A rational pipeline for Epitope Immunogenicity Characterization

What is EpIC?

EpIC is a software program that is designed to enable optimization of peptide epitopes for vaccine applications. Peptide-based vaccines offer many advantages over traditional vaccine platforms in terms of cost, safety, and ease of production. Difficulties arise when the peptide lacks sufficient immunogenicity, which can occur even with the use of effective carrier proteins. However, many poorly immunogenic peptides can be translated into effective vaccine candidates through subtle manipulations in the target protein sequence. EpIC allows the user to easily, quickly, and accurately increase the immunogenicity of peptide epitopes through selective inclusion of endogenous B-cell epitopes that exist within the target protein sequence near the epitope of interest. EpIC identifies the optimal iteration of your target peptide antigen through sequential single amino acid-based expansion of your peptide sequence and analysis of the resulting antigen using the BepiPred program. For more information, refer to the original manuscript (Bioinformatics, under review).

NOTE: In situations where optimization of epitope presentation in the absence of sequence expansion is desired, perform the analysis as follows. Upload the desired epitope sequence for both the target protein sequence and the core epitope sequence files. Indicate the linker sequences and presentation pattern as desired and enter “0” for the before and after expansion residues. The EpIC algorithm will generate an immunogenicity score for the repeat pattern. Comparative analysis of immunogenicity prediction scores with varying antigen presentation patterns can be performed by modifying the presentation input in consecutive runs.

Target sequence input

  1. Upload your FASTA file containing the full target protein sequence or a partial sequence that includes the core epitope and sufficient flanking residues for expansion analysis. Multiple sequences can be included in the FASTA file. The immunogenicity analysis will be performed against the first protein sequence and sequence conservation of epitopes will be analyzed across all of the sequences. Click here to download an example sequence.

  2. Upload your file containing the core epitopes, which represent the minimal target sequences from which the expansion-based analysis should be performed. There should be one core epitope per line. If a given core epitope occurs more than once in the sequence, then you may also specify the position in the protein sequence of the first amino acid in the core epitope. For instance, if a line contains "YML", then the first instance of YML will be used. If, however, the line contains "YML:131", then the YML that begins at position 131 will be used. Click here to download an example file.

Antigen presentation input

  1. Enter the amino acids to be included in any linker sequences. Default = "GS".

  2. Enter the desired repeat pattern and location of the linker sequences in the final complete antigen sequence. Specify the number of repeats, the orientation of each epitope repeat and the amino acids present in any desired linkers using the following code. "F" refers to the forward sequence of the epitope. "R" indicates the reverse presentation of the epitope. "1" will insert the first amino acid in your linker sequence described in part 3. "2" will insert the second amino acid in your linker sequence, and so on. Default presentation pattern = "12FRR212FRR122FRR212FRR212FRR"

  3. Enter the maximum number of residues before and after the core epitope sequence to use in generating expanded epitope sequences.