Biology subjects

Hsu, W.-H.

Publications and source records attributed to Hsu, W.-H..

6 recordsLinked to original sources

bioRxiv2026

Transcriptional networks underlying tumour plasticity in small-cell lung cancer

Across human malignancies, the ability of cancer cells to switch states (plasticity) drives progression, metastasis, and therapy resistance 1-3. Here we investigated the transcriptional and epigenetic basis of plasticity in small-cell lung cancer (SCLC), an aggressive, treatment-refractory cancer 4, 5. SCLC tumours display plasticity along a neuroendocrine (NE) to nonNE axis; however, the trajectories of lineage transition and the gene regulatory network underlying it, remain poorly defined 6. Using single-cell multi-omics, we resolved distinct transcriptional SCLC cell states, including a previously unrecognised Intermediate state comprised of low-identity immunogenic SCLC cells that serve as an obligatory route in NE to nonNE lineage transition. Using single-cell gene expression and chromatin accessibility data, we next developed a Boolean Bayes model for transcription factor networks (BoBa-T) to predict regulators of SCLC cell states. We validated RORB as a novel gatekeeper of the NE state that represses the nonNE identity in SCLC. RORB inactivation drives NE cells into the Intermediate state, upregulates immunogenic programs, and inhibits tumour growth in immunocompetent hosts. Our work identifies a plastic, immunogenic waypoint for SCLC lineage switching and reveals strategies to target it therapeutically.

cancer biology↗

bioRxiv2025

A 3D Amphioxus Brain Atlas Illuminates the Blueprint of the Ancestral Chordate Brain

Comparative studies on highly complex vertebrate brains have provided insights into the evolutionary history of morphological diversity. However, a long-standing question in vertebrate brain evolution is how the fundamental blueprint emerged. To probe the cellular and molecular origins of brain architecture in the chordate lineage, we performed single-nucleus RNA-seq combined with spatial transcriptomics and generated a three-dimensional cell atlas of the basal chordate amphioxus central nervous system (CNS). This atlas reveals a tripartite organization along the anterior-posterior axis of the adult amphioxus brain, with a rostral retinal/hypothalamic region followed by a di-mesencephalon and caudally, the hindbrain and spinal cord. Notably, we show that the amphioxus brain contains cell clusters resembling the zona limitans intrathalamica and midbrain-hindbrain boundary, both of which demarcate the major brain compartments. Furthermore, expression profiling and gene ontology enrichment analyses support that the cell clusters located in the rostral part of the amphioxus forebrain correspond to vertebrate retinal primordium and hypothalamic cells. However, the absence of key telencephalic marker expression in the amphioxus anterior forebrain suggests that the telencephalon likely represents a vertebrate innovation. Together, our findings establish a spatial transcriptomic framework for the amphioxus CNS and provide a critical link for understanding the evolution of the complex vertebrate brain.

evolutionary biology↗

bioRxiv2023

qTAG: An adaptable CRISPR-based endogenous tagging protocol using optimized repair cassettes

Endogenous tagging makes it possible to study a proteins localization, dynamics, and function within its native regulatory context. This is typically accomplished via CRISPR, which involves inserting a sequence encoding a functional tag into the reading frame of a gene. However, this process is often inefficient. Here, we introduce the "quickTAG," or qTAG system, a versatile collection of optimized repair cassettes designed to make CRISPR-mediated tagging more accessible. By including a desired tag sequence linked to a selectable marker in the cassette, integrations can be quickly isolated post-editing. The core sequence scaffold within these constructs incorporates several key features that enhance flexibility and ease of use, such as: specific cassette designs for N- and C-terminus tagging; standardized cloning sequences to simplify the incorporation of homology arms for HDR or MMEJ-based repairs; restriction sites next to each genetic element within the cassette for easy modification of tags and selectable markers; and the inclusion of lox sites flanking the selectable marker to allow for marker gene removal following integration. We showcase the versatility of these cassettes with a diverse range of tags, demonstrating their applications in fluorescence imaging, proximity-dependent biotinylation, epitope tagging, and targeted protein degradation. The adaptability of this scaffold is also exhibited by incorporating novel tags such as mStayGold, which offer enhanced brightness and photostability, reconciling prolonged live-cell imaging of proteins at their endogenous levels. Finally, by leveraging the restriction sites, entirely distinct cassette structures and editing schemes were developed. These enabled scenarios that included conditional expression tagging, selectable knockout tagging, and safe-harbor expression. Our existing and forthcoming collection of plasmids will be accessible through Addgene. It includes ready-to-use constructs targeting common subcellular marker genes, as well as an assortment of tagging cassettes for the tagging of genes of interest. The qTAG system offers an accessible framework to streamline endogenous tagging and will serve as an open resource for researchers to adapt and tailor for their own experiments.

molecular biology↗

bioRxiv2023

Anaplerotic nutrient stress drives synergy of angiogenesis inhibitors with therapeutics targeting tumor metabolism

Tumor angiogenesis is a cancer hallmark, and its therapeutic inhibition has provided meaningful, albeit limited, clinical benefit. While anti-angiogenesis inhibitors deprive the tumor of oxygen and essential nutrients, cancer cells activate metabolic adaptations to diminish therapeutic response. Despite these adaptations, angiogenesis inhibition incurs extensive metabolic stress, prompting us to consider such metabolic stress as an induced vulnerability to therapies targeting cancer metabolism. Metabolomic profiling of angiogenesis-inhibited intracranial xenografts showed universal decrease in tricarboxylic acid cycle intermediates, corroborating a state of anaplerotic nutrient deficit or stress. Accordingly, we show strong synergy between angiogenesis inhibitors (Avastin, Tivozanib) and inhibitors of glycolysis or oxidative phosphorylation through exacerbation of anaplerotic nutrient stress in intracranial orthotopic xenografted gliomas. Our findings were recapitulated in GBM xenografts that do not have genetically predisposed metabolic vulnerabilities at baseline. Thus, our findings cement the central importance of the tricarboxylic acid cycle as the nexus of metabolic vulnerabilities and suggest clinical path hypothesis combining angiogenesis inhibitors with pharmacological cancer interventions targeting tumor metabolism for GBM tumors.

cancer biology↗

bioRxiv2023

Can motional dynamics account for the cytotoxicity of beta amyloid oligomers?

The underlying biophysical principle governing the cytotoxicity of the oligomeric aggregates of {beta}-amyloid (A{beta}) peptides has long been an enigma. Here we show that the size of A{beta}40 oligomers can be actively controlled by incubating the peptides in reverse micelles. Our approach allowed for the first time a detailed comparison of the structures and dynamics of two A{beta}40 oligomers of different size, viz., 10 and 23 nm, by solid-state NMR. From the chemical shift data, we infer that the conformation of the residues from K16 to K28 are different between the 10-nm and 23-nm oligomers. We find that the 10-nm oligomers are more cytotoxic, and the molecular motions of their charged residues are more dynamic. Interestingly, the residue A21 exhibits an unusually high structural rigidity. Our data raise the interesting possibility that the cytotoxicity of A{beta}40 oligomers could also be correlated to the motional dynamics of the charged residues.

biophysics↗

bioRxiv2020

You-Gui-Wan ameliorates house dust mite-induced allergic asthma via modulating amino acid metabolic disorder and gut dysbiosis

IntroductionAllergic asthma is a worldwide health problem, and its etiology remains incompletely understood. Besides, as current therapies for allergic asthma mainly rely on administration of glucocorticoids and have many side effects, new therapy is needed. You-Gui-Wan (YGW), a traditional Chinese herbal remedy, has been used for boosting Yang, enhancing immunity and treating allergic asthma. ObjectivesThis study aims to explore the molecular changes during the development of allergic asthma and investigate the potential bio-signatures and the effect of YGW on house dust mite (HDM)-induced chronic allergic asthma in mice. MethodsDermatophagoides pteronyssinus (Der p), one of HDMs, was intratracheally administered once a week for a total of 7 treatments over 6 consecutive weeks to induce allergic asthma in mice. Serum metabolomics was analyzed by LC-QTOF-MS/MS. 16S rRNA-based microbiome profiling was used to analyze gut microbiota, and the correlation between metabolomic signatures and microbial community profiling was explored by Spearman correlation analysis. ResultsSerum metabolomic analysis revealed that 10 identified metabolites -- acetylcarnitine, carnitine, hypoxanthine, tryptophan, phenylalanine, norleucine, isoleucine, betaine, methionine, and valine, were markedly elevated by Der p. These metabolites are mainly related to branch-chain amino acid (BCAA) metabolism, aromatic amino acid (AAA) biosynthesis, and phenylalanine metabolism. YGW administration reversed 7 of the 10 identified metabolites and chiefly affected BCAA metabolism. 16S DNA sequencing revealed that YGW profoundly changed Der p-induced gut microbiota composition. Multiple correlation analysis indicated 10 selected metabolites have a good correlation with gut microbiota. ConclusionDer p induced BCAA metabolic deviation in allergic asthma mice, and YGW administration effectively ameliorated the AA metabolic disorder, and improved gut dysbiosis. This study paves the way towards the interactions of Der-p on microbiome and gut microbiota, and the effects of YGW treatment as well as provides a support for YGW administration with potential benefits for allergic asthma.

systems biology↗