Abstract 126: The transcriptome landscape of high-risk neuroblastoma
Authors: Wei Jun S. , Zhang Shile , Song Young K. , Asgharzadeh Shahab , Sindiri Sivasish , Wen Xinyu , Patidar Rajesh , Guidry Auvil Jaime M. , Gerhard Daniela S. , Seeger Robert , Maris John M. , Khan Javed 
Published: July 2016

Abstract
Despite the success of multimodal therapies, the mortality and morbidity remains substantial for patients with high-risk neuroblastoma (NBL). Sequencing of paired tumor/normal DNA of NBL has revealed a low somatic mutation burden and few recurrent somatically-mutated genes. Here we hypothesize that the integrated analysis of DNA sequencing with whole transcriptome sequencing (WTS) in patients with high-risk NBL tumor will yield valuable insights into the biology of this disease. We performed WTS of 139 NBLs (118 high-risk stage 4 and 21 stage 4S tumors) which had whole genome sequencing or whole exome sequencing of case-matched tumor/normal pairs through the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. We identified expressed mutations, fusion genes, and correlations between gene expression and clinical parameters of patients such as survival to provide understandings of high-risk NBL biology.
Out of 1500 protein-coding changing somatic nucleotide variants detected by DNA sequencing, 614 variants (41%) were also detected in the transcriptome. Twenty-four genes known to be recurrently mutated in NBL showed the exact mutations in their transcriptome as seen in the DNA, including ALK (9.4%), ATRX (2.2%) and MYCN (1.4%). Fusion gene analysis identified in-frame fusions involving ALK (n = 2) and FOXR1 genes (n = 4). All tumors positive for ALK- and FOXR1-fusions expressed transcripts containing ALK or FOXR1 sequences at much higher levels (&gt;10 folds) than those without fusion in these respective genes. Consensus clustering using tumor gene expression profiles revealed 4 subgroups with distinct survival probability. Among them, several molecular signatures including MYC activation and tumor microenvironment were observed. Intriguingly, 58% tumors without MYCN-amplification showed a MYC activation signature significantly associated with worse overall survival (p = 0.0017). Further examination of these tumors with the MYC activation signature revealed different somatic alterations including MYCN P44L mutations, high expression of other MYC family members (MYC and MYCL), mutations in the RAS pathway, and FOXR1 fusions. Interestingly, a gene expression signature representing tumor-associated macrophages (TAM) and regulatory T-cells significantly correlated with a worse outcome in NBLs with normal MYCN copy number, similar to that seen in tumors with the MYC activation signature. In contrast, NBL patients with tumors showing a signature of cytotoxic T-cells and B-cells have better outcomes. Furthermore, tumors of the latter subgroup express significantly more somatic SNVs comparing to the other two subgroups of worse outcome with MYC activation or TAM signatures, suggesting that expressed neo-antigens may elevate cytotoxic T-cell response in these tumors. Our study suggests that patients with high-risk neuroblastoma may benefit from immune-based therapies including check point inhibitors in the future trials.
Citation Format: Jun S. Wei, Shile Zhang, Young K. Song, Shahab Asgharzadeh, Sivasish Sindiri, Xinyu Wen, Rajesh Patidar, Jaime M. Guidry Auvil, Daniela S. Gerhard, Robert Seeger, John M. Maris, Javed Khan. The transcriptome landscape of high-risk neuroblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 126.