A Toolkit for Profiling the Immune Landscape of Pediatric Central Nervous System Malignancies

Abstract

The prognosis of pediatric central nervous system (CNS) malignancies remains dismal due to limited treatment options, resulting in high mortality rates and long-term morbidities. Immunotherapies, including checkpoint inhibition, cancer vaccines, engineered T cell therapies, and oncolytic viruses, have promising results in some hematological and solid malignancies, and are being investigated in clinical trials for various high-grade CNS malignancies. However, the role of the tumor immune microenvironment (TIME) in CNS malignancies is mostly unknown for pediatric cases. In order to successfully implement immunotherapies and to eventually predict which patients would benefit from such treatments, in-depth characterization of the TIME at diagnosis and throughout treatment is essential. In this review, we provide an overview of techniques for immune profiling of CNS malignancies, and detail how they can be utilized for different tissue types and studies. These techniques include immunohistochemistry and flow cytometry for quantifying and phenotyping the infiltrating immune cells, bulk and single-cell transcriptomics for describing the implicated immunological pathways, as well as functional assays. Finally, we aim to describe the potential benefits of evaluating other compartments of the immune system implicated by cancer therapies, such as cerebrospinal fluid and blood, and how such liquid biopsies are informative when designing immune monitoring studies. Understanding and uniformly evaluating the TIME and immune landscape of pediatric CNS malignancies will be essential to eventually integrate immunotherapy into clinical practice.

Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing

“…Even though microglia are the most dominant immune cells in the brain (80%), other immune cell types have been identified in the brain including B cells, dendritic cells, macrophages, monocytes, myeloid cells, natural killer (NK) cells, and T cells [ 12 , 36 – 38 ]. Nevertheless, the limited number of tumor-infiltrating immune cells compared to the high density of tumor cells can limit the sensitivity of bulk techniques [ 39 ]. The estimation of immune cell types in the samples by NanoString and RNA sequencing shows mostly incomparable results (Fig.…”

Pediatric Solid Cancers: Dissecting the Tumor Microenvironment to Improve the Results of Clinical Immunotherapy

“…Analysis of immune cell infiltration in pediatric gliomas demonstrated that myeloid cells are major components of the TME and show enrichment of CD8+ T cells and CD45+ leukocytes in low-grade gliomas compared to high-grade gliomas [ 77 ]. While the percentage of tumor-associated CD68+ macrophages is comparable across subgroups, diffuse midline gliomas have the lowest number of infiltrating CD8+ T cells and CD163+ macrophages, which contributes to their immunosuppressive phenotype [ 78 ].…”

“…In pediatric patients, ependymomas comprise ~10% of primary central nervous system tumors, with the majority arising in the posterior fossa [ 96 ]. Pediatric ependymomas with higher infiltration of CD3+ and CD8+ T cells in the microenvironment at diagnosis had a longer progression-free survival, while elevated Forkhead box P3 regulatory T cells and CD68+ macrophages were correlated with a shorter survival rate [ 78 ].…”

“…Tumor Type Technique FindingsSample n. Ref.Brain tumors FCEnrichment of CD8+ T cells and CD45+ leukocytes in low-grade gliomas compared to high-grade gliomas.Lowest number of infiltrating CD8+ T cells and CD163+ macrophages in diffuse midline gliomas.62[77,78] …”