MicroRNA expression in ex vivo ventilated human lungs
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA727089 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14415987.fastq.gz | Fastqsanger.gz | |||
| SRR14415988.fastq.gz | Fastqsanger.gz | |||
| SRR14415989.fastq.gz | Fastqsanger.gz | |||
| SRR14415990.fastq.gz | Fastqsanger.gz | |||
| SRR14415991.fastq.gz | Fastqsanger.gz |
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Project description:RNA expression in ex vivo ventilated human lungs
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Project description:Rationale: Overstretching of lung parenchyma may lead to tissue injury, especially during mechanical ventilation. There are no specific biomarkers of lung stretch. Objectives: To identify transcriptomic signatures of micro-RNAs and genes specifically related to lung stretch and validate them in preclinical models. Methods: Data on micro-RNA expression in response to stretch in experimental models were systematically pooled. Signatures were identified as those micro-RNAs or genes with differential expression in samples from stretched cells, and optimized using a greedy algorithm. Transcriptomic scores were calculated as the difference of geometric means in expression of up- and down-regulated features, and compared among different magnitudes of stretch. The accuracy of these scores was validated in animal models of lung injury, ex vivo mechanically ventilated human lungs and in bronchoalveolar lavage fluid (BALF) from patients under different ventilatory conditions. Measurements and main results: Eight micro-RNAs were differentially expressed in stretched cell cultures (n=24). Amongst the genes regulated by these micro-RNAs, a 180-gene signature was identified in ex vivo models (n=106) and refined using data from animal models (n=143) to obtain a 4-gene signature. The corresponding scores were significantly higher in samples submitted to stretch or injurious mechanical ventilation. The microRNA signatures were validated in human tissue and BALF, with areas under the ROC curve between 0.89 and 1 respectively to identify lung overdistention. Conclusions: Lung cell stretch induces the expression of specific micro-RNA and genes. These signatures may be used to obtain an index of lung overstretching that can be measured at the bedside.
2025-05-01 | GSE173803 | GEO
Project description:Rationale: Overstretching of lung parenchyma may lead to tissue injury, especially during mechanical ventilation. There are no specific biomarkers of lung stretch. Objectives: To identify transcriptomic signatures of micro-RNAs and genes specifically related to lung stretch and validate them in preclinical models. Methods: Data on micro-RNA expression in response to stretch in experimental models were systematically pooled. Signatures were identified as those micro-RNAs or genes with differential expression in samples from stretched cells, and optimized using a greedy algorithm. Transcriptomic scores were calculated as the difference of geometric means in expression of up- and down-regulated features, and compared among different magnitudes of stretch. The accuracy of these scores was validated in animal models of lung injury, ex vivo mechanically ventilated human lungs and in bronchoalveolar lavage fluid (BALF) from patients under different ventilatory conditions. Measurements and main results: Eight micro-RNAs were differentially expressed in stretched cell cultures (n=24). Amongst the genes regulated by these micro-RNAs, a 180-gene signature was identified in ex vivo models (n=106) and refined using data from animal models (n=143) to obtain a 4-gene signature. The corresponding scores were significantly higher in samples submitted to stretch or injurious mechanical ventilation. The microRNA signatures were validated in human tissue and BALF, with areas under the ROC curve between 0.89 and 1 respectively to identify lung overdistention. Conclusions: Lung cell stretch induces the expression of specific micro-RNA and genes. These signatures may be used to obtain an index of lung overstretching that can be measured at the bedside.
2025-05-01 | GSE234463 | GEO
Project description:microRNA profiling of RBC transcriptome during ex vivo storage
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Project description:Rationale: Overstretching of lung parenchyma may lead to tissue injury, especially during mechanical ventilation. There are no specific biomarkers of lung stretch. Objectives: To identify transcriptomic signatures of micro-RNAs and genes specifically related to lung stretch and validate them in preclinical models. Methods: Data on micro-RNA expression in response to stretch in experimental models were systematically pooled. Signatures were identified as those micro-RNAs or genes with differential expression in samples from stretched cells, and optimized using a greedy algorithm. Transcriptomic scores were calculated as the difference of geometric means in expression of up- and down-regulated features, and compared among different magnitudes of stretch. The accuracy of these scores was validated in animal models of lung injury, ex vivo mechanically ventilated human lungs and in bronchoalveolar lavage fluid (BALF) from patients under different ventilatory conditions. Measurements and main results: Eight micro-RNAs were differentially expressed in stretched cell cultures (n=24). Amongst the genes regulated by these micro-RNAs, a 180-gene signature was identified in ex vivo models (n=106) and refined using data from animal models (n=143) to obtain a 4-gene signature. The corresponding scores were significantly higher in samples submitted to stretch or injurious mechanical ventilation. The microRNA signatures were validated in human tissue and BALF, with areas under the ROC curve between 0.89 and 1 respectively to identify lung overdistention. Conclusions: Lung cell stretch induces the expression of specific micro-RNA and genes. These signatures may be used to obtain an index of lung overstretching that can be measured at the bedside.
2025-05-01 | GSE197752 | GEO
Project description:RNA expression in ventilated preterm lamb lungs [RNA-seq]
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Project description:Ex vivo lung perfusion restores normothermia, ventilation and circulation to donor lungs, typically after a period of cold ischemia. This allows donor lungs to be evaluated prior to transplantation. We used microarrays to study the biological response of human lungs to Ex Vivo Lung Perfusion. Samples were collected from donor lungs at Toronto General Hospital. Lungs were donation after brain death (DBD)
2020-06-22 | GSE127055 | GEO
Project description:Proteins that were newly-synthesized during ex vivo lung perfusion were labeled with an azido-sugar Ac4GalNAz in the perfusate. These proteins were enriched using click chemistry to attach an alkyne-desthiobiotin group to the azido-labeled proteins, then pulled out of solution using streptavidin beads. The overall goal is to better understand the effects of warm ischemia injury in lungs destined for lung transplantation.
2022-10-07 | MSV000090491 | MassIVE
Project description:Purpose: ATAC-seq was performed on preterm lambs that were ventilated by invasive mechanical ventilation or noninvasive respiratory support utilizing a mask and compared to gestation-age-matched preterm lambs that were not ventilated and naturally delivered term lambs. Methods: Lung chromatin access profiles were generated for: 1) Unventilated preterm lamb, 2) preterm lambs delivered at gd131 and intubated and mechanically ventilated for 3 days, 3) preterm lambs delivered at gd131 and not intubated and resuscitated by placing a face mask over the nose and mouth and controlling O2 delivery via a computer-controlled electronic blower device, 4) unventilated naturally delivered full-term lambs. Results: Using an optimized data analysis workflow, we mapped between 76 and 96 million sequence reads per sample to the sheep genome Conclusions: Our study represents the first detailed analysis of ventilated preterm lung chromatin access, with biologic replicates, generated by ATAC-seq
2021-06-30 | GSE163807 | GEO