Poster Presentation 29th Lorne Cancer Conference 2017

Systematic identification of dysregulated microRNAs in soft-tissue sarcomas through integrative expression analysis (#261)

Regina Ryan 1 , David Goldstein , Philip J Crowe 1 , Jia-Lin Yang 1 , Jason Wong 1
  1. Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia

Background: Soft-tissue sarcomas (STSs) are rare malignant tumours that occur as a result of aberrant differentiation of mesenchymal stem cells (MSCs) (1). Current theories suggest the loss of post-transcriptional control in gene expression leads to the development of sarcomas (2,3). Post-transcriptional regulators, specifically microRNAs (miRNAs), are involved in differentiation and aberrantly expressed in STS (2,4). Characterising miRNA expression may reveal underlying gene regulatory mechanisms involved in the tumorigenesis of sarcomas.

Methods: Publicly available high-throughput sequencing data from MSCs undergoing adipogenesis (5) was used to identify miRNAs related to differentiation. To correlate miRNAs with STS pathogenesis, differential expression and log-rank tests were applied to a cohort of 256 STS patients from The Cancer Genome Atlas. Bootstrapping was applied to evaluate the enrichment of differentiation specific miRNAs that predict survival. Potential gene regulatory pathways were explored by identifying target genes anti-correlated with miRNA expression based on parallel expression profiling data.

Results: The set of miRNAs related to differentiation identified 13 candidates (i.e., hsa-let-7g, hsa-mir-130b, hsa-mir-18a, hsa-mir-181a, hsa-mir-186, hsa-mir-25, hsa-mir-30a, hsa-mir-324, hsa-mir-335, hsa-mir-503, hsa-mir-625, hsa-mir-652, and hsa-mir-93) that can independently predict STS patient survival. The bootstrapping analysis confirmed that miRNAs that are differentially expressed between MSCs and adipocytes are significantly (p< 0.001) more likely to also predict patient survival compared with other miRNAs. Several oncogenes were predicted to be targets of these miRNAs and inversely correlated with their expression. These include CDK6, FGFR3, HMGA1, LPP, MYCN and PDGFRA. Pathway analysis suggests these miRNAs also affect multiple genes involved in critical pathways. For example, let-7g upregulation predicted worse survival in STS patients and nine genes (BMP7, FGF5, LEF1, SERPINE1, TP73, WNT7/16, WWC1, and YAP1) of the Hippo signalling pathway were inversely correlated with miRNA expression, suggesting an involvement in the regulation of apoptosis.

Conclusion: The systematic analysis identified differentiation-related miRNAs that predict patient survival. This supports the hypothesis that miRNAs are important in STS patient outcomes. Pathways related to miRNA activity suggest involvement in STS pathogenesis. Thus a better understanding of miRNA-gene regulatory networks in STS will enable the development of targeted therapies for patients.

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  2. Subramanian, S., Lui, W. O., Lee, C. H., Espinosa, I., Nielsen, T. O., Heinrich, M. C., Corless, C. L., Fire, A. Z. & Van De Rijn, M. 2008, 'MicroRNA expression signature of human sarcomas', Oncogene, vol. 27(14), pp 2015-2026.
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  4. Schoolmeesters, A., Eklund, T., Leake, D., Vermeulen, A., Smith, Q., Aldred, S. F. & Fedorov, Y. 2009, 'Functional profiling reveals critical role for miRNA in differentiation of human mesenchymal stem cells', PLoS ONE, vol. 4(5), e5605.
  5. Mikkelsen, T. S., Xu, Z., Zhang, X., Wang, L., Gimble, J. M., Lander, E. S. & Rosen, E. D. 2010, 'Comparative epigenomic analysis of murine and human adipogenesis', Cell, vol. 143, pp 156-169.