Plasma immunopeptidomic landscape in patients with alpha-1 antitrypsin deficiency

Alpha-1 antitrypsin deficiency (AATD) is an autosomal monogenic defect that causes misfolding and a secretory defect of alpha-1 antitrypsin (AAT) in the producing hepatocyte cell. This can lead to variable symptoms both in the liver as well as in the periphery, predominantly the lung. Consequences can be severe liver fibrosis or even cirrhosis as well as pulmonary emphysema.

In a previous study we discovered that a healthy human has a stable soluble human leukocyte class I (HLA-) immunopeptidomic signature, representative of various organ systems (Wahle et al. PMID 38043703). AATD is associated with the remodeling of various intracellular processes potentially reflected by different proteome compositions and as a consequence by the presented immunopeptides. We here apply our recently introduced IMBAS-MS immunopeptidomics workflow for the efficient enrichment of soluble immunopeptides from plasma of 120 homozygous AATD patients and their heterozygous genetic relatives. We leverage the speed and flexibility of the Orbitrap Astral mass spectrometer in analyzing immunopeptidomics samples separated over a 31 min nanoflow gradient (Whisper 40) using the Evosep One liquid chromatography system. We also acquired the neat plasma proteome of all patients on a Orbitrap Exploris 480. Raw files were analyzed with DIANN 1.8.1 or AlphaDIA using predicted spectral libraries and peptide quality was assessed using MHCVizPipe.

We identify on average more than 4000 HLA-I immunopeptides per patient. We now aim to assess whether the soluble immunopeptidome can be indicative of cellular stress and hepatocyte damage as a consequence of AAT accumulation in those cells. Findings of biomarker candidate would enhance the precise monitoring of the disease status in patients with alpha-1 antitrypsin deficiency with clinical impact for this large disease group.