From HLA-C peptide processing to NK cell recognition: unveiling mechanisms controlling KIR interactions with human cytomegalovirus infected cells

• Applicant: Dr. Anne Halenius
• Subject Area: Virology ; Immunology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 563322053

Classical human leucocyte antigen class I (HLA-I) molecules, encoded by the HLA-A, HLA-B, and HLA-C genes, are the most polymorphic genes in humans. They display peptide ligands on the cell surface, unique to each individual. HLA-I peptide presentation is fundamental for the action of CD8+ T cells, but also natural killer (NK) cells interact with HLA-I through killer-cell immunoglobulin-like receptors (KIRs). KIRs are polymorphic receptors that have both inhibiting and stimulating effects on NK cells. Of all HLA-I molecules interacting with KIRs, HLA-C allotypes play a dominant role and communicate with KIRs in a peptide-dependent manner. However, the mechanisms governing HLA-C/peptide quality, affecting subsequent KIR-recognition, remain largely elusive. In this project, we want to address this knowledge gap. We developed a highly specific and sensitive KIR-reporter cell system and analyzed recognition of human cytomegalovirus (HCMV)-infected fibroblasts. A strong engagement of KIR2DL1, KIR2DS1 and KIR2DS4 with the common HLA-C ligand HLA-C*05:01 was observed, although HLA-C was markedly downregulated by HCMV. This discrepancy is particularly interesting given the reported single (polarized) KIR expression in the adaptive NK cell population that is uniquely induced in HCMV-infected individuals. Moreover, IFNγ-treatment of fibroblasts reduced KIR2DL1-recognition of HLA-C*05:01 despite high HLA-C*05:01 surface density. Together, these results indicated that the immunological condition of the target cell, such as IFNγ-stimulated or HCMV-infected, alters the quality of presented HLA-C/peptide complexes and modifies the outcome of KIR interaction. The findings provide us excellent tools to mechanistically investigate how HLA-C ligandomes form and impact KIR engagement. Using SILAC labeling techniques, we will quantitatively analyze HLA-C ligandomes and evaluate the KIR binding potential of HLA-C/peptide complexes using HLA-C single-chain trimers. We will probe key steps in the HLA-I antigen processing and presentation pathway to define mechanisms that constitute and regulate the quality of HLA-C/peptide complexes and shape KIR recognition of target cells.

• DFG Programme: Research Grants