Decoding the epigenome and its regulation in neuroblastoma

Neuroblastoma (NB) is a pediatric cancer of the sympathetic nervous system and one of the most common solid tumors in infancy. Several studies have provided insights into the genetic complexity underlying NB, however, the heterogeneous nature of the disease and lack of recurrent somatic mutations reinforces the need to understand the interplay between the genetic factors and epigenetic alterations in the context of NB. Epigenetic modifications are heritable changes that occur on the DNA, without altering the DNA sequence per se. Epigenetic mechanisms play a pivotal role in normal and disease settings. Thus, understanding the epigenetic architecture and genes governed by these modifications provides an alternative approach to identifying novel underlying mechanisms associated with NB. In this project, we will systematically investigate the impact of the various epigenetic layers in several NB models through an array of molecular biology and biochemistry technologies. We expect that our findings will provide a platform to generate novel biomarkers that allow for better diagnostic approaches as well as screening of new drugs in real time, which will pave the way for innovative and better lines of treatment.

Neuroblastoma (NB) is one of the most common pediatric cancers, where >90% of metastatic stage NB tumors disseminate to the bone marrow (BM), resulting in an unfavorable clinical outcome. The BM provides a unique microenvironment that promotes the growth of tumors, however, the role of different BM cells, their molecular features, and their interactions with tumor cells are poorly defined. We employed single-cell transcriptomic and epigenomic profiling of BM aspirates in various NB subgroups to: (i) study differences in cellular plasticity across NB subtypes in metastatic and primary tumors, (ii) investigate interactions between tumor cells and the BM cell communities, and (iii) unravel metastasis-induced alterations in the BM. Our studies showed that tumor phenotype is conserved upon metastasis across different NB subtypes when compared to primary tumors. The interrogation of the BM microenvironment composition in NB subtypes revealed an aberrant presence of various immune cells in NB metastases compared to controls. Moreover, NB cells signal to the BM microenvironment, leading to local reactions, characterized by activation of pro- and anti-inflammatory programs, and expression of tumor-promoting factors. Finally, the molecules identified in this study that mediate the communication between tumor and BM cells have been under intense investigations in recent years as emerging therapeutic targets in various tumors. The current genetic studies provide a framework for a classic panel for genetic screening of NB, but only roughly 30% of the NB cases have a well-defined genetic driver. Epigenetic changes are present in all diseases and identification of an epigenetic component will pave the way for better detection and treatment approaches in NB. To capture the intricate interplay between chromatin and the associated epigenetic mechanisms in the control of gene expression and cell fate decisions, as well as their role in NB pathogenesis, we: (1) investigated how ATRX mutations affect this chromatin remodeler's function and interactions with other epigenetic regulatory elements, resulting in an aberrant chromatin landscape and downstream gene expression found in high-risk NB. Considering the developmental aspect of NB, we: (2) bridged the gaps in identifying the stages during sympathoadrenal differentiation, where ATRX mutations distort the developmental trajectory, leading to the onset of tumorigenesis. Ultimately, these studies identified the ATRX-associated proteins that regulate the epigenome in the developing tissues of NB. Further, we provided a comprehensive characterization of ATRX-related transcriptional and epigenetic developmental changes capturing NB formation. In conclusion, our work provides a cellular atlas of NB across all subgroups that defines the cellular states underlying each NB subgroup, disentangling determinants of intra- and inter-tumoral heterogeneity. Importantly, the ligand/receptor pairs and members of the ATRX protein complex identified in our study play pleiotropic roles in normal and disease settings and offer novel molecular targets for therapeutic opportunities in NB.