Project description:The objective of this study is to map early time-response in of estrogen regulated genes using precision cut liver slices (PCLS). PCLS from juvenile male cod were exposed to ethynylestradiol (EE2) in culture for 12, 24 and 48 h and the transcriptome responses were studied using RNA-seq
Project description:This study was done to show the utility of precision-cut lung slices (PCLS) in supporting the survival of Pneumocystis murina in vitro.
Project description:The study aimed to mimic inflamm-aging using ex vivo precision-cut lung slices (PCLS) from young and old mice, and to investigate the influence of aging on inflammation upon infection with the P. aeruginosa standard lab strain PAO1 and a clinical P. aeruginosa isolate, D61. Genome-wide transcriptome analysis revealed that genes associated with processes of immune system were strongly regulated with aging upon P. aeruginosa infection. Very early events of pulmonary inflamm-aging can be mimicked ex vivo in tissue slices of distal lungs and aging promotes pulmonary inflammation upon P. aeruginosa infection
Project description:Transcriptional changes of mouse precision-cut liver slices (PCLS) after three days of culture were determined using RNA sequencing. PCLS were cultured for three days in the absence or presence of 2.5 mM valproic acid sodium salt (VPA). Illumina NovaSeq SP was used for sequencing.
Project description:Transcriptome analysis revealed miRNA profiles from PCLS of tumor-free tissue comparable to normal lung tissue Suitability of human PCLS as a model for lung-specific miRNA investigations by RTqPCR and microarray analyses
Project description:Gremlin-1 has been implicated in liver fibrosis in metabolic dysfunction-associated steatohepatitis (MASH) via inhibition of bone-morphogenetic protein (BMP) signalling and has thereby been identified as a potential therapeutic target. Using human cirrhotic precision-cut liver slices (PCLS) as an ex vivo model systems of MASH fibrosis, we show that neutralisation of Gremlin-1 activity with monoclonal therapeutic antibodies does not reduce liver inflammation or liver fibrosis. Overall, our findings suggest a redundant role for Gremlin-1 in the pathogenesis of liver fibrosis, which is unamenable to therapeutic targeting.
Project description:Precision-cut lung slices (PCLS) are increasingly utilized for ex-vivo disease modeling, but a high-resolution characterization of cellular-phenotype stability in PCLS has not been reported. Comparing the single cell transcriptomic profile of human PCLS after five days of culture to freshly isolated human lung tissue, we found striking changes in endothelial cells and alveolar epithelial cell programs, reflecting both injury and pathways activated in static culture, while immune cell frequencies and programs remained largely intact and similar to the native lung. These baseline changes should be considered when utilizing PCLS as a model of the human lung.
Project description:Purpose: The objective of this study is to use Atlantic cod (Gadus morhua) PCLS culture and RNA-seq analysis to map gene expression responses to BaP and EE2 exposure in Atlantic cod. Methods: A total of 8 (3 females and 5 males) juvenile cod (G. morhua) (average body weight 498 g) were used for PCLS (n = 6-8 per group). PCLS preparation and chemical exposure in the culture was performed as previously described (Eide et al., 2014). Cod liver slices were cultured in 24-well plates in the growth medium containing DMSO vehicle (CAS No: 67-68-5), BaP (CAS No: 50-32-8) (10 or 1000 nm), EE2 (CAS No: 57-63-6) (10 or 1000 nm) or BaP and EE2 mixture (10 or 1000 nm each). After 48 hors of culture, the slices were collected and snap frozen in liquid nitrogen and stored at -80 °C for RNA extraction. Results: In total, we had 47 high-quality samples, which were aligned to the published CDS of Atlantic cod (ftp://ftp.ensembl.org/pub/release-90/fasta/gadus_morhua/cds/Gadus_morhua.gad) using HISAT2 v2.1.0 (Kim et al., 2015). Counts were generated from the alignments using SAMtools v1.4.1 (Li et al., 2009). Differential expression analysis was performed using edgeR v3.18.1 (McCarthy et al., 2012) between control group and each treated group using paired test, after removing the genes with all-zero counts across all samples of the two compared groups. Differentially expressed genes were defined by p-value < 0.05 after adjustment using the Benjamini-Hochberg multiple testing correction. Several genes were differentially expressed in the BaP and EE2 and mixture treatment groups compared to the group. Hierarchical clustering showed that signature expression profile of top differentially expressed genes in response to the single treatment was distinctly maintained also in the equimolar binary mixtures. Conclusions: Combining high-throughput RNA-seq analysis and PCLS culture in Atlantic cod, we have shown that BaP and EE2 differentially regulated many genes in the AHR and ER pathways. The results show that omics data can be generated using an efficient PCLS in vitro culture system.
Project description:Expression data from mouse precision cut lung slices (PCLS) after human rhinovirus (RV) infection and after treatment with bronchobini (BRO).