Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA260426 | ENA |
REPOSITORIES: ENA
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Project description:Type II cell differentiation and expression of the major surfactant protein, SP-A, in midgestation human fetal lung (HFL) are markedly induced by cAMP and inhibited by TGF-β. cAMP induction of SP-A promoter activity is mediated by increased phosphorylation and in vivo binding of TTF-1/Nkx2.1, a critical transcription factor in lung development. To further define mechanisms for developmental induction of surfactant synthesis in HFL, herein, we investigated the potential role of microRNAs (miRNAs, miRs). To identify and characterize differentially regulated miRNAs in mid-gestation HFL explants during type II pneumocyte differentiation in culture, we performed miRNA microarray analysis of RNA isolated from epithelial cells from midgestation HFL explants before and after culture ± Bt2cAMP. Interestingly, the miR-200 family was significantly upregulated during type II cell differentiation; miR-200 family induction was inversely correlated with expression of its known targets, transcription factors ZEB1 and ZEB2, and TGF-b2. miR-200 antagonists inhibited TTF-1 and SP-A expression and upregulated TGF-β2 and ZEB1 expression in type II cells. Overexpression of ZEB1 in cultured type II cells decreased DNA binding of endogenous TTF-1, blocked cAMP stimulation of SP-A and inhibited miR-200 expression,whereas, cAMP markedly inhibited ZEB1/2 and TGF-β. Importantly, overexpression of ZEB1 or miR-200 antagonists in HFL type II cells markedly suppressed accumulation of lamellar bodies, organelles that store surfactant. Our findings suggest that the miR-200 family and ZEB1, which exist in a double-negative feedback loop regulated by TGF-β, serve important regulatory roles in the developmental regulation of type II cell differentiation and SP-A expression in HFL.
2015-10-01 | GSE61183 | GEO
Project description:To investigate the roles of miR-200 family memebrs in the regulation of lung cancer-associated fibroblasts (CAFs), we overexpressed miR-200b/a/429 cluster in murine lung CAFs through lentiviral infection. We then performed gene expression profiling analysis using data obtained from RNA-seq of control and miR-200-overexpressed CAFs.
2024-04-08 | GSE226886 | GEO
Project description:Transcription factors such as Tbx5, Gata4, Mef2c and Pitx2 are required during cardiac development, and in adult cardiac homeostasis. We demonstrate that the gene dosage and modulation of these factors are mediated in vivo by the miR-200 family. These microRNAs (miRs) are expressed during early stages of heart development, and they regulate a highly complex gene regulatory network (GRN). To study the in vivo and in vitro function of specific miR-200 family members we inhibited individual members of the miR-200 family during embryonic development. Inhibition of a single miR-200 family member within the cluster caused defects in the left ventricle and cardiomyocyte maturation during development. Inhibition of the entire miR-200 family resulted in a ventral septal defect and embryonic lethality by embryonic day (E)16.5. In cardiomyocytes, the miR-200 family targets the transcripts of Tbx5, Gata4, Mef2c and Pitx2. Inhibition of this family increased expression of Tbx5, Gata4, Mef2c and Pitx2 in both the left ventricle and atria across multiple stages of cardiac development. Embryos with reduced levels of a single miR-200 family member were non-lethal and pups survived into adulthood. At postnatal day (P) 1 these pups had a reduced heart rate and increased ventricular wall thickness. Each miR-200 family has distinct heart phenotypes in cell specific differentiation and maturation. snRNA-sequencing revealed a new cardiomyocyte cell state, suggesting these cells were less differentiated due to inhibition of the miR-200 family. We have identified several new transcription factors regulated by miR-200 during heart development. The miR-200 family are critical regulators of early cardiac development through maintaining gene dosage of Tbx5, Gata4, Mef2c and Pitx2, which affects cardiomyocyte differentiation and maturation. The multiomics analyses of early heart development after miR-200 inhibition reveals a new cardiomyocyte less differentiated cell state and chromatin modifications due to the function of the miR-200 family.
2025-07-12 | GSE272154 | GEO
Project description:The objective of this study was to identify miR-200 family member target sites. Of note, CLEAR-CLIP captures all miRNAs, not one family specifically. So data for all miRNAs is included. CLEAR-CLIP on murine keratinocytes grown in culture. Keratinocytes were either wild type, miR-200 family double knock out or miR-200b/miR-200a/miR-429 cluster inducible.
2018-03-16 | GSE102716 | GEO
Project description:Mechanical forces are essential for normal fetal lung development. However, the cellular and molecular mechanisms regulating this process remain largely unknown. In the present study, we used oligonucleotide microarray technology to investigate gene expression profile in cultured E19 rat fetal lung type II epithelial cells exposed to a level of mechanical strain similar to that observed in utero. Significance Analysis of Microarrays (SAM) identified 92 genes differentially expressed by strain. Interestingly, several members of the solute carrier family of amino acid transporters, genes involved in amino acid synthesis and development, and amiloride-sensitive epithelial sodium channel gene were induced by strain. These results were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). Thus, this study identifies genes induced by strain that may be important for amino acid signaling pathways, protein synthesis and development in fetal type II cells. In addition, these data suggest that mechanical forces may contribute to facilitate lung fluid reabsorption in preparation for birth. Taken together, the present investigation provides further insights into how mechanical forces may modulate fetal lung development. Keywords: lung development, fetal type II epithelial cells, strain response, microarray
2006-04-29 | GSE3541 | GEO
Project description:The cAMP response element binding protein (Creb) is a member of a leucine zipper transcription factor family that regulates gene expression primarily in response to the intracellular cAMP signalling pathway. Previous studies have shown Creb1-null mice suffer respiratory failure with lung atelectasis and a large reduction in Sftpd mRNA. Using a new line of Creb1-null mice we have further investigated Creb function in the developing mouse lung, focussing on differentiation of the airway epithelium. The lungs of Creb1-null fetal mice showed normal respiratory development until E17.5 when proximal and distal airways fail to inflate. Subsequent ultrastructural analysis of the lungs of E17.5 Creb1-null fetal mice revealed a defect in AEC differentiation with a reduction in proportions of type-II AECs and in particular, a very large reduction in type-I AECs. Furthermore, immunostaining for the proximal epithelial cell markers Scgb1a1 (also known as CC10) (Clara cells), Foxj1 (Ciliated cells), and CGRP (Neuroendocrine cells) showed delayed or defective proximal epithelial differentiation in Creb1-null fetal lungs. Quantitative real time PCR (qRT-PCR) analysis at E17.5 in Creb1-null fetal lungs showed differential expression of mRNAs for Creb/Atf1 subfamily members, surfactant-associated proteins, type-I AEC markers and proximal epithelial markers. Furthermore, whole-genome microarray analysis at E17.5 in Creb1-null fetal lungs has provided novel genes which will prove useful to further investigate Creb-mediated signalling in lung development. Together these results demonstrate that Creb plays a key role in determining cell lineages and differentiation of the developing lung epithelium.
2009-04-30 | E-MEXP-1295 | biostudies-arrayexpress
Project description:Studies of human fetal lung in explant culture and in isolated epithelial cells have demonstrated that both glucocorticoids and cyclic AMP promote differentiated alveolar type II cell phenotype as assessed by ultrastructural morphology and surfactant production. This project profiles changes in gene expression associated with hormone induced differentiation. Undifferentiated human fetal lung (13-20 wk) epithelial cells were cultured in serum-free medium (control) or with dexamethasone/8-Bromo cyclic AMP/isobutylmethylxanthine (DCI) to promote type II cell differentiation. RNA from five sets of experiments (10 samples) was evaluated using the U133A Affymetrix GeneChip set. Keywords: Hormone treatment
2005-09-21 | GSE3306 | GEO
Project description:We used transcription activator-like effector nucleases (TALENs) to generate knockout cells for two related microRNAs (miRNAs), mir-141 and mir-200c, which belong to the deeply conserved mir-200 family. By carrying out deep sequencing, we identified the target genes of each miRNA. Interestingly, miR-141 and miR-200c, despite their overall similarity, suppressed largely non-overlapping groups of targets. Analysis of global mRNA level change in mir-141 and mir-200c knockout compared to wild type cells
2013-09-27 | E-GEOD-51217 | biostudies-arrayexpress
Project description:Cell-specific gene expression is achieved by a combination of mechanisms including transcriptional and post-transcriptional regulation. The transcription factor Nkx2-1, essential for lung cell differentiation, mainly acts in transcriptional activation but can directly or indirectly repress gene expression. microRNAs are a class of small non-coding RNA that control one of the major mechanisms of gene repression. To identify miRNAs regulated by Nkx2-1 that may mediate its repressing effects, we knocked-down Nkx2-1 in mouse lung epithelial cell lines and systematically identified targets by genome-wide miR and mRNA expression analyses. Nkx2-1 controls expression of miRs known to contribute to lung cell differentiation in development and disease and others not previously described. Amongst the significantly altered miRs, the mir-106a-363 cluster, miR-1195, miR-378, and miR-346 are directly correlated with the levels of Nkx2-1, whereas miR-200c/b, miR-221, and miR- 222 are inversely correlated. These miRNAs are expressed in embryonic lung at day E11.5, and/or E19.5 determined by in-situ hybridization. Expression of predicted targets of mir-1195, mir-346 and miR-200c and mir-221/222 were evaluated by mRNA expression microarrays in Nkx2-1 knockdown cells identifying those anti-correlated to the corresponding miRNA expression. Genes regulated by mir-1195, Cyp2s1 and Map3k2, by mir-346, Klf6, and miR-200c, Myb, Nfib, and Six1, were validated by qRT-PCR. Inhibition of mir-1195 confirms the inverse correlation of this miRNA with its putative targets Cyp2s1 and Map3k2. This miRNA-mRNA expression analysis identifies potential paths of Nkx2-1 mediated gene repression, and contributes to the understanding of gene regulation in lung epithelial differentiation and development. Nkx2-1 mRNA was knocked down in lung epithelial cells using a lentivirus expressing a shRNA targeting Nkx2-1 (n=3) and compared to empty vector controls (n=3).
2015-12-22 | E-GEOD-47054 | biostudies-arrayexpress
Project description:Cell-specific gene expression is achieved by a combination of mechanisms including transcriptional and post-transcriptional regulation. The transcription factor Nkx2-1, essential for lung cell differentiation, mainly acts in transcriptional activation but can directly or indirectly repress gene expression. microRNAs are a class of small non-coding RNA that control one of the major mechanisms of gene repression. To identify miRNAs regulated by Nkx2-1 that may mediate its repressing effects, we knocked-down Nkx2-1 in mouse lung epithelial cell lines and systematically identified targets by genome-wide miR and mRNA expression analyses. Nkx2-1 controls expression of miRs known to contribute to lung cell differentiation in development and disease and others not previously described. Amongst the significantly altered miRs, the mir-106a-363 cluster, miR-1195, miR-378, and miR-346 are directly correlated with the levels of Nkx2-1, whereas miR-200c/b, miR-221, and miR- 222 are inversely correlated. These miRNAs are expressed in embryonic lung at day E11.5, and/or E19.5 determined by in-situ hybridization. Expression of predicted targets of mir-1195, mir-346 and miR-200c and mir-221/222 were evaluated by mRNA expression microarrays in Nkx2-1 knockdown cells identifying those anti-correlated to the corresponding miRNA expression. Genes regulated by mir-1195, Cyp2s1 and Map3k2, by mir-346, Klf6, and miR-200c, Myb, Nfib, and Six1, were validated by qRT-PCR. Inhibition of mir-1195 confirms the inverse correlation of this miRNA with its putative targets Cyp2s1 and Map3k2. This miRNA-mRNA expression analysis identifies potential paths of Nkx2-1 mediated gene repression, and contributes to the understanding of gene regulation in lung epithelial differentiation and development. Nkx2-1 mRNA was knocked down in lung epithelial cells using a lentivirus expressing a shRNA targeting Nkx2-1 (n=3) and compared to empty vector controls (n=3).
2015-12-22 | E-GEOD-47053 | biostudies-arrayexpress