Biology subjects

Lee, H.-G.

Publications and source records attributed to Lee, H.-G..

5 recordsLinked to original sources

bioRxiv2026

A Reaction-Driven Condensate-to-Vesicle Transition Selects, Activates, and Spatially Organizes RNA

Living systems depend on the selective concentration of informational polymers within membrane-bound compartments. Liquid-liquid phase-separated condensates efficiently concentrate biomolecules, whereas membrane-bound vesicles provide persistent compartment boundaries. However, direct chemical mechanisms that couple these organizational states remain largely unexplored. Here we report a reaction-driven pathway linking condensates to RNA-enriched lipid vesicles. Electrostatic interactions between cationic thioesters and RNA drive phase separation into reactive condensates. Reaction with cysteine generates membrane lipids and transforms the condensates into unilamellar bilayer vesicles with near-uniform size distribution. The vesicles encapsulate >90% of the RNA from the initial solution and concentrate it by more than two orders of magnitude to >100 {micro}M. Encapsulation is strongly dependent on RNA length, with short oligonucleotides excluded while longer RNAs are selectively retained. Under spatial gradients of the chemical trigger, sharply defined vesicle populations with distinct RNA compositions emerge. Reaction-driven compartmentalization raises local ribozyme and substrate concentrations above the threshold required for catalytic activity, enabling function from otherwise inactive dilute solutions. These findings establish a mechanism by which chemical reactions generate selective, functional, and spatially organized RNA-enriched membrane-bound compartments from heterogeneous molecular mixtures.

biochemistry↗

bioRxiv2026

Repeat expansions in C9orf72 rewire the 3D chromatin landscape in ALS

Amyotrophic lateral sclerosis (ALS) is frequently driven by GGGGCC short tandem repeat (STR) expansions in C9orf72, yet the mechanisms by which these expansions lead to neurodegeneration remain incompletely understood. Here, we propose a novel mechanism involving higher-order chromatin architecture where C9orf72-STR expansions induce widespread, neuron-specific gains in chromatin loops that are closely linked to transcriptomic dysregulation in ALS. These ectopic loops colocalize with the genomic binding sites of C9orf72-STR RNAs and the architectural protein CTCF, supporting a model in which RNA-DNA interactions promote aberrant loop formation. Together, our findings demonstrate how C9orf72-STR expansions remodel the neuronal genome and disrupt gene expression, uncovering an RNA-driven mechanism of chromatin reorganization in C9-ALS that connects altered nuclear topology to gene dysregulation in neurodegeneration.

genomics↗

bioRxiv2024

Disease-associated astrocyte epigenetic memory promotes CNS pathology

Astrocytes play important roles in the central nervous system (CNS) physiology and pathology. Indeed, astrocyte subsets defined by specific transcriptional activation states contribute to the pathology of neurologic diseases, including multiple sclerosis (MS) and its pre-clinical model experimental autoimmune encephalomyelitis (EAE)1-8. However, little is known about the stability of these disease-associated astrocyte subsets, their regulation, and whether they integrate past stimulation events to respond to subsequent challenges. Here, we describe the identification of an epigenetically controlled memory astrocyte subset which exhibits exacerbated pro-inflammatory responses upon re-challenge. Specifically, using a combination of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing (ChIP-seq), focused interrogation of cells by nucleic acid detection and sequencing (FIND-seq), and cell-specific in vivo CRISPR/Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) used by the histone acetyltransferase p300 to control chromatin accessibility. ACLY+p300+ memory astrocytes are increased in acute and chronic EAE models; the genetic targeting of ACLY+ p300+ astrocytes using CRISPR/Cas9 ameliorated EAE. We also detected responses consistent with a pro-inflammatory memory phenotype in human astrocytes in vitro; scRNA-seq and immunohistochemistry studies detected increased ACLY+ p300+ astrocytes in chronic MS lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, MS. These findings may guide novel therapeutic approaches for MS and other neurologic diseases.

immunology↗

bioRxiv2023

Engineered probiotics limit CNS autoimmunity by stabilizing HIF-1α in dendritic cells

Dendritic cells (DCs) control the generation of self-reactive pathogenic T cells. Thus, DCs are considered attractive therapeutic targets for autoimmune diseases. Using single-cell and bulk transcriptional and metabolic analyses in combination with cell-specific gene perturbation studies we identified a negative feedback regulatory pathway that operates in DCs to limit immunopathology. Specifically, we found that lactate, produced by activated DCs and other immune cells, boosts NDUFA4L2 expression through a mechanism mediated by HIF-1. NDUFA4L2 limits the production of mitochondrial reactive oxygen species that activate XBP1-driven transcriptional modules in DCs involved in the control of pathogenic autoimmune T cells. Moreover, we engineered a probiotic that produces lactate and suppresses T-cell autoimmunity in the central nervous system via the activation of HIF-1/NDUFA4L2 signaling in DCs. In summary, we identified an immunometabolic pathway that regulates DC function, and developed a synthetic probiotic for its therapeutic activation.

immunology↗

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↗