Biology subjects

Wuestefeld, T.

Publications and source records attributed to Wuestefeld, T..

3 recordsLinked to original sources

bioRxiv2026

Gut microbial phenylalanine metabolism contributes to MASLD in a dietary protein-dependent manner

Metabolic dysfunction-associated steatotic liver disease (MASLD) affects nearly a third of adults worldwide, yet how diet shapes the microbiota's contribution remains unclear. In a diet-induced mouse model varying protein content independently of caloric intake, microbiota depletion ameliorated hepatic steatosis and liver injury under protein- sufficient but not protein-restricted conditions. Caecal and plasma metabolomics implicated microbial phenylalanine catabolism and its host conjugates phenylacetylglutamine (PAGln) and phenylacetylglycine (PAGly). PAGln supplementation exacerbated steatosis and liver injury without altering body weight, adiposity or glucose homeostasis. Individual-antibiotic perturbation with metagenomics linked bacterial phenylalanine catabolic capacity to disease severity, and in gnotobiotic mice, genetic disruption of bacterial phenylalanine-to-phenylacetic acid conversion lowered circulating conjugates and attenuated steatosis and fibrosis. In a human cohort, circulating PAGln was selectively elevated in cardiometabolic MASLD. These findings identify dietary protein availability as a modifier of the contribution of microbial phenylalanine metabolism to MASLD and highlight PAGln as a microbiota-derived metabolite that exacerbates hepatic disease.

microbiology↗

bioRxiv2025

Tirzepatide reduces diet-induced senescence and NETosis-mediated liver fibrosis in mice

Lipofuscin, a protein-lipid complex that progressively accumulates in senescent cells, was commonly observed in the liver biopsies from patients with liver fibrosis or cirrhosis regardless of the etiological insults. However, whether and how lipofuscin contributes to the development of liver fibrosis remains unknown. Using a mouse model of liver fibrosis induced by choline-deficient L-amino acid-defined high-fat diet (HFD), we found that lipofuscin accumulation preceded the emergence of liver fibrosis. A significant, positive and strong correlation was observed between the hepatic lipofuscin levels and liver fibrosis severity. Neutrophils were recruited to the liver in mice fed HFD, and those that were in close proximity to lipofuscin-laden hepatocytes displayed higher susceptibility to produce neutrophil extracellular traps (NETs). We revealed that lipofuscin-laden hepatocytes generated CXCL5, which promoted NETosis. When mice defective in NETosis (Vav1-Cre Padi4fl/fl) were fed HFD, they had significantly less collagen deposition in the liver, indicating the critical role of NETs in the development of liver fibrosis associated with lipofuscin accumulation. Notably, we showed that tirzepatide, the latest glucagon-like peptide-1 receptor and glucose-dependent insulinotropic polypeptide receptor dual agonist recently approved for type 2 diabetes, attenuated NETosis-dependent liver fibrosis by preventing hepatic lipofuscin accumulation, and reduced other hepatic senescence signatures as well. In summary, our study unveiled the pathogenic, NETosis-enhancing effect of lipofuscin in liver fibrosis, and demonstrated the potential of repurposing tirzepatide for combating liver fibrosis associated with lipofuscin and for preventing organ senescence.

molecular biology↗

bioRxiv2021

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing. To systematically evaluate the ability to study the transcriptome at a resolution of individual isoforms we profiled 5 human cell lines with short read cDNA sequencing and Nanopore long read direct RNA, amplification-free direct cDNA, PCR-cDNA sequencing. The long read protocols showed a high level of consistency, with amplification-free RNA and cDNA sequencing being most similar. While short and long reads generated comparable gene expression estimates, they differed substantially for individual isoforms. We find that increased read length improves read-to-transcript assignment, identifies interactions between alternative promoters and splicing, enables the discovery of novel transcripts from repetitive regions, facilitates the quantification of full-length fusion isoforms and enables the simultaneous profiling of m6A RNA modifications when RNA is sequenced directly. Our study demonstrates the advantage of long read RNA sequencing and provides a comprehensive resource that will enable the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.

genomics↗