Redefining functional MYCN gene signatures in neuroblastoma

Comprehensive analysis and validation reveal potential MYCN regulatory biomarkers associated with neuroblastoma prognosis

Neuroblastoma (NB) is an embryonic malignant tumor that occurs in the sympathetic nervous system. The treatment results of patients in the high-risk group are poor, and relapse and treatment failure can occur even with multiple combination treatments. The proto-oncogene MYCN is a BHLH Transcription Factor used as an independent prognostic factor for NB. The proportion of MYCN amplification in tumor tissues of high-risk patients reaches 40-50%. Hence, exploring new MYCN target genes is a meaningful approach in developing treatment for high-risk NB patients. The microarray datasets were obtained from Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and miRPathDB were used for enrichment analysis. STRING and Cytoscape were used to construct a protein-protein interaction (PPI) network and for modular analysis. The miRNet and NetworkAnalyst databases were used to predict and construct gene-miRNA and gene-TFs networks. The R2 database was used for expression, correlation, and prognostic analyses. The diagnostic value of the biomarkers was predicted by ROC analysis, and RT-qPCR was used to validate the identified hub genes. Finally, using specific MYCN siRNA and overexpressing plasmids, the correlation between the identified hub genes and MYCN was investigated. Our results showed that FBXO9, HECW2, MIB2, RNF19B, RNF213, TRIM36, and ZBTB16 are novel biomarkers that affect the prognosis of the NB patients. In addition, FBXO9, RNF19B, and TRIM36 were preliminarily confirmed as potential target genes of MYCN. Overall, FBXO9, HECW2, MIB2, RNF19B, RNF213, TRIM36, and ZBTB16 are expected to become novel biomarkers for the treatment of high-risk NB patients.Communicated by Ramaswamy H. Sarma.

Lipid Metabolic Reprogramming in Embryonal Neoplasms with MYCN Amplification

Tumor cells reprogram their metabolism, including glucose, glutamine, nucleotide, lipid, and amino acids to meet their enhanced energy demands, redox balance, and requirement of biosynthetic substrates for uncontrolled cell proliferation. Altered lipid metabolism in cancer provides lipids for rapid membrane biogenesis, generates the energy required for unrestricted cell proliferation, and some of the lipids act as signaling pathway mediators. In this review, we focus on the role of lipid metabolism in embryonal neoplasms with MYCN dysregulation. We specifically review lipid metabolic reactions in neuroblastoma, retinoblastoma, medulloblastoma, Wilms tumor, and rhabdomyosarcoma and the possibility of targeting lipid metabolism. Additionally, the regulation of lipid metabolism by the MYCN oncogene is discussed.

Distillation of the clinical algorithm improves prognosis by multi-task deep learning in high-risk Neuroblastoma

We introduce the CDRP (Concatenated Diagnostic-Relapse Prognostic) architecture for multi-task deep learning that incorporates a clinical algorithm, e.g., a risk stratification schema to improve prognostic profiling. We present the first application to survival prediction in High-Risk (HR) Neuroblastoma from transcriptomics data, a task that studies from the MAQC consortium have shown to remain the hardest among multiple diagnostic and prognostic endpoints predictable from the same dataset. To obtain a more accurate risk stratification needed for appropriate treatment strategies, CDRP combines a first component (CDRP-A) synthesizing a diagnostic task and a second component (CDRP-N) dedicated to one or more prognostic tasks. The approach leverages the advent of semi-supervised deep learning structures that can flexibly integrate multimodal data or internally create multiple processing paths. CDRP-A is an autoencoder trained on gene expression on the HR/non-HR risk stratification by the Children’s Oncology Group, obtaining a 64-node representation in the bottleneck layer. CDRP-N is a multi-task classifier for two prognostic endpoints, i.e., Event-Free Survival (EFS) and Overall Survival (OS). CDRP-A provides the HR embedding input to the CDRP-N shared layer, from which two branches depart to model EFS and OS, respectively. To control for selection bias, CDRP is trained and evaluated using a Data Analysis Protocol (DAP) developed within the MAQC initiative. CDRP was applied on Illumina RNA-Seq of 498 Neuroblastoma patients (HR: 176) from the SEQC study (12,464 Entrez genes) and on Affymetrix Human Exon Array expression profiles (17,450 genes) of 247 primary diagnostic Neuroblastoma of the TARGET NBL cohort. On the SEQC HR patients, CDRP achieves Matthews Correlation Coefficient (MCC) 0.38 for EFS and MCC = 0.19 for OS in external validation, improving over published SEQC models. We show that a CDRP-N embedding is indeed parametrically associated to increasing severity and the embedding can be used to better stratify patients’ survival.

microRNA-221 Enhances MYCN via Targeting Nemo-like Kinase and Functions as an Oncogene Related to Poor Prognosis in Neuroblastoma

Purpose:MYCN is one of the most well-characterized genetic markers of neuroblastoma. However, the mechanisms as to how MYCN mediate neuroblastoma tumorigenesis are not fully clear. Increasing evidence has confirmed that the dysregulation of miRNAs is involved in MYCN-mediated neuroblastoma tumorigenesis, supporting their potential as therapeutic targets for neuroblastoma. Although miR-221 has been reported as one of the upregulated miRNAs, the interplay between miR-221 and MYCN-mediated neuroblastoma progression remains largely elusive.Experimental Design: The expression of miR-221 in the formalin-fixed, paraffin-embedded tissues from 31 confirmed patients with neuroblastoma was detected by locked nucleic acid-in situ hybridization and qRT-PCR. The correlation between miR-221 expression and clinical features in patients with neuroblastoma was assessed. The mechanisms as to how miR-221 regulate MYCN in neuroblastoma were addressed. The effect of miR-221 on cellular proliferation in neuroblastoma was determined both in vitro and in vivoResults: miR-221 was significantly upregulated in neuroblastoma tumor cells and tissues that overexpress MYCN, and high expression of miR-221 was positively associated with poor survival in patients with neuroblastoma. Nemo-like kinase (NLK) as a direct target of miR-221 in neuroblastoma was verified. In addition, overexpression of miR-221 decreased LEF1 phosphorylation but increased the expression of MYCN via targeting of NLK and further regulated cell cycle, particularly in S-phase, promoting the growth of neuroblastoma cells.Conclusions: This study provides a novel insight for miR-221 in the control of neuroblastoma cell proliferation and tumorigenesis, suggesting potentials of miR-221 as a prognosis marker and therapeutic target for patients with MYCN overexpressing neuroblastoma. Clin Cancer Res; 23(11); 2905-18. ©2016 AACR.

Chemoresistance, cancer stem cells, and miRNA influences: the case for neuroblastoma

Neuroblastoma is a type of cancer that develops most often in infants and children under the age of five years. Neuroblastoma originates within the peripheral sympathetic ganglia, with 30% of the cases developing within the adrenal medulla, although it can also occur within other regions of the body such as nerve tissue in the spinal cord, neck, chest, abdomen, and pelvis. MicroRNAs (miRNAs) regulate cellular pathways, differentiation, apoptosis, and stem cell maintenance. Such miRNAs regulate genes involved in cellular processes. Consequently, they are implicated in the regulation of a spectrum of signaling pathways within the cell. In essence, the role of miRNAs in the development of cancer is of utmost importance for the understanding of dysfunctional cellular pathways that lead to the conversion of normal cells into cancer cells. This review focuses on highlighting the recent, important implications of miRNAs within the context of neuroblastoma basic research efforts, particularly concerning miRNA influences on cancer stem cell pathology and chemoresistance pathology for this condition, together with development of translational medicine approaches for novel diagnostic tools and therapies for this neuroblastoma.