Cancer treatment strategies targeting the tumor microenvironment and corresponding immune cell infiltrate (i.e., immunotherapy) have recently proven effective against many solid tumors. In pediatric brain cancers, there is little known about the immune tumor microenvironment. We aim to characterize immune cell populations of pediatric brain tumors, which will better inform us about immune cell infiltration in different brain cancer subtypes and may indicate potential for patient response to immunotherapy. The Institute for Genomic Medicine at Nationwide Children’s Hospital has recently initiated a translational protocol to evaluate tumor specimens from pediatric patients with rare or refractory brain cancers in a focused N-of-1 manner. We performed RNA-seq and NanoString™ PanCancer Immune expression profiling on extracted tumor RNA from 22 patients comprising eight distinct brain cancer subtypes. We used CIBERSORT algorithm for deconvolution of RNA-seq global gene expression data and NanoString™ expression profiling to investigate methods of quantifying tumor-infiltrating leukocytes (TIL) and expression of immune genes. Our analyses identified a subset of pediatric brain tumors with evidence of immune infiltration. Using CIBERSORT, four gliomas were predicted to harbor significant TIL populations. Overall, we observed high correlation (Pearson R2 = 0.884) between expression values derived from RNA-seq and NanoString™ methods. Similarly, the two methods produced comparable predictions for TIL composition in the glioma tumors. Further genomic analysis identified one patient, with a diagnosis of glioblastoma and Neurofibromatosis type 1 (NF1), with marked infiltration of macrophages and neutrophils. Overexpression of tumor-associated macrophage/microglia genes (CD14, CD163, CD68, ITGAM, PTPRC) and other immune markers (PD-L1, CCL2/MCP-1, IL1B) was observed relative to all other samples. More specifically, overexpression of CD204, CD206, and CD163 suggested the infiltrating macrophages represent the M2/protumor phenotype. CIBERSORT allows more “granularity” in macrophage population prediction and indicated an equal representation of M2 and M0/uncommitted macrophages. Given the M2 phenotype, it is likely that the infiltrating macrophages contributed to tumor progression and radiation resistance observed in this patient. If confirmed, the presence of M0 macrophages and/or overexpression of PD-L1 could indicate potential for immunotherapy in this patient (e.g., oncolytic viral therapy, strategies focusing on M0 to M1/antitumor polarization, or combination targeted therapy with PD-L1 inhibitor). In summary, we identified a patient with progressive glioblastoma tumor growth and significant macrophage tumor infiltration as a likely candidate for immunotherapy.

Citation Format: Katherine E. Miller, Kathleen Schieffer, James Fitch, Vincent Magrini, Amy Wetzel, Anthony R. Miller, Daniel R. Boue, Jeffrey Leonard, Jonathan L. Finlay, Diana S. Osorio, Mohamed S. AbdelBaki, Christopher R. Pierson, Annie Drapeau, Jonathan Pindrik, Kristen Leraas, Elizabeth Varga, Devon Dishman, Lauren Shoemaker, Nicole Ross, Jeremy Pitts, Julie Gastier-Foster, Peter White, Catherine E. Cottrell, Richard K. Wilson, Elaine R. Mardis. Expression profiling-based characterization of immune cell populations in pediatric brain cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4551.