Biology subjects

Hwang, D.-W.

Publications and source records attributed to Hwang, D.-W..

4 recordsLinked to original sources

bioRxiv2026

Quantitative Optimization of Sensitivity and Specificity in Targeted and Whole-Exome Sequencing Using Reference-Standard DNA Mixtures

BackgroundWe previously developed a benchmarking strategy using mixtures of homozygote and heterozygote DNAs as reference standards to simultaneously assess sensitivity and false positive (FP) error rates in targeted next-generation sequencing (T-NGS) and whole-exome sequencing (WES), revealing substantial variability across commercial platforms. However, optimal analytic conditions for clinical application remain undefined. MethodsWe systematically evaluated multiple sequencing kits and bioinformatics pipelines across various variant allele fraction (VAF) thresholds to identify conditions that maximize both sensitivity and specificity. Recurrent error-prone alleles were defined and filtered to enhance specificity. ResultsOptimal performance was achieved using the DRAGEN pipeline with recurrent FP allele filtering. For T-NGS, a 1% VAF cutoff yielded a 95% detection threshold of 2.99% and 1.21 FPs per megabase (FP/Mb); for WES, a 2% cutoff yielded a 95% threshold of 5.02% and 1.15 FP/Mb. These settings improved sensitivity >3-fold and reduced FP rates >96% versus suboptimal pipelines. Notably, VAF thresholds flattened sensitivity differences across platforms, obscuring key performance disparities--challenging assumptions that T-NGS is inherently more sensitive than WES. In-house and conventional pipelines undercalled up to 10% of true variants. Restricting reporting of 1-4% VAF variants to [~]1,000 predefined actionable sites enabled recovery of clinically relevant mutations while reducing FP risk >99%. ConclusionsThis study provides a quantitative framework for optimizing NGS performance. Our findings support actionable strategies to improve diagnostic accuracy in clinical genomics through tailored pipeline selection, VAF thresholding, and artifact filtering.

bioinformatics↗

bioRxiv2025

Single-molecule imaging reveals activity-dependent regulation of Camk2a mRNAs at dendritic spines

AbstractPostsynaptic calcium/calmodulin-dependent protein kinase type II (CaMKII) integrates fleeting Ca2+ transients into long-term synaptic potentiation (LTP). A persistent presence of CaMKII at dendritic spines during the maintenance of LTP facilitates the prolongation of synaptic transmission. Yet, it remains unclear how the perpetuation of CaMKII, despite protein turnover, is achieved at dendritic spines. By visualizing endogenous Camk2a mRNAs at single molecule resolution using a newly developed mouse model, we identified a rapid activity-dependent localization of mRNAs to stimulated spines near the postsynaptic density (PSD) of hippocampal neurons. This spine localization was conferred by cis-acting regulatory elements termed cytoplasmic polyadenylation elements (CPEs) in Camk2a mRNA. Spine-localized Camk2a underwent on-site translation, which persisted for extended periods. These findings uncovered a novel local regulation of Camk2a mRNA, which serves to supply dendritic spines with a steady pool of highly concentrated CaMKII for maintaining long-lasting synaptic plasticity.

neuroscience↗

bioRxiv2025

Identification and classification of abundant RNA-binding proteins in the mouse lens and interactions of Carhsp1, Igf2bp1/ZBP1, and Ybx1 with crystallin and β-actin mRNAs

RNA-binding proteins (RBPs) are critical regulators of mRNAs controlling all processes such as RNA transcription, transport, localization, translation, mRNA:ncRNA interactions, and decay. Cellular differentiation is driven by tissue-specific and/or tissue-preferred expression of proteins needed for the optimal function of mature cells, tissues and organs. Lens fiber cell differentiation is marked by high levels of expression of crystallin genes encoding critical proteins for lens transparency and light refraction. Herein we performed proteomic and transcriptomic analyses of RBPs in differentiating mouse lenses to identify the most abundant RBPs and establish dynamic changes of their expression in differentiating lens. Expression analyses include highly abundant RBPs, including Carhsp1, Igf2bp1/ZBP1, Ybx1, Pabpc1, Ddx39, and Rbm38. Binding sites of Carhsp1, Ybx1, and Igf2bp1/ZBP1 were predicted in various crystallin and {beta}-actin mRNAs. Immunoprecipitations using antibodies against Carhsp1, Igf2bp1/ZBP1, and Ybx1 confirmed their interactions with A-, B-, and {gamma}A-crystallin mRNAs. A combination of single molecule RNA FISH (smFISH) and immunofluorescence was used to probe in vivo interactions of these RBPs with A-, B-crystallin, and {beta}-actin mRNAs in cytoplasm and nucleoplasm of cultured mouse lens epithelial cells. Together, these results open new avenues to perform comprehensive genetic, cell, and molecular biology studies of individual RBPs in the lens.

developmental biology↗

bioRxiv2023

Dopamine D2 receptors in mossy cells reduce excitatory transmission and are essential for hippocampal function

Hilar mossy cells (MCs) are principal excitatory neurons of the dentate gyrus (DG) that play critical roles in hippocampal function and have been implicated in brain disorders such as anxiety and epilepsy. However, the mechanisms by which MCs contribute to DG function and disease are poorly understood. Expression from the dopamine D2 receptor (D2R) gene (Drd2) promoter is a defining feature of MCs, and previous work indicates a key role for dopaminergic signaling in the DG. Additionally, the involvement of D2R signaling in cognition and neuropsychiatric conditions is well-known. Surprisingly, though, the function of MC D2Rs remain largely unexplored. In this study, we show that selective and conditional removal of Drd2 from MCs of adult mice impaired spatial memory, promoted anxiety-like behavior and was proconvulsant. To determine the subcellular expression of D2Rs in MCs, we used a D2R knockin mouse which revealed that D2Rs are enriched in the inner molecular layer of the DG, where MCs establish synaptic contacts with granule cells. D2R activation by exogenous and endogenous dopamine reduced MC to dentate granule cells (GC) synaptic transmission, most likely by a presynaptic mechanism. In contrast, removing Drd2 from MCs had no significant impact on MC excitatory inputs and passive and active properties. Our findings support that MC D2Rs are essential for proper DG function by reducing MC excitatory drive onto GCs. Lastly, impairment of MC D2R signaling could promote anxiety and epilepsy, therefore highlighting a potential therapeutic target. SIGNIFICANCEGrowing evidence indicates that hilar mossy cells (MCs) of the dentate gyrus play critical but incompletely understood roles in memory and brain disorders, including anxiety and epilepsy. Dopamine D2 receptors (D2Rs), implicated in cognition and several psychiatric and neurological disorders, are considered to be characteristically expressed by MCs. Still, the subcellular localization and function of MC D2Rs are largely unknown. We report that removing the Drd2 gene specifically from MCs of adult mice impaired spatial memory and was anxiogenic and proconvulsant. We also found that D2Rs are enriched where MCs synaptically contact dentate granule cells (GC) and reduce MC-GC transmission. This work uncovered the functional significance of MC D2Rs, thus highlighting their therapeutic potential in D2R- and MC-associated pathologies.

neuroscience↗