Biology subjects

Geiser, T.

Publications and source records attributed to Geiser, T..

5 recordsLinked to original sources

bioRxiv2025

A Human Alveolus-on-Chip Recapitulates SARS-CoV-2-mediated Lung Injury in an Organ-relevant Context for Pre-clinical Applications

Respiratory viruses pose a constant threat to public health as highlighted by the pandemic outbreak of COVID-19. The most severe manifestation of COVID-19 is observed in the distal lung, where SARS-CoV-2 infection can result in massive inflammation and barrier breakdown. To date, few therapies are approved for clinical use in COVID-19 patients partially due to the lack of highly translational pre-clinical models of the alveoli. Human-derived microphysiological systems pose a promising new class of in vitro models to study viral infection in a relevant context. Therefore, we aimed to develop a Lung-on-Chip (LOC) model for studying SARS-CoV-2 infection at the alveolar barrier. Using an immortalized alveolar epithelial cell line, AXiAEC, and human lung microvascular endothelial cells (hLMVEC) we established a SARS-CoV-2 infection model on a LOC system. The LOC models the alveolar epithelial/endothelial barrier under physiological breathing motion. Our results demonstrated that AXiAEC maturation at the air-liquid interface (ALI) is essential for SARS-CoV-2 infection. SARS-CoV-2 infected the breathing LOC model and induced breakdown of the air-blood barrier. Finally, we evaluated the application of the LOC SARS-CoV-2 infection model for efficacy testing and demonstrated the antiviral effect of remdesivir. Drug treatment not only inhibited viral replication but also protected the alveolar barrier from damage and partially reverted SARS-CoV-2-mediated transcriptional dysregulation in AXiAEC. This novel LOC infection model recapitulates aspects of COVID-19. Our results highlight the importance of physiological cues such as ALI and stretch to accurately model host-pathogen interactions in the distal lung. Application of LOC models in pre-clinical drug testing may facilitate candidate compound selection at an early stage, allowing the allocation of resources to a few promising candidate compounds raising the potential to accelerate drug development and reduce costs and animal testing.

cell biology↗

bioRxiv2023

Comparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota.

Streptococci are one of the predominant and the most diverse genus in the human lung. Previously, we isolated human distal lung Streptococci from bronchoalvolear lavage fluid (BALF) as part of the human Lung Microbiota culture Collection (LuMiCol). Here, we performed whole genome sequencing, comparative phylogenomics and phenotypic characterization of six Streptococcal isolates representing the phylogenetic diversity of the genus in distal human lung. Here, we report five new species and one new subspecies including phylogenetic intermediates of commonly found Streptococci not limited to human lung. Pangenome analysis reveals gene content, evolutionary relationships, and metabolic functions shedding light on contribution of these Streptococci to lung microbial metabolism. Antimicrobial resistance gene analysis followed by MIC determination revealed macrolide, lincosamide and tetracycline resistance in lung Streptococci. We show the presence of capsular genes in lung streptococci both matching to the prototypical capsular genes (cps) and unique genes. Interestingly, the new Streptococcus isolate sp. nov. P2E5, genetically identical to the most prevalent Streptococcus in the human distal lung was revealed to be a phylogenetic intermediate between the S. mitis group and S. pneumoniae. It also harbors the pneumolysin (ply) gene and was found to have the serotype 21E. Finally, core genome phylogeny reveals that lung Streptococci the are evolutionary distinct from oral Streptococcal isolates in expanded Human Oral Microbiome Database (eHOMD). Hence, these findings we reveal new phylogenetically distinct Streptococcal species from the human distal lung microbiota and its genetic diversity and metabolism to understand the microbial ecology of human lung. ImportanceA healthy human distal lung harbour characteristic microbial communities mostly composed of oropharyngeal taxa, which are facultative or obligative anaerobes despite lung being the medium of oxygen intake. However, little is known about the genetic and functional diversity of these bacteria owing to the lack of resources including availability of primary lung isolate from human samples. Therefore, we have established a large bacterial collection that covers all major phyla by cultivating human bronchoalveolar lavage fluid (BALF) under various conditions. Streptococcus is the most prevalent and diverse genera in the human lung microbiota. Using genetic and biochemical approaches, we studied six diverse lung isolates from our collection representing the actual Streptococcal diversity and identify these as new species and subspecies. We hypothesize that learning about the phylogenetic genetic diversity, preferred metabolism and molecular structures of these Streptococci will provide with new insights on the understudied microbial ecosystem of the human lung.

microbiology↗

bioRxiv2021

Circadian patterns of energy metabolism are only partially reconstituted in gnotobiotic mice

The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known to greatly improve the recovery of energy from food. This has led to the hypothesis that increased digestive efficiency may underlie the contribution of the microbiome to obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat-mass than germ-free or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, energy expenditure and respiratory quotient using a novel isolator-housed metabolic cage system which allows long-term measurements without contamination risk. This demonstrated that microbiota- released calories are perfectly balanced by decreased food intake in fully colonized versus gnotobiotic OligoMM12 and germ-free mice fed a standard chow diet, i.e., microbiota-released calories can in fact be well-integrated into appetite control. We also observed no significant difference in energy expenditure per gram lean mass between the different microbiota groups, suggesting that cumulative very small differences in energy balance, or altered energy storage must underlie fat accumulation in OligoMM12 mice. Consistent with altered energy storage, major differences were observed in the type of respiratory substrates used in metabolism over the circadian cycle: in germ-free mice the respiratory exchange ratio was consistently lower than that of fully colonized mice at all times of day, indicative of more reliance on fat and less on glucose metabolism. Intriguingly the RER of OligoMM12-colonized gnotobiotic mice phenocopied fully colonized mice during the dark (active/eating) phase but phenocopied germ-free mice during the light (fasting/resting) phase. Further, OligoMM12-colonized mice showed a germ-free-like drop in liver glycogen storage during the light cycle and both liver and plasma metabolomes of OligoMM12 mice clustered closely with germ-free mice. This implies the existence of microbiota functions that are required to maintain normal host metabolism during the resting/fasting phase of circadian cycle, and which are absent in the OligoMM12 consortium.

microbiology↗

bioRxiv2020

In vitro culture of aberrant basal-like cells from fibrotic lung tissue

RationaleIn idiopathic pulmonary fibrosis (IPF) atypical epithelial cells are present in the alveolar compartment. Their origin and contribution to IPF pathogenesis is unknown. We recently cultured a distinct population of cells, which readily grew from fibrotic lung tissue, but only rarely from non-fibrotic tissue. Here we aimed to characterize these fibrosis-enriched cells and determine transcriptomic differences between cells derived from IPF and patients with other interstitial lung diseases (ILD). MethodsCells were cultured from peripheral lung tissue of ILD patients and analysed by bulk or single cell RNA sequencing (scRNA-seq), TaqMan-PCR, immunofluorescence (IF), immunoblotting or electron microscopy (EM). ResultsscRNA-seq demonstrated an overall homogeneity and epithelial origin of the cells. The majority of cells expressed basal cell markers (Cytokeratin (KRT) 5 and 17, TP63), of which a fraction co-expressed mesenchymal cell markers (VIM, FN1, CDH2), alveolar (SLC34A2, ABCA3, LPCAT1, EMP2, HOPX) and/or secretory epithelial cell markers (SCGB1A1, MUC4). Interestingly, most of the cells showed closest transcriptomic similarity to recently described aberrant basal-like cells. Cells derived from IPF versus other ILD patients revealed significant transcriptomic differences with an up-regulation of fibrosis-associated and a down-regulation of inflammatory pathways in IPF cells. ConclusionWe here confirm the presence of aberrant basal-like cells in fibrotic lung tissue and, importantly, are the first to describe their in vitro characteristics and a way of culturing these cells in vitro. Cultured basal-like cells co-express epithelial and mesenchymal markers, suggesting a partial epithelial to mesenchymal transition (EMT). A subset of cells co-express alveolar, ciliated or secretory epithelial cell markers, possibly indicating differentiation towards these cell linages. Furthermore, cultured basal-like cells display a disease-specific transcriptome, possibly induced by their specific microenvironment. Our findings will contribute to a better understanding of the cells origin and their potential contribution to IPF pathogenesis.

cell biology↗

bioRxiv2019

Second-generation lung-on-a-chip array with a stretchable biological membrane

The complex architecture of the lung parenchyma and the air-blood barrier is difficult to mimic in-vitro. Recently reported lung-on-a-chips used a thin, porous and stretchable PDMS membrane, to mimic the air-blood barrier and the rhythmic breathing motions. However, the nature, the properties and the size of this PDMS membrane differ from the extracellular matrix of the distal airways. Here, we present a second-generation lung-on-a-chip with an array of in vivo-like sized alveoli and a stretchable biological membrane. This nearly absorption free membrane allows mimicking in vivo functionality of the lung parenchyma at an unprecedented level. The air-blood barrier is constituted by human primary lung alveolar epithelial cells from several patients and co-cultured with primary lung endothelial cells. Typical markers of lung alveolar epithelial cells could be observed in the model, while barrier properties were preserved for up to three weeks. This advanced lung alveolar model reproduces some key features of the lung alveolar environment in terms of composition, alveolar size, mechanical forces and biological functions, which makes this model a more analogous tool for drug discovery, diseases modeling and precision medicine applications.

bioengineering↗