Biology subjects

Huang, K.-T.

Publications and source records attributed to Huang, K.-T..

6 recordsLinked to original sources

bioRxiv2025

gAIRR-wgs: An Algorithm to Genotype T Cell Receptor Alleles Using Whole Genome Sequencing Data

T cell receptor (TR) genes, including variable (TR_V), diversity (TR_D), and joining (TR_J) segments, exhibit allelic diversity that is critical to adaptive immunity. Growing evidence has identified associations between TR genes and immune-related diseases. Germline variants may influence TR gene function and subsequent usage, highlighting the importance of accurate TR allele profiling. However, accurately identifying germline TR from standard WGS data remains challenging due to short read lengths, limited depth, and high sequence similarity. To address these challenges, we developed gAIRR-wgs, for WGS-based TR allele typing. By incorporating novel alleles from HPRC individuals, gAIRR-wgs exhibited excellent performance in allele calling, with F1 scores of 100.0% for TR_D, 99.8% for TR_J, and 98.3% for TR_V. Applying this pipeline to 1,492 individuals from the Taiwan Biobank (TWB), we identified 449 novel TR alleles, 277 of which overlapped with HPRC release 1 data of mixed ethnicity and are absent in the IMGT database. Further population comparison analysis revealed significant TR allele distribution differences across global populations, showing population-specific patterns and diversity variations between ethnic groups. We also discovered TWB-specific deletion polymorphisms affecting contiguous TRGV and TRBV genes, which are not recorded in the gnomAD database and undetected by standard structural variant callers, highlighting the need for tailored approaches to resolve complex immune gene regions. In conclusion, gAIRR-wgs enables accurate TR allele calling from standard WGS data using feasible computational resources and reveals substantial immunogenetic diversity in population cohorts.

bioinformatics↗

bioRxiv2025

Unmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite

The adaptive immune receptor repertoire (AIRR), composed of V(D)J-recombined T cell receptors (TR) and immunoglobulins (IG), is central to adaptive immunity. Accurate AIRR profiling depends on a comprehensive and diverse germline gene set encoding AIRR (gAIRR). Furthermore, gAIRR alleles themselves are associated with immune-related phenotypes and diseases. However, for TR genes, the IMGT database - the primary gAIRR reference - has not been updated since 2020 and lacks sufficient population diversity and complete flanking sequences. To address these limitations, we investigated 47 high-quality genomes from the Human Pangenome Reference Consortium (HPRC) using the gAIRR Suite and identified 335 novel TR alleles - 305 TRV and 30 TRJ - representing 91.6% and 30.9% increases over IMGT records. All novel alleles were crosschecked using two orthogonal pipelines. We also established a comprehensive flanking sequence database, including recombination signal sequences (RSS). We have made all resources publicly available to support immunogenomics research and clinical applications.

genomics↗

bioRxiv2024

Dysregulated Ca2+ signaling, fluid secretion, and mitochondrial function in a mouse model of early Sjögren's syndrome

Saliva is essential for oral health. The molecular mechanisms leading to physiological fluid secretion are largely established, but factors that underlie secretory hypofunction, specifically related to the autoimmune disease Sjogrens syndrome (SS) are not fully understood. A major conundrum is the lack of association between the severity of inflammatory immune cell infiltration within the salivary glands and glandular hypofunction. In this study, we investigated in a mouse model system, mechanisms of glandular hypofunction caused by the activation of the stimulator of interferon genes (STING) pathway. Glandular hypofunction and SS-like disease were induced by treatment with 5,6-Dimethyl-9-oxo-9H-xanthene-4-acetic acid (DMXAA), a small molecule agonist of murine STING. Contrary to our expectations, despite a significant reduction in fluid secretion in DMXAA-treated mice, in vivo imaging demonstrated that neural stimulation resulted in greatly enhanced spatially averaged cytosolic Ca2+ levels. Notably, however, the spatiotemporal characteristics of the Ca2+ signals were altered to signals that propagated throughout the entire cytoplasm as opposed to largely apically confined Ca2+ rises observed without treatment. Despite the augmented Ca2+ signals, muscarinic stimulation resulted in reduced activation of TMEM16a, although there were no changes in channel abundance or absolute sensitivity to Ca2+. However, super-resolution microscopy revealed a disruption in the intimate colocalization of Inositol 1,4,5-trisphosphate receptor Ca2+ release channels in relation to TMEM16a. TMEM16a channel activation was also reduced when intracellular Ca2+ buffering was increased. These data are consistent with altered local coupling between the channels contributing to the reduced activation of TMEM16a. Appropriate Ca2+ signaling is also pivotal for mitochondrial morphology and bioenergetics and secretion is an energetically expensive process. Disrupted mitochondrial morphology, a depolarized mitochondrial membrane potential, and reduced oxygen consumption rate were observed in DMXAA-treated animals compared to control animals. We report that early in SS disease, dysregulated Ca2+ signals lead to decreased fluid secretion and disrupted mitochondrial function contributing to salivary gland hypofunction and likely the progression of SS disease.

physiology↗

bioRxiv2024

Mitochondrial membrane potential regulates nuclear DNA methylation and gene expression through phospholipid remodeling

Maintenance of the mitochondrial inner membrane potential ({Delta}{Psi}M) is critical for many aspects of mitochondrial function, including mitochondrial protein import and ion homeostasis. While {Delta}{Psi}M loss and its consequences are well studied, little is known about the effects of increased {Delta}{Psi}M. In this study, we used cells deleted of ATPIF1, a natural inhibitor of the hydrolytic activity of the ATP synthase, as a genetic model of mitochondrial hyperpolarization. Our data show that chronic {Delta}{Psi}M increase leads to nuclear DNA hypermethylation, regulating transcription of mitochondria, carbohydrate and lipid metabolism genes. Surprisingly, remodeling of phospholipids, but not metabolites or redox changes, mechanistically links the {Delta}{Psi}M to the epigenome. These changes were also observed upon chemical exposures and reversed by decreasing the {Delta}{Psi}M, highlighting them as hallmark adaptations to chronic mitochondrial hyperpolarization. Our results reveal the {Delta}{Psi}M as the upstream signal conveying the mitochondrial status to the epigenome to regulate cellular biology, providing a new framework for how mitochondria can influence health outcomes in the absence of canonical dysfunction. HighlightsO_LIMitochondria hyperpolarization leads to nuclear DNA hypermethylation C_LIO_LIDNA methylation regulates expression of mitochondrial and lipid metabolism genes C_LIO_LIPhospholipid remodeling mediates the epigenetic effects of mitochondrial hyperpolarization C_LI

genomics↗

bioRxiv2022

Z-REX uncovers a bifurcation in function of Keap1 paralogs

Studying electrophile signaling is marred by difficulties in parsing changes in pathway flux attributable to on-target, vis-a-vis off-target, modifications. By combining bolus dosing, knockdown, and Z-REX--a tool investigating on-target/on-pathway electrophile signaling, we document that electrophile labeling of one zebrafish-Keap1-paralog (zKeap1b) stimulates Nrf2-driven antioxidant response (AR) signaling (like the human-ortholog). Conversely, zKeap1a is a dominant-negative regulator of electrophile-promoted Nrf2-signaling, and itself is nonpermissive for electrophile-induced Nrf2-upregulation. This behavior is recapitulated in human cells, wherein following electrophile treatment: (1) zKeap1b-transfected cells are permissive for augmented AR-signaling through reduced zKeap1b-Nrf2 binding; (2) zKeap1a-transfected cells are non-permissive for AR-upregulation, as zKeap1a-Nrf2 binding capacity remains unaltered; (3) 1:1 ZKeap1a:zKeap1b-transfected cells show no Nrf2-release from the Keap1-complex, rendering these cells unable to upregulate AR. We identified a zKeap1a-specific point-mutation (C273I) responsible for zKeap1as behavior. Human-Keap1(C273I), of known diminished Nrf2-regulatory capacity, dominantly muted electrophile-induced Nrf2-signaling. These studies highlight divergent and interdependent electrophile signaling behaviors, despite conserved electrophile sensing. Impact statementHow electrophile-sensing versus -signaling marshal stress responses: two zebrafish Keap1-paralogs are equally adept at electrophile-sensing but manifest divergent and co-regulatory electrophile-signaling behaviors.

pharmacology and toxicology↗

bioRxiv2022

Z-REX: Shepherding Reactive Electrophiles to Specific Proteins Expressed either Tissue-Specifically or Ubiquitously, and Recording the Resultant Functional Electrophile-Induced Redox Responses in Larval Fish

Summary of the Protocol ExtensionThis Protocol Extension describes the adaptation of an existing Nature Protocol detailing the use of T-REX (targetable reactive electrophiles and oxidants)--an on-demand redox targeting toolset in cultured cells. The adaptation described here is for use of REX technologies in live zebrafish embryos (Z-REX). Zebrafish embryos expressing a Halo-tagged protein of interest (POI)--either ubiquitously or tissue-specifically--are treated with a HaloTag-specific small-molecule probe housing a photocaged reactive electrophile (either natural electrophiles or synthetic electrophilic drug-like fragments). The reactive electrophile is then photouncaged at a user-defined time, enabling proximity-assisted electrophile-modification of a POI. Functional and phenotypic ramifications of POI-specific modification can then be monitored, by coupling to standard downstream assays, such as, Click chemistry-based POI-labeling and target-occupancy quantification; immunofluorescence or live imaging; RNA-Seq and qRT-PCR analyses of downstream-transcript modulations. Transient expression of requisite Halo-POI in zebrafish embryos is achieved by mRNA injection. Procedures associated with generation of transgenic zebrafish expressing a tissue-specific Halo-POI are also described. The Z-REX experiments can be completed in <1-week using standard techniques. To successfully execute Z-REX, researchers should have basic skills in fish husbandry, imaging, and pathway analysis. Experience with protein or proteome manipulation is useful. This protocol extension is aimed at helping chemical biologists study precision redox events in a model organism and fish biologists perform redox chemical biology.

biochemistry↗