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

Abstract

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 (i) triggering host anti-viral responses, (ii) hijacking host processes, and (iii) 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 following influenza infection, we compared by mass spectrometry (MS) peptides eluted from the HLA of naïve and infected cells. We identified 20 peptide ligands unique to infected cells and 347 peptides with increased presentation following 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 in order to access the same host cell processes.

Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity

“…In contrast to previous MS efforts to identify IAV peptides in association with A2 (21,22), the highly conserved M1 58-66 peptide GILGFVFTL was not only detected, but shown to be abundantly presented by infected lung epithelium. Previously unrecognized IAV epitopes were identified and characterized by their copy number on infected cells.…”

“…S23). Whereas the other six peptides are not fully conserved, variability is still finite, with three variants each covering the HA 431-439 stem region segment and PB2 463-471 and eight peptide variants covering NA [18][19][20][21][22][23][24][25][26] and NS1 [122][123][124][125][126][127][128][129][130] . M1 134-142 global strain variability is accounted for by three peptides but the RMGAVTTES variant found in 13% is predicted to be a very weak A2 binder, potentially permitting viral escape.…”

“…Although relative ion amplitudes by static nanospray MS ranged over factors of 2-3 when the peptides were directly diluted, similar relative amplitudes are not observed when these peptides are spiked into affinity-purified complexes at the acid elution step and analyzed by LC-DIAMS. In particular, surface exposure and poorly characterized electrospray factors strongly suppress the hydrophobic NA [18][19][20][21][22][23][24][25][26] and M1 58-66 peptides. Optimal quantitation would use isotopically labeled analogs as internal standards for all peptides but considering expense and anticipating the discussion to follow, this was restricted to the M1 58-66 peptide.…”

Enhanced Direct Major Histocompatibility Complex Class I Self-Antigen Presentation Induced by Chlamydia Infection

“…Viruses, including HIV (10), measles virus (11), influenza virus (12), and respiratory syncytial virus (13), often alter the self-peptide repertoire on MHC class I molecules. Changes in cellular metabolic activity can also skew the repertoire of self-peptides displayed at the cell surface (14).…”

Identification of Human Host Proteins Contributing to H5N1 Influenza Virus Propagation by Membrane Proteomics

“…9,49 ANXA2 can be incorporated into the IAV particles and supports virus replication by converting plasminogen into plasmin, which can serve as an alternative protease for the cleavage of the hemagglutinin (HA) outside of the respiratory tract. 50−52 In this study, ANXA2 was found to be down-regulated during HPAI H5N1 virus infection (Supplementary Figure 2, Supporting Information).…”