Biology subjects

Chang, T.-Y.

Publications and source records attributed to Chang, T.-Y..

11 recordsLinked to original sources

bioRxiv2025

deCYPher: Star Allele-Resolution Computational Framework of Pharmacogenes for Haplotype-Resolved Long-Read Assemblies

Although existing next-generation sequencing (NGS) tools, such as Aldy and Cyrius, have been applied for allele typing, they cannot achieve complete accuracy due to various genomic challenges including pseudogenes, structural variations, hybrid genes, copy number variations, and gene deletions. These complexities make accurate pharmacogene interpretation more challenging, despite the crucial role pharmacogenomics plays in precision medicine. We developed deCYPher, a tool that generates personalized pharmacogenomic reports from haplotype-resolved assemblies. The tool enables analysis of all PharmVar 1A level genes, such as CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, CYP4F2, DPYD, NUDT15, and SLCO1B1. Applied to all HPRC haplotypes (including both release 1 and release 2 data), deCYPher demonstrated high accuracy in resolving complex gene structures. In the case of CYP2D6, release 1 identified 6% gene multiplications, 6% full gene deletions, and 4% CYP2D6/CYP2D7 hybrids. By contrast, release 2 demonstrated an increased prevalence of multiplications (14%) and hybrids (11%), while the frequency of full gene deletions remained comparable at 5%. Comparison with pb-StarPhase revealed discrepancies in 12 of 94 assemblies in the release 1 dataset. For instance, in sample HG02257, Aldy, Cyrius, and deCYPher consistently identified the genotype as *2/*35, whereas pb-StarPhase reported *2/*2. Notably, the *35-defining variants were present in the BAM and VCF files in the pb-StarPhase pipeline, but the local read depth over the *35-specific region was only 5x in HG02257-p, suggesting that the misclassification likely resulted from insufficient coverage - a known limitation of pb-StarPhase under low-depth conditions.

bioinformatics↗

bioRxiv2025

TypeAssembly: Copy number estimation and allele typing for haplotype assemblies

Accurately annotating complex genes in the human genome, particularly from haplotype assemblies, remains a significant challenge. To overcome this, we developed TypeAssembly, a local alignment-based framework for copy number estimation and allele typing. Operating in two modes, mode-FASTA and mode-VCF, TypeAssembly can define alleles by either sequence or variant information. We successfully applied it to annotate 41 genes in the MHC locus, 17 KIR genes, and, for the first time, 15 pharmacogenes across 466 haplotype assemblies. This study establishes TypeAssembly as a robust method for accurately annotating complex genomic regions and provides an evaluation of existing gene annotations and callers.

bioinformatics↗

bioRxiv2025

Integrated Spatial Analysis of Ovarian Precancerous Lesions

Studying precancerous lesions is essential for improving early detection and prevention, particularly in aggressive cancers such as ovarian carcinoma. Here, we conducted integrated and spatial analyses of transcriptomes, aneuploidy, and clinic-pathological features in 166 ovarian precancerous lesions. Four pre-cancerous subtypes were identified transcriptomically: proliferative, immunoreactive, dormant, and mixed. These subtypes varied in their frequency of germline-BRCA1/2 mutations, aneuploidy, CCNE1/MYC amplification, proliferative activity, immune-regulatory gene expression, and histological features. Notably, the immunoreactive subtype upregulated immune-regulatory genes, exhibited chronic inflammation, and was enriched in cases with germline-BRCA1/2 mutations, deletions of chromosomes 17 (harboring TP53 and BRCA1) and 13 (harboring BRCA2), leading to a double "two-hit" involving TP53 and BRCA1/2. Tumor invasion was associated with the activation of interferon response pathways, epithelial-mesenchymal transition, and extracellular matrix remodeling. In summary, our results elucidate the earliest molecular landscape of ovarian precancerous lesions, serving as the foundation for future risk stratification to identify aggressive pre-cancerous lesions.

molecular biology↗

bioRxiv2025

Inhibition of Glutamine Metabolism Suppresses Tumor Progression through Remodeling of the Macrophage Immune Microenvironment

BackgroundTargeting glutamine metabolism has emerged as a promising strategy in cancer therapy. However, several barriers, such as in vivo anti-tumor efficacy, drug toxicity, and safety, remain to be overcome to achieve clinical utility. Prior preclinical in vivo studies had generated encouraging data showing promises of cancer metabolism targeting drugs, although most were performed on immune-deficient murine models. It is being recognized that aside from tumor cells, normal cells such as immune cells in the tumor microenvironment may also utilize glutamine for maintaining physiological functions. To provide an in-depth view of glutamine antagonist (GLNi) treatment on the tumor immune microenvironment, the current study made several unique approaches. MethodFirst, to evaluate GLNi treatment modality that potentially involves immune cells, the study was performed on immunocompetent murine models of gynecological cancers. Second, to enhance safety and reduce potential off-target effects, we developed a GLNi prodrug, JHU083, which is bio-activated restrictively in cancer tissues. Third, to unbiasedly decode the response of single cells in the tumor microenvironment to GLNi treatment, single-cell RNA sequencing (scRNA-seq) was performed on cells prepared from tumors of the JHU083 or vehicle control-treated mice. ResultsIn both immunocompetent murine tumor models, we observed a significant anti-tumor efficacy, resulting in reduced tumor burden and impeded tumor progression. Similarly, in both tumor models, scRNA-seq revealed significantly impeded immunosuppressive M2-like macrophages by JHU083, while the treatment spared pro-inflammatory M1-like tumor macrophages. In many tumor microenvironment (TME) cells, JHU083 downregulated genes regulated by Myc and hypoxia. M2 macrophages greater sensitivity to glutamine antagonism when compared to M1 macrophages or monocytes was further validated on ex vivo cultures of bone marrow-derived macrophages. ConclusionOur findings support a converged mechanism of glutamine metabolism antagonists. JHU083 exerted its anti-tumor efficacy through not only direct targeting of glutamine-addicted cancer cells but also by suppressing glutamine-dependent M2 macrophages, leading to a shift in the M1/M2 macrophage landscape in favor of an immune-stimulatory microenvironment.

cancer biology↗

bioRxiv2024

HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo

STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of [~]50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.

genomics↗

bioRxiv2022

Parallel processing, hierarchical transformations, and sensorimotor associations along the 'where pathway

Visually guided behaviors require the brain to transform ambiguous retinal images into object-level spatial representations and implement sensorimotor transformations. These processes are supported by the dorsal where pathway. However, the specific functional contributions of areas along this pathway remain elusive due in part to methodological differences across studies. We previously showed that macaque caudal intraparietal (CIP) area neurons possess robust three-dimensional (3D) visual representations, carry choice-related and presaccadic activity, and exhibit experience-dependent sensorimotor associations (Chang et al., 2020b). Here, we used a common experimental design to reveal parallel processing, hierarchical transformations, and the formation of sensorimotor associations along the where pathway by extending the investigation to V3A, a major feedforward input to CIP. Higher-level 3D representations and choice-related activity were more prevalent in CIP than V3A. Both areas contained presaccadic activity that predicted the direction/timing of eye movements. Intriguingly, the time-course of presaccadic activity in CIP aligned with the temporally integrated V3A output. Sensorimotor associations between 3D orientation and saccade direction preferences were strongest in CIP and moderated by choice signals in both areas. Together, the results explicate parallel representations, hierarchical transformations, and functional associations of visual and presaccadic signals at a key juncture in the where pathway.

neuroscience↗

bioRxiv2020

Acat1 gene KO restores TGN cholesterol deficiency in mutant NPC1 cells and expands mutant Npc1 mouse lifespan

Niemann-Pick type C (NPC) is a neurological disorder with no cure. NPC proteins deliver cholesterol from endosomes to other compartments including trans-Golgi network (TGN) and endoplasmic reticulum (ER). Acyl-coenzyme A:cholesterol acyltransferase 1 (ACAT1) is a resident ER enzyme that converts cholesterol to cholesteryl esters for storage. Here, we report the surprising finding that in a mutant Npc1 mice, Acat1-deficiency delayed the onset of weight loss and declining motor skill, prolonged lifespan, delayed Purkinje neuron death, and improved hepatosplenic pathology. Furthermore, syntaxin 6, a cholesterol-binding t-SNARE normally localized to TGN, is mislocalized in mutant NPC cells. However, upon ACAT1 inhibition this mislocalization is corrected, and increase the level of a few proteins further downstream. Our results imply that ACAT1 inhibition diverts a cholesterol storage pool in a way that replenished the low cholesterol level in NPC-deficient TGN. Taking together, we identify ACAT1 inhibition as a potential therapeutic target for NPC treatment.

neuroscience↗

bioRxiv2020

Choice activity stabilizes sensory representations and mediates sensorimotor associations in parietal cortex

Selecting actions which achieve desired goals often requires three-dimensional (3D) representations of the environment. Because the sensory epithelia cannot directly encode the worlds 3D spatial features, sensory signals must be converted into 3D representations. Here we investigated the relationships between the quality of 3D visual representations, choice-related activity, and motor-related activity in the parietal cortex of macaque monkeys using an eight-alternative 3D orientation discrimination task, visually guided saccade task, and laminar probe recordings. We found that choice activity was preferentially carried by caudal intraparietal area neurons with more robust 3D representations. Choice activity further stabilized the 3D representations, rather than attenuating information not directly relevant to the behavioral task (nuisance variables). An experience-dependent, sensorimotor association additionally aligned sensory and saccade direction preferences, particularly for neurons with choice activity. These findings reveal novel roles for choice activity in improving the fidelity of ecologically relevant object representations and mediating sensorimotor associations.

neuroscience↗

bioRxiv2020

Inhibition mechanism of human sterol O-acyltransferase 1 by competitive inhibitor

Sterol O-acyltransferase 1 (SOAT1) is an endoplasmic reticulum (ER) resident, multi-transmembrane enzyme that belongs to the membrane-bound O-acyltransferase (MBOAT) family 1. It catalyzes the esterification of cholesterol to generate cholesteryl esters for cholesterol storage 2. SOAT1 is a target to treat several human diseases 3. However, its structure and mechanism remain elusive since its discovery. Here, we report the structure of human SOAT1 (hSOAT1) determined by cryo-EM. hSOAT1 is a tetramer consisted of a dimer of dimer. The structure of hSOAT1 dimer at 3.5 [A] resolution reveals that the small molecule inhibitor CI-976 binds inside the catalytic chamber and blocks the accessibility of the active site residues H460, N421 and W420. Our results pave the way for future mechanistic study and rational drug design of SOAT1 and other mammalian MBOAT family members.

biochemistry↗

bioRxiv2019

Optimized but not maximized cue integration for 3D visual perception

Reconstructing three-dimensional (3D) scenes from two-dimensional (2D) retinal images is an ill-posed problem. Despite this, our 3D perception of the world based on 2D retinal images is seemingly accurate and precise. The integration of distinct visual cues is essential for robust 3D perception in humans, but it is unclear if this mechanism is conserved in non-human primates, and how the underlying neural architecture constrains 3D perception. Here we assess 3D perception in macaque monkeys using a surface orientation discrimination task. We find that perception is generally accurate, but precision depends on the spatial pose of the surface and available cues. The results indicate that robust perception is achieved by dynamically reweighting the integration of stereoscopic and perspective cues according to their pose-dependent reliabilities. They further suggest that 3D perception is influenced by a prior for the 3D orientation statistics of natural scenes. We compare the data to simulations based on the responses of 3D orientation selective neurons. The results are explained by a model in which two independent neuronal populations representing stereoscopic and perspective cues (with perspective signals from the two eyes combined using nonlinear canonical computations) are optimally integrated through linear summation. Perception of combined-cue stimuli is optimal given this architecture. However, an alternative architecture in which stereoscopic cues and perspective cues detected by each eye are represented by three independent populations yields two times greater precision than observed. This implies that, due to canonical computations, cue integration for 3D perception is optimized but not maximized.\n\nAuthor summaryOur eyes only sense two-dimensional projections of the world (like a movie on a screen), yet we perceive the world in three dimensions. To create reliable 3D percepts, the human visual system integrates distinct visual signals according to their reliabilities, which depend on conditions such as how far away an object is located and how it is oriented. Here we find that non-human primates similarly integrate different 3D visual signals, and that their perception is influenced by the 3D orientation statistics of natural scenes. Cue integration is thus a conserved mechanism for creating robust 3D percepts by the primate brain. Using simulations of neural population activity, based on neuronal recordings from the same animals, we show that some computations which occur widely in the brain facilitate 3D perception, while others hinder perception. This work addresses key questions about how neural systems solve the difficult problem of generating 3D percepts, identifies a plausible neural architecture for implementing robust 3D vision, and reveals how neural computation can simultaneously optimize and curb perception.

neuroscience↗

bioRxiv2018

Real-time experimental control using network-based parallel processing

Modern neuroscience research often requires the coordination of multiple processes such as stimulus generation, real-time experimental control, as well as behavioral and neural measurements. The technical demands required to simultaneously manage these processes with high temporal fidelity limits the number of labs capable of performing such work. Here we present an open-source network-based parallel processing framework that eliminates these barriers. The Real-Time Experimental Control with Graphical User Interface (REC-GUI) framework offers multiple advantages: (i) a modular design agnostic to coding language(s) and operating system(s) that maximizes experimental flexibility and minimizes researcher effort, (ii) simple interfacing to connect measurement and recording devices, (iii) high temporal fidelity by dividing task demands across CPUs, and (iv) real-time control using a fully customizable and intuitive GUI. Testing results demonstrate that the REC-GUI framework facilitates technically demanding, behavior-contingent neuroscience research. Sample code and hardware configurations are downloadable, and future developments will be regularly released.

neuroscience↗