Search bioRxiv⌕ Search

Biology subjects

Wolters, J.

Publications and source records attributed to Wolters, J..

3 recordsLinked to original sources

cGAS-STING drives alveolar epithelial cell dysfunction in cigarette smoke-induced lung injury

Chronic inflammation induced by cigarette smoke (CS) plays a central role in the pathogenesis of chronic obstructive pulmonary disease (COPD), but its impact on lung epithelial progenitor function and regenerative capacity remains incompletely understood. Here, we combined in vivo and in vitro approaches to dissect how CS exposure and subsequent inflammatory insults shape epithelial repair dynamics. A 6-week whole-body CS exposure model in mice induced lung function impairment and altered gene expression profiles in alveolar epithelial cells, prominently activating interferon (IFN)-related pathways and the cGAS-STING axis. Alveolar epithelial cells from CS-exposed mice generated a similar number, but larger organoids with reduced alveolar differentiation compared to air-exposed mice. Notably, these cells obtained from CS-exposed mice displayed resistance to IFN{gamma}-induced suppression of organoid growth, contrasting with the strong inhibitory effect of IFN{gamma} observed in controls. This phenotype was recapitulated in a two-hit in vitro model using cigarette smoke extract (CSE), in which chronic CSE exposure impaired regeneration and differentiation while inducing resistance to IFN{gamma}. Gene expression and proteomic analyses revealed upregulation of Zbp1, Irf7, and other upstream IFN regulators, correlating negatively with alveolar differentiation potential. Inhibition of the cGAS-STING pathway with RU.521 partially rescued organoid formation, increased proliferation, and alveolar differentiation. Together, our data reveal that CS exposure alters the alveolar epithelial landscape, inducing a stress-adapted, IFN{gamma}-resistant state that compromises alveolar regeneration, with cGAS-STING activation as a key driver of early CS-associated alveolar type 2 cell dysfunction. These findings provide new insight into how chronic inflammation reshapes progenitor cell function during early lung injury.

Cell Biology↗

Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts

Antifungal drug resistance is a major challenge in fungal infection management. Numerous genomic changes are known to contribute to acquired drug resistance in clinical isolates of specific pathogens, but whether they broadly explain natural resistance across entire lineages is unknown. We leveraged genomic, ecological, and phenotypic trait data from naturally sampled strains from nearly all known species in subphylum Saccharomycotina to examine the evolution of resistance to eight antifungal drugs. The phylogenetic distribution of drug resistance varied by drug; fluconazole resistance was widespread, while 5-fluorocytosine resistance was rare, except in Lipomycetales. A random forest algorithm trained on genomic data predicted drug-resistant yeasts with 54-75% accuracy. In general, frequency of drug resistance correlated with prediction accuracy, with fluconazole resistance being consistently predicted with the highest accuracy (74.9%). Fluconazole resistance accuracy was similar between models trained on genome-wide variation in the presence and number of InterPro protein annotations across Saccharomycotina (74.9% accuracy) and those trained on amino acid sequence alignment data of Erg11, a protein known to be involved in fluconazole resistance (74.3-74.9% accuracy). Interestingly, the top Erg11 residues for predicting fluconazole resistance across Saccharomycotina do not overlap with, are not spatially close to, and are less conserved than those previously linked to resistance in clinical isolates of Candida albicans. In silico deep mutational scanning of the C. albicans Erg11 protein revealed that amino acid variants implicated in clinical cases of resistance are almost universally destabilizing while variants in our most informative residues are energetically more neutral, explaining why the latter are much more common than the former in natural populations. Importantly, previous experimental analyses of C. albicans Erg11 have shown that amino acid variation in our most informative residues, despite having never been directly implicated in clinical cases, can directly contribute to resistance. Our results suggest that studies of natural resistance in yeast species never encountered in the clinic will yield a fuller understanding of antifungal drug resistance.

microbiology↗

A yeast with muscle does not run faster: full humanization of the glycolytic pathway in Saccharomyces cerevisiae

While transplantation of single genes in yeast plays a key role in elucidating gene functionality in metazoans, technical challenges hamper the humanization of full pathways and processes. Empowered by advances in synthetic biology, this study demonstrates the feasibility and implementation of full humanization of glycolysis in yeast. Single gene and full pathway transplantation revealed the remarkable conservation of both glycolytic and moonlighting functions and, combined with evolutionary strategies, brought to light novel, context-dependent responses. Remarkably, human hexokinase 1 and 2, but not 4, required mutations in their catalytic or allosteric sites for functionality in yeast, while hexokinase 3 was unable to complement its yeast ortholog. Comparison with human tissues cultures showed the preservation of turnover numbers of human glycolytic enzymes in yeast and human cell cultures. This demonstration of transplantation of an entire, essential pathway paves the way to the establishment of species, tissue and disease-specific metazoan models. One Sentence SummaryThis work demonstrates the successful humanization of an entire pathway in Saccharomyces cerevisiae and establishes an attractive strategy to study (human) glycolysis architecture and regulation. HighlightsO_LIThe successful humanization of the entire glycolytic pathway in yeast offers new microbial models for both fundamental and applied studies. C_LIO_LIBoth glycolytic and moonlighting functions and turnover numbers of glycolytic enzymes are highly conserved between yeast and human. C_LIO_LIFunctionality of human hexokinases 1 and 2 in yeast requires mutations in the catalytic or allosteric binding sites. C_LIO_LICombination of single gene and full transplantation with laboratory evolution reveals context-dependent activity and evolution of glycolytic enzymes. C_LI

systems biology↗