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Longitudinal analysis of phenotype-transcriptome correlations in AAV-TGFb1- and Bleomycin-induced lung fibrosis

ABSTRACT: Longitudinal analysis of phenotype-transcriptome correlations in AAV-TGFb1- and Bleomycin-induced lung fibrosis

PROVIDER: PRJEB50439 | ENA |

REPOSITORIES: ENA

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Longitudinal analysis of phenotype-transcriptome correlations in AAV-TGFb1- and Bleomycin-induced lung fibrosis

Project description:Longitudinal analysis of phenotype-transcriptome correlations in AAV-TGFb1- and Bleomycin-induced lung fibrosis

| PRJNA802142 | ENA

Longitudinal analysis of phenotype-transcriptome correlations in AAV-TGFb1- and Bleomycin-induced lung fibrosis

Project description:We have previously established a novel mouse model of lung fibrosis based on Adeno-associated virus (AAV)-mediated pulmonary overexpression of TGFβ1. Here, we provide an in-depth characterization of phenotypic and transcriptomic changes (mRNA and miRNA) in a head-to-head comparison with Bleomycin-induced lung injury over a 4-week disease course. The analyses delineate the temporal state of model-specific and commonly altered pathways, thereby providing detailed insights into the processes underlying disease development. They further guide appropriate model selection as well as interventional study design. Overall, Bleomycin-induced fibrosis resembles a biphasic process of acute inflammation and subsequent transition into fibrosis (with partial resolution), whereas the TGFβ1-driven model is characterized by pronounced and persistent fibrosis with concomitant inflammation and an equally complex disease phenotype as observed upon Bleomycin instillation. Finally, based on an integrative approach combining lung function data, mRNA/miRNA profiles, their correlation and miRNA target predictions, we identify putative drug targets and miRNAs to be explored as therapeutic candidates for fibrotic diseases. Taken together, we provide a comprehensive analysis and rich data resource based on RNA-sequencing, along with a strategy for transcriptome-phenotype coupling. The results will be of value for TGFβ research, drug discovery and biomarker identification in progressive fibrosing interstitial lung diseases.

2022-07-15 | GSE195773 | GEO

Longitudinal single-cell transcriptomics analysis of mouse lung upon bleomycin-induced injury

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VLDL Proteome in Control-AAV and PSS1(Q353R)-AAV

Project description:Fractionated VLDL from Control-AAV and PSS1(Q353R)-AAV.

2024-10-21 | PXD047916 | Pride

Longitudinal single-cell transcriptomics analysis of mouse lung upon bleomycin-induced injury

Project description:Two single-cell RNA sequencing data sets were generated called "Whole lung" and "High Resolution". The "Whole lung" single-cell mRNAseq libraries were generated with Drop-Seq from whole mouse lungs upon bleomycin-induced injury and followed over time. Samples were taken at days 3 (n = 3), 7 (n = 5), 10 (n = 3), 14 (n = 4), 21 (n = 4) and 28 (n = 2). Control samples (n = 7) were administered saline only, also indicated with PBS or day0. The "High resolution" single-cell mRNAseq libraries were generated with Drop-Seq from the epithelial compartment of mouse lungs upon bleomycin-induced injury and followed over time. Samples were taken daily for two weeks and at days 21, 28, 36, 54 after injury. Control samples (n = 2) were administered saline only, also indicated with PBS or day0.

2019-12-02 | GSE141259 | GEO

Longitudinal prediction of DNA methylation to forecast epigenetic outcomes

Project description:We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty.

2025-05-14 | GSE254135 | GEO

Bleomycin-injured alveolospheres

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mRNA reponse to bleomycin instillation

Project description:Gene expression analysis of C57BL/6 mice challenged by intratracheal bleomycin instillation: mRNA expression profiles were established from lungs following a 14-days PBS or bleomycin administration. One color -experiment with 1 strain of mice (C57BL/6) following a 14-days PBS or bleomycin administration (n=5), corresponding to a total of 10 samples.

2013-02-01 | E-GEOD-34814 | biostudies-arrayexpress

Profiling fibrotic lung in TGFb1-Tg mice

Project description:Transgenic (Tg) mice over-expressing TGFb1 in a lung-specific manner display airway inflammation and fibrosis, phenotypes relevant to human COPD and asthma. This model system provides a platform for identifying and validating genes/pathways involved in these disease pathogeneses. The TGFb1-Tg mice lung profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the lung of TGFb1-Tg mice compared to the corresponding wild type controls.

2013-03-22 | E-GEOD-31950 | biostudies-arrayexpress

miRNA reponse to bleomycin instillation

Project description:Comparison of C57BL/6 (sensitive) and BALB/c (resistant) mice challenged by intratracheal bleomycin instillation: miRNA expression profiles were established from lungs derived from the two strains, following a 7- or 14-days PBS or bleomycin administration. One color -experiment with 2 strains of mice (C57BL/6 and BALB/c) following a 7- or 14-days PBS or bleomycin administration (n=3), corresponding to a total of 24 samples.

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