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Purpose  RNA and DNA sequencing data are traditionally used to discern intrinsic cellular pathways in cancer pathogenesis, their utility for investigating the tumor microenvironment (TME) has not been fully explored. This study explores the use of sequencing data to investigate immunity within the TME.    Experimental design  Here, we use immune cell fraction estimation analysis to determine the immune profiles in the microenvironment of neuroblastoma (NB) based on RNA-seq data in the TARGET database. The correlation between immune cell transcripts and prognosis in pediatric NB is also investigated.    Results   In silico  analysis revealed a strong inverse correlation between  MYCN  amplification and leukocyte infiltration. This finding was validated by immunohistochemistry analysis in tumor samples. Moreover, the abundance of CD4 T cells strongly associated with better patient survival regardless of  MYCN  gene amplification, while those of CD8 T cells, NK or B cells do not. Based on characteristic cytokine expression of CD4 subsets in tumors, the Th2 rather than Th1 levels were associated with better prognosis.    Conclusion  We found that the  in silico  analysis of TARGET database reflected tumor immunity and was validated by the immunohistochemical tumor data. Our results reveal the association of  MYCN  amplification with repressed cellular immunity and the potential prognostic value of infiltrating CD4 T cell transcripts in pediatric NB. This analysis illustrates the potential role of  MYCN  in NB as a regulator of immune privilege and characterizes the power of  in silico  analysis for delineating cancer immunology and risk stratification.

MYCN Amplification Is Associated with Repressed Cellular Immunity in Neuroblastoma: An In Silico Immunological Analysis of TARGET Database