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MiRNA profiling in human precision-cut lung slices (PCLS)

ABSTRACT: miRNA profiling in human precision-cut lung slices (PCLS)

PROVIDER: PRJNA705600 | ENA |

REPOSITORIES: ENA

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Precision Cut Lung Slices as an ex vivo model to study Pneumocystis murina survival and antimicrobial susceptibility

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miRNA profiling in human precision-cut lung slices (PCLS)

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Gene expression data from precision cut lung slices (PCLS) of old and young mice infected with two strains of Pseudomonas aeruginosa

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

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RNA sequencing from mouse, pig and human precision cut lung slices (PCLS)

Project description:RNA sequencing from mouse, pig and human precision cut lung slices (PCLS)

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Transcriptional changes of precision-cut liver slices after 3 days of cultures in the absence or presence of 2.5 mM valproic acid sodium salt.

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.

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scRNA-seq of human PCLS

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.

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A modified protocol for successful miRNA profiling in human precision-cut lung slices (PCLS).

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

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