Biology subjects

Wu, C.-J.

Publications and source records attributed to Wu, C.-J..

6 recordsLinked to original sources

bioRxiv2025

Phylogenetic Insights into Antifungal Susceptibility: Comparing Environmental and Clinical Scedosporium and Lomentospora Isolates from Taiwan

ObjectivesScedosporium and Lomentospora species are intrinsically resistant molds increasingly implicated in invasive infections with poor outcomes. Olorofim, a novel orotomide antifungal, has demonstrated potent activity against various molds. This study evaluated the antifungal susceptibility of clinical and environmental isolates, focusing on olorofim, and examined these data in a phylogenetic context. MethodsA total of 216 isolates (Scedosporium spp., n=205; L. prolificans, n=11) were collected from clinical and environmental sources across Taiwan. Species identification was confirmed by sequencing of the ITS and {beta}-tubulin regions, followed by maximum-likelihood phylogenetic analysis. Antifungal susceptibility was determined using CLSI M38-A3 method. Cross-resistance was evaluated using correlation analyses. Phylogenetic signal, Mantel tests, and variance partitioning were applied to assess the evolutionary structuring of minimum inhibitory concentrations (MICs). ResultsScedosporium apiospermum (46.3%) and S. boydii (15.7%) were the predominant species, exhibiting comparable triazole susceptibility profiles (MIC90: voriconazole 1-2 mg/L, posaconazole 4 mg/L, and isavuconazole 8 mg/L). L. prolificans displayed pan-resistance to all agents except olorofim. Among triazoles, voriconazole yielded the lowest MICs for most Scedosporium isolates. Olorofim exhibited the lowest MICs across Scedosporium spp. and L. prolificans (all MIC90 [≤]0.12 mg/L). Rare taxa (S. marinum, S. haikouense, S. multisporum, S. minutisporum, S. sp. nov.1) were also identified, exhibiting variable triazole MICs but consistently low olorofim MICs. The association between antifungal susceptibility and species relatedness varied by drug: moderate for posaconazole, amphotericin B, and voriconazole; intermediate for olorofim; weak for isavuconazole; and absent for itraconazole. Most MIC variability (72.5-89.2%) occurred within rather than between species. ConclusionsAntifungal susceptibility among Scedosporium spp. and L. prolificans was drug dependent. Olorofim demonstrated consistently low MICs across species, whereas amphotericin B and triazoles showed variable, species-specific activity. These findings highlight olorofim as a promising therapeutic option and emphasize the need for target gene-based investigations to elucidate the evolutionary basis of antifungal resistance.

microbiology↗

bioRxiv2025

High-Resolution Characterization of rAAV Genomes for Vector Quality Using Long-Read Sequencing

Recombinant adeno-associated virus (rAAV)-mediated gene therapy has been applied for human diseases. However, the rAAV capsids contain heterogeneous mixtures of full-length and truncated genomes and, depending on the manufacturing process, residual host cell and plasmid DNA. Therefore, a method is needed to characterize the encapsidated DNA of rAAV in order to support process development and batch release. The emerging long-read sequencing (LRS) has achieved AAV single-genome resolution. Here we propose a Python-based LRS profiling framework to classify and quantitate residual DNA species in rAAV products. We designed a reference that contains universal genetic components that are commonly used in rAAV production, including AmpR, KanR, Rep and Cap genes along with HPV18, Ad5 and hg38 genomes. We accessed the impurities of rAAV production from public and in-house LRS datasets. Analyzing the lambda fragments supplemented in these datasets showed that sequencing introduced size biases, which couldnt be fully corrected by regression but is improvable within library preparation. Functional potential of impurities were assessed through indicators derived from long-read alignments, which enabled us to quantitatively compare impurities between manufacturing batches. We demonstrated that LRS provides informative metrics for rAAV production and can facilitate process development to ensure therapeutic product safety and quality.

genomics↗

bioRxiv2024

Inter- and intra-tumor heterogeneous immune presentation in primary uterine carcinosarcoma determined by digital spatial profiling

Uterine carcinosarcoma (UCS) is a rare gynecologic cancer with unfavorable prognosis. Its biphasic histologic components are known to associated with outcomes. Dissecting the tumor heterogeneity within UCS is crucial to discover molecular biomarkers for patient stratification. The aim of this study was to utilize spatial profiling technology to analyze immune presentation in different histological components within UCS tumors. The study included 23 UCS patients whose tumor sections were subjected to nanoString GeoMx Digital Spatial Profiling (DSP) to profile 30 immune-related proteins in 491 segments. We identified distinct cluster-labeled subtypes showing varied immune marker expressions. The immune presentations within the carcinoma and sarcoma components showed significant differences. Markers indicating M2 macrophages (CD45+CD163+) and epithelial-mesenchymal transition (EMT) (SMA, fibronectin) were highly expressed in the sarcoma components. The immune presentation subtypes within each histological component also differed between patients with recurrence in 5 years and without recurrence over 5 years. The cluster-labeled subtype with high Neutrophil/PMN-MDSC marker expression (CD66b) was associated with longer survival, whereas the subtype with high NK cell marker expressions (CD56) was linked to poor prognosis. Our result suggested that immune features within the carcinoma component of UCS tumors would determine patient outcomes and should be considered as a strategy for patient stratification.

immunology↗

bioRxiv2023

Selective IL-27 production by intestinal regulatory T cells permits gut-specific regulation of Th17 immunity

Regulatory T (Treg) cells are instrumental in establishing immunological tolerance. However, the precise effector mechanisms by which Treg cells control a specific type of immune response in a given tissue remains unresolved. By simultaneously studying Treg cells from different tissue origins under systemic autoimmunity, here we show that IL-27 is specifically produced by intestinal Treg cells to regulate Th17 immunity. Selectively increased intestinal Th17 responses in mice with Treg cell-specific IL-27 ablation led to exacerbated intestinal inflammation and colitis-associated cancer, but also helped protect against enteric bacterial infection. Furthermore, single-cell transcriptomic analysis has identified a CD83+TCF1+ Treg cell subset that is distinct from previously characterized intestinal Treg cell populations as the main IL-27 producers. Collectively, our study uncovers a novel Treg cell suppression mechanism crucial for controlling a specific type of immune response in a particular tissue, and provides further mechanistic insights into tissue-specific Treg cell-mediated immune regulation.

immunology↗

bioRxiv2019

Bivalent and Broad Chromatin Domains Regulate Pro-metastatic Drivers in Melanoma

Chromatin deregulation is an emerging hallmark of cancer. However, the extent of epigenetic aberrations during tumorigenesis and their relationship with genetic aberrations are poorly understood. Using ChIP-sequencing for enhancers (H3K27ac and H3K4me1), promoters (H3K4me3), active transcription (H3K79me2) and polycomb (H3K27me3) or heterochromatin (H3K9me3) repression we generated chromatin state profiles in metastatic melanoma using 46 tumor samples and cell lines. We identified a strong association of NRAS, but not BRAF mutations, with bivalent states harboring H3K4me3 and H3K27me3 marks. Importantly, the loss and gain of bivalent states occurred on important pro-metastasis regulators including master transcription factor drivers of mesenchymal phenotype including ZEB1, TWIST1, SNAI1 and CDH1. Unexpectedly, a subset of these and additional pro-metastatic drivers (e.g. POU3F2, SOX9 and PDGFRA) as well as melanocyte-specific master regulators (e.g. MITF, ZEB2, and TFAP2A) were regulated by exceptionally wide H3K4me3 domains that can span tens of thousands of kilobases suggesting roles of this new epigenetic element in melanoma metastasis. Overall, we find that BRAF, NRAS and WT melanomas may use bivalent states and broad H3K4me3 domains in a specific manner to regulate pro-metastatic drivers. We propose that specific epigenetic traits - such as bivalent and broad domains - get assimilated in the epigenome of pro-metastatic clones to drive evolution of cancer cells to metastasis.

cancer biology↗

bioRxiv2019

Bone regeneration in Ds-Red pig calvarial defect using allogenic transplantation of EGFP-pMSCs - a comparison of host cells and seeding cells in the scaffold

BackgroundCells, scaffolds, and factors are the triad of regenerative engineering; however, it is difficult to distinguish whether cells in the regenerative construct are from the seeded cells or host cells via the host blood supply. We performed a novel in vivo study to transplant enhanced green fluorescent pig mesenchymal stem cells (EGFP-pMSCs) into calvarial defect of DsRed pigs. The cell distribution and proportion were distinguished by the different fluorescent colors through the whole regenerative period.\n\nMethod/ResultsEight adult domestic Ds-Red pigs were treated with five modalities: empty defects without scaffold (group 1); defects [fi]lled only with scaffold (group 2); defects [fi]lled with osteoinduction medium-loaded scaffold (group 3); defects filled with 5 x 103 cells/scaffold (group 4); and defects filled with 5 x 104 cells/scaffold (group 5). The in vitro cell distribution, morphology, osteogenic differentiation, and [fl]uorescence images of groups 4 and 5 were analyzed. Two animals were sacri[fi]ced at 1, 2, 3, and 4 weeks after transplantation. The in vivo [fl]uorescence imaging and quantification data showed that EGFP-pMSCs were represented in the scaffolds in groups 4 and 5 throughout the whole regenerative period. A higher seeded cell density resulted in more sustained seeded cells in bone regeneration compared to a lower seeded cell density. Host cells were recruited by seeded cells if enough space was available in the scaffold. Host cells in groups 1 to 3 did not change from the 1st week to 4th week, which indicates that the scaffold without seeded cells cannot recruit host cells even when enough space is available for cell ingrowth. The histological and immunohistochemical data showed that more cells were involved in osteogenesis in scaffolds with seeded cells.\n\nConclusionOur in vivo results showed that more seeded cells recruit more host cells and that both cell types participate in osteogenesis. These results suggest that scaffolds without seeded cells may not be effective in bone transplantation.

cell biology↗