Biology subjects

Huang, C.-K.

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

8 recordsLinked to original sources

bioRxiv2025

RhoV Promotes Proliferation, Migration, and MAPK Activation in Pancreatic Ductal Adenocarcinoma

Background and AimsPancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy characterized by diagnosis at advanced stages, limited therapeutic options, and frequent resistance to therapies. Although oncogenic KRAS mutations are central drivers of PDAC, alternative pathways indisputably contribute to its tumorigenesis and progression. RhoV, a member of the Rho family of small GTPases, has been implicated in tumor development in other cancer types, such as breast cancer and lung adenocarcinoma; however, its role in PDAC remains unclear. MethodsIn this study, we investigated the expression and functional impact of RhoV on PDAC. Analysis of publicly available datasets and immunohistochemical profiling of 114 PDAC patient specimens were used to evaluate the expression of RhoV in PDAC and its prognostic impact. Overexpression and CRISPR-Cas9-mediated knockout of RhoV were established in three pancreatic cancer cell lines. Functional analyses, such as cell proliferation, migration, invasion, colony formation, spheroid growth, and mouse xenograft, were used to evaluate the role of RhoV in PDAC cells. ResultsRhoV overexpression was associated with reduced overall and recurrence-free survival in public datasets and our own patient cohort. Functional assays demonstrated that RhoV overexpression promoted PDAC cell proliferation, colony formation, and spheroid growth, whereas knockout of RhoV suppressed these changes. Moreover, RhoV enhanced PDAC cell migration and invasion in vitro, accompanied by downregulation of E-cadherin and upregulation of N-cadherin and vimentin, indicating induction of epithelial-mesenchymal transition. Mechanistically, RhoV overexpression activated key MAPK pathway components, including phosphorylation of ERK, JNK, and p38. In vivo, xenograft models confirmed that RhoV drives tumor growth and increases tumor burden. ConclusionThese results establish RhoV as a novel oncogenic factor in PDAC progression and highlight its potential as a biomarker and therapeutic target, warranting further investigation into combinatorial targeting strategies to overcome KRAS inhibitor resistance.

cancer biology↗

bioRxiv2025

Microscopy-Guided Spatial Proteomics Reveals Novel Proteins at the Mitochondria-Lipid Droplet Interface and Their Role in Lipid Metabolism

Mitochondria-lipid droplet (LD) interactions play a critical role in lipid metabolism and the progression of metabolic diseases such as non-alcoholic fatty liver disease (NAFLD). However, the dynamic nature of these interactions has hindered the identification of novel protein constituents and their functional roles. Here, we employed Microscoop Mint, an advanced microscopy-guided spatial proteomics platform, to isolate proteins localized at mitochondria-LD contact sites in oleic acid (OA)-treated HepG2 cells, an in vitro model for studying fatty liver disease. Microscoop Mint integrates high-resolution image analysis and two-photon illumination to achieve precise biotinylation of proteins at subcellular regions of interest. Coupled with mass spectrometry, this approach identified a proteome enriched at the mitochondria-LD interface, including both well-characterized lipid-associated proteins and previously unrecognized candidates. Among the 373 common proteins identified across replicates, five novel candidates with no prior association to lipid metabolism were selected for validation. Immunofluorescence staining confirmed their localization at mitochondria-LD contact sites, with more pronounced association in OA-treated cells. Notably, suppression of one candidate, FHL3, led to reduced LD size, elongated mitochondrial morphology, and diminished mitochondria-LD interactions, suggesting its role in regulating fatty acid {beta}-oxidation. Our findings demonstrate the utility of Microscoop Mint in unveiling novel molecular players at organelle contact sites. This study not only provides insights into the functional dynamics of mitochondria-LD interactions but also highlights potential therapeutic targets for lipid metabolic disorders and NAFLD.

cell biology↗

bioRxiv2023

Microscopy-guided subcellular proteomic discovery by high-speed ultra-content photo-biotinylation

Microscopy-guided proteomics at an organelle-dimension resolution is desired for revealing unknown protein constituents at specific disease- or functional-associated regions at the molecular-molecular interactions level. Here, we achieve protein spatial purification by introducing a firmware-integrated microscopy platform that triggers in situ subcellular photo-biotinylation of proteins at user-defined regions of interest (ROIs) one field of view (FOV) at a time for thousands of FOVs fully automatically. An illumination pattern at the analogous ROIs of each FOV is calculated on the fly by either machine learning or traditional image processing. Photoactivatable amino acid crosslinkers are activated by a two-photon focal light one spot at a time at a sub-millisecond illumination duration per spot. Imaging, pattern generation, targeted illumination, and FOV movement are coordinated and cycled with high-speed mechatronic control to complete illumination on millions of ROI spots within hours. Once enough proteins are biotinylated in a cell or tissue sample, the sample is scraped and lysed, and avidin pulldown is used to enrich proteins to achieve spatial protein scooping at a 240-nm precision. Subsequent LC-MS/MS is implemented to reveal the subcellular proteome in high sensitivity, specificity, and resolution. Using this technology termed optoproteomics, we have revealed novel stress granule-localized and amyloid {beta}-localized proteins validated by immunostaining. Together, spatial purification by ultra-content, high-speed microscopy-targeted photo-biotinylation enables unprecedented subcellular spatial proteomics discovery in any microscopically recognizable regions.

cell biology↗

bioRxiv2023

Gel-Shrink Softlithography: Enabling 3D Tissue Culture Microstructure Miniaturization and Tacky Super-Soft Material Molding

In this study, we introduce an innovative hydrogel soft lithography technique that leverages the significant volume change of hydrogels during hydration. Through a systematic desiccation process applied to hydrogels containing microfeatures, we achieved a remarkable 2-fold reduction in feature dimensions. These shrunken hydrogel structures were then readily molded using standard soft lithography methods. Furthermore, we demonstrated the techniques utility in rectifying surface imperfections commonly found in 3D printed structures, offering promising prospects in fields like tissue engineering. Additionally, our study discovered a unique capability of hydrated hydrogel molds in molding super-soft, tacky elastomeric materials, exemplified by CY25-276 and low cross-linker ratio PDMS. This development opens doors to studying cellular forces through traction force microscopy to a broader spectrum of 3D structural contexts. In support of our efforts in microfabrication advancement, we explored multicellular responses to surface curvatures of diminishing dimensions. Our findings reveal a curvature-dependent alignment pattern: cells residing on convex surfaces align with the direction of least curvature, while those in concave regions align with the direction of the strongest curvature. These results underscore the critical influence of geometric complexity in biological systems and highlight the need for continuously improving methods to replicate geometric qualities relevant to these environments.

bioengineering↗

bioRxiv2022

Surface curvature and basal hydraulic stress induce spatial bias in cell extrusion

Epithelial cell extrusion is employed in maintaining a healthy epithelium. It remains unclear how environmental conditions specific to various epithelial tissues, such as geometry and fluid osmolarity, affect cell extrusions. We found that, over curved surfaces, epithelial monolayers exhibited higher extrusion rates in concave regions than convex ones. This difference, and overall extrusions, decreased when osmotically induced basal hydraulic stress was reduced by increasing media osmolarity or by culturing monolayers on hydrogels. Mechanistically, basal fluid accumulation antagonized cell-substrate adhesions and the subsequent FAK-Akt survival pathway, leading to apoptotic cell death. Convex surfaces induced cellular forces that acted against osmosis, thereby promoting adhesions and lowering apoptosis. This effect was reversed in concave regions, and together, resulted in a curvature induced spatial bias in cell extrusions.

cell biology↗

bioRxiv2020

Evaluating institutional open access performance: Methodology, challenges and assessment

Open Access to research outputs is becoming rapidly more important to the global research community and society. Changes are driven by funder mandates, institutional policy, grass-roots advocacy and culture change. It has been challenging to provide a robust, transparent and updateable analysis of progress towards open access that can inform these interventions, particularly at the institutional level. Here we propose a minimum reporting standard and present a large-scale analysis of open access progress across 1,207 institutions world-wide that shows substantial progress being made. The analysis detects responses that coincide with policy and funding interventions. Among the striking results are the high performance of Latin American and African universities, particularly for gold open access, whereas overall open access levels in Europe and North America are driven by repository-mediated access. We present a top-100 of global universities with the worlds leading institutions achieving around 80% open access for 2017 publications.

scientific communication and education↗

bioRxiv2020

Evaluating institutional open access performance: Sensitivity analysis

In the article “Evaluating institutional open access performance: Methodology, challenges and assessment” we develop the first comprehensive and reproducible workflow that integrates multiple bibliographic data sources for evaluating institutional open access (OA) performance. The major data sources include Web of Science, Scopus, Microsoft Academic, and Unpaywall. However, each of these databases continues to update, both actively and retrospectively. This implies the results produced by the proposed process are potentially sensitive to both the choice of data source and the versions of them used. In addition, there remain the issue relating to selection bias in sample size and margin of error. The current work shows that the levels of sensitivity relating to the above issues can be significant at the institutional level. Hence, the transparency and clear documentation of the choices made on data sources (and their versions) and cut-off boundaries are vital for reproducibility and verifiability.View Full Text

scientific communication and education↗

bioRxiv2019

Comparison of bibliographic data sources: Implications for the robustness of university rankings

Universities are increasingly evaluated, both internally and externally on the basis of their outputs. Often these are converted to simple, and frequently contested, rankings based on quantitative analysis of those outputs. These rankings can have substantial implications for student and staff recruitment, research income and perceived prestige of a university. Both internal and external analyses usually rely on a single data source to define the set of outputs assigned to a specific university. Although some differences between such databases are documented, few studies have explored them at the institutional scale and examined the implications of these differences for the metrics and rankings that are derived from them. We address this gap by performing detailed bibliographic comparisons between three key databases: Web of Science (WoS), Scopus and, the recently relaunched Microsoft Academic (MSA). We analyse the differences between outputs with DOIs identified from each source for a sample of 155 universities and supplement this with a detailed manual analysis of the differences for fifteen universities. We find significant differences between the sources at the university level. Sources differ in the publication year of specific objects, the completeness of metadata, as well as in their coverage of disciplines, outlets, and publication type. We construct two simple rankings based on citation counts and open access status of the outputs for these universities and show dramatic changes in position based on the choice of bibliographic data sources. Those universities that experience the largest changes are frequently those from non-English speaking countries and those that are outside the top positions in international university rankings. Overall MSA has greater coverage than Scopus or WoS, but has less complete affiliation metadata. We suggest that robust evaluation measures need to consider the effect of choice of data sources and recommend an approach where data from multiple sources is integrated to provide a more robust dataset.

scientific communication and education↗