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The HLA class-I immunopeptidomes of AAV capsid proteins

ABSTRACT: Introduction: Cellular immunity is one of the main factors affecting sustained expression of gene therapies. AAV capsid-specific CD8+ T cells recognize peptides that are loaded on HLA class I molecules by cells that have been infected or transduced with AAVs. Previous studies performed by others have identified several peptides that activate CD8+ T cells, however the entire repertoire of naturally displayed peptides is unknown. Methods: Using MHC-associated peptide proteomics, we describe the HLA class I immunopeptidomes of AAV2, AAV6 and AAV9 capsids. Monocyte-derived dendritic cells (MDDCs) were isolated from a panel of 13 healthy donors that have diverse alleles representing more than 50% of the US population. MDDCs were transfected with mRNA encoding for the different AAV capsids. 6 hours post transfection, cells were lysed and peptide:HLA complexes were immunoprecipitated. Peptides were eluted and analyzed by mass spectrometry and PEAKS bioinformatic algorithms. Results: The HLA-I peptides are distributed along the entire capsids but the number of AAV9-derived peptides was significantly higher than for AAV2 or AAV6. We identified a few peptides that had been described before and are immunogenic. We also observed 14 peptides that are highly conserved among the serotypes. Finally, we observed that more than 60% of the HLA-I peptides are contained within HLA-II clusters. Discussion: This work is the first comprehensive study identifying the naturally displayed HLA class I peptides derived from the capsid of AAVs and expands on previous studies that have identified immunogenic peptides. The results from this study can be used to generate peptide pools to assess immunogenicity risk of gene therapies in the clinic.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Adeno-associated Virus - 6 (ncbitaxon:68558) Homo Sapiens (ncbitaxon:9606) Adeno-associated Virus 9 (ncbitaxon:235455) Adeno-associated Virus - 2 (ncbitaxon:10804)

SUBMITTER: Carlos Brito

PROVIDER: MSV000091389 | MassIVE | Wed Mar 01 14:48:00 GMT 2023

SECONDARY ACCESSION(S): PXD040535

REPOSITORIES: MassIVE

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The HLA class-I immunopeptidomes of AAV capsid proteins

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