RNA sequencing of tumor tissue from DAOY xenograft study

The embryonic brain tumor medulloblastoma is a highly malignant tumor of the cerebellum and the most common CNS malignancy of childhood and multimodal treatment has improved the survival rates considerably. Unfortunately, the intense treatment often leads to neurological morbidity and the risk of a resistant relapse is significant and therefore improvement of the treatment regiments is needed to increase the survival rates and reduce the late side effects. Our study shows that the ?3-fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) decreased medulloblastoma cell viability and colony forming ability dose-dependently and furthermore, treatment with DHA-oil reduced tumor growth in a medulloblastoma xenograft study. Additionally, DHA decreased prostaglandin E2 (PGE2) production from medulloblastoma cells in vitro and PGE2 and prostacyclin were significantly decreased in tumor tissue from ?3-fatty acid treated mice compared to control animals. RNA sequencing showed 10 commonly downregulated genes (CRYAB, CASQ1, MYH13, ATP2A1, POTEI, APOBEC2, CKM, TNNC2, MYLPF, PVALB) in tumors from mice revieving treatment with DHA alone or in combination with EPA. Overall design: Medulloblastoma cell line DAOY were implanted on the flank of nude mice and randomized into three groups: treatment with docosahexaenoic acid (DHA)- or a combination of DHA and Eicosapentaenoic acid (EPA) or control eating ordinary chow. Bulk RNA sequencing was performed on fresh frozen tumors from the study. The Illumina TruSeq Stranded mRNA sample preparation protocol was used to construct libraries suitable for Illumina sequencing and then sequenced on the Illumina Nextseq 550 for a 75-cycle v2 sequencing run generating 75 bp single-end reads.