Phosphopeptide Neoantigens as Emerging Targets in Cancer Immunotherapy

Abstract

Protein post-translational modifications play a vital role in various cellular events essential for maintaining cellular physiology and homeostasis. In cancer cells, aberrant post-translational modifications such as glycosylation, acetylation, and phosphorylation on proteins can result in the generation of antigenic peptide variants presented in complex with MHC molecules. These modified peptides add to the class of tumorspecific antigens and offer promising avenues for targeted anti- cancer therapies. In this review, we focus on the role of phosphorylated peptides (p-peptides) in cancer immunity. We discuss the mechanisms by which the phosphorylated moiety modifies the structural features and binding properties of p-peptides with MHC, compared to their non-phosphorylated counterparts. Additionally, we review recent work on how the HLA-B*07-specific p-peptide, pMLL_747-755, interacts with its cognate TCR. Altogether, p-peptides are emerging as a novel class of tumor-specific antigens, expanding the range of targets in cancer immunotherapy.

Keywords: Immune checkpoint blockade therapies; Immunopeptidome; Neoantigens; Phosphorylation; Post-translational modifications.

Figure 1.

Phosphorylated antigen generation and their utilization for antigen-based treatment workflow in cancers. (A) Phosphorylated proteins are intracellularly processed and presented in complex with MHC I or MHC II molecules on cell surface. (B) The immunopeptidome purification and enrichment from cancer and normal tissues is done and peptide sequences are tested by Liquid Chromatography with tandem mass spectrometry (LC/MS-MS). The phosphorylated peptides from the immunopeptidome are evaluated using in silico tools for data mining and mechanistic studies and validated by both, in vitro and in vivo assays before selection for cancer vaccines. Created with BioRender.com.

Figure 2.

Binding between phosphopeptides and HLA class I molecules. (A) The most typical binding pattern between p-peptide and HLA with phosposerine at position P4 and/or P8 of a 9-mer peptide. The arrows show anchor residues (down) or non-anchor residues (up). P2 and P9 are primary anchor residues, others are usually optional and vary between different peptides. (B) The binding pattern between p-peptides with a consensus sequence of R/KQx(pS)xxxxΨ and HLA-A*02:01. Hydrogen bonds shown as dotted lines. (C) Superimposition between the two typical binding patterns observed for p-peptides in complex with HLA-A*02:01. (D) Schematic representation of the interface between HLA-B*07:02, pMLL p-peptide and TCR27 (variable region only). The TCR residues involved in hydrogen bonding with p-peptide are depicted. Ψ - aliphatic amino acid residues. Created with BioRender.com.