M. A. Applebaum, A. R. Jha, K. Hernandez, C. J. Mariani, B. E. Stranger, S. L. Cohn; University of Chicago, Chicago, IL
BACKGROUND: Hypoxia, a hallmark of malignant tumors, induces treatment resistance and an aggressive phenotype. Increased expression of hypoxia inducible factor (HIF) is highly correlated with poor survival in neuroblastoma. Hypoxia also results in specific adaptive genetic changes in Drosophila melanogaster and many other species. We hypothesized that an evolutionarily conserved transcriptional program exists in Drosophila, neuroblastoma cell lines, and primary neuroblastoma tumors conferring both a survival advantage in Drosophila bred in hypoxia and aggressive tumor behavior.
METHODS: RNA-seq of neuroblastoma cells grown in normoxia or hypoxia were analyzed for differentially expressed genes (DEG) using Cufflinks and CuffDiff. These data were overlapped with previously identified human orthologous DEG from Drospohila bred in normoxia or hypoxia. Microarrays of 163 high-risk neuroblastoma tumors were analyzed by patient outcome with the oligo and limma packages in R.
RESULTS: Pathway analysis of neuroblastoma cells grown in hypoxia shows changes in steroid biosynthesis (p = 1.3e-13), HIF-1 transcription network (p = 3.3e-13), and sugar metabolism (p = 3.2e-6). 55 of the 2,156 DEG in these cells are present in the Drosophila data set and are enriched for tyrosine kinase signaling pathways (p = 1.9e-5). In primary tumors, transcriptional up-regulation of the AP-1/MAPK and HIF-1 pathways correlates with worse survival (p = 1.3e-4 and p = 0.001, respectively).
CONCLUSION: Hypoxia induces transcriptional changes that provide a survival advantage for Drosophila and drive aggressive neuroblastoma tumor growth. A deeper understanding of these genes and their regulation may allow us to identify patients at high risk of death and ultimately provide insight to personalize therapy.