The impact of intratumor heterogeneity on anti-tumor immunity

Abstract

Cancer immunotherapies, notably checkpoint blockade therapy (CBT), have proven efficacy to control cancer growth, with a fraction of patients exhibiting durable responses. However, the majority of patients do not respond to CBT and the molecular determinants of resistance have not been fully characterized. Many of these therapies depend on cytotoxic CD8+ T cells, which recognize specific tumor cells and kill them. Specific recognition is bestowed by the presence of neoantigens, derived from mutated sequences arising during tumorigenesis. They are attractive targets because they are specific to tumor cells and have not been subjected to central immune tolerance mechanisms. However, there is mounting evidence from clinical data that the clonal status of neoantigens impacts the anti-tumor immune response. High intratumor heterogeneity (ITH), where the majority of neoantigens is expressed subclonally, is correlated with poor clinical response to CBT and weaker anti-tumor immunity. The mechanism by which ITH blunts tumor-reactive CD8+ T cells is still unknown.

To study the effect clonal and subclonal expression of neoantigens has on resulting neoantigen-specific responses we developed a transplantable murine cancer model to characterize the immune response against a defined set of neoantigens expressed either clonally or subclonally to model low or high ITH, respectively. We find that clonal expression of a weakly immunogenic neoantigen with a relatively strong neoantigen increased the immunogenicity of tumors. Mechanistically we found that clonal neoantigen expression allowed cross-presenting dendritic cells to acquire and present both neoantigens. Dual neoantigen presentation was associated with a more mature DC phenotype and a higher stimulatory capacity.

These data suggest that clonal neoantigen expression can induce more potent anti-tumor responses due to more mature dendritic cells : T cell interactions and highlights the therapeutic potential of targeting subclonal neoantigens using vaccination and modulating the tumor immune microenvironment to increase response to CBT. The model we developed is being used to recapitulate more complex subclonal neoantigen architectures found in patients to identify and refine the rules that determine the quality and structure of anti-tumor immune responses. Identifying these rules and the mechanisms that drive them will inform therapeutic strategies to circumvent poor anti-tumor immune responses.