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MiR-29 targets in human fetal lung fibroblast IMR-90 cells

ABSTRACT: TGFβ is one of most intensively studied regulators of extracellular matrix formation, and has been implicated in the development of pulmonary fibrosis in different models. However, little is know about the role of miRNAs in TGFβ mediated fibrogenic gene regulation. By using miRNA qRT-PCR array, we have identified miRNAs whose expression are regulated by TGFβ in IMR-90 cells. Among those down-regulated miRNAs are miR-29 family members. Knockdown miR-29 in IMR-90 cells results in up-regulation of a large number of extracellular matrix and fibrogenic genes including family members of collagen, laminin, integrin, ADAM and MMP, many of them are predicted or confirmed miR-29 targets. Hierarchichal clustering analysis of mRNA array data revealed that many extracellular matrix and fibrogenic genes up-regulated by TGFβ in IMR-90 cells, are also up-regulated in miR-29 KD cells. Moreover, the similar set of extracellular matrix and fibrogenic genes is also significantly up-regulated in bleomycin treated mouse lungs. Together, our data strongly suggest that downstream of the TGFβ, miR-29 is a master modulator of genes involved in extracellular matrix formation and might play a significant role in pulmonary fibrosis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE18651 | GEO | 2010/03/01

SECONDARY ACCESSION(S): PRJNA121587

REPOSITORIES: GEO

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Homo sapiens

Project description:miR-29 targets in human fetal lung fibroblast IMR-90 cells

| PRJNA121587 | ENA

Expression data in the presence of miR-29a inhibition in human dermal fibroblast cells

2013-10-28 | GSE45564 | GEO

Expression data in the presence of miR-29a inhibition in human dermal fibroblast cells

Project description:miR-29 can target many gene transcripts encoding extracellular matrix proteins. To unravel novel targets, we used microarray analysis to detect global gene expression changes when inhibiting endogenous miR-29. Total RNA from human dermal fibroblast cells after 48 h treatment with miR-29a inhibitor or control inhibitor were isolated and subjected to whole gene expression microarray analysis.

2013-10-28 | E-GEOD-45564 | biostudies-arrayexpress

Homo sapiens

Project description:IMR-90 methylome

| PRJDB2885 | ENA

Age-dependent increase of oxidative stress regulates microRNA-29 family preserving cardiac health

Project description:The short-lived turquoise killifish Nothobranchius furzeri (Nfu) is a valid model for aging studies. Here, we investigated its age-associated cardiac function. We observed oxidative stress accumulation and an engagement of microRNAs (miRNAs) in the aging heart. MiRNA-sequencing of 5 week (young), 12-21 week (adult) and 28-40 week (old) Nfu hearts revealed 23 up-regulated and 18 down-regulated miRNAs with age. MiR-29 family turned out as one of the most up-regulated miRNAs during aging. MiR-29 family increase induces a decrease of known targets like collagens and DNA methyl transferases (DNMTs) paralleled by 5´methyl-cytosine (5mC) level decrease. To further investigate miR-29 family role in the fish heart we generated a transgenic zebrafish model where miR-29 was knocked-down. In this model we found significant morphological and functional cardiac alterations and an impairment of oxygen dependent pathways by transcriptome analysis leading to hypoxic marker up-regulation. To get insights the possible hypoxic regulation of miR-29 family, we exposed human cardiac fibroblasts to 1% O2 levels. In hypoxic condition we found miR-29 down-modulation responsible for the accumulation of collagens and 5mC. Overall, our data suggest that miR-29 family up-regulation might represent an endogenous mechanism aimed at ameliorating the age-dependent cardiac damage leading to hypertrophy and fibrosis.

2018-02-27 | GSE107003 | GEO

Modulation of miR-29 influences myocardial compliance likely through coordinated regulation of calcium handling and extracellular matrix

Project description:MicroRNAs (miRs) control the expression of diverse subsets of target mRNAs, and studies have found miR dysregulation in failing hearts. Expression of miR-29 is abundant in heart, increased with aging, and altered in cardiomyopathies. Prior studies demonstrate that miR-29 reduction via genetic knockout or pharmacologic blockade can blunt cardiac hypertrophy and fibrosis in mice. Surprisingly, this depended on specifically blunting miR-29 actions in cardiomyocytes versus fibroblasts. To begin developing more translationally-relevant vectors, we generated a novel transgene-encoded miR-29 inhibitor (TuD-29) that can be incorporated into a viral-mediated gene therapy for cardioprotection. Herein, we corroborate that miR-29 expression and activity is higher in cardiomyocytes versus fibroblasts and demonstrate that TuD-29 effectively blunts hypertrophic responses in cultured cardiomyocytes and mouse hearts. Furthermore, we found that adeno-associated viral (AAV)-mediated miR-29 overexpression in mouse hearts induces early diastolic dysfunction, whereas AAV:TuD-29 treatment improves cardiac output by increasing end-diastolic and stroke volumes. Integration of RNA-seq and miR-target interactomes reveals that miR-29 regulates genes involved in calcium handling, cell stress and hypertrophy, metabolism, ion transport, and extracellular matrix remodeling. These investigations support a likely versatile role for miR-29 in influencing myocardial compliance and relaxation, potentially providing a unique therapeutic avenue to improve diastolic function in heart failure patients.

2023-11-21 | GSE241423 | GEO

TGFβ-Induced Proteins in Non-Endocrine Mouse Pituitary Cell Line TtT/GF

Project description:TtT/GF is a mouse pituitary cell line derived from radiothyroidectomy-induced thyrotropic pituitary tumor and has been recognized as a model of folliculostellate cells. Our previous studies suggested that TtT/GF cells have cellular plasticity, rather than representing a model only for folliculostellate cells. We found that transforming growth factor beta (TGFβ) reinforces pericyte properties (Tsukada et al. Cell and Tissue Research, 371: 339-350, 2018). In order to extensively identify TGFβ-induced proteins in TtT/GF cells, the present study performed mass spectrometry analysis combined with the stable isotope labeling of amino acids in cell culture (SILAC) system. TtT/GF cells were cultured in either light medium (containing normal Arg/Lys) or heavy medium (containing 13C6-labelled Arg/Lys) in the presence of vehicle (light), TGFβ (heavy), or selective TGFβ receptor I inhibitor (SB431542, heavy). Collected proteins were then analyzed by mass spectrometry. We successfully found 51 up-regulated and 112 down-regulated proteins, which are related to actin cytoskeleton, cell adhesion, extracellular matrix, and DNA replication. The result also showed up-regulation of many pericyte markers/pointers, supporting our previous hypothesis. Intriguingly, we found down-regulation of several pituitary adenoma markers. Mass spectrometry data using SILAC will provide valuable information about pathological processes in pituitary adenomas, as well as pericyte differentiation.

2019-03-19 | PXD009245 | JPOST Repository

Transcriptome analysis of IMR-90 human fibroblasts following oncogene-induced and replicative senescence

Project description:By transcriptome analysis of IMR-90 human fibroblasts following oncogene-induced senescence (OIS) and replicative senescence (RS), we identified commonly regulated genes in both conditions.

2017-03-30 | GSE86546 | GEO

Sequencing of human IMR-90 at 27 and 55 population doublings

Project description:Comparisong of gene expression of human IMR-90 at 27 and 55 population doublings. RNA-seq data comprises 2 groups: 27 and 55 population doublings of IMR-90. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

2021-10-19 | GSE117813 | GEO

Inhibition of miR-29 has a significant lipid-lowering benefit through suppression of lipogenic programs in liver

Project description:MicroRNAs (miRNAs) are important regulators and potential therapeutic targets of metabolic disease. In this study we show by in vivo administration of locked nucleic acid (LNA) inhibitors that suppression of endogenous miR-29 lowers plasma cholesterol levels by ~40%, commensurate with the effect of statins, and reduces fatty acid content in the liver by ~20%. Whole transcriptome sequencing of the liver reveals 883 genes dysregulated (612 down, 271 up) by inhibition of miR-29. The set of 612 down-regulated genes are most significantly over-represented in lipid synthesis pathways. Among the up-regulated genes are the anti-lipogenic deacetylase sirtuin 1 (Sirt1) and the anti-lipogenic transcription factor aryl hydrocarbon receptor (Ahr), the latter of which we demonstrate is a direct target of miR-29. In vitro radiolabeled acetate incorporation assays confirm that pharmacologic inhibition of miR-29 significantly reduces de novo cholesterol and fatty acid synthesis. Our findings indicate that miR-29 controls hepatic lipogenic programs, likely in part through regulation of Ahr and Sirt1, and therefore may represent a candidate therapeutic target for metabolic disorders such as dyslipidemia.

2015-08-07 | GSE63493 | GEO

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