Biology subjects

Wu, M.-S.

Publications and source records attributed to Wu, M.-S..

4 recordsLinked to original sources

bioRxiv2026

Integrated Proteo-Metabolomics of Urinary Extracellular Vesicles Reveals Early Molecular Divergence and Temporal Pathogenesis of Sepsis-Associated AKI

BackgroundSepsis-associated acute kidney injury (S-AKI) is a major contributor to morbidity and mortality in critically ill patients. However, the molecular mechanisms underlying its temporal progression remain poorly understood because conventional biomarkers primarily reflect renal dysfunction rather than disease pathogenesis. Urinary extracellular vesicles (uEVs), which carry kidney-derived molecular cargo, provide a promising platform for monitoring renal-specific biological alterations during disease progression. MethodsWe conducted a longitudinal multi-omics study of uEVs collected from 81 patients with sepsis, including 48 patients with S-AKI and 33 sepsis-only controls. Patients were randomly assigned to a discovery cohort (n = 52) and an independent validation cohort (n = 29). Urine samples were collected at Day 1, Day 4, and Day 8 after AKI diagnosis. High-resolution proteomic and metabolomic profiling was performed to characterize temporal molecular alterations. Enriched pathways identified in the discovery cohort were evaluated in the validation cohort using pathway-level concordance analysis. ResultsComparative analysis between S-AKI and sepsis-only patients identified distinct stage-specific molecular alterations throughout disease progression. At the early stage (Day 1), validated pathways included complement and coagulation cascades, ferroptosis, HIF-1 signaling, sphingolipid metabolism, and arachidonic acid metabolism, highlighting coordinated inflammatory, hypoxic, and lipid metabolic responses. During the mid-stage (Day 4), persistent activation of complement and coagulation cascades, ferroptosis, and HIF-1 signaling was accompanied by metabolic reprogramming involving alanine, aspartate and glutamate metabolism and tyrosine metabolism. Although limited sample availability reduced statistical power at Day 8, phenylalanine metabolism remained validated in the metabolomic analysis, suggesting persistent metabolic dysregulation during late-stage disease progression. ConclusionsThis study provides the first longitudinal, independently validated multi-omics characterization of human uEVs in S-AKI. By integrating proteomic and metabolomic profiling, we reveal the temporal evolution of renal-specific molecular pathways from early inflammatory and hypoxic responses to subsequent metabolic reprogramming. These findings establish uEV-based multi-omics as a promising strategy for molecular phenotyping of S-AKI beyond conventional clinical biomarkers and provide a valuable resource for future biomarker discovery and therapeutic target identification.

biochemistry↗

bioRxiv2021

Dietary Exposure to Antibiotic Residues Facilitates Metabolic Disorder by Altering the Gut Microbiota and Bile Acid Composition

Antibiotics used as growth promoters in livestock and animal husbandry can be detected in animal-derived food. Epidemiological studies have implicated that exposure to these antibiotic residues in food may be associated to childhood obesity. Herein, the effect of exposure to residual dose of tylosin--an antibiotic growth promoter--on host metabolism and gut microbiota was explored in vivo. Theoretical maximal daily intake (TMDI) doses of tylosin were found to facilitate high-fat diet-induced obesity, induce insulin resistance, and perturb the composition of gut microbiota in mice. The obesity-related phenotypes were transferrable to germ-free recipient mice, indicating that the effects of TMDI dose of tylosin on obesity and insulin resistance occurred mainly via alteration of the gut microbiota. Tylosin TMDI exposure restricted to early life, which is the critical period of gut microbiota development, altered the abundance of specific bacteria related to host metabolic homeostasis later in life. Moreover, early-life exposure to tylosin TMDI was sufficient to modify the ratio of primary to secondary bile acids, thereby inducing lasting metabolic consequences via the downstream FGF15 signaling pathway. Altogether, these findings demonstrate that exposure to very low dose of antibiotic residues, whether continuously or in early life, can exert long-lasting effects on host metabolism by altering gut microbiota and its metabolites. ImportanceEvidence has indicated that chronic exposure to antibiotic residues in food could contribute to obesity. However, few studies have investigated the effect of chronic exposure to very low-dose antibiotic residue in food (~1000-fold lower than the therapeutic dose) on gut microbiota and host metabolism. Our study demonstrates that even with limited exposure in early life, a residual dose of tylosin causes lasting metabolic disturbances through altering gut microbiota and its metabolites. Our findings reveal that the gut microbiota is susceptible to previously ignored environmental factors.

microbiology↗

bioRxiv2020

Evaluation of Compatibility of 16S rRNA V3V4 and V4 Amplicon Libraries for Clinical Microbiome Profiling

Sequencing of the 16S rRNA gene by Illumina next-generation sequencing is broadly used in microbiome studies. Different hypervariable regions of the 16S rRNA gene, V3V4 (amplified with primers 341F-805R) or V4 (V4O; primers 515F-806R), are selected, depending on the targeted resolution. However, in population-based clinical studies, combining V3V4 and V4 data from different studies for a meta-analysis is challenging. Reads generated by short-read (150-bp) high-throughput sequencing platforms do not fully recover the V4 region read-length. Here, we evaluated the compatibility of 16S rRNA V3V4 and V4 amplicons for microbiome profiling. We compared taxonomic compositions obtained by the analysis of V3V4 and V4 amplicons, and V4 fragments trimmed from V3V4 amplicons. We also evaluated an alternative V4 region (V4N; primers 519F-798R) designed for efficient stitching with 150-bp paired-end sequencing. First, we simulated a global investigation of environmental prokaryotes in silico. This revealed that V4O primers recovered the highest proportion of fragments (81.7%) and most phyla, including archaea. Empirical sequencing of standard (mock) and human fecal samples revealed biased patterns of each primer that were similar to the ones determined by in silico simulation. Further, for human fecal microbiome profiling, the between-sample variance was greater than the systematic bias of each primer. The use of trimmed V4 fragments and single-end amplicons resulted in the same systematic bias. In conclusion, paired-end V4O sequencing yielded the most accurate data for both, simulation and mock community sequencing; the V4O amplicons were compatible with trimmed V4 sequences for microbiome profiling. IMPORTANCENext-generation sequencing of the 16S rRNA gene is a commonly used approach for clinical microbiome studies. Different amplicons of the 16S rRNA hypervariable regions are used in different studies, which creates incompatible sequence features when comparing and integrating data among studies by using 16S denoising pipelines. Here we compared the type of data and coverage obtained when different 16S rRNA amplicons were analyzed. In silico and empirical analyses of the human fecal microbiome revealed that the V3V4 amplicons are compatible with V4 amplicons after trimming up to the same region. These observations demonstrate that reconciling the compatibility of clinical microbiome data from different studies improve not only the sample size but also the confidence of the hypothesis tested.

microbiology↗

bioRxiv2018

Nifedipine Modulated Renal Lipogenesis via AMPK-SREBP Transcriptional Pathways

Lipid accumulation in renal cells has been implicated in the pathogenesis of obesity-related kidney disease, and lipotoxicity occurring in the kidney can be a surrogate marker for renal failure or renal fibrosis. Nifedipine-induced renal lipotoxicity has never been cited, although a few studies have shown that nifedipine inhibits lipogenesis via activation of the LKB1-AMPK pathway. Therefore, we utilized NRK52E cell models to examine this further. We pre-treated cells with varying concentrations of nifedipine (7.5, 15, or 30 M) for 24 or 48 h prior to examining the activity of lipogenesis enzymes and lipotoxicity.\n\nNifedipine was found to activate acetyl CoA synthetase, acetyl CoA carboxylase, long chain fatty acyl CoA elongase, ATP-citrate lyase, and HMG CoA reductase, suggesting elevated production of cholesterol, triacylglycerides, and phospholipids. Nifedipine exposure induced a vast accumulation of cytosolic free fatty acids (FFA) and stimulated the production of reactive oxygen species, upregulated CD36 and KIM-1 (kidney injury molecule-1) expression, inhibited p-AMPK activity, and triggered the transcription of SREBP-1/2 and lipin-1, underscoring the potential of nifedipine to induce lipotoxicity with renal damage.\n\nIn the present study, we elucidated the mechanism of action of nifedipine that leads to renal lipotoxicity via the AMPK-SREBP-1/2 pathway. To our knowledge, this is the first report demonstrating nifedipine-induced lipid accumulation in the kidney.

biochemistry↗