This month’s study focuses on the role of IGF-1, Cytokines, and miR-181D in Glioblastoma progression, and comes from the lab of Ku-Chung Chen and others at Taipei Medical University in Taiwan. The article was published 7 April 2017 in the journal Scientific Reports and includes miRNA expression data generated by the Phalanx Biotech service lab using our Human miRNA OneArray Microarray platform.
Glioblastoma is aggressive cancer that accounts for nearly 15% of all brain cancers. More specifically, the authors look at cytokine and miRNA expression within the larger cellular signaling network mediated by insulin-like growth factor 1 (IGF-1). Many studies indicate a role for IGF1, cytokines, and miRNAs in glioblastoma progression, but no one has ever sought to connect these players into a functional cellular signaling axis.
Integrated Analysis of mRNA and miRNA Expression
The authors start by performing an integrated analysis of mRNA and miRNA expression using existing genome data collected from human patients as part of the Cancer Genome Atlas (TCGA). They divide the patient data into 2 groups (low and high IGF-1 expression), identify differentially expressed genes (DEGs) between these 2 groups (nearly 6000), and look for enriched gene ontologies among the DEGs. Interestingly, they find that the most significantly enriched gene ontology associated with IGF-1 expression is “cytokine-cytokine receptor interaction,” containing 125 DEGs total. Of these 125 DEGs, the authors further focus on 48 core cytokines that are up-regulated in patients with elevated IGF-1 expression.
The authors then repeat this same analysis of TCGA data but query RNA-Seq data, rather than microarray data. Consistent with the microarray results, they find a large number of DEGs (nearly 4600) between patients grouped by high and low IGF-1 expression. The list of DEGs contains 138 genes involved in “cytokine-cytokine receptor interaction,” of which 87 are core cytokines. Most notably, there is an overlap of 32 core cytokines with the microarray data analysis. The Venn diagram showing the overlap between the microarray and RNA-Seq data sets, along with the core 32 cytokine-related genes is presented above.
To delve into the miRNA part of the picture, the authors analyze TCGA miRNA data. They find 6 miRNAs significantly down-regulated in patients with elevated IGF-1 expression. To help identify “core” miRNAs involved in the IGF-1 pathway, the authors use the Human miRNA OneArray Microarray to profile miRNA expression in IGF-1-stimulated U87-MG glioma cells. This experiment identifies 179 down-regulated miRNAs, of which 4 overlap with the TCGA data – miR-9-5p, miR-9-3p, miR-181d, and miR-130b.
miR-181d and IGF-1 are Prognostic Indicators for Glioblastoma
miR-181d becomes the next focus, as this miRNA putatively targets many of the cytokine-related DEGs identified in the TCGA mRNA expression data analysis. The authors treat glioma cell lines with IGF-1 and show that miR-181d decreases in a dose-dependent fashion as IGF-1 levels increase. They also show that endogenous miR-181d is down-regulated in glioma cells lines relative to normal human astrocytes. Going back to the TCGA data, the authors ask whether patient survival is correlated with IGF-1 and miR-181d expression level. Interestingly, they find that low IGF-1/high miR-181d patients demonstrated significantly longer survival compared to high IGF-1/low miR-181d patients. These results ultimately point to IGF-1 and miR-181d being strong prognostic indicators for glioblastoma.
CCR1 and IL1B are Targets of miR-181d
Two of the core cytokines regulated by IGF-1 are CCR1 and IL1B. Using miRNA target prediction tools, the authors find that these genes are putative targets of miR-181d. They further show evidence that CCR1 and IL1B are indeed direct targets of miR-181d, and that treatment with exogenous miR-181d decreases the expression of CCR1 and IL1B transcripts and protein in a dose-dependent fashion. Lastly, they further elucidate this signaling axis by showing that IGF-1 induces dose-dependent increases in both mRNA and protein levels of IL-1b and CCR1, and that miR-181d overexpression significantly attenuates IGF-1-upregulated IL-1b and CCR1 levels.
In summary, the authors have uncovered a potent cell signaling axis underlying glioblastoma development. They took a genomic approach by utilizing publically available microarray and RNA-Seq data sets and by generating new microarray data on the Human miRNA OneArray Microarray. The most exciting results discussed here include: 1) IGF-1 and miR-181d as prognostic indicators for gliobastoma; and 2) concrete evidence that miR-181d targets transcripts of CCR1 and IL1B.
At Phalanx Biotech, we help you achieve success in your research. Please contact us if you’re interested in our miRNA expression profiling services on either Agilent or our own OneArray platforms. We are also experts in NGS services, qPCR services, and gene expression microarray services. No matter what genomics approach you need, contact us, and we’ll be sure to accelerate the pace of your research.
Ho KH et al. Identification of IGF-1-enhanced cytokine expressions targeted by miR-181d in glioblastomas via an integrative miRNA/mRNA regulatory network analysis (2017). Scientific Reports 7: 732.