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Comparative evaluation of miRNA expression between in vitro and in vivo airway epithelium demonstrates widespread differences.

ABSTRACT: Airway epithelial cells cultured at an air-liquid interface bear many hallmarks of in vivo cells and are used extensively to study the biology of the lung epithelium. Because miRNAs regulate many cellular functions, we postulated that miRNA profiling would provide an unbiased assessment of the effects of in vitro culturing. RNA was extracted from primary airway epithelial cells either immediately after cell procurement (in vivo condition) or after air-liquid interface culture was established (in vitro condition). We assessed 742 miRNAs and determined differential expression between in vivo and in vitro conditions. Air-liquid interface culturing of airway epithelial cells caused widespread changes in miRNA expression. A similarly extensive alteration in gene expression was observed in an independent set of publicly available microarray data. We integrated miRNA and gene expression results to identify culture-induced differences in transcriptional programs (including several involved in epithelial injury and repair). Air-liquid interface cultures are useful models for studying airway biology, but the present findings indicate that, despite phenotypic similarities with primary cells, these culture systems profoundly perturb miRNA and gene expression. Studies of lung epithelium based on in vitro culture should therefore be designed and interpreted with an appreciation of the limitations of air-liquid interface culture systems.

SUBMITTER: Chen P

PROVIDER: S-EPMC3814685 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

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Comparative evaluation of miRNA expression between in vitro and in vivo airway epithelium demonstrates widespread differences.

Chen Peter P Edelman Jeffrey D JD Gharib Sina A SA

The American journal of pathology 20130831 5

Airway epithelial cells cultured at an air-liquid interface bear many hallmarks of in vivo cells and are used extensively to study the biology of the lung epithelium. Because miRNAs regulate many cellular functions, we postulated that miRNA profiling would provide an unbiased assessment of the effects of in vitro culturing. RNA was extracted from primary airway epithelial cells either immediately after cell procurement (in vivo condition) or after air-liquid interface culture was established (in ...[more]

PMID: 24001474

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Project description:BackgroundPair bonding with a reproductive partner is rare among mammals but is an important feature of human social behavior. Decades of research on monogamous prairie voles (Microtus ochrogaster), along with comparative studies using the related non-bonding meadow vole (M. pennsylvanicus), have revealed many of the neural and molecular mechanisms necessary for pair-bond formation in that species. However, these studies have largely focused on just a few neuromodulatory systems. To test the hypothesis that neural gene expression differences underlie differential capacities to bond, we performed RNA-sequencing on tissue from three brain regions important for bonding and other social behaviors across bond-forming prairie voles and non-bonding meadow voles. We examined gene expression in the amygdala, hypothalamus, and combined ventral pallidum/nucleus accumbens in virgins and at three time points after mating to understand species differences in gene expression at baseline, in response to mating, and during bond formation.ResultsWe first identified species and brain region as the factors most strongly associated with gene expression in our samples. Next, we found gene categories related to cell structure, translation, and metabolism that differed in expression across species in virgins, as well as categories associated with cell structure, synaptic and neuroendocrine signaling, and transcription and translation that varied among the focal regions in our study. Additionally, we identified genes that were differentially expressed across species after mating in each of our regions of interest. These include genes involved in regulating transcription, neuron structure, and synaptic plasticity. Finally, we identified modules of co-regulated genes that were strongly correlated with brain region in both species, and modules that were correlated with post-mating time points in prairie voles but not meadow voles.ConclusionsThese results reinforce the importance of pre-mating differences that confer the ability to form pair bonds in prairie voles but not promiscuous species such as meadow voles. Gene ontology analysis supports the hypothesis that pair-bond formation involves transcriptional regulation, and changes in neuronal structure. Together, our results expand knowledge of the genes involved in the pair bonding process and open new avenues of research in the molecular mechanisms of bond formation.

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Comparative evaluation of miRNA expression between in vitro and in vivo airway epithelium demonstrates widespread differences.

Publications

Comparative evaluation of miRNA expression between in vitro and in vivo airway epithelium demonstrates widespread differences.

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