TOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification.

T cell recognition of human leukocyte antigen (HLA)-presented tumor-associated peptides is central for cancer immune surveillance. Mass spectrometry (MS)-based immunopeptidomics represents the only unbiased method for the direct identification and characterization of naturally presented tumor-associated peptides, a key prerequisite for the development of T cell-based immunotherapies. This study reports on the implementation of ion mobility separation-based time-of-flight (TOFIMS) MS for next-generation immunopeptidomics, enabling high-speed and sensitive detection of HLA-presented peptides. Applying TOFIMS-based immunopeptidomics, a novel extensive benignTOFIMS dataset was generated from 94 primary benign samples of solid tissue and hematological origin, which enabled the expansion of benign reference immunopeptidome databases with > 150,000 HLA-presented peptides, the refinement of previously described tumor antigens, as well as the identification of frequently presented self antigens and not yet described tumor antigens comprising low abundant mutation-derived neoepitopes that might serve as targets for future cancer immunotherapy development.

Autoradiography on deparaffinized tissue sections - A feasibility study with 68Ga-labeled PET-tracers.

Tissue available for retrospective research questions is often already paraffin-embedded for better preservation. However, in vitro autoradiography (AURA) is normally performed on cryopreserved tissue sections. We hypothesized a) that it would also be feasible with deparaffinized tissue sections, enabling the use of human paraffin-embedded tissue for in vitro AURA and b) that the results would be comparable to those obtained with corresponding cryosections. For that purpose, the clinically relevant oncological targets CXCR4, SSTR and PSMA were evaluated. In vitro AURA on deparaffinized tissue sections was feasible, but only with the two receptor ligands [68Ga]Ga-PentixaFor and [68Ga]Ga-DOTANOC. [68Ga]Ga-PSMA-11 did not show any binding on deparaffinized tissue sections, suggesting that native tissue is required for an interaction between this inhibitor and the enzyme.