Computational protocol: Immunogenicity of HLA Class I and II Double Restricted Influenza A-Derived Peptides

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Protocol publication

[…] Epitope predictions were performed on the basis of datasets obtained from the Influenza Sequence Database (www.flu.land.gov). Only peptides from influenza A-derived constant proteins such as M1, M2, NS1, PB1, PB2, PA and NP proteins were included in the analysis, while the variable proteins N and H were excluded. Bioinformatic analyses were used to identify double binding influenza A-derived peptides, i.e. peptides predicted to bind to both HLA-A*02:01 and to HLA-DRB1*01:01. Binding to HLA-A*02:01 was performed using NetMHCpan-2.8 [,]. Binding to HLA-DRB1*01:01 was performed using NetMHCIIpan-3.0 [,] and both prediction methods are available at www.cbs.dtu.dk/services. Analyses were performed using the Influenza strain A/Puerto Rico/8/1934(H1N1) [Refseq accession numbers:NP_040978.1,NP_040979.2,NP_040980.1,NP_040981.1,NP_040982.1,NP_040983.1,NP_040984.1,NP_040985.1,NP_040986.1,NP_040987.1].Peptides were selected based on the following strategy. First peptides of length 9–11 amino acids with predicted binding to HLA-A*02:01 stronger than 50nM were selected. Next this list was filtered to include only peptides that either were predicted to bind HLA-DRB1*01:01 or were part of a 15mer peptides that was predicted to bind HLA-DRB1*01:01 with an affinity stronger than rank 10% (the IEDB recommended threshold for MHC class II peptide binding classification). Finally, the selection was extended by a peptide that is part of a 15mer with very strong binding to HLA-DRB1*01:01 even though it lacked binding to HLA-A*02:01, and a peptide with strong binding to HLA-A*02:01 even though it lacked binding to HLA-DRB1*01:01 (details on the peptide selection and predicted binding values are given ). These peptides were all present in the influenza strain A/Puerto Rico/8/34 H1N1 used for the challenge of mice. […]

Pipeline specifications

Software tools NetMHCpan, NetMHCIIpan
Databases IEDB
Application Immune system analysis
Organisms Mus musculus
Diseases Influenza, Human