Biology subjects

Lukassen, S.

Publications and source records attributed to Lukassen, S..

7 recordsLinked to original sources

bioRxiv2024

Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus

BackgroundTBX1 is required for the development of the pharyngeal apparatus. In the mouse, fish, and ascidian, Tbx1 is a marker of cardiopharyngeal mesoderm (CPM), a cell population that provides progenitors to the heart and branchiomeric muscles. However, in mammals: a) the molecular cascade that drives the diversification of this multipotent cell population, and b) the role of Tbx1 therein, are not well defined. Material and methodsWe used in vitro differentiation of WT and Tbx1-/- mouse embryonic stem cells into precardiac mesoderm, and performed single cell RNA-seq and ATAC-seq at two differentiation stages. We then used WT and Tbx1-/- mouse embryos for in vivo validation of the key findings. Results and conclusionsWe found that the response to loss of TBX1 is cell sub-population-specific, both in terms of gene expression and chromatin remodeling. We show that Tbx1 regulates chromatin accessibility and gene expression of an ancient transcriptional module that orchestrates the development of the trunk, pharynx and heart across evolution. This module is co-regulated and includes genes encoding the conserved transcription factor families of Tea Shirt (Tshz), Sine Oculis (Six), Eye absent (Eya), and Ebf/Collier. Analysis of putative regulatory regions of these genes, which were selected using a machine-learning computational procedure, predicted a feed-forward regulatory relationship between TBX1 and SIX factors that drives or stabilizes the module. Most surprisingly, we found a drift in the differentiation trajectory of the Tbx1 mutant CPM that led to a relative expansion of cells with epithelial-like transcriptional features in the cell culture model and in mouse embryos. We conclude that TBX1 is a critical factor for maintaining the transcriptional profile of the CPM.

developmental biology↗

bioRxiv2024

Population dynamics after pancreatitis dictates long-lasting epigenetic reprogramming and mediates tumor predisposition

Local inflammation in the pancreas is transient but imprints a durable epigenetic memory on epithelial cells, making them more amenable to oncogenic transformation. However, it is unclear whether epithelial cell heterogeneity is impacted by acute pancreatitis (AP) or whether population dynamics during regeneration contributes to the establishment of inflammation memory. To tackle those questions, we deployed experimental pancreatitis in mice and performed paired sequencing of transcriptomic and chromatin accessibility profiles at single nucleus resolution. We documented cell type abundance but also applied integrative analyses to infer phenotypically-distinct clusters of mesenchymal and exocrine cells. We found that AP perturbs a subset of "idling" acinar cells, which separate from more canonical "secretory" acini based on a more diversified proteome, which include elevated expression of signal transduction receptors. We linked acinar cell heterogeneity to epigenetic differences that also endow idling cells with superior plasticity. These constitute about 40% of acinar cells but can proliferate and skew their phenotype in response to AP. This leads to a remarkable recovery of pancreas histology and function, but also to the dissemination of idling-like features across the exocrine parenchyma. Mechanistically, idling acinar cells are characterized by enhanced transcriptional activity and protein synthesis. After recovery from pancreatitis, acini show elevation of both and establishment of chronic Unfolded Protein Response (UPR). We finally demonstrated that AP-primed pancreata show signs of elevated UPR and that ER stress promotes acinar cell metaplasia. Our data interrogate phenotypical dynamics during tissue regeneration to identify cell states amenable to epigenetic imprinting. They also suggest that UPR-alleviating strategies might curtail the risk of developing pancreatic cancer for individuals who experiences AP.

cell biology↗

bioRxiv2023

Enhanced Airway Epithelial Response to SARS-CoV-2 Infection in Children is Critically Tuned by the Cross-Talk Between Immune and Epithelial Cells

To cope with novel virus infections to which no prior adaptive immunity exists, the body strongly relies on the innate immune system. In such cases, including infections with SARS-CoV-2, children tend to fair better than adults. In the context of COVID-19, it became evident that a rapid interferon response at the site of primary infection is key for successful control of the virus and prevention of severe disease. The airway epithelium of children was shown to exhibit a primed state already at homeostasis and to respond particularly well to SARS-CoV-2 infection. However, the underlying mechanism for this priming remained elusive. Here we show that interactions between airway mucosal immune cells and epithelial cells are stronger in children, and via cytokine-mediated signaling lead to IRF-1-dependent upregulation of the viral sensors RIG-I and MDA5. Based on a cellular in vitro model we show that stimulated human peripheral blood mononuclear cells (PBMC) can induce a robust interferon-beta response towards SARS-CoV-2 in a lung epithelial cell line otherwise unresponsive to this virus. This is mediated by type I interferon, interferon-gamma and TNF, and requires induction of both, RIG-I and MDA5. In single cell-analysis of nasal swab samples the same cytokines are found to be elevated in mucosal immune cells of children, correlating with elevated epithelial expression of viral sensors. In vitro analysis of PBMC derived from healthy adolescents and adults confirm that immune cells of younger individuals show increased cytokine production and potential to prime epithelial cells. In co-culture with SARS-CoV-2-infected A549 cells, PBMC from adolescents significantly enhance the antiviral response. Taken together, our study suggests that higher numbers and a more vigorous activity of innate immune cells in the airway mucosa of children tune the set-point of the epithelial antiviral system. This likely is a major contributor to the robust immune response to SARS-CoV-2 in children. Our findings shed light on the molecular underpinnings of the stunning resilience of children towards severe COVID-19, and may propose a novel concept for immunoprophylactic treatments.

immunology↗

bioRxiv2020

The COVID-19 PHARMACOME: Rational Selection of Drug Repurposing Candidates from Multimodal Knowledge Harmonization

The SARS-CoV-2 pandemic has challenged researchers at a global scale. The scientific communitys massive response has resulted in a flood of experiments, analyses, hypotheses, and publications, especially in the field of drug repurposing. However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from which a rational selection of drug repurposing candidates can be made. In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of 10 separate disease maps and sources of experimental data focused on SARS-CoV-2 / COVID-19 pathophysiology. By applying our systematic approach, we were able to predict the synergistic effect of specific drug pairs, such as Remdesivir and Thioguanosine or Nelfinavir and Raloxifene, on SARS-CoV-2 infection. Experimental validation of our results demonstrate that our graph can be used to not only explore the involved mechanistic pathways, but also to identify novel combinations of drug repurposing candidates.

bioinformatics↗

bioRxiv2020

SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches

The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. While TMPRSS2 is expressed in both tissues, in the subsegmental bronchial branches ACE2 is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.

genomics↗

bioRxiv2019

Gene set inference from single-cell sequencing data using a hybrid of matrix factorization and variational autoencoders

Recent advances in single-cell RNA sequencing (scRNA-Seq) have driven the simultaneous measurement of the expression of 1,000s of genes in 1,000s of single cells. These growing data sets allow us to model gene sets in biological networks at an unprecedented level of detail, in spite of heterogenous cell populations. Here, we propose an unsupervised deep neural network model that is a hybrid of matrix factorization and conditional variational autoencoders (CVA), which utilizes weights as matrix factorizations to obtain gene sets, while class-specific inputs to the latent variable space facilitate a plausible identification of cell types. This artificial neural network model seamlessly integrates functional gene set inference, experimental batch effect correction, and static gene identification, which we conceptually prove here for three single-cell RNA-Seq datasets and suggest for future single-cell-gene analytics.

bioinformatics↗

bioRxiv2019

Single nucleus RNA sequencing maps acinar cell states in a human pancreas cell atlas

Molecular evidence of cellular heterogeneity in the human exocrine pancreas has not been established, due to the local concentration of hydrolytic enzymes that can rapidly degrade cells and RNA upon resection. Here we innovated single-nucleus RNA sequencing protocols, and profiled more than 120,000 cells from adult and neonatal human donors to create the first comprehensive atlas of human pancreas cells, including epithelial and non-epithelial constituents. Adult and neonatal pancreata shared common features, including the presence of previously undetected acinar subtypes, but also showed marked differences in the composition of the endocrine, endothelial, and immune compartments. Spatial cartography, including cell proximity mapping through in situ sequencing, revealed dynamic developmental cell topographies in the endocrine and exocrine pancreas. Our human pancreas cell atlas can be interrogated to understand pancreatic cell biology, and provides a crucial reference set for future comparisons with diseased tissue samples to map the cellular foundations of pancreatic diseases.

genomics↗