Samuels Lab

Aberrant peptides presented by major histocompatibility complex (MHC) molecules are targets for tumor eradication, as these peptides can be recognized as foreign by T cells. Protein synthesis in malignant cells is dysregulated, which may result in the generation and presentation of aberrant peptides that can be exploited for T cell-based therapies. To investigate the role of translational dysregulation in immunological tumor control, we disrupt translation fidelity by deleting tRNA wybutosine (yW)-synthesizing protein 2 (TYW2) in tumor cells and characterize the downstream impact on translation fidelity and immunogenicity using immunopeptidomics, genomics, and functional assays. These analyses reveal that TYW2 knockout (KO) cells generate immunogenic out-of-frame peptides. Furthermore, Tyw2 loss increases tumor immunogenicity and leads to anti-programmed cell death 1 (PD-1) checkpoint blockade sensitivity in vivo. Importantly, reduced TYW2 expression is associated with increased response to checkpoint blockade in patients. Together, we demonstrate that defects in translation fidelity drive tumor immunogenicity and may be leveraged for cancer immunotherapy.

Low intratumor heterogeneity correlates with increased patient survival and immunotherapy response. However, even highly homogeneous tumors are vari-ably aggressive, and the immunologic factors impacting aggressiveness remain understudied. In this study, we analyzed the mechanisms underlying immune escape in murine tumors with low intratumor heterogeneity. We used immunophenotyping and single-cell RNA sequencing to compare the temporal growth of in vivo transplanted, genetically similar, rejected and nonrejected single-cell clones. Nonrejected clones showed high infiltration of tumor-associated macrophages, lower T cell infiltra-tion, and increased T cell exhaustion when compared with rejected clones. Comparative analysis of rejection-associated gene expression programs, combined with in vivo CRISPR knockout screens of candidate regulators, identified macrophage migration inhibitory factor (Mif) as a major con-tributor to preventing immune rejection. Mif knockout resulted in smaller tumors and reduced tumor-associated macrophage infiltration. These results were validated in patients with melanoma. Overall, our homogeneous tumor system can uncover factors regulating growth variability and identifies Mif as critical in aggressive melanoma. Significance: In this study, we find that Mif expression is associated with tumor growth and aggressiveness, specifically in tumors with low heterogeneity. These findings could facilitate the development of new strategies to treat patients with homogeneous, high MIFexpressing tumors that are unresponsive to immune checkpoint therapy.

Neoantigen immunogenicity prediction is a burgeoning field with vast potential; however, the shortage of high-quality data and biases in current datasets limit model generalizability. Here we discuss some of the pitfalls that may underly this limited performance and propose a path forward.