MiRNA profiling in human precision-cut lung slices (PCLS)
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ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE167705 | GEO | 2021/06/22
REPOSITORIES: GEO
Similar Datasets
Project description:miRNA profiling in human precision-cut lung slices (PCLS)
| PRJNA705600 | ENA
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.
2021-08-22 | GSE181388 | GEO
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
2024-01-05 | GSE208375 | GEO
Project description:RNA sequencing from mouse, pig and human precision cut lung slices (PCLS)
| PRJEB39914 | ENA
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.
2024-01-24 | GSE247615 | GEO
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.
2019-03-06 | GSE106968 | GEO
Project description:BackgroundMonitoring cellular processes across different levels of complexity, from the cellular to the tissue scale, is important for understanding tissue structure and function. However, it is challenging to monitor and estimate these structural and dynamic interactions within three-dimensional (3D) tissue models.ObjectiveThe aim of this study was to design a method for imaging, tracking, and quantifying 3D changes in cell morphology (shape and size) within liver tissue, specifically a precision-cut liver slice (PCLS). A PCLS is a 3D model of the liver that allows the study of the structure and function of liver cells in their native microenvironment.MethodsHere, we present a method for imaging liver tissue during anisosmotic exposure in a multispectral four-dimensional manner. Three metrics of tissue morphology were measured to quantify the effects of osmotic stress on liver tissue. We estimated the changes in the volume of whole precision cut liver slices, quantified the changes in nuclei position, and calculated the changes in volumetric responses of tissue-embedded cells.ResultsDuring equilibration with cell-membrane-permeating and non-permeating solutes, the whole tissue experiences shrinkage and expansion. As nuclei showed a change in position and directional displacement under osmotic stress, we demonstrate that nuclei could be used as a probe to measure local osmotic and mechanical stress. Moreover, we demonstrate that cells change their volume within tissue slices as a result of osmotic perturbation and that this change in volume is dependent on the position of the cell within the tissue and the duration of the exposure.ConclusionThe results of this study have implications for a better understanding of multiscale transport, mechanobiology, and triggered biological responses within complex biological structures.
| S-EPMC10903333 | biostudies-literature
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
2023-02-23 | E-MTAB-12605 | biostudies-arrayexpress
Project description:ObjectiveHuman precision cut lung slices (PCLS) are widely used as an ex vivo model system for drug discovery and development of new therapies. PCLS reflect the functional heterogeneity of lung tissue and possess relevant lung cell types. We thus determined the use of PCLS in studying non-coding RNAs notably miRNAs, which are important gene regulatory molecules. Since miRNAs play key role as mediators of respiratory diseases, they can serve as valuable prognostic or diagnostic biomarkers, and in therapeutic interventions, of lung diseases. A technical limitation though is the vast amount of agarose in PCLS which impedes (mi)RNA extraction by standard procedures. Here we modified our recently published protocol for RNA isolation from PCLS to enable miRNA readouts.ResultsThe modified method relies on the separation of lysis and precipitation steps, and a clean-up procedure with specific magnetic beads. We obtained successfully quality miRNA amenable for downstream applications such as RTqPCR and whole transcriptome miRNA analysis. Comparison of miRNA profiles in PCLS with published data from human lung, identified all important miRNAs regulated in IPF, COPD, asthma or lung cancer. Therefore, this shows suitability of the method for analyzing miRNA targets and biomarkers in the valuable human PCLS model.
| S-EPMC8252208 | biostudies-literature
Project description:Respiratory infections caused by mycoplasma species in ruminants lead to considerable economic losses. Two important ruminant pathogens are Mycoplasma mycoides subsp. Mycoides (Mmm), the aetiological agent of contagious bovine pleuropneumonia and Mycoplasma mycoides subsp. capri (Mmc), which causes pneumonia, mastitis, arthritis, keratitis, and septicemia in goats. We established precision cut lung slices (PCLS) infection model for Mmm and Mmc to study host-pathogen interactions. We monitored infection over time using immunohistological analysis and electron microscopy. Moreover, infection burden was monitored by plating and quantitative real-time PCR. Results were compared with lungs from experimentally infected goats and cattle. Lungs from healthy goats and cattle were also included as controls. PCLS remained viable for up to two weeks. Both subspecies adhered to ciliated cells. However, the titer of Mmm in caprine PCLS decreased over time, indicating species specificity of Mmm. Mmc showed higher tropism to sub-bronchiolar tissue in caprine PCLS, which increased in a time-dependent manner. Moreover, Mmc was abundantly observed on pulmonary endothelial cells, indicating partially, how it causes systemic disease. Tissue destruction upon prolonged infection of slices was comparable to the in vivo samples. Therefore, PCLS represents a novel ex vivo model to study host-pathogen interaction in livestock mycoplasma.
| S-EPMC6631151 | biostudies-literature