Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma

Abstract

Despite intensive study, many mysteries remain about the MYCN oncogene's functions. Here we focus on MYCN's role in neuroblastoma, the most common extracranial childhood cancer. MYCN gene amplification occurs in 20% of cases, but other recurrent somatic mutations are rare. This scarcity of tractable targets has hampered efforts to develop new therapeutic options. We employed a multi-level omics approach to examine MYCN functioning and identify novel therapeutic targets for this largely un-druggable oncogene. We used systems medicine based computational network reconstruction and analysis to integrate a range of omic techniques: sequencing-based transcriptomics, genome-wide chromatin immunoprecipitation, siRNA screening and interaction proteomics, revealing that MYCN controls highly connected networks, with MYCN primarily supressing the activity of network components. MYCN's oncogenic functions are likely independent of its classical heterodimerisation partner, MAX. In particular, MYCN controls its own protein interaction network by transcriptionally regulating its binding partners.Our network-based approach identified vulnerable therapeutically targetable nodes that function as critical regulators or effectors of MYCN in neuroblastoma. These were validated by siRNA knockdown screens, functional studies and patient data. We identified β-estradiol and MAPK/ERK as having functional cross-talk with MYCN and being novel targetable vulnerabilities of MYCN-amplified neuroblastoma. These results reveal surprising differences between the functioning of endogenous, overexpressed and amplified MYCN, and rationalise how different MYCN dosages can orchestrate cell fate decisions and cancerous outcomes. Importantly, this work describes a systems-level approach to systematically uncovering network based vulnerabilities and therapeutic targets for multifactorial diseases by integrating disparate omic data types.

Wnt signalling is a major determinant of neuroblastoma cell lineages

“…It therefore follows that ADRN-LR genes, strongly associated with neural development, may be Wnt/Hedgehog regulated genes repressed by MYCN. This informs and extends the suggestion that MYCN represses signalling pathways driving differentiation during NB tumorigenesis (Duffy et al 2015).…”

Unveiling MYCN regulatory networks in neuroblastoma via integrative analysis of heterogeneous genomics data

“…To this end, integration of various regulatory interactions and the construction of comprehensive MYCN regulatory networks in NB are required. A few studies have used integrative omics approaches to identify the critical regulators or effector of MYCN in NB and potential therapeutic targets [18, 19]. In this study, we performed chromatin immunoprecipitation following by sequencing (ChIP-seq) and small RNA sequencing to identify MYCN binding sites and MYCN-associated miRNAs, and then used an integrative approach to dissect the MYCN regulatory networks.…”

Precision wildlife medicine: applications of the human‐centred precision medicine revolution to species conservation

“…By profiling the global activity status of all of the turtle and viral genes being expressed in healthy tissue and FP tumours across multiple stages, using deep sequencing‐based transcriptomics, we can determine the oncogenic events driving tumour formation and progression. By computationally integrating this data at the pathway, gene ontology and inferred regulator level, using approaches validated for human cancers (Duffy et al ., ; Duffy, ), we can reconstruct the oncogenic signalling and effector networks promoting tumour growth. This approach not only identifies the relevant regulators and pathways but computationally infers their degree of activation or inhibition, by collating the changes in the expression of their target genes.…”

“…Precision medicine can be defined as treatments targeted to the needs of disease groups on the basis of genetic, biomarker, phenotypic or psychosocial characteristics (Jameson & Longo, 2015). This rapidly emerging field is revolutionizing our understanding of disease, drug development and repurposing, human patient care and treatment decisions by emphasizing disease prevention and tailoring precision treatments targeted to stratified patient cohorts or even individual patients (Committee on a Framework for Developing a new Taxonomy of Disease, 2011;Hood & Friend, 2011;Flores et al, 2013;Vandamme et al, 2013;CASyM Consortium, 2014;Collins & Varmus, 2015;Duffy et al, 2015;Byron et al, 2016;Duffy, 2016). Precision medicine incorporates a number of new technologies (Table 1) with advanced computational analysis (Duffy, 2016) to improve our understanding of disease and predict in advance the response of disease groups and individual patients to therapy.…”