Bioinformatics and Regression Analyses Manifest Tumor-Specific miRNA Expression Dynamics in Pediatric Embryonal Malignancies

Co-Deregulated miRNA Signatures in Childhood Central Nervous System Tumors: In Search for Common Tumor miRNA-Related Mechanics

Simple Summary

Childhood tumors of the central nervous system (CNS) constitute a grave disease and their diagnosis is difficult to be handled. To gain better knowledge of the tumor’s biology, it is essential to understand the underlying mechanisms of the disease. MicroRNAs (miRNAs) are small noncoding RNAs that are dysregulated in many types of CNS tumors and regulate their occurrence and development through specific signal pathways. However, different types of CNS tumors’ area are characterized by different deregulated miRNAs. Here, we hypothesized that CNS tumors could have commonly deregulated miRNAs, i.e., miRNAs that are simultaneously either upregulated or downregulated in all tumor types compared to the normal brain tissue, irrespectively of the tumor sub-type and/or diagnosis. The only criterion is that they are present in brain tumors. This approach could lead us to the discovery of miRNAs that could be used as pan-CNS tumoral therapeutic targets, if successful.

Abstract

Despite extensive experimentation on pediatric tumors of the central nervous system (CNS), related to both prognosis, diagnosis and treatment, the understanding of pathogenesis and etiology of the disease remains scarce. MicroRNAs are known to be involved in CNS tumor oncogenesis. We hypothesized that CNS tumors possess commonly deregulated miRNAs across different CNS tumor types. Aim: The current study aims to reveal the co-deregulated miRNAs across different types of pediatric CNS tumors. Materials: A total of 439 CNS tumor samples were collected from both in-house microarray experiments as well as data available in public databases. Diagnoses included medulloblastoma, astrocytoma, ependydoma, cortical dysplasia, glioblastoma, ATRT, germinoma, teratoma, yoc sac tumors, ocular tumors and retinoblastoma. Results: We found miRNAs that were globally up- or down-regulated in the majority of the CNS tumor samples. MiR-376B and miR-372 were co-upregulated, whereas miR-149, miR-214, miR-574, miR-595 and miR-765 among others, were co-downregulated across all CNS tumors. Receiver-operator curve analysis showed that miR-149, miR-214, miR-574, miR-595 and miR765 could distinguish between CNS tumors and normal brain tissue. Conclusions: Our approach could prove significant in the search for global miRNA targets for tumor diagnosis and therapy. To the best of our knowledge, there are no previous reports concerning the present approach.

Bioinformatics Analysis Reveals Ki-67 Specific microRNA Functions in Pediatric Embryonal Tumors

Pediatric Central Nervous System (CNS) neoplasms are the second most prevalent tumors of childhood. CNS malignancies are considered as the most notorious type of tumors, due to their anatomic position manifesting an imminent threat to the patients' life. miRNAs are molecules that play a significant role in CNS tumor biology. At the same time diagnostic markers such as Ki-67 have played an important role in CNS tumor diagnosis. In a previous study we have identified several miRNAs, common to different subtypes of pediatric embryonal CNS malignancies as well as, we have identified miRNAs that manifest significant dynamics with respect to their expression and the neoplasmatic subtype. Among the previously reported miRNAs, several have manifested significant differences with respect to Ki-67 expression. Those miRNAs, were further analyzed bioinformatically and related functions were revealed, where some of them confirmed Ki-67 role as a proliferation marker but also predicted novel miRNAs functions in pediatric embryonal tumors.