Angela R. Wahl

HLA class I molecules reflect an altered host proteome after influenza virus infection

Class I HLA sample and display peptides from thousands of endogenous proteins at the cell surface. During infection, the influenza virus modifies the host cell proteome by triggering host antiviral responses, hijacking host processes, and inhibiting host mRNA processing. In turn, the catalog of HLA class I peptides that decorate the surface of an infected cell is positioned to reflect an altered host cell proteome. To understand the host-encoded peptides presented by class I molecules after influenza infection, we compared by mass spectrometry (MS) the peptides eluted from the HLA of naive and infected cells. We identified 20 peptide ligands unique to infected cells and 347 peptides with increased presentation after infection. Infection with different influenza strains demonstrated that proteome changes are predominantly strain-specific, with few individual cellular interactions observed for multiple viral strains. Modeling by pathway analysis, however, revealed that strain specific host peptide changes represent different routes to the same destination; host changes mediated by influenza are found predominantly clustered around HLA-B, ACTB, HSP90AB1, CDK2, and ANXA2. The class I HLA proteome scanning of influenza-infected cells therefore indicates how divergent strains of influenza pursue alternate routes to access the same host cell processes.

Direct class I HLA antigen discovery to distinguish virus-infected and cancerous cells

Class I human leukocyte antigen molecules are nature’s proteome-scanning chips, presenting thousands of endogenously loaded peptides on the surface of virtually every cell in the body. Cytotoxic T cells survey the class I human leukocyte antigen peptide cargo presented, recognize peptides unique to unhealthy cells and destroy diseased cells. A precise understanding of how class I molecules distinguish diseased cells is positioned to drive immune-based diagnostics, therapies and vaccines. When identifying epitopes unique to unhealthy cells, the most experimentally direct approach is to examine the class I-presented peptides of infected/cancerous cells. Here we discuss the strategies adapted for protein production, protein/peptide purification, peptide separation and for maintaining experimental reproducibility during the direct characterization of class I human leukocyte antigen peptides.

The Immune Response Under Stress: Class I HLA Presentation of Host-Derived Peptides

Major histocompatibility complex (MHC) class I molecules are found at the surface of all nucleated cells. Class I molecules function as immune sentries by scanning the intracellular proteome and then reflecting the proteome at the cell surface. Through class I presented peptides, T lymphocytes and other immune effector cells can continuously survey the intracellular proteome. Viral infection and cancerous transformation results in the presentation of peptides not found on healthy cells. Class I presented peptides therefore act to distinguish infected and cancerous cells in the eyes of the immune response. Here, we review how class I molecules reflect host cell stress resulting from infection and cancerous transformation. Class I molecules display peptides derived from heat shock proteins on both cancerous and virus-infected cells, and these peptides are clearly recognized by the immune response. The class I of diseased cells also reveal less obvious stress-related signals: Peptide fragments of proteins involved in cell homeostasis act to distinguish infected or cancerous cells. Finally, peptides derived from particular host proteins act as broad indicators of cellular stress, distinguishing both cancerous and virus-infected cells. These class I presented peptides are positioned to influence adaptive and innate immune responses to cellular stress