Deregulation of microRNAs in medulloblastoma

Medulloblastoma (MB) is one of the most malignant and frequent childhood brain tumors consisting of four distinct molecular subtypes: Wingless (WNT), Sonic Hedgehog (SHH), Group 3 and Group 4. microRNAs (miRNAs) are 21-25 nucleotide long small non-coding RNAs which regulate the gene expression post transcriptionally by base pairing with the complementary mRNA sequence. It is speculated that miRNAs target about 60% of the human genes. A deregulation of miRNA expression was found in various cancer types and is linked with tumorigenesis, chemoresistance, invasion and metastasis. A comparative approach to identify the deregulation of miRNAs in medulloblastomas was not performed. To establish a miRNA expression profile 150 tissue samples of the known MB subgroups and subtypes within the main subgroups will be analyzed via sequencing of the small RNA fraction. The overall miRNA expression patterns will be compared to the different subgroups/ subtypes to identify a specific miRNA signature. The identified deregulated miRNAs will be validated via RT-qPCR and tested upon their biomarker suitability as a serum/CSF based biomarker for early detection, prognosis or monitoring the disease. Traditional invasive biomarkers have been widely used for personalized treatment but there is urgent need for new noninvasive markers. Extracellular vesicles (EVs) are small membrane encapsulated vesicles massively secreted by cancer cells, containing all kind of information about the tumor. EVs represent a liquid biopsy platform for minimal-invasive diagnosis of tumors. Therefore highly upregulated miRNAs will be selected to detect them in the serum/CSF of MB patients or in EVs isolated from serum/CSF of MB patients. The novelty of this approach is to use a sample set of more than 150 medulloblastomas to identify a deregulated miRNA signature and link it to a well-defined subgroup/subtype. This will ultimately result in a better understanding of tumor biogenesis, a critical step in providing lasting and effective treatments for children. The possibility to use deregulated miRNAs as a liquid biopsy platform for a minimal-invasive diagnosis of tumors for early detection might improve the life of many children.

Central nervous system (CNS) tumors are the second most common malignancies in childhood and the leading cause of cancer related deaths among children. Medulloblastoma (MB) is one of the most malignant and frequent childhood brain tumors consisting of four distinct molecular subgroups: Wingless (WNT), Sonic Hedgehog TP53-mutated/TP53-wildtype (SHH), Group 3 and Group 4. Recently, these subgroups could further be divided into various subtypes. microRNAs (miRNAs) are 21-25 nucleotide long small non-coding RNAs which regulate the gene expression post transcriptionally by base pairing with the complementary mRNA sequence. By using a miRNA expression dataset consisting of 80 samples we could cluster MB according to their subgroup and identify subgroup specific miRNAs. Extracellular vesicles (EVs) are small membrane encapsulated vesicles massively secreted by cancer cells, containing all kind of tumor information. Therefore, EVs represent a "liquid biopsy" platform for minimal-invasive diagnosis of tumors. The goal was to use a miRNA signature for liquid biopsy and to distinguish between different pediatric brain tumors. To achieve this, we isolated EVs from various tumor cell lines, short-term cultures, fresh tumor resections as well as CSF samples and performed small RNA sequencing. In the EV fraction of Group 3 MBs, we identified upregulated miRNAs, including members of the miR-183/182/96 family, miR-1290, and miR-375-3p. Furthermore, EVs isolated from an ETMR cell line exhibited significant upregulation of members from the C19MC. Across all cerebrospinal fluid (CSF) samples, we identified miRNAs, but samples from tumor patients exhibited a greater number of individual miRNAs compared to control samples. By clustering the samples based on their EV miRNA signature, we observed distinct grouping of MB and other pediatric brain tumors. The majority of cell lines and short-term cultures used belong to subtype II, which shows upregulation of the miR-183/182/96 cluster. Subsequently, we assessed the suitability of these miRNAs as potential liquid biopsy tools. Within our cohort, consisting of 20 group 3 tumors, only 5 belonged to the subtypes showing increased expression. In general, miR-182-5p and miR-183-5p demonstrated higher expression in group 3 MB patients. In one patient with MYC amplification, we were able to track disease progression, from diagnosis to progression and metastasis, based on the expression patterns of miR-182-5p and miR-183-5p. Currently, we are working towards expanding our cohort size to further enhance our research efforts. Notably, highly aggressive and lethal brain tumors called ETMRs exhibited a unique cell-free miRNA signature. These tumors are characterized by amplification of the C19MC miRNA cluster, which comprises 58 miRNAs. By utilizing miR-517a, we developed a reliable and efficient method for rapid detection of tumor-derived miRNA specifically in ETMR patients. This method offers the advantages of minimal cost and equipment requirements, providing test results within a rapid turnaround time of only 4 hours.