Insights into anti-tumor immunity via the polyomavirus shared across human Merkel cell carcinomas

Abstract

Understanding and augmenting cancer-specific immunity is impeded by the fact that most tumors are driven by patient-specific mutations that encode unique antigenic epitopes. The shared antigens in virus-driven tumors can help overcome this limitation. Merkel cell carcinoma (MCC) is a particularly interesting tumor immunity model because (1) 80% of cases are driven by Merkel cell polyomavirus (MCPyV) oncoproteins that must be continually expressed for tumor survival; (2) MCPyV oncoproteins are only ~400 amino acids in length and are essentially invariant between tumors; (3) MCPyV-specific T cell responses are robust and strongly linked to patient outcomes; (4) anti-MCPyV antibodies reliably increase with MCC recurrence, forming the basis of a standard clinical surveillance test; and (5) MCC has one of the highest response rates to PD-1 pathway blockade among all solid cancers. Leveraging these well-defined viral oncoproteins, a set of tools that includes over 20 peptide-MHC class I tetramers has been developed to facilitate the study of anti-tumor immunity across MCC patients. Additionally, the highly immunogenic nature of MCPyV oncoproteins forces MCC tumors to develop robust immune evasion mechanisms to survive. Indeed, several immune evasion mechanisms are active in MCC, including transcriptional downregulation of MHC expression by tumor cells and upregulation of inhibitory molecules including PD-L1 and immunosuppressive cytokines. About half of patients with advanced MCC do not persistently benefit from PD-1 pathway blockade. Herein, we (1) summarize the lessons learned from studying the anti-tumor T cell response to virus-positive MCC; (2) review immune evasion mechanisms in MCC; (3) review mechanisms of resistance to immune-based therapies in MCC and other cancers; and (4) discuss how recently developed tools can be used to address open questions in cancer immunotherapy. We believe detailed investigation of this model cancer will provide insight into tumor immunity that will likely also be applicable to more common cancers without shared tumor antigens.

Keywords: Merkel cell carcinoma; Merkel cell polyomavirus; anti-tumor T cells; immunotherapy; oncoproteins; skin cancer.

Figure 1

Virus-driven MCC is a unique model cancer for studying anti-tumor T cell responses. (A) Virus-driven MCC arises when MCPyV undergoes a truncation and integrates into the host genome. The integration site is thought to be random as it varies greatly among patients. Following the truncation and integration, two oncoproteins (large and small T antigens), which share a common region, are persistently expressed and drive tumorigenesis. (B) These viral oncoproteins are small (~400 amino acids), and this antigenic space has been rigorously studied to identify immunogenic peptides presented by common MHC types. The areas of immunogenicity are highlighted with pink stars. (C) Based on these functional studies, multimer tools to identify cancer-specific T and B cells have been developed and validated. The immunogenic peptides, the MHC molecules that can present them, the relevant oncoprotein region, and an approximation of the prevalence of these MHC molecules in patients with MCC are summarized in the table.

Figure 2

Insights into anti-tumor T cell responses gained by studying virus-driven MCC. Several lines of evidence have shown that virus-driven MCC is targetable by CD8 T cells and the presence of the MCPyV oncoprotein-specific T cells in patients can be linked to improved clinical outcomes. (A) Increased number of MCPyV oncoprotein-specific T cells, diverse T cell clonotypes that target MCPyV oncoprotein antigens, and CD8 T cells with high functional avidity found in the tumor are linked to improved patient outcomes in the absence of immunotherapy. (B) Circulating peripheral blood T cell characteristics that are associated with response to immunotherapy include the presence of MCPyV oncoprotein-specific CD8 T cells before initiation of anti-PD-1 therapy as assessed by MHC-peptide tetramer, and the presence of CD8 T cells that co-express CD39 and CLA before initiation of anti-PD-1 therapy.

Figure 3

Summary of mechanisms of resistance to immunotherapy identified to-date. Several mechanisms can prevent response to immunotherapy altogether (primary resistance), while other mechanisms are acquired later in the disease course and lead to tumor relapse (secondary resistance). (A) Oncoproteins can induce immune suppressive environments that recruit tumor-promoting macrophages and T regulatory cells, prevent infiltration of antigen-presenting cells, and prevent infiltration and priming of effector T cells. (B) Tumor cells can prevent T cell recruitment via downregulation of inflammatory pathways and cell surface integrins (e.g., E-selectin) that mediate T cell entry into inflamed tissues. (C) Tumors often downregulate or develop mutations in genes responsible for antigen presentation (e.g., MHC, IFN-γ receptor), preventing tumor engagement with T cells. (D) Chronic exposure to their cognate antigens leads to activation of evolutionarily protective, immunosuppressive mechanisms that convert effector T cells to a hypofunctional phenotype. (E) Increased glucose uptake by the tumor leads to T cell activation in a nutrient-poor environment, which seems to prime T cells to attain a hyporesponsive phenotype. This phenotype cannot be reversed even if T cells are subsequently stimulated in nutrient-rich conditions. (F) Lack of TLS can prevent appropriate T cell priming and is linked to poor outcomes and poor response to immunotherapy. (G) Cancer and immune cells co-exist in balance with each other. Thus, immune pressure can lead to deletion of immunogenic neoantigens not required for tumor survival. This “hides” the tumor from the immune system. (H) Tumors can also downregulate or mutate cell surface receptors and intracellular proteins responsible for recognizing and responding to immune effector signals (e.g., PTPN2, ADAR1, SETDB1, TBK1, JAK1/2, and PTEN), thus preventing immune-mediated cancer cell death. (I) ICI has been demonstrated to re-invigorate the effector functions of T cells but may not induce memory cell formation. This would allow metastases and microtumors to grow after initial disease has been controlled.