.

microbiology↗

bioRxiv2025

The mycobacterial ATP burst is a lysis artifact and serves as an assay for drug-induced cell wall damage

Antibiotics targeting the mycobacterial cell wall are a cornerstone of tuberculosis treatment. Understanding how these drugs facilitate bacterial killing has important implications for identifying novel therapeutic targets and optimizing drug combinations. Previous studies on mycobacteria using the BacTiter-Glo luminescence assay have reported increased ATP levels after treatment with cell wall inhibitors such as isoniazid, a phenomenon referred to as an ATP burst. This phenomenon has been proposed to contribute to drug-induced killing. In this study, we demonstrate that the ATP burst is not a biological response but rather an experimental artifact resulting from enhanced cell lysis induced by cell wall-targeting drugs. The addition of a bead-beating lysis step prior to luminescence measurement abolishes the ATP burst, enabling a more reliable assessment of intracellular ATP levels with this assay. Our findings thus establish a direct link between the ATP burst and the canonical mechanism of action of cell wall inhibitors. We further demonstrate the utility of this approach as a functional readout for identifying compounds that disrupt the mycobacterial cell wall and for screening synergistic or antagonistic interactions with known cell wall-targeting agents. Together, our results elucidate the mechanistic basis of the ATP burst and provide a valuable tool for antimycobacterial drug discovery and development.

microbiology↗

bioRxiv2025

Psychedelics Relax Priors and Reshape Orbitofrontal Dynamics

Psychedelics such as psilocybin and ketamine are gaining attention as rapid-acting treatments for psychiatric disorders, yet the mechanisms by which they alter cognition remain unclear. A key hypothesis--the REBUS model--proposes that psychedelics relax high-level priors, allowing bottom-up sensory information to exert greater influence over perception and behavior. Here, we test this model in mice performing a free-response perceptual decision-making task that disambiguates prior-driven and sensory-driven decision strategies. Acute administration of psilocybin or ketamine significantly slowed decision times and improved accuracy. Behavioral modeling that combined drift diffusion and GLM-HMM frameworks revealed that these changes were mediated by increased decision thresholds and a marked shift into sensory-engaged cognitive states. Whole-brain c-Fos mapping identified a distributed decision-making network, with psychedelics selectively modulating cortical and subcortical nodes. Calcium imaging in the orbitofrontal cortex (OFC)--a key region for integrating priors and sensory inputs--revealed preserved decision-related selectivity under psychedelics, while exhibiting reduced neuronal correlations--population-level signatures of weakened top-down influence and relaxed priors. Together, these results provide circuit-level support for the REBUS model, showing that psychedelics reconfigure brain-wide and local dynamics to promote more deliberate, flexible, and sensory-driven decision policies.

neuroscience↗

bioRxiv2025

A PBD-dimer containing antibody drug conjugate targeting CCRL2 for high-risk MDS/AML

Patients with myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML) with high-risk features including TP53 mutations and deletions have poor outcomes due to lack of effective therapies. The atypical chemokine surface receptor C-C motif chemokine receptor-like 2 (CCRL2) is overexpressed in MDS and secondary AML (sAML) compared to healthy hematopoietic cells and we recently found that TP53-mutated MDS/AML and AML with erythroid features express the highest levels of this receptor across MDS/AML subtypes. To illustrate the therapeutic potential of CCRL2 as a therapeutic target, we developed an anti-CCRL2 antibody-drug conjugate (ADC) by conjugating an anti-CCRL2 antibody with the cytotoxic drug pyrrolobenzodiazepine (PBD), which causes DNA double-strand breaks leading to cancer cell death. The anti-CCRL2 ADC demonstrated strong CCRL2-selective cytotoxicity against cell lines derived from MDS/AML patients with TP53 mutations and erythroid features, surpassing the cytotoxic effects observed with gemtuzumab and PBD-conjugated anti-CD33 and anti-CD123 ADCs. It also induced apoptosis and suppressed the clonogenicity of primary MDS/AML bone marrow samples without affecting the survival, differentiation and clonogenicity of healthy hematopoietic stem and progenitor cells. This agent also suppressed the leukemic growth of TP53-mutated MDS/AML cell line xenografts, improving mice survival and decreasing the leukemic burden in patient-derived TP53-mutated MDS/AML xenografts. In conclusion, our study introduces CCRL2 as a potential new therapeutic target in high-risk MDS/AML. Statement of significancePyrrolobenzodiazepine(PBD)-conjugated anti-CCRL2 ADC shows anti-leukemic effect in MDS/AML models including TP53-mutated disease without affecting healthy hematopoietic cells supporting that it is a promising candidate for single-agent or combination therapies in high-risk MDS/AML.

cancer biology↗

bioRxiv2024

'Mitotic' kinesin-5 is a dynamic brake for axonal growth

During neuronal development, neurons undergo significant microtubule reorganization to shape axons and dendrites, establishing the framework for efficient wiring of the nervous system. Previous studies from our laboratory demonstrated the key role of kinesin-1 in driving microtubule-microtubule sliding, which provides the mechanical forces necessary for early axon outgrowth and regeneration in Drosophila melanogaster. In this study, we reveal the critical role of kinesin-5, a mitotic motor, in modulating the development of postmitotic neurons. Kinesin-5, a conserved homotetrameric motor, typically functions in mitosis by sliding antiparallel microtubules apart in the spindle. Here, we demonstrate that the Drosophila kinesin-5 homolog, Klp61F, is expressed in larval brain neurons, with high levels in ventral nerve cord (VNC) neurons. Knockdown of Klp61F using a pan-neuronal driver leads to severe locomotion defects and complete lethality in adult flies, mainly due to the absence of kinesin-5 in VNC motor neurons during early larval development. Klp61F depletion results in significant axon growth defects, both in cultured and in vivo neurons. By imaging individual microtubules, we observe a significant increase in microtubule motility, and excessive penetration of microtubules into the axon growth cone in Klp61F-depleted neurons. Adult lethality and axon growth defects are fully rescued by a chimeric human-Drosophila kinesin-5 motor, which accumulates at the axon tips, suggesting a conserved role of kinesin-5 in neuronal development. Altogether, our findings show that at the growth cone, kinesin-5 acts as a brake on kinesin-1-driven microtubule sliding, preventing premature microtubule entry into the growth cone. This regulatory role of kinesin-5 is essential for precise axon pathfinding during nervous system development.

cell biology↗

bioRxiv2024

EB-SUN, a New Microtubule Plus-End Tracking Protein in Drosophila.

Microtubule (MT) regulation is essential for oocyte development. In Drosophila, MT stability, polarity, abundance, and orientation undergo dynamic changes across developmental stages. In our effort to identify novel microtubule-associated proteins (MAPs) that regulate MTs in the Drosophila ovary, we identified a previously uncharacterized gene, CG18190, encoding a novel MT end-binding (EB) protein, which we propose to name EB-SUN. We show that EB-SUN colocalizes with EB1 at growing microtubule plus-ends in Drosophila S2 cells. Tissue-specific and developmental expression profiles from Paralog Explorer reveal that EB-SUN is predominantly expressed in the ovary and early embryos, while EB1 is ubiquitously expressed. Furthermore, as early as oocyte determination, EB-SUN comets are highly concentrated in oocytes during oogenesis. EB-SUN knockout (KO) results in a decrease in MT density at the onset of mid-oogenesis (Stage 7) and delays oocyte growth during late mid-oogenesis (Stage 9). Combining EB-SUN KO with EB1 knockdown (KD) in germ cells significantly further reduced MT density at Stage 7. Notably, all eggs from EB-SUN KO/EB1 KD females fail to hatch, unlike single gene depletion, suggesting a functional redundancy between these two EB proteins during embryogenesis. Our findings indicate that EB-SUN and EB1 play distinct roles during early embryogenesis. Significance StatementO_LIOur study identified a novel microtubule end-binding (EB) protein, which is highly expressed in the Drosophila ovary, and we propose to name it EB-SUN. C_LIO_LIWe demonstrate the functional redundancy of EB-SUN and EB1 during oocyte development, while highlighting their distinct roles in early embryogenesis. C_LIO_LIGiven the high conservation of MT-dependent mechanisms in oogenesis and EB proteins across species, these findings provide insights into the differential regulation and tissue-specific functions of the EB family, using Drosophila as a model system, potentially benefiting future research on MT regulation in higher organisms. C_LI

cell biology↗

bioRxiv2023

Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape

Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen implicated disruption of kinase SMG1s phosphorylation of UPF1 as a potential disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro. Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases. One Sentence SummaryDisruption of the nonsense-mediated decay pathway with a newly developed SMG1 inhibitor with in-vivo activity increases the expression of T-cell targetable cancer neoantigens resulting from truncating mutations.

cancer biology↗

bioRxiv2022

The assessment of cortical hemodynamical responses induced by tubuloglomerular feedback using in vivo imaging

The tubuloglomerular feedback (TGF) mechanism is crucial in modulating renal hemodynamics and glomerular filtration rate in individual nephrons. Our study aimed to evaluate the TGF-induced vascular responses by comparing the effects of two transport inhibitors with different sites and mechanisms of action. We assessed cortical hemodynamics with high-resolution laser speckle contrast imaging, which enabled the evaluation of blood flow individual micro-vessels and analysis of their dynamical patterns in the time-frequency domain. We demonstrated that a systemic administration of a loop diuretic abolishes TGF-mediated hemodynamic responses. Furthermore, we showed that the local microcirculatory blood flow decreased, and the TGF reset in response to reduced proximal reabsorption elicited by systemic administration of a sodium-glucose co-transporter 2 inhibitor, phlorizin.

physiology↗

bioRxiv2020

Anatomical modeling of brain vasculature in two-photon microscopy by generalizable deep learning

Objective and Impact StatementSegmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis. IntroductionVascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems, or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems, and is able to segment large-scale angiograms. MethodsWe employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and a total variation regularization on the networks output. Its effectiveness is demonstrated on experimentally acquired in-vivo angiograms from mouse brains of dimensions up to 808x808x702 m. ResultsTo demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope, and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10x faster computation in terms of voxels-segmented-per-second and 3x larger depth compared to the state-of-the-art. ConclusionOur work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.

neuroscience↗