Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data.
The process of adipogenesis is controlled in a highly orchestrated manner, including transcriptional and post-transcriptional events. In developing 3T3-L1 pre-adipocytes, this program can be interrupted by all-trans retinoic acid (ATRA). To examine this inhibiting impact by ATRA, we generated large-scale transcriptomic data on the microRNA and mRNA level. Non-coding RNAs such as microRNAs represent a field in RNA turnover, which is very important for understanding the regulation of mRNA gene expression. High throughput mRNA and microRNA expression profiling was performed using mRNA hybridisation microarray technology and multiplexed expression assay for microRNA quantification. After quantitative measurements we merged expression data sets, integrated the results and analysed the molecular regulation ofin vitroadipogenesis. For this purpose, we applied local enrichment analysis on the integrative microRNA-mRNA network determined by a linear regression approach. This approach includes the target predictions of TargetScan Mouse 5.2 and 23 pre-selected, significantly regulated microRNAs as well as Affymetrix microarray mRNA data. We found that the cellular lipid metabolism is negatively affected by ATRA. Furthermore, we were able to show that microRNA 27a and/or microRNA 96 are important regulators of gap junction signalling, the rearrangement of the actin cytoskeleton as well as the citric acid cycle, which represent the most affected pathways with regard to inhibitory effects of ATRA in 3T3-L1 preadipocytes. In conclusion, the experimental workflow and the integrative microRNA-mRNA data analysis shown in this study represent a possibility for illustrating interactions in highly orchestrated biological processes. Further the applied global microRNA-mRNA interaction network may also be used for the pre-selection of potential new biomarkers with regard to obesity or for the identification of new pharmaceutical targets.
Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
Katharina
K
Stoecker
Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Oberschleißheim, Germany.
Steffen
S
Sass
Institute of Computational Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Oberschleißheim, Germany; Department of Mathematics, Technical University of Munich, Garching, Germany.
Fabian J
FJ
Theis
Else-Kröner-Fresenius-Centre for Nutritional Medicine, ZIEL Research Center for Nutrition and Food Sciences, Technical University of Munich, Freising, Germany; Else Kröner-Fresenius-Centre for Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.
Hans
H
Hauner
Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
Michael W
MW
Pfaffl
3T3-L1 cells; Adipogenesis; All-trans retinoic acid (ATRA); MicroRNA–mRNA interaction; Multiple linear regression models; Regulation of biological pathways