Identification of immunogenic mutant peptides using genomic, transcriptomic and proteomic information
The present disclosure provides methods of identifying a disease-specific immunogenic peptide through a series of selection steps. Immunogenic epitopes identified by methods of the present disclosure are applicable for use in peptide-based immunotherapy, preferably cancer therapy. Furthermore, the methods of the present disclosure may be performed in a high-throughput manner and serve as a means of personalized vaccine development and therapy. Also provided are compositions of immunogenic peptides as well as methods of treatment comprising said compositions.
1. A method of identifying a disease-specific immunogenic mutant peptide from a disease tissue in an individual, comprising:
(a) obtaining a first set of variant-coding sequences based on the genomic sequences of the disease tissue in the individual, each variant-coding sequence of the first set having a sequence variation compared to a reference sample;
(b) selecting a second set of expression variant-coding sequences from the first set based on transcriptomic sequences of the disease tissue in the individual;
(c) selecting a third set of epitope variant-coding sequences from the second set based on predicted ability of the peptides encoded by the second set to bind to an MHC class I molecule (MHCI);
(d) obtaining a plurality of peptides that are bound to an MHCI from the disease tissue;
(e) subjecting the MHCI-bound peptides to mass spectrometry-based sequencing,
wherein mass spectrometry-based sequencing comprises identifying MHCI-bound peptides based on transcriptomic sequence information of the disease tissue; and
(f) correlating the mass spectrometry-derived sequence information of the MHCI-bound peptides with the third set of epitope variant-coding sequences, thereby identifying the disease-specific immunogenic mutant peptide.
2. The method of claim 1 , wherein the obtaining the first set of variant-coding sequences based on genomic sequences of the disease tissue in the individual comprises:
(i) obtaining a set of sequences based on the genomic sequences of the disease tissue in the individual; and
(ii) identifying the first set of variant-coding sequences from the set of sequences,
wherein each variant-coding sequence of the first set of variant-coding sequences comprises a variation in the sequence compared to the reference sample.
3. The method of claim 1 , further comprising synthesizing a nucleic acid encoding a peptide based on the sequence of the identified disease-specific immunogenic mutant peptide.
4. The method of claim 1 , wherein the disease is cancer.
5. The method of claim 1 , wherein the individual is human.
6. A method of stimulating an immune response in the individual of claim 1 with the disease of claim 1 comprising:
(a) identifying according to claim 1 the disease-specific immunogenic mutant peptide from the disease tissue in the individual;
(b) producing a composition comprising a peptide or a nucleic acid encoding the peptide based on the sequence of the identified disease-specific immunogenic mutant peptide; and
(c) administering the composition to the individual.
7. The method of claim 6 , further comprising administering an anti-PD-1 antibody to the individual.
8. The method of claim 6 , further comprising administering to the individual an anti-PD-L1 antibody to the individual.
9. The method of claim 1 , further comprising predicting immunogenicity of peptides identified in step (f).
10. The method of claim 9 , wherein predicting immunogenicity is based on one or more of the following parameters:
(i) binding affinity of the peptide to the MHCI molecule;
(ii) protein level of a peptide precursor containing the peptide;
(iii) expression level of the transcript encoding the peptide precursor;
(iv) processing efficiency of the peptide precursor by an immunoproteasome;
(v) timing of expression of the peptide precursor;
(vi) binding affinity of the peptide to a TCR molecule;
(vii) position of a variant amino acid within the peptide;
(viii) solvent exposure of the peptide when bound to a MHCI molecule;
(ix) solvent exposure of the variant amino acid when bound to a MHCI molecule;
(x) content of aromatic residues in the peptide;
(xi) property of the variant amino acid when compared to the wild type residue; and
(xii) nature of the peptide precursor.
11. The method of claim 10 , wherein the prediction of immunogenicity further comprises HLA-typing analysis.