Biology subjects

Min, J. K.

Publications and source records attributed to Min, J. K..

4 recordsLinked to original sources

bioRxiv2026

DTCAMD, a disease-associated truncated form of CRYAB in neovascular age-related macular degeneration: a potential driver of subretinal fibrosis

Abstract Purpose: Subretinal fibrosis causes irreversible vision loss in neovascular age-related macular degeneration (nAMD) and remains poorly controlled by anti-vascular endothelial growth factor (VEGF) therapy. We investigated the role of B-crystallin (CRYAB) in angiogenic and fibrotic pathology and evaluated disease-associated CRYAB truncation as a therapeutic target. Methods: Aqueous humor from patients with nAMD was analyzed by quantitative proteomics and receiver operating characteristic (ROC) analysis. CRYAB function was assessed using knockout and knockdown approaches in a choroidal neovascularization (CNV) mouse model. CRYAB truncation and associated proteins were examined by immunoblotting, co-immunoprecipitation, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). C-terminal truncation was further examined in mouse retinal tissue using antibodies generated against full-length CRYAB and its C-terminal region. Primary human retinal pigment epithelial (hRPE)-THP-1 co-cultures were used to examine CRYAB truncation under fibrosis-associated conditions. Pharmacological effects were tested using ({+/-})-threo-3-methylglutamic acid (T3MG) and 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF). Results: CRYAB was upregulated in the aqueous humor of patients with nAMD. Higher CRYAB levels were associated with persistent lesions after initial anti-VEGF treatment. CRYAB knockout or knockdown reduced CNV pathology and decreased VEGFA and -smooth muscle actin (SMA) expression, without a significant substrain effect between C57BL/6N and C57BL/6J mice. A Ser45-phosphorylated truncated CRYAB species was detected in mouse laser-induced CNV model. We termed this species disease-associated truncated CRYAB in AMD (DTCAMD). Peptide mapping showed reproducible loss of distal C-terminal peptide coverage in truncated CRYAB. Consistent with this finding, C-terminal antibody recognition was reduced in CNV lesions. In hRPE-THP-1 co-cultures, DTCAMD accumulated with increased SMA expression. Proteomic analysis identified Prss1 as a candidate CRYAB-associated serine protease linked to truncation under CNV conditions. T3MG and AEBSF reduced DTCAMD-associated signals and CNV pathology. Conclusions: CRYAB contributes to angiogenic and fibrotic pathology in CNV. Disease-associated CRYAB truncation, particularly Ser45-phosphorylated DTCAMD, represents a potential therapeutic target for fibrotic remodeling in nAMD.

pathology↗

bioRxiv2024

The regulatory potential of transposable elements in maize

The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read-sequencing have hindered our understanding of their regulatory potential. We demonstrate that long-read chromatin fiber sequencing (Fiber-seq) comprehensively identifies accessible chromatin regions (ACRs) and CpG methylation across the maize genome. We uncover stereotypical ACR patterns at young TEs that degenerate with evolutionary age, resulting in TE-enhancers preferentially marked by a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility. We show that TE ACRs are co-opted as gene promoters and that ACR-containing TEs can facilitate gene amplification. Lastly, we uncover a pervasive epigenetic signature - hypo-5mCpG methylation and diffuse chromatin accessibility - directing TEs to specific loci, including the loci that sparked McClintocks discovery of TEs.

genomics↗

bioRxiv2022

An in silico method to assess antibody fragment polyreactivity

Antibodies are essential biological research tools and important therapeutic agents, but some exhibit non-specific binding to off-target proteins and other biomolecules. Such polyreactive antibodies compromise screening pipelines, lead to incorrect and irreproducible experimental results, and are generally intractable for clinical development. We designed a set of experiments using a diverse naive synthetic camelid antibody fragment ( nanobody) library to enable machine learning models to accurately assess polyreactivity from protein sequence (AUC > 0.8). Moreover, our models provide quantitative scoring metrics that predict the effect of amino acid substitutions on polyreactivity. We experimentally tested our models performance on three independent nanobody scaffolds, where over 90% of predicted substitutions successfully reduced polyreactivity. Importantly, the model allowed us to diminish the polyreactivity of an angiotensin II type I receptor antagonist nanobody, without compromising its pharmacological properties. We provide a companion web-server that offers a straightforward means of predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.

pharmacology and toxicology↗

bioRxiv2021

MaveDB v2: a curated community database with over three million variant effects from multiplexed functional assays

A central problem in genomics is understanding the effect of individual DNA variants. Multiplexed Assays of Variant Effect (MAVEs) can help address this challenge by measuring all possible single nucleotide variant effects in a gene or regulatory sequence simultaneously. Here we describe MaveDB v2, which has become the database of record for MAVEs. MaveDB now contains a large fraction of published studies, comprising over two hundred datasets and three million variant effect measurements. We created tools and APIs to streamline data submission and access, transforming MaveDB into a hub for the analysis and dissemination of these impactful datasets.

genomics↗