Biology subjects

Schmeck, B.

Publications and source records attributed to Schmeck, B..

8 recordsLinked to original sources

bioRxiv2026

First Genome-Scale Metabolic Model for Understanding HMPV-Host Interaction

BackgroundHuman Metapneumovirus (HMPV) is a major contributor to acute respiratory tract infections. Currently, no approved vaccines or specific antiviral therapies are available worldwide. Genome-scale metabolic models (GEMs), when integrated with Viral Biomass Objective Functions (VBOFs), provide a robust computational framework for identifying host metabolic dependencies essential for viral replication. This approach enables systematic prioritization of potential antiviral drug targets. ResultsThe first comprehensive VBOF for HMPV was constructed by integrating stoichiometric data from the viral genome, including structural proteins with defined copy numbers, amino acid residues per virion, envelope lipids, and glycan modifications. The reconstructed VBOF was incorporated into the human bronchial epithelial cell model, iHBEC1, to analyze metabolic changes between uninfected and infected host cells. Knockout analysis identified two selective antiviral gene targets: PGM3 (phosphoacetylglucosamine mutase) and GNPNAT1 (N-acetylglucosamine-6-phosphate acetyltransferase), as well as seven selective reaction targets primarily within the hexosamine biosynthesis and nucleotide sugar pathways. Knockout of PGM3 or GNPNAT1 completely abolished viral production while preserving complete host cell viability. Additionally, guanylate kinase (GUK1/GK1) emerged as a highly selective target for HMPV, confirming findings from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) studies and suggesting a conserved vulnerability across respiratory viruses. ConclusionsUDP-GlcNAc, the vital end-product of the hexosamine biosynthesis pathway (HBP), is computationally predicted as a critical metabolic hub. This pathway represents the primary metabolic vulnerability of HMPV, due to the extensive glycosylation requirements of the HMPV attachment protein. The host-directed antiviral targets PGM3 and GNPNAT1 are high-priority candidates for experimental validation and may provide novel strategies to combat this respiratory infection.

Systems Biology↗

bioRxiv2026

Lifespan Analysis of the Lung Epithelium Reveals Inflammatory Reprogramming and Regenerative Decline

Aging is a major risk factor for chronic lung diseases, associated with chronic low-grade inflammation (inflammaging) and impaired epithelial regeneration. How epithelial-intrinsic aging intersects with inflammaging across the lifespan remains poorly understood. Here, we systematically analyzed lung epithelial cells from neonatal, young adult, and aged mice to define age-dependent changes in regenerative capacity. RNA sequencing revealed lifespan-associated shifts characterized by early repression of developmental and WNT/{beta}-catenin programs and progressive activation of DNA damage, inflammation, and senescence signatures. Functionally, neonatal epithelial cells exhibited markedly enhanced organoid-forming capacity compared with young and aged cells. Aged organoids maintained a pro-inflammatory secretory profile indicative of cell-intrinsic inflammaging, and transfer of the aged secretome or TNF- to young cultures significantly impaired regeneration. Comparison of freshly isolated cells and long-term organoid cultures revealed sustained repression of regenerative pathways with age, consistent with stable epigenetic imprinting. Pharmacological inhibition of DNA methylation and WNT signalling partially restored regenerative capacity in adult organoids. Together, these findings identify epigenetic reprogramming and epithelial-intrinsic inflammaging as key determinants of age-dependent regenerative decline.

cell biology↗

bioRxiv2025

Ketone and glycolytic metabolism are key modulators of inflammation during neonatal sepsis

Neonatal sepsis is a life-threatening condition in preterm infants, primarily due to a dysregulated immunometabolic response to infection. Sepsis and infection mortality are associated with excessive glycolysis-induced inflammation, impaired mitochondrial oxidative phosphorylation (OXPHOS) and loss of disease tolerance. Reduced glucose intake can reverse these dysregulations, but it is unclear how the mechanistic control of glycolysis-OXPHOS balance drives defense strategies and infection outcomes. Here, in a preterm piglet model of neonatal sepsis, glycolysis inhibition with 2-deoxyglucose (2-DG) completely prevents acute infection mortality, reduces systemic inflammation and markers of liver injury, accompanied by enhanced mitochondrial metabolism and disease tolerance. Strikingly, this protection by 2-DG is conferred despite elevated blood glucose levels and higher bacterial burdens than the infected controls. Alternatively, partial replacement of glucose intake with the ketone beta-hydroxybutyrate (BHB) abolishes sepsis-related mortality via improving disease tolerance and clinical parameters. This intervention also shifts the hepatic transcriptome away from inflammatory signaling and towards mitochondrial metabolism. In macrophages in vitro, BHB also exerts anti-inflammatory effects independently of metabolic modulation via the HCAR2 receptor. Finally, data from a cohort of 700 infants confirm an association of plasma BHB levels and anti-inflammatory state. These findings demonstrate that metabolic reprogramming through glycolysis inhibition or ketone supplementation is a promising therapeutic strategy to enhance disease tolerance and improve sepsis outcomes in neonates.

immunology↗

bioRxiv2025

Engineering site-specific nucleic acid-protein conjugates by utilizing a natural RNAylation reaction

Nucleic acid-protein conjugates are valuable for synthetic biology, therapeutics, and nanotechnology, but current methods often lack site specificity and rely on non-natural linkages. RNAylation, a one-step enzymatic reaction catalyzed by the bacteriophage T4 enzyme ModB where first discovered in vivo during phage infection, enables site-specific conjugation of nucleic acids to proteins via a natural N-glycosidic bond. Here, we establish RNAylation as a novel and robust in vitro platform for generating nucleic acid-protein conjugates, overcoming key limitations of existing strategies. We define design principles for this approach, demonstrate enhanced nucleic acid stability in human cell lysates, and develop an efficient purification workflow. Furthermore, we achieve successful delivery of purified conjugates into human cells, highlighting the potential for functional in vivo applications. Our work expands RNAylation from a phage-specific phenomenon to a versatile, biologically relevant strategy with broad biotechnological potential.

bioengineering↗

bioRxiv2025

Raman spectroscopy reveals growth phase-dependent molecular differences in bacterial membrane vesicles

Bacterial membrane vesicles (BMVs) have attracted significant attention as highly efficient transport vehicles for molecules crossing biological barriers and as key mediators in infection processes. As interest in BMVs increases, the need for standardized isolation protocols and comprehensive analytical approaches becomes apparent. This study introduces Raman spectroscopy as a novel, chemically selective monitoring approach for the analysis of subtle biochemical changes in BMVs across different bacterial growth phases. BMVs derived from Pseudomonas aeruginosa, a Gram-negative human pathogen responsible for severe nosocomial infections, were isolated at six different time points and analyzed via established physicochemical and functional assays, as well as Raman spectroscopy. While established analytics revealed growth phase-dependent variations in protein content, surface charge, and immunogenic effects on human immune cells, Raman spectroscopy enabled the comprehensive analysis of molecular-level changes between isolation time points. Significant shifts in protein-to-lipid ratios, higher lipid saturation, and changes in protein secondary structure were detected in BMVs isolated from later growth phases. Further, the absence of spectral markers for nucleic acids enabled the identification of BMVs as outer membrane vesicles. These findings emphasize the critical influence of the isolation time point on BMV properties and highlight Raman spectroscopy as a powerful tool for semi-quantitative chemical profiling, revealing minuscule yet biologically significant changes in BMVs depending on isolation time points.

cell biology↗

bioRxiv2023

NAD+ metabolism is a key modulator of bacterial respiratory epithelial infections

1.Lower respiratory tract infections caused by StreptococcusOpneumoniae (Spn) are a leading cause of death globally. Here we investigate the bronchial epithelial response to Spn infection on a transcriptomic, proteomic and metabolic level. We found the NAD+ salvage pathway to be dysregulated upon infection in a cell line model, primary human lung tissue and in vivo in rodents, leading to a reduced production of NAD+. Knockdown of NAD+ salvage enzymes (NAMPT, NMNAT1) increased bacterial replication. NAD+ treatment of Spn inhibited its growth while growth of other respiratory pathogens improved. Boosting NAD+ production increased NAD+ levels in immortalized and primary cells and decreased bacterial replication upon infection. NAD+ treatment of Spn dysregulated the bacterial metabolism and reduced intrabacterial ATP. Enhancing the bacterial ATP metabolism abolished the antibacterial effect of NAD+. Thus, we identified the NAD+ salvage pathway as an antibacterial cascade in Spn infections, predicting a novel antibacterial mechanism of NAD+.

immunology↗

bioRxiv2022

Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides

Bioactive peptides are key molecules in health and medicine. Deep learning holds a big promise for the discovery and design of bioactive peptides. Yet, suitable experimental approaches are required to validate candidates in high throughput and at low cost. Here, we established a cell- free protein synthesis (CFPS) pipeline for the rapid and inexpensive production of antimicrobial peptides (AMPs) directly from DNA templates. To validate our platform, we used deep learning to design thousands of AMPs de novo. Using computational methods, we prioritized 500 candidates that we produced and screened with our CFPS pipeline. We identified 30 functional AMPs, which we characterized further through molecular dynamics simulations, antimicrobial activity and toxicity. Notably, six de novo-AMPs feature broad-spectrum activity against multidrug-resistant pathogens and do not develop bacterial resistance. Our work demonstrates the potential of CFPS for production and testing of bioactive peptides within less than 24 hours and <10$ per screen.

synthetic biology↗

bioRxiv2021

Single cell RNA-seq uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19

The systemic immune response to viral infection is shaped by master transcription factors such as NF{kappa}B or PU.1. Although long non-coding RNAs (lncRNAs) have been suggested as important regulators of transcription factor activity, their contributions to the systemic immunopathologies observed during SARS-CoV-2 infection have remained unknown. Here, we employed a targeted single-cell RNA-seq approach to reveal lncRNAs differentially expressed in blood leukocytes during severe COVID-19. Our results uncover the lncRNA PIRAT as a major PU.1 feedback-regulator in monocytes, governing the production of the alarmins S100A8/A9 - key drivers of COVID-19 pathogenesis. Knockout and transgene expression, combined with chromatin-occupancy profiling characterized PIRAT as a nuclear decoy RNA, diverting the PU.1 transcription factor from alarmin promoters to dead-end pseudogenes in naive monocytes. NF{kappa}B-dependent PIRAT down-regulation during COVID-19 consequently releases a transcriptional brake, fueling alarmin production. Our results suggest a major role of nuclear noncoding RNA circuits in systemic antiviral responses to SARS-CoV-2 in humans.

immunology↗