To underscore the importance of the observed genetic rearrangements in aggressive disease, we first clarified their biological functions, network and communal molecular orchestrations, and their documented role in any tumor progression systems. IPA “pathway interaction analysis” revealed a complex yet well-organized signal transduction network of
MAL2, A4GALT, POLDIP3, RPL3, EP300, CD1C, CFHR3, APOBEC3B, RALYL, NBPF20, FOXP2, MDFIC, TTL1, and
MGAT3 (Additional file
3: Figure S1). Evidently, genes with genetic rearrangements in coding regions play concomitant roles in multiple tumor systems, such as chronic myeloid leukemia, melanoma, small cell carcinoma, lung carcinoma, mammary tumor, prostate cancer, pancreatic cancer, colon adenocarcinoma, squamous cell carcinoma, and non-small cell lung adenocarcinoma. Moreover, “IPA-Core-Analysis” revealed that this small subset of tightly inter-regulated molecular targets showed influential participation in many canonical signaling pathways and demonstrated defined roles in multifarious biological functions. IPA-data mining considering only relationships where confidence = experimentally observed, these molecules exhibited their role in at least 67 different canonical pathways exerting >150 biological functions. Interestingly, in the light of tumor progression and dissemination, we observed a significant association of these molecules in key pathways of cancer progression viz., ATM Signaling, cAMP-mediated signaling, Cell Cycle:Checkpoint Regulation, CREB Signaling in Neurons, Dendritic Cell Maturation, EIF2 Signaling, ERK/MAPK Signaling, ERK5 Signaling, Estrogen Receptor Signaling, FGF Signaling, FLT3 Signaling in Progenitor Cells, G-Protein Coupled Receptor Signaling, Granzyme A Signaling, HIF1a Signaling, ILK Signaling, Neurotrophin/TRK Signaling, NFkB Signaling, p38 MAPK Signaling, p53 Signaling, Phospholipase C Signaling, PPAR Signaling, PPARa/RXRa Activation, Protein Kinase A Signaling, RAR Activation, Pyrimidine Deoxyribonucleotides, TGF-b Signaling, VDR/RXR Activation, Wnt/Ca + pathway, Wnt/b-catenin Signaling
etc., (Additional file
4: Figure S2A). In addition to their role in molecular signaling events, these molecules also exercise their defined (
P < 0.05) roles in cancer progression related bio-functions including Cancer Cell Morphology, Progression of tumor, Cell Cycle-replicative senescence, Cellular Assembly DNA Replication, Cell Cycle arrest, Cell Death and Survival, Cellular Function and Maintenance, Post-Translational Modification, Cell-To-Cell Signaling, Cellular Assembly/Organization, Cellular Growth and Proliferation, Cellular Movement, Cellular Response to Therapeutics
etc., (Additional file
4: Figure S2B). To that note, all-encompassing overview of these molecules including information on their symbol, name, subcellular location, protein functions, binding, regulating, regulated by, targeted by miRNA, role in cell, molecular function, biological process, cellular component, disease, role in tumor progression and metastasis
etc., are provided in Additional file
5: Table S1.
To demonstrate the relevance of these genetic rearrangements to high-risk neuroblastoma and poor clinical outcomes, we examined the correlation of individual gene expression with overall (OS) and relapse-free survival in patients with neuroblastoma. We utilized a web-based microarray analysis and visualization platform (
http://r2.amc.nl) that correlates a select gene expression profile with clinical outcomes for samples from multiple cohorts of patients with neuroblastoma. Kaplan-Meier plots showed a significant association between increased expression of
CFHR3, MDFIC, CSMD3, FOXP2, or
RALYL (genes with gains in coding regions) and poor OS in patients with neuroblastoma (Additional file
6: Figure S3A). This inverse association of
CFHR3-, MDFIC-, CSMD3-, FOXP2-, or
RALYL-gain also reflects poor relapse-free survival in these patients (Additional file
6: Figure S3A). Interestingly,
SLC25A17, POLDIP3, SERHL, LOC400927, MGAT3, or
TTLL1 (genes with CNV-loss in coding regions) demonstrated a definite association with their loss and poor OS (Additional file
6: Figure S3B). The loss in any of these genes individually results in poor relapse-free survival in children with neuroblastoma (Additional file
6: Figure S3B). Clinical outcome association analysis also revealed a strong correlation between the expressional variations of both groups of genes listed above and stage progression, favorable → unfavorable disease and alive → died-of-disease (data not shown). It is pertinent to mention that gains in
CD1C, NBPF20, and
MAL2, and losses in
ADAM5, RPL3, L3MBTL2, A4GALT, EP300, and
APOBEC3B were not associated with poor clinical outcomes (Additional file
7: Figure S4). Together, these data demonstrate the direct, definite influence of genetic rearrangements in aggressive disease on poor clinical outcomes in children with neuroblastoma.