Considerable recent interest lies in the immunogenicity of non-canonical neoantigens harboured in alternative open reading frames generated by non-synonymous mutations, nucleotide insertions / deletions, exonization of untranslated regions of the genome, non-coding transcripts, transposable elements, etc. Amongst these ‘cryptic’ epitopes, those generated by chimeric transcripts [CTs], which represent sequences from more than one gene remain undefined, and their translational potential and immunogenicity is relatively unexplored. In the present study, we predicted and assessed neoepitopes generated by CTs in ovarian cancer. Development and application of a customized targeted peptide database, further led to the identification of unique peptides and reading-frame isoforms [sense/anti-sense] of such transcripts. Prediction of antigenicity of these novel peptides and proteins was achieved considering their stability, proteasomal processing, and likelihood of being presented to MHC-I in an allele-specific manner. Further docking of peptide MHC and peptide-MHC-TCR complexes provided validation and proof-of-concept of generation of a small number of putative neoepitopes of CTs that are recognized by specific TCRs. Importantly, our findings identify that relaxed/perturbed rigidity of canonical transcription and translation in cancer may present new opportunities in immunotherapy.

Peptides identified in a customized targeted database were assessed for antigenicity. Further docking of peptide – MHC as well as peptide-MHC-TCR complexes provided proof-of-concept of antigenicity. Considerable recent interest lies in the immunogenicity of non-canonical neoantigens generated by alternative ORFs emerging from non-synonymous mutations or nucleotide insertions and deletions, exonization of untranslated regions of the genome, non-coding transcripts, transposable elements, etc. Amongst these ‘cryptic’ epitopes, those derived from chimeric transcripts which harbor sequences derived from more than one gene remain undefined, since the translational potential and immunogenicity of these transcripts is relatively unexplored. The present study was hence designed to predict and assess the neoepitopes generated by chimeric transcripts in ovarian cancer. Using a customized targeted database, we identified peptides uniquely generated by such transcripts, expressed either as reading-frame or sense/anti-sense isoforms. Further assessment of the antigenicity of these peptides identified a small number of putative neoepitopes that are likely to be presented to MHC-I in an allele-specific manner, and further recognized by specific TCRs. Effectively, such generation of chimeric molecules by relaxed rigidity of canonical transcription and translation may present opportunities in immunotherapy.

Background: Considerable recent interest lies in the immunogenicity of non-canonical neoantigens generated by alternative ORFs emerging from non-synonymous mutations or nucleotide insertions and deletions, exonization of untranslated regions of the genome, non-coding transcripts, transposable elements, etc. Amongst these ‘cryptic’ epitopes, those derived from chimeric transcripts which harbor sequences derived from more than one gene remain undefined, since the translational potential and immunogenicity of these transcripts is relatively unexplored.Methods: The present study was hence designed to predict and assess the neoepitopes generated by chimeric transcripts in ovarian cancer. Peptides identified in a customized targeted database were assessed for antigenicity. Further docking of peptide – MHC as well as peptide-MHC-TCR complexes provided proof-of-concept of antigenicity.Results: We identified peptides uniquely generated by chimeric transcripts, expressed by reading-frame as well as sense/anti-sense isoforms. Further assessment of the antigenicity of these peptides identified a small number of putative neoepitopes that are likely to be presented to MHC-I in an allele-specific manner, and further recognized by specific TCRs.Conclusions:Such generation of chimeric molecules by relaxed rigidity of canonical transcription and translation may present opportunities in immunotherapy.

Considerable recent interest lies in the immunogenicity of non-canonical neoantigens harboured in alternative open reading frames generated by non-synonymous mutations, nucleotide insertions / deletions, exonization of untranslated regions of the genome, non-coding transcripts, transposable elements, etc. Amongst these ‘cryptic’ epitopes, those generated by chimeric transcripts [CTs], which represent sequences from more than one gene remain undefined, and their translational potential and immunogenicity is relatively unexplored. In the present study, we predicted and assessed neoepitopes generated by CTs in ovarian cancer. Development and application of a customized targeted peptide database, further led to the identification of unique peptides and reading-frame isoforms [sense/anti-sense] of such transcripts. Prediction of antigenicity of these novel peptides and proteins was achieved considering their stability, proteasomal processing, and likelihood of being presented to MHC-I in an allele-specific manner. Further docking of peptide MHC and peptide-MHC-TCR complexes provided validation and proof-of-concept of generation of a small number of putative neoepitopes of CTs that are recognized by specific TCRs. Importantly, our findings identify that relaxed/perturbed rigidity of canonical transcription and translation in cancer may present new opportunities in immunotherapy.