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MicroRNA and mRNA expression profiling in rat acute respiratory distress syndrome.

Huang C, Xiao X, Chintagari NR, Breshears M, Wang Y, Liu L - BMC Med Genomics (2014)

Bottom Line: The expression of 27 miRNAs and 37 mRNAs were found to be significantly changed.While Sod2 was inversely correlated with Let-7a, b, c, f., Ebf1 and Apc were inversely correlated with miR-24 and miR-26a, respectively. miR-26a, miR-346, miR-135b, miR-30a/b, miR-344, and miR-18a targeted multiple altered mRNAs.Gabrb1, Sod2, Eif2ak1, Fbln5, and Tspan8 were targeted by multiple altered miRNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Physiological Sciences, Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Stillwater, OK, USA. lin.liu@okstate.edu.

ABSTRACT

Background: Acute respiratory distress syndrome (ARDS) is characterized by pulmonary epithelial injury and extensive inflammation of the pulmonary parenchyma. Systematic analyses of microRNA (miRNA) and mRNA expression profiling in ARDS provide insights into understanding of molecular mechanisms of the pathogenesis of ARDS. The objective of this study was to identify miRNA and mRNA interactions in a rat model of ARDS by combining miRNA and mRNA microarray analyses.

Methods: Rat model of ARDS was induced by saline lavage and mechanical ventilation. The expression profiles of both mRNAs and miRNAs in rat ARDS model were performed by microarray analyses. Microarray data were further verified by quantitative RT-PCR. Functional annotation on dys-regulated mRNAs and miRNAs was carried out by bioinformatics analysis.

Results: The expression of 27 miRNAs and 37 mRNAs were found to be significantly changed. The selected miRNAs and genes were further verified by quantitative real-time PCR. The down-regulated miRNAs included miR-24, miR-26a, miR-126, and Let-7a, b, c, f. The up-regulated miRNAs were composed of miR-344, miR-346, miR-99a, miR-127, miR-128b, miR-135b, and miR-30a/b. Gene ontology and functional annotation analyses indicated that up-regulated mRNAs, such as Apc, Timp1, and Sod2, were involved in the regulation of apoptosis. Bioinformatics analysis showed the inverse correlation of altered miRNAs with the expression of their predicted target mRNAs. While Sod2 was inversely correlated with Let-7a, b, c, f., Ebf1 and Apc were inversely correlated with miR-24 and miR-26a, respectively. miR-26a, miR-346, miR-135b, miR-30a/b, miR-344, and miR-18a targeted multiple altered mRNAs. Gabrb1, Sod2, Eif2ak1, Fbln5, and Tspan8 were targeted by multiple altered miRNAs.

Conclusion: The expressions of miRNAs and mRNAs were altered in a rat model of ARDS. The identified miRNA-mRNA pairs may play critical roles in the pathogenesis of ARDS.

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Related in: MedlinePlus

Validation of mRNA microarray data by real-time PCR. Total RNA was extracted from control (CON) and ARDS rat lungs. The expression of mRNAs relative to 18S rRNA was determined by real-time PCR. The results were expressed as a ratio of ARDS to CON. Data are presented as means ± SD from 4 animals, each assay performed in duplicate. *p < 0.05, v.s. CON. Microarray: SAM test; Real time PCR: t-test.
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Figure 3: Validation of mRNA microarray data by real-time PCR. Total RNA was extracted from control (CON) and ARDS rat lungs. The expression of mRNAs relative to 18S rRNA was determined by real-time PCR. The results were expressed as a ratio of ARDS to CON. Data are presented as means ± SD from 4 animals, each assay performed in duplicate. *p < 0.05, v.s. CON. Microarray: SAM test; Real time PCR: t-test.

Mentions: DNA microarray was performed to identify the altered mRNAs in ARDS using an in-house printed DNA microarray containing 10,000 rat genes. The microarray data were deposited to the GEO database: http://www.ncbi.nlm.nih.gov/geo/, GSE57011. The expression of 37 genes was significantly changed based on a q value of <0.05 (SAM test) and a fold change of ≥ 2 (Table 3). Among them, eleven genes were up-regulated and twenty six genes were down-regulated. Sod2 (Superoxide dismutase 2) and Timp1 (Metalloproteinase inhibitor 1) modulate lung injury [26,27]. Ramp2 [Receptor (calcitonin) activity modifying protein 2], Acaa2 (Acetyl-Coenzyme A acyltransferase 2), Mdh1 (Malate dehydrogenase 1, NAD), and Tspan8 (Tetraspanin 8) are enriched mRNAs in the lungs and are involved in lung disease [28,29]. These mRNAs were selected for validation by qRT-PCR. The results in Figure 3 showed that Sod2 and Timp1 were confirmed to be up-regulated in ARDS. Ramp2, Acaa2, Mdh1, and Tspan8 were confirmed to be down-regulated in ARDS.


MicroRNA and mRNA expression profiling in rat acute respiratory distress syndrome.

Huang C, Xiao X, Chintagari NR, Breshears M, Wang Y, Liu L - BMC Med Genomics (2014)

Validation of mRNA microarray data by real-time PCR. Total RNA was extracted from control (CON) and ARDS rat lungs. The expression of mRNAs relative to 18S rRNA was determined by real-time PCR. The results were expressed as a ratio of ARDS to CON. Data are presented as means ± SD from 4 animals, each assay performed in duplicate. *p < 0.05, v.s. CON. Microarray: SAM test; Real time PCR: t-test.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4128536&req=5

Figure 3: Validation of mRNA microarray data by real-time PCR. Total RNA was extracted from control (CON) and ARDS rat lungs. The expression of mRNAs relative to 18S rRNA was determined by real-time PCR. The results were expressed as a ratio of ARDS to CON. Data are presented as means ± SD from 4 animals, each assay performed in duplicate. *p < 0.05, v.s. CON. Microarray: SAM test; Real time PCR: t-test.
Mentions: DNA microarray was performed to identify the altered mRNAs in ARDS using an in-house printed DNA microarray containing 10,000 rat genes. The microarray data were deposited to the GEO database: http://www.ncbi.nlm.nih.gov/geo/, GSE57011. The expression of 37 genes was significantly changed based on a q value of <0.05 (SAM test) and a fold change of ≥ 2 (Table 3). Among them, eleven genes were up-regulated and twenty six genes were down-regulated. Sod2 (Superoxide dismutase 2) and Timp1 (Metalloproteinase inhibitor 1) modulate lung injury [26,27]. Ramp2 [Receptor (calcitonin) activity modifying protein 2], Acaa2 (Acetyl-Coenzyme A acyltransferase 2), Mdh1 (Malate dehydrogenase 1, NAD), and Tspan8 (Tetraspanin 8) are enriched mRNAs in the lungs and are involved in lung disease [28,29]. These mRNAs were selected for validation by qRT-PCR. The results in Figure 3 showed that Sod2 and Timp1 were confirmed to be up-regulated in ARDS. Ramp2, Acaa2, Mdh1, and Tspan8 were confirmed to be down-regulated in ARDS.

Bottom Line: The expression of 27 miRNAs and 37 mRNAs were found to be significantly changed.While Sod2 was inversely correlated with Let-7a, b, c, f., Ebf1 and Apc were inversely correlated with miR-24 and miR-26a, respectively. miR-26a, miR-346, miR-135b, miR-30a/b, miR-344, and miR-18a targeted multiple altered mRNAs.Gabrb1, Sod2, Eif2ak1, Fbln5, and Tspan8 were targeted by multiple altered miRNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Physiological Sciences, Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Stillwater, OK, USA. lin.liu@okstate.edu.

ABSTRACT

Background: Acute respiratory distress syndrome (ARDS) is characterized by pulmonary epithelial injury and extensive inflammation of the pulmonary parenchyma. Systematic analyses of microRNA (miRNA) and mRNA expression profiling in ARDS provide insights into understanding of molecular mechanisms of the pathogenesis of ARDS. The objective of this study was to identify miRNA and mRNA interactions in a rat model of ARDS by combining miRNA and mRNA microarray analyses.

Methods: Rat model of ARDS was induced by saline lavage and mechanical ventilation. The expression profiles of both mRNAs and miRNAs in rat ARDS model were performed by microarray analyses. Microarray data were further verified by quantitative RT-PCR. Functional annotation on dys-regulated mRNAs and miRNAs was carried out by bioinformatics analysis.

Results: The expression of 27 miRNAs and 37 mRNAs were found to be significantly changed. The selected miRNAs and genes were further verified by quantitative real-time PCR. The down-regulated miRNAs included miR-24, miR-26a, miR-126, and Let-7a, b, c, f. The up-regulated miRNAs were composed of miR-344, miR-346, miR-99a, miR-127, miR-128b, miR-135b, and miR-30a/b. Gene ontology and functional annotation analyses indicated that up-regulated mRNAs, such as Apc, Timp1, and Sod2, were involved in the regulation of apoptosis. Bioinformatics analysis showed the inverse correlation of altered miRNAs with the expression of their predicted target mRNAs. While Sod2 was inversely correlated with Let-7a, b, c, f., Ebf1 and Apc were inversely correlated with miR-24 and miR-26a, respectively. miR-26a, miR-346, miR-135b, miR-30a/b, miR-344, and miR-18a targeted multiple altered mRNAs. Gabrb1, Sod2, Eif2ak1, Fbln5, and Tspan8 were targeted by multiple altered miRNAs.

Conclusion: The expressions of miRNAs and mRNAs were altered in a rat model of ARDS. The identified miRNA-mRNA pairs may play critical roles in the pathogenesis of ARDS.

Show MeSH
Related in: MedlinePlus