Biology subjects

Lee, I.-H.

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

10 recordsLinked to original sources

bioRxiv2026

Systems-Scale Structural Modeling Reveals the Germline Architecture of Immunodominance

The adaptive immune system generates diverse antibodies to protect against infection, yet responses often focus on a limited number of antigenic sites, a phenomenon called immunodominance. Using the SARS-CoV-2 receptor-binding domain as a model, this study combines large-scale antibody sequencing, deep mutational scanning, and AlphaFold 3 structural modeling to investigate the basis of immunodominant epitope selection. The results show that germline-encoded antibody features are a primary driver of immunodominance. Specifically, 76% of RBD-targeting antibodies display conserved gene segment usage and/or germline-encoded HCDR3 motifs. Structural analyses identified recurrent germline-encoded residues within these regions that interact with immunodominant epitopes, and mutating these residues eliminated binding. Mutations in SARS-CoV-2 variants frequently disrupt these interactions and are associated with immune escape; other mutations enable germline-mediated recognition and generate new immunodominant epitopes. These findings indicate that innate features, rather than diverse somatic mutations, determine binding specificity for the large majority of the antibody response and underlie antibody immunodominance.

immunology↗

bioRxiv2025

Astrocytic FKBP5 Regulates Neuroinflammation and Cognitive Outcomes in Excitotoxic Brain Injury

FK506-binding protein 51 (FKBP51, encoded by FKBP5) is a multisignaling cochaperone that regulates cellular responses to stress. FKBP51 is upregulated in reactive astrocytes; however, the role of FKBP51 in excitotoxic brain injury remains unknown. Here, we investigated how both global and astrocyte-specific Fkbp5 deletion influence seizure susceptibility, astrogliosis, neuroinflammation, and cognition in male mice subjected to a kainic acid (KA)-induced epilepsy mouse model. Global Fkbp5 knockout (Fkbp5-KO) presented lower seizure activity along with decreased neuronal loss and astrogliosis in the hippocampus compared with the wild-type mice. Astrocyte-specific Fkbp5 conditional knockout (aFkbp5-cKO) mice similarly attenuated seizure severity, decreased astrogliosis, improved novel object recognition, and preserved glutamate transporter 1 (GLT-1) expression in hippocampal CA3. Glia-neuron mixed cultures derived from Fkbp5-KO brains showed reduction of NMDA-induced neurotoxicity, astrogliosis, accompanied by decreased NF-{kappa}B p65 phosphorylation. Notably, overexpression of an Fkbp5 quadruple mutant that disrupts the FKBP51-NF-{kappa}B interaction inhibited proinflammatory lipopolysaccharide (LPS)-induced astrogliosis and NF-{kappa}B activation. The hippocampal transcriptome of the LPS-treated Fkbp5-KO mice revealed suppression of NF-{kappa}B signaling. In summary, this study highlights FKBP51 as a key mediator of excitotoxin-induced neuroinflammation and GLT-1 dysfunction and underlines NF-{kappa}B-mediated inflammatory astrogliosis as a potential intervention target for excitotoxic brain injury.

neuroscience↗

bioRxiv2025

Bone marrow mesenchymal stromal cells mediate cellular inflammation in HFpEF

During the genesis of heart failure, the myocardium recruits an abundance of bone marrow-derived leukocytes, primarily monocytes, with various disease-promoting functions. Increased hematopoiesis fuels these unfavorable changes in cardiac leukocyte origin, number and phenotype. Here we examine hematopoietic niche cells, which regulate blood progenitor proliferation and systemic monocyte supply, in obese, hypertensive mice that develop heart failure with preserved ejection fraction (HFpEF). Single cell transcriptomics revealed that in HFpEF, stromal bone marrow niche cells expand and respond strongly to IFN{gamma}. Deleting the IFN{gamma} receptor in stromal cells of Prrx1CreERT2;Ifngr1fl/fl mice reduced hematopoietic progenitor proliferation and systemic monocytes in both the steady state and HFpEF and also increased the canonical hematopoietic maintenance factor CXCL12, resulting in reduced fibrosis and improved diastolic function. CD8+ T cells in adipose tissue were a major source of IFN{gamma} in mice with HFpEF; their depletion restored CXCL12 expression and lowered monocyte numbers. ScRNA-seq in mice with ischemic heart disease uncovered a diverging marrow response. These data indicate that in HFpEF, adipose tissue, bone marrow and adaptive and innate immune cells conspire to expand harmful macrophage subsets in the heart.

immunology↗

bioRxiv2024

A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer

Whether metastasis in humans can be accomplished by most primary tumor cells or requires the evolution of a specialized trait remains an open question. To evaluate whether metastases are founded by non-random subsets of primary tumor lineages requires extensive, difficult-to-implement sampling. We have realized an unusually dense multi-region sampling scheme in a cohort of 26 colorectal cancer patients with peritoneal metastases, reconstructing the evolutionary history of on average 28.8 tissue samples per patient with a microsatellite-based fingerprinting assay. To assess metastatic randomness, we evaluate inter- and intra-metastatic heterogeneity relative to the primary tumor and find that peritoneal metastases are more heterogeneous than liver metastases but less diverse than locoregional metastases. Metachronous peritoneal metastases exposed to systemic chemotherapy show significantly higher inter-lesion diversity than synchronous, untreated metastases. Projection of peritoneal metastasis origins onto a spatial map of the primary tumor reveals that they often originate at the deep-invading edge, in contrast to liver and lymph node metastases which exhibit no such preference. Furthermore, peritoneal metastases typically do not share a common subclonal origin with distant metastases in more remote organs. Synthesizing these insights into an evolutionary portrait of peritoneal metastases, we conclude that the peritoneal-metastatic process imposes milder selective pressures onto disseminating cancer cells than the liver-metastatic process. Peritoneal metastases unique evolutionary features have potential implications for staging and treatment.

genetics↗

bioRxiv2024

Phase Separation Clustering of Poly Ubiquitin Cargos on the Ternary Mixture Lipid Membranes by Synthetically Cross-Linked Ubiquitin Binder Peptides.

Ubiquitylation is involved in various physiological processes in our bodies such as signaling and vesicle trafficking, thus Ubiquitin (UB) is an important medical target system of interest. Polymeric addition of UB allows cargo molecules to be recognized specifically by multivalent binding interaction with UB binding proteins leading to various downstream processes. Recently, implication of protein condensate formation by Ubiquitylated proteins have been reported in many independent UB processes suggesting its potential role in governing the spatial organization of Ubiquitylated cargo proteins. We created modular polymeric UB binder motifs and polymeric UB cargos by synthetic bioconjugation and protein purification. Giant unilamellar vesicles with lipid raft composition were created to reconstitute polymeric UB cargo organization on the membranes. Fluorescence imaging was used to observe the outcome. We found that polymeric UB cargos clustered on the membranes by forming phase separation codomains in interaction with multivalent UB binder conjugate. This phase separation was valency dependent and was strongly correlated to their potency to form protein condensate droplets in solution. Multivalent UB binding interactions showed a general trend toward the formation of phase separated condensates, and the resulting condensates were either in liquid-like or solid-like state depending on the conditions and interactions used. It implies that polymeric UB cargos on the plasma and endosomal membranes may use the codomain phase separation to assist clustering of UB cargos on the membranes for cargo sorting. Our work also shows that model systems of such phase behavior can be created by modular synthetic approach that can potentially be used to further engineer biomimetic interactions in vitro. Graphical abstracts (TOC) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/608403v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@eca49dorg.highwire.dtl.DTLVardef@2b64d2org.highwire.dtl.DTLVardef@e82b98org.highwire.dtl.DTLVardef@862558_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Therapeutic Spp1 silencing in TREM2+ cardiac macrophages suppresses atrial fibrillation

Atrial fibrillation (AFib) and the risk of its lethal complications are propelled by fibrosis, which induces electrical heterogeneity and gives rise to reentry circuits. Atrial TREM2+ macrophages secrete osteopontin (encoded by Spp1), a matricellular signaling protein that engenders fibrosis and AFib. Here we show that silencing Spp1 in TREM2+ cardiac macrophages with an antibody-siRNA conjugate reduces atrial fibrosis and suppresses AFib in mice, thus offering a new immunotherapy for the most common arrhythmia.

immunology↗

bioRxiv2023

Spontaneous transfer of small peripheral peptides between supported lipid bilayer and giant unilamellar vesicles

Vesicular trafficking facilitates material transport between membrane-bound organelles. Membrane protein cargos are trafficked for relocation, recycling, and degradation during various physiological processes. In vitro fusion studies utilized synthetic lipid membranes to study the molecular mechanisms of vesicular trafficking and to develop synthetic materials mimicking the biological membrane trafficking. Various fusogenic conditions which can induce vesicular fusion have been used to establish synthetic systems that can mimic biological systems. Despite these efforts, the mechanisms underlying vesicular trafficking of membrane proteins remain limited and robust in vitro methods that can construct synthetic trafficking systems for membrane proteins between large membranes (>1 m2) are unavailable. Here, we provide data to show the spontaneous transfer of small membrane-bound peptides ([~]4 kD) between a supported lipid bilayer (SLB) and giant unilamellar vesicles (GUVs). We found that the contact between the SLB and GUVs led to the occasional but notable transfer of membrane-bound peptides in a physiological saline buffer condition (pH 7.4, 150 mM NaCl). Quantitative and dynamic time-lapse analyses suggested that the observed exchange occurred through the formation of hemi-fusion stalks between the SLB and GUVs. Larger protein cargos with a size of [~]77 kD could not be transferred between the SLB and GUVs, suggesting that the larger-sized cargos limited diffusion across the hemi-fusion stalk, which was predicted to have a highly curved structure. Our system serves as an example synthetic platform that enables the investigation of small-peptide trafficking between synthetic membranes and reveals hemi-fused lipid bridge formation as a mechanism of peptide transfer. Graphical abstracts O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=56 SRC="FIGDIR/small/544237v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1f72d8corg.highwire.dtl.DTLVardef@cf7ed5org.highwire.dtl.DTLVardef@8fee0forg.highwire.dtl.DTLVardef@1565484_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

CRFalign: A Sequence-structure alignment of proteins based on a combinationof HMM-HMM comparison and conditional random fields

We built a method of sequence-structure alignment (called CRFalign) which improves upon a base alignment model based on HMM-HMM comparison by employing pairwise conditional random fields (pCRF) in combination with nonlinear scoring functions of structural and sequence features. The total scoring function consists of a base scoring part based on HMM-HMM profile comparison plus additional nonlinear scoring part which is implemented by a set of gradient boosted regression trees. In addition to sequence profile features, various structural features are employed including secondary structures, solvent accessibilities, environment-dependent properties that give rise to position-dependent as well as environment-dependent match scores and gap penalties. Training is performed on reference alignments at superfamily levels or twilight zone chosen from the SABmark benchmark set. We found that our alignment method produce relative improvement in terms of average alignment accuracies, especially for the alignment of remote homologous proteins. We found that our alignment method produced (by using Modeller) better modeling results especially in the relatively hard targets compared with other methods. CRFalign was successfully applied to the stages of fold recognition and multiple sequence alignment in CASP11 and CASP12 competition on protein structure predictions.

bioinformatics↗

bioRxiv2018

WEScover: whole exome sequencing vs. gene panel testing

MotivationWhole exome sequencing (WES) is widely adopted in clinical and research settings. However, there is potential for false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known phenotype associated genes. We developed a tool for quickly gauging whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should instead be considered to minimize false negatives in candidate genes. ResultsWEScover is a novel web application that provides an interface for discovering breadth and depth of coverage across population scale WES datasets, searching either by phenotype, by targeted gene panels and by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. ConclusionWEScover allows users to efficiently query genes and phenotype for exome coverage of associated exons, and recommends use of panel tests for genes that are potentially not well covered by WES.

bioinformatics↗

bioRxiv2018

ATP-dependent force generation and membrane scission by ESCRT-III and Vps4

The ESCRTs catalyze reverse-topology scission from the inner face of membrane necks in HIV budding, multivesicular endosome biogenesis, cytokinesis, and other pathways. We encapsulated a minimal ESCRT module consisting of ESCRT-III subunits Snf7, Vps24, and Vps2, and the AAA+ ATPase Vps4 such that membrane nanotubes reflecting the correct topology of scission could be pulled from giant vesicles. Upon ATP release by photo-uncaging, this system was capable of generating forces within the nanotubes in a manner dependent upon Vps4 catalytic activity, Vps4 coupling to the ESCRT-III proteins, and membrane insertion by Snf7. At physiological concentrations, single scission events were observed that correlated with forces of ~6 pN, verifying predictions that ESCRTs are capable of exerting forces on membranes. Imaging of scission with subsecond resolution revealed Snf7 puncta at the sites of membrane cutting, directly verifying longstanding predictions for the ESCRT scission mechanism.\n\nOne Sentence SummaryESCRT-III and Vps4 were reconstituted from within the interior of nanotubes pulled from giant vesicles, revealing that this machinery couples ATP-dependent force production for membrane scission.

biophysics↗