Publications by authors named "Eric Chuang"
Grey mullet (Mugil cephalus) aquaculture is economically vital due to the high value of its roe. However, it faces significant risks from disease outbreaks, particularly from Nocardia seriolae. Current reliance on antibiotics has drawbacks, highlighting the potential of probiotics as a promising alternative.
View Article and Find Full Text PDFCurrent genome-wide association studies (GWAS) for kidney function lack ancestral diversity, limiting the applicability to broader populations. The East-Asian population is especially under-represented, despite having the highest global burden of end-stage kidney disease. We conducted a meta-analysis of multiple GWASs (n = 244,952) on estimated glomerular filtration rate and a replication dataset (n = 27,058) from Taiwan and Japan.
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- Current research is limited on how combined exposure to multiple pollutants affects epigenetics, specifically DNA methylation, in relation to cancer and chronic diseases.
- The study discovered numerous DNA methylation probes linked to exposure to heavy metals and PAHs, revealing potential early markers for health risks.
- Key findings included a correlation between hypomethylation of the AHRR gene and increased lung cancer risk, as well as significant interactions between specific SNPs and pollutant exposure, impacting disease progression.
The therapeutic efficacy of immunotherapy is limited in the majority of colorectal cancer patients due to the low mutational and neoantigen burdens in this immunogenically "cold" microsatellite stability-colorectal cancer (MSS-CRC) cohort. Here, we showed that DNA methyltransferase (DNMT) inhibition upregulated neoantigen-bearing gene expression in MSS-CRC, resulting in increased neoantigen presentation by MHC class I in tumor cells and leading to increased neoantigen-specific T-cell activation in combination with radiotherapy. The cytotoxicity of neoantigen-reactive T cells (NRTs) to DNMTi-treated cancer cells was highly cytotoxic, and these cells secreted high IFNγ levels targeting MSS-CRC cells after ex vivo expansion of NRTs with DNMTi-treated tumor antigens.
View Article and Find Full Text PDFNURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition.
IEEE/ACM Trans Comput Biol Bioinform
April 2024
Article Synopsis
- Dietary habits significantly influence the gut microbiota, which in turn can affect human health through metabolite production.
- Researchers have created an analytical platform called NURECON that predicts nutrient deficiencies by comparing an individual's gut microbiome data to a baseline from healthy subjects.
- NURECON combines advanced analytical tools and databases to identify nutrient gaps and offers personalized dietary recommendations, making it useful for dietitians and researchers.
Objective: To assess the efficacy of injecting various amounts of fluid into the shoulder joints for capsule distension in patients with adhesive capsulitis.
Design: A randomized controlled trial.
Setting: Outpatient clinic of a tertiary care centre.
Article Synopsis
- Recent advancements in next generation sequencing (NGS) technology have made studying bacterial genomes in the environment more affordable and effective, allowing for the identification of previously unknown microbiome species.
- An efficient NGS data analysis pipeline needs to combine various bioinformatics tools, which can be complex and resource-intensive, presenting challenges for biologists and clinicians.
- Twnbiome, a public gut microbiome database developed from healthy Taiwanese subjects, provides an interactive and user-friendly platform for microbiota research, enabling easy data analysis and customizable results for users without a bioinformatics background.
Article Synopsis
- Breast cancer shows significant genetic variation, with existing research primarily focused on Caucasian populations, prompting a study in a Taiwanese cohort to broaden understanding.
- A study analyzing 152,534 participants narrowed down to 2,496 cases and 9,984 controls conducted genome-wide association studies and polygenic risk score analyses encompassing four breast cancer subtypes.
- The findings revealed 113 SNPs linked to breast cancer risk, including 50 novel variants, with strong correlations found between polygenic risk scores and the likelihood of developing breast cancer, especially for the luminal A subtype.
Article Synopsis
- Changes in the oral microbiome are linked to oral squamous cell carcinoma (OSCC) recurrence, with specific microbial signatures identified as potential biomarkers for predicting recurrence.
- A study analyzed oral swab samples from OSCC patients and found significant differences in bacterial compositions between those with and without recurrence, highlighting certain microbes that were enriched in recurring cases.
- A prediction model using five microbial signatures showed high accuracy in distinguishing OSCC recurrence, performing better than traditional clinical indicators, thus suggesting a promising noninvasive approach for OSCC prognosis and treatment.
Article Synopsis
- Frailty is a common syndrome in older adults, linked to poor health outcomes and assessed using the Frailty Phenotype (FP) and Frailty Index (FI), but its biological mechanisms are still not well understood.
- Researchers analyzed genetic and health data from UK Biobank participants (aged 60-73), identifying significant genetic links to frailty, including notable associations with known genes related to aging and metabolism.
- The study utilized machine learning to create models that effectively distinguish between frail and non-frail individuals, achieving a high accuracy of 85%, highlighting the polygenic nature of frailty and its connections to cognitive function and cholesterol metabolism.
Article Synopsis
- Genotype imputation is important for understanding disease variants in Asian populations, which have been underrepresented in genetic studies compared to Caucasian populations.
- A new web platform called Multi-ethnic Imputation System (MI-System) has been developed to facilitate easy genotype imputation for East-Asians, providing multiple established pipelines and a unique reference panel for Taiwanese-Chinese ancestry.
- MI-System allows researchers to upload their data for imputation with minimal effort, contributing to faster research in Asian population genetics without needing extensive computational resources or bioinformatics expertise.
Aims: Atrial fibrillation (AF) is one of the major causes of ischaemic stroke. In addition to clinical risk evaluated by the CHA2DS2-VASC score, the impact of genetic factors on the risk of AF-related thromboembolic stroke has been largely unknown. We found several copy number variations (CNVs) in novel genes that were associated with thromboembolic stroke risk in our AF patients by genome-wide approach.
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- Analyzing 16S rRNA sequences helps researchers understand the types of bacteria present in different environments, especially using third-generation sequencing technology for full-length analysis.
- Major databases like RDP, SILVA, and Greengenes are commonly used for taxonomic classification of these sequences, but they have limitations in species-level resolution.
- To enhance accuracy, researchers manually curated these databases by removing sequences lacking species names and created an integrated database, which showed improved results for species-level taxonomy when tested with a mock community.
Article Synopsis
- Next generation sequencing data allows for the analysis of low-frequency and rare genetic variants, which are crucial for understanding complex diseases that can't be fully explained by common variants. CLIN_SKAT is an R package developed to address the challenges of analyzing this data efficiently.
- The package provides four user-friendly functions for obtaining clinically relevant variants, conducting gene-based association analyses, and visualizing results, making it easier to interpret findings.
- CLIN_SKAT includes pre-analysis steps and customizable features to enhance the clinical relevance of its results, and it's available for free on multiple operating systems for users to download and use in R.
Article Synopsis
- Hypoxia is a common condition in tumors that negatively impacts cancer progression, and long noncoding RNAs (lncRNAs) are gaining attention for their roles in cancer biology, specifically NDRG1-OT1 in breast cancer.
- The study found that NDRG1-OT1 is upregulated under hypoxia, regulated by HIF-1α, which binds to its promoter, thereby enhancing its expression.
- NDRG1-OT1 acts as a miRNA sponge for miR-875-3p, promoting tumor growth and migration while also producing a small peptide, highlighting its potential as a contributor to breast cancer malignancy.
Nicotinamide adenine dinucleotide (NAD) is an important coenzyme in various physiological processes, including sirtuins (SIRTs) and kynurenine pathway (KP). Previous studies have shown that lower NAD levels can be indicative of increased risks of cancer and psychiatric disorders. However, there has been no prior study exploring the link between NAD homeostasis and psychiatric disorders from a genetic perspective.
View Article and Find Full Text PDFMore than 40% of patients undergoing percutaneous nephrolithotomy (PCNL) are left with residual stone fragments and often require secondary procedures. Portable CT (PCT) technology allows surgeons to obtain intraoperative cross-sectional imaging, identify and extract residual stones immediately, and thereby reduce the need for subsequent procedures. This prospective trial evaluates how incorporation of PCT during PCNL affects perioperative outcomes.
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- The study investigates the gut microbiota of healthy Taiwanese individuals and compares it to that of chronic kidney disease (CKD) patients on different dialysis treatments to understand how kidney disease affects gut health.
- Researchers analyzed fecal samples using advanced sequencing methods to identify bacterial species and their relationships with certain demographic factors like age and gender.
- Results showed significant differences in gut microbiome composition between healthy individuals and dialysis patients, with specific bacteria linked to CKD complications, highlighting the potential of gut microbiota as a therapeutic target in managing non-communicable diseases.
Article Synopsis
- Taxonomic assignment is crucial for analyzing bacterial 16S rRNA, but focusing only on specific regions limits the ability to distinguish species, prompting the need for full-length sequence analysis with new sequencing technologies.
- This study compares the accuracy of seven different 16S sequence classifiers, using various training datasets to determine which ones perform best for taxonomic classification.
- Results showed that SINTAX and SPINGO, when trained with RDP sequences, achieved the highest accuracy, indicating that the choice of training dataset significantly impacts classifier performance.
Article Synopsis
- This study investigates the link between gut microbiome changes and acute myocardial infarction (AMI) by analyzing fecal samples from 44 subjects (19 with AMI and 25 controls).
- Findings show that certain bacteria were more abundant in AMI patients, while Selenomonadales were less so, suggesting significant microbiome differences associated with AMI.
- The research indicates a potential new avenue for preventing and treating AMI by focusing on the role of specific gut bacteria and seleno-compounds.
(1) Background: The role of using artificial intelligence (AI) with electrocardiograms (ECGs) for the diagnosis of significant coronary artery disease (CAD) is unknown. We first tested the hypothesis that using AI to read ECG could identify significant CAD and determine which vessel was obstructed. (2) Methods: We collected ECG data from a multi-center retrospective cohort with patients of significant CAD documented by invasive coronary angiography and control patients in Taiwan from 1 January 2018 to 31 December 2020.
View Article and Find Full Text PDFBackground/purpose: Previously we had identified concurrent genes, which highlighted the interplay between copy number variation (CNV) and differential gene expression (GE) for Han Chinese breast cancers. The merit of the approach is to discovery biomarkers not identifiable by conventional GE only data, for which phenotype-correlation or gene variability is the criteria of gene selection.
Materials And Methods: Thirty-one comparative genomic hybridization (CGH) and 83 GE microarrays were performed, with 29 breast cancers assayed from both platforms.
Lidocaine and Bupivacaine Downregulate MYB and lncRNA by Upregulating in MCF-7 Cells.
Front Med (Lausanne)
January 2022
Article Synopsis
- Breast cancer is a prevalent cancer in women and often requires surgery, with emerging evidence linking anaesthetic techniques to patient outcomes.
- The study explored how two local anaesthetics, lidocaine and bupivacaine, affect MCF-7 breast cancer cells, finding that they reduce cell proliferation and impact the expression of various microRNAs (miRNAs).
- The research identified a potential biomarker through next-generation sequencing and confirmed interactions between specific lncRNAs and miRNAs, suggesting that local anaesthetics may play a role in suppressing tumor growth via a particular molecular pathway.
Article Synopsis
- - The study investigates Semaphorin 5A (SEMA5A), which was found to act as a tumor suppressor in lung cancer, specifically in nonsmoking women, by inhibiting cell proliferation and migration.
- - Researchers focused on evaluating different domains of SEMA5A to understand their roles in lung adenocarcinoma cell lines, observing that overexpression of the full-length protein and its extracellular domain effectively reduced growth and movement of lung cancer cells.
- - Microarray analysis revealed that SEMA5A influences the expression of genes related to the 'Interferon Signaling' pathway, which was confirmed through various validation methods, highlighting its importance in SEMA5A's tumor-suppressive effects. *