P07.03 A gene co-expression network analysis for Snail and Slug identifies IL1R1, an inflammatory interleukin to be preferentially expressed in ST-EPN-RELA and PF-EPN-A molecular subgroups of intracranial ependymomas
Authors: P. Malgulwar, A. Tomar, M. Singh, V. Suri, C. Sarkar, M. Sharma
Journal: Neuro-Oncology (2017)

Introduction: Ependymomas are rare glial tumors which displays a dismal prognosis with higher occurrence in children and intracranial location. Accumulating evidences has proposed molecular grouping for ependymomas where ST-EPN-RELA and PF-EPN-A, are the two molecular subgroups associated with worst prognosis. Snail and Slug are the cardinal EMT-transcription factors and its overexpression has been reported in several CNS tumors. We hypothesized up-regulation of Snail and Slug expressions and gene sets/modules that are co-expressed with Snail and Slug may have significant impact in pathogenesis of ependymomas. Materials and Methods: We performed bioinformatics analysis of 4 independent ependymoma cohorts for Snail and Slug gene expression(n=284). Co-expression network analysis for Snail and Slug was constructed using R2 software and pathway analysis was performed using KEGG. qRT-PCR was performed for expression validation of Snail, Slug and IL1R1(n=84). RELA fusion analysis was done using PCR followed by Sanger Sequencing. Methylation data for IL1R1 was analyzed using GSE65362. Survival analysis was constructed on in-house data and on external cohort(GSE27287). Results: We observed upregulation for Snail and Slug expressions in intracranial ependymomas across 4 datasets. Construction of co-expression network identified 634 genes for Snail with TGF-β, PPAR signaling and Phosphatidylinositol signaling and 757 genes for Slug with Focal adhesion, ECM-receptor interaction and Regulation of actin cytoskeleton related pathways.Of 37 genes common for Snail and Slug, IL1R1, a cytokine receptor from interleukin-1 receptor family, was found to have significant positive correlation with Snail and Slug expressions (R=0.671; p=0.003) and was preferentially expressed in ST-EPN-RELA and PF-EPN-A molecular groups. Pathway interactor analysis showed IL1R1 interacts with members of NF-kB, MAPK and JAK-STAT signaling pathways. Comparison of IL1R1 expression with other CNS tumors (glioblastomas, medulloblastomas, meningioma and CNS/PNET) reported an overexpression favorably in ependymomas. Interestingly, 62% of neural stem cells (NSCs) markers (R=0.739; p=0.039) and 71% of non-classical EMT markers (R=0.451; p=0.021) showed a significant positive correlation with IL1R1 expressions. Methylation data suggested hypermethylation of IL1R1 in ST-EPN-RELA and PF-EPN-A at TSS as compared to ST-EPN-YAP1 and PF-EPN-B groups. Prognostically, high expression of IL1R1 showed worst survival in in-house (p=0.043) as well as in external cohort (p=0.027). CONCLUSION: Taken together, using co-expression network approach for Snail and Slug, we have identified an inflammatory marker, IL1R1, to be associated with ependymoma prognosis. Molecular dissection of IL1R1 may provide a promising opportunity for ependymoma treatment as it is involved in stem cells and EMT-like phenotype.