In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors

Suzanne Vanhauwaert,Sara De Brouwer,Frank Speleman,Jo Vandesompele,Bieke Decaesteker,Pieter Mestdagh,Kaat Durinck,Christophe Van Neste,Katleen De Preter,Karen Sermon,Carina Leonelli,Geertrui Denecker

doi:10.1038/s41598-018-35868-5

Abstract

Chemotherapy resistance is responsible for high mortality rates in neuroblastoma. MYCN, an oncogenic driver in neuroblastoma, controls pluripotency genes including LIN28B. We hypothesized that enhanced embryonic stem cell (ESC) gene regulatory programs could mark tumors with high pluripotency capacity and subsequently increased risk for therapy failure. An ESC miRNA signature was established based on publicly available data. In addition, an ESC mRNA signature was generated including the 500 protein coding genes with the highest positive expression correlation with the ESC miRNA signature score in 200 neuroblastomas. High ESC m(i)RNA expression signature scores were significantly correlated with poor neuroblastoma patient outcome specifically in the subgroup of MYCN amplified tumors and stage 4 nonamplified tumors. Further data-mining identified FOXM1, as the major predicted driver of this ESC signature, controlling a large set of genes implicated in cell cycle control and DNA damage response. Of further interest, re-analysis of published data showed that MYCN transcriptionally activates FOXM1 in neuroblastoma cells. In conclusion, a novel ESC m(i)RNA signature stratifies neuroblastomas with poor prognosis, enabling the identification of therapy-resistant tumors. The finding that this signature is strongly FOXM1 driven, warrants for drug design targeted at FOXM1 or key components controlling this pathway.

Highlights

Chemotherapy resistance is responsible for high mortality rates in neuroblastoma
Using signature score analysis, we could validate the signature in an independent dataset of embryonic stem cell (ESC) with high miRNA signature scores for the ESC samples compared to differentiated somatic tissue (Supplemental Fig. 1)[24]
The normal counterpart cells, i.e. the normal neuroblasts isolated from fetal adrenal glands, have ESC miRNA signature scores in the higher range of the scores identified in neuroblastoma tumors samples

Summary

Introduction

Chemotherapy resistance is responsible for high mortality rates in neuroblastoma. MYCN, an oncogenic driver in neuroblastoma, controls pluripotency genes including LIN28B. Childhood cancers have been considered as developmental disorders and differ in many aspects from adult cancers, including an undifferentiated cellular phenotype and a remarkable low mutational burden[1] Embryonal tumors such as medulloblastoma, Wilms’ tumor, embryonal rhabdomyosarcoma and neuroblastoma arise due to disruption of normal early developmental pathways in immature progenitor cells causing differentiation arrest and formation of pre-malignant lesions that can subsequently develop to full blown tumors that retain distinct stemness characteristics[1,2]. We explored the stemness features of neuroblastoma tumor cells using an in silico analysis starting from a normal embryonal stem cell (ESC) driven miRNA signature. This approach was based on three important concepts. Several miRNAs have been shown to play a role in chemoresistance in neuroblastoma[19]

Methods

Results

Conclusion