Tumor-infiltrating lymphocytes in glioblastoma are associated with specific genomic alterations and related to transcriptional class

Abstract

Purpose: Tumor-infiltrating lymphocytes (TIL) have prognostic significance in many cancers, yet their roles in glioblastoma have not been fully defined. We hypothesized that TILs in glioblastoma are associated with molecular alterations, histologies, and survival.

Experimental design: We used data from The Cancer Genome Atlas (TCGA) to investigate molecular, histologic, and clinical correlates of TILs in glioblastomas. Lymphocytes were categorized as absent, present, or abundant in histopathologic images from 171 TCGA glioblastomas. Associations were examined between lymphocytes and histologic features, mutations, copy number alterations, CpG island methylator phenotype, transcriptional class, and survival. We validated histologic findings using CD3G gene expression.

Results: We found a positive correlation between TILs and glioblastomas with gemistocytes, sarcomatous cells, epithelioid cells, and giant cells. Lymphocytes were enriched in the mesenchymal transcriptional class and strongly associated with mutations in NF1 and RB1. These mutations are frequent in the mesenchymal class and characteristic of gemistocytic, sarcomatous, epithelioid, and giant cell histologies. Conversely, TILs were rare in glioblastomas with small cells and oligodendroglioma components. Lymphocytes were depleted in the classical transcriptional class and in EGF receptor (EGFR)-amplified and homozygous PTEN-deleted glioblastomas. These alterations are characteristic of glioblastomas with small cells and glioblastomas of the classical transcriptional class. No association with survival was shown.

Conclusions: TILs were enriched in glioblastomas of the mesenchymal class, strongly associated with mutations in NF1 and RB1 and typical of histologies characterized by these mutations. Conversely, TILs were depleted in the classical class, EGFR-amplified, and homozygous PTEN-deleted tumors and rare in histologies characterized by these alterations.

Figure 1

Representative examples of permanent section histologic slides from TCGA cases. Lymphocytes were identified as small round cells with scant cytoplasm and darkly staining nuclei. Cases with a complete absence of lymphocytes were labeled 0 (absent) (top). Cases with lymphocytes present in <50% of tumor tissue were categorized 1+ (present) (middle).Cases with lymphocytes present in ≥50% were categorized 2+ (abundant) (bottom).

Figure 2

Representative examples of GBM morphologic subtypes associated with the presence of lymphocytes in TCGA permanent section histologic slides. TILs are enriched in GBMs with sarcomatous cells (top), gemistocytes (middle) and giant cells (bottom).

Figure 3

Kaplan–Meier estimates of survival according to absent (0), present (1+) or abundant (2+) lymphocytes. TILs are not associated with improved survival (log-rank p>0.05).