Transcriptional Hallmarks Of Tumor Infiltrating Lymphocyte Responses To Melanoma

Tumor-infiltrating lymphocytes (TIL) are found in a subset of melanomas. Patients with pronounced TIL responses have an excellent prognosis, suggesting that for those patients, the infiltrating immune cells are part of an effective adaptive and/or innate response to cancer. However, the molecular features of brisk TIL infiltrates have not been analyzed in situ. Moreover, it is not clear whether the features of the immune response to melanoma are shared by other tumors. Here, we used histological grading of TIL infiltrates in melanoma samples from The Cancer Genome Atlas combined with analysis of immune signatures in transcriptional profiles from the same tumors to characterize the molecular features of the immune response to melanoma. To categorize the histological grade of immune infiltrate, we reviewed digital images of 156 melanoma samples, and assigned a TIL grade (0 - 3) based on established criteria. We found that the distribution of TIL grades in our dataset was consistent with previously published analyses. We first tested whether tumors with brisk infiltrate (TIL Grade 2 or 3) showed enrichment of immune signatures relative to those with non-brisk infiltrates (TIL Grade 0 or 1) using gene-set enrichment analysis (GSEA) with a collection of ∼2000 immune-related gene-sets manually curated from published studies of adaptive and innate immunity. We found that 493 immune signatures enriched in brisk tumors (FDR<0.25), while none enriched in non-brisk tumors, suggesting that the histological TIL grade was strongly associated with transcriptional features of an immune response. Gene-sets that enriched in tumors with brisk infiltrates included those derived from CD4 and CD8 T cells (evidenced by increased expression of T cell lineage-specific genes such as CD3G, ZAP70, CD28, TBX21, PRDM1, GZMB, PRF1); those related to monocytes (CD14); as well as Type I interferon response genes (OAS1, IFI44). Surprisingly we did not find enrichment of gene-sets related to CD8 T cell exhaustion. Instead, we found highly significant enrichment of effector CD8 T cell gene-sets that featured effector cytokines, such as IFNG and TNF, and cytokine receptors such as IL-15R and IL-2RB, genes that which are normally decreased in expression in exhausted T cells. This suggests that the transcriptional profile of brisk immune infiltrates in melanoma includes features of highly functional CD8 effector T cell responses and lacks transcriptional features of exhaustion. We next tested whether the signatures of immune response to melanoma were enriched in other tumors. We identified a core set of “TIL hallmark genes” comprised of GSEA leading-edge genes from multiple gene-sets enriched in brisk vs. non-brisk melanoma samples. We then grouped the gene expression profiles of other tumor histologies according to their expression of TIL hallmark genes using single-sample GSEA. In thyroid cancer, for example, we found that the enrichment of melanoma TIL hallmark genes was strongly correlated with the presence of lymphocyte infiltrates, suggesting that there are common features of the immune response to cancer in different tumor types. Our results show that integrated analysis of histology and gene expression profiles from melanoma samples can identify the molecular features of the TIL response. We find evidence for signatures of effective CD8 T cell responses in brisk infiltrate melanomas that are shared by other tumor types. These TIL hallmark genes may help identify molecular subsets of immunogenic tumors, providing novel outcome predictors, and opportunities to stratify immunotherapeutic treatment options. More broadly, this approach can help deconvolve tumor/host gene expression profiles and better characterize the human immune response to cancer.