MHC Class I–Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia

Abstract

Deregulation of signaling pathways involving phosphorylation is a hallmark of malignant transformation. Degradation of phosphoproteins generates cancer-specific phosphopeptides that are associated with MHC-I and II molecules and recognized by T-cells. We identified 95 phosphopeptides presented on the surface of primary hematological tumors and normal tissues, including 61 that were tumor-specific. Phosphopeptides were more prevalent on more aggressive and malignant samples. CD8 T-cell lines specific for these phosphopeptides recognized and killed both leukemia cell lines and HLA-matched primary leukemia cells ex vivo. Healthy individuals showed surprisingly high levels of CD8 T-cell responses against many of these phosphopeptides within the circulating memory compartment. This immunity was significantly reduced or absent in some leukemia patients, which correlated with clinical outcome, and was restored following allogeneic stem cell transplantation. These results suggest that phosphopeptides may be targets of cancer immune surveillance in humans, and point to their importance for development of vaccine-based and T-cell adoptive transfer immunotherapies..

Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD)

“…A preferred bias was found for a basic residue on P1 and the phosphate group on P4 of peptide sequence (SI Appendix, Fig. S9)-characteristics similar to those previously reported (24,25). Mapping the data to phosphorylation-specific motifs that are commonly associated with specific kinases resulted in the assignment of 72% of the phosphopeptides to a prolinedirected kinase motif (PxTP, PxSP), similar to those reported by Cobbold et al (24), or basophilic kinase motif (RxxS) (SI Appendix, Fig.…”

“…S9). Comparison with previous studies revealed that 16 HLA-B7-associated phosphopeptides had been reported previously (16,24,26), whereas a total of 24 phosphorylation sites are annotated in the Uniprot protein database (www.uniprot.org/). The correct identification of selected phosphopeptides could be nicely confirmed by the spectra we generated from their synthetic peptide counterparts (SI Appendix, Fig.…”

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

“…MS-based approaches, together with MHC peptide ligand prediction algorithms (e.g. SYFPEITHI, Net-MHC, smm) (120 -122) were particularly helpful to better understand the molecular mechanisms that process cellular proteins into the immunopeptidome as well as for the detection of disease-related peptides and phosphopeptides that could be used for the rational design of immunotherapeutic interventions (123)(124)(125). Since a comprehensive survey of the literature is not within the scope of this mini-review, we focus below on selected landmark papers and applications of outstanding interest.…”

The Flipside of the Power of Engineered T Cells: Observed and Potential Toxicities of Genetically Modified T Cells as Therapy

“…Furthermore, new molecular methods that allow for the analysis of post-translationally modified (PTM) proteins has further increased the repertoire of new candidates amenable for T cell recognition. Cobbold et al 31 emphasized the increasing importance of these post-translational modifications in human malignancies. They demonstrated that phosphopeptide antigens derived from cancer-related phosphoproteins could serve as immunologic signatures of the "transformed self" and were immunogenic in patients with and without cancer.…”

“…These neo-antigen phosphopeptides were then identified on primary human malignant tissue and were often derived from oncogenes linked to leukemogenesis, making them exciting targets for future T cell-targeted therapy independent of overall mutational load. 31 Most of the neoantigens studied are derived from modified intracellular proteins and have been proposed and tested as candidates for TCR-engineered T cells. Nevertheless, the discovery of neoantigens on the surface of cancer cells will likely provide a valuable source of targets for CAR T cells.…”