Shared Neoantigens: Ideal Targets for Off-The-Shelf Cancer Immunotherapy

References

• Forbes SA , BeareD , BoutselakisHet al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res.45(D1), D777–D783 (2017).
   PubMed Web of Science ®Google Scholar
• Matthew H , BaileyMH , TokheimCet al. Comprehensive characterization of cancer driver genes and mutations. Cell173(2), 371–385.e18 (2018).
   PubMed Web of Science ®Google Scholar
• Chapman PB , HauschildA , RobertCet al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N. Eng. J. Med.364(26), 2507–2516 (2011).
   PubMed Web of Science ®Google Scholar
• Longitudinal S , StructuralM , ModelsW. Immune checkpoint targeting in cancer therapy: towards combination strategies with curative potential. Cell2(2), 147–185 (2015).
   Google Scholar
• Rosenberg SA , RestifoNP. Adoptive cell transfer as personalized immunotherapy for human cancer. Science348(6230), 62–68 (2015).
   PubMed Web of Science ®Google Scholar
• de Plaen E , LurquinC , van PelAet al. Immunogenic (tum-) variants of mouse tumor P815: cloning of the gene of tum- antigen P91A and identification of the tum- mutation. Proc. Natl Acad. Sci.85(7), 2274–2278 (1988).
   PubMed Web of Science ®Google Scholar
• Zhou J , DudleyME , RosenbergSA , RobbinsPF. Persistence of multiple tumor-specific T-cell clones is associated with complete tumor regression in a melanoma patient receiving adoptive cell transfer therapy. J. Immunother.28(1), 53–62 (2005).
   PubMed Web of Science ®Google Scholar
• Dennis MK , FieldAS , BuraiRet al. Association of the autoimmune disease scleroderma with an immunologic response to cancer. Science127(6167), 358–366 (2012).
   Google Scholar
• Klebanoff CA , WolchokJD. Shared cancer neoantigens: making private matters public. J. Exp. Med.215(1), 5–7 (2018).
   PubMed Web of Science ®Google Scholar
• Ballhausen A , PrzybillaMJ , JendruschMet al. The shared neoantigen landscape of MSI cancers reflects immunoediting during tumor evolution. bioRxiv10.1101/691469 (2019) ( Epub ahead of print).
   Google Scholar
• Nielsen M , LundegaardC , LundO , KeşmirC. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics57(1–2), 33–41 (2005).
   PubMed Web of Science ®Google Scholar
• Bhasin M , LataS , RaghavaGP. TAPPred prediction of TAP-binding peptides in antigens. Methods Mol. Biol.409, 381–386 (2007).
   PubMedGoogle Scholar
• Larsen MV , LelicA , ParsonsRet al. Identification of CD8+ T cell epitopes in the west Nile virus polyprotein by reverse-immunology using NetCTL. PLoS ONE5(9), 1–11 (2010).
   Web of Science ®Google Scholar
• Hoof I , PetersB , SidneyJet al. NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics61(1), 1–13 (2009).
   PubMed Web of Science ®Google Scholar
• Liu G , LiD , LiZet al. PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity. Gigascience6(5), 1–11 (2017).
   Web of Science ®Google Scholar
• Andreatta M , NielsenM. Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics32(4), 511–517 (2015).
   PubMed Web of Science ®Google Scholar
• O’Donnell TJ , RubinsteynA , BonsackM , RiemerAB , LasersonU , HammerbacherJ. MHCflurry: open-source class I MHC binding affinity prediction. Cell Syst.7, 129–132 (2018).
   PubMed Web of Science ®Google Scholar
• Wu J , WangW , ZhangJet al. DeepHLApan: a deep learning approach for neoantigen prediction considering both HLA-peptide binding and immunogenicity. Front. Immunol.10, 2559 (2019).
   PubMed Web of Science ®Google Scholar
• Zhou Z , LyuX , WuJet al. TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection. R. Soc. Open Sci.4(4), 170050 (2017).
   PubMed Web of Science ®Google Scholar
• Wu J , ZhaoW , ZhouBet al. TSNAdb: a database for tumor-specific neoantigens from immunogenomics data analysis. Genomics, Proteomics Bioinforma.16(4), 276–282 (2018).
   PubMed Web of Science ®Google Scholar
• Yarchoan M , JohnsonBA , LutzER , LaheruDA , JaffeeEM. Targeting neoantigens to augment antitumour immunity. Nat. Rev. Cancer.17(4), 209–222 (2017).
   PubMed Web of Science ®Google Scholar
• Kumai T . Peptide vaccines in cancer-old concept revisited. Curr. Opin. Immunol.33(2), 557–573 (2017).
   Google Scholar
• Aldous AR , DongJZ. Personalized neoantigen vaccines: a new approach to cancer immunotherapy. Bioorganic Med. Chem.26(10), 2842–2849 (2018).
   PubMed Web of Science ®Google Scholar
• Ott PA , HuZ , KeskinDBet al. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature547(7662), 217–221 (2017).
   PubMed Web of Science ®Google Scholar
• Sahin U , DerhovanessianE , MillerMet al. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature547(7662), 222–226 (2017).
   PubMed Web of Science ®Google Scholar
• Keskin DB , AnandappaAJ , SunJet al. Neoantigen vaccine generates intratumoral T cell responses in Phase Ib glioblastoma trial. Nature565(7738), 234–239 (2019).
   PubMed Web of Science ®Google Scholar
• Hilf N , Kuttruff-CoquiS , FrenzelKet al. Actively personalized vaccination trial for newly diagnosed glioblastoma. Nature565(7738), 240–245 (2019).
   PubMed Web of Science ®Google Scholar
• Tran E , TurcotteS , GrosAet al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science344(6184), 641–645 (2014).
   PubMed Web of Science ®Google Scholar
• Tran E , AhmadzadehM , LuYet al. Immunogenicity of somatic mutations in human gastrointestinal cancers. Science350(6266), 1387–1391 (2015).
   PubMed Web of Science ®Google Scholar
• Tran E , RobbinsPF , LuY-Cet al. T-cell transfer therapy targeting mutant KRAS in cancer. N. Engl. J. Med.375(23), 2255–2262 (2016).
   PubMed Web of Science ®Google Scholar
• van der Lee DI , ReijmersRM , HondersMWet al. Mutated nucleophosmin 1 as immunotherapy target in acute myeloid leukemia. J. Clin. Invest129(2), 774–785 (2019).
   PubMed Web of Science ®Google Scholar
• Wang QJ , YuZ , GriffithK , HanadaK-i , RestifoNP , YangJC. Identification of T-cell receptors targeting KRAS-mutated human tumors. Cancer Immunol. Res.4(3), 204–214 (2016).
   PubMed Web of Science ®Google Scholar
• Malekzadeh P , PasettoA , RobbinsPFet al. Neoantigen screening identifies broad TP53 mutant immunogenicity in patients with epithelial cancers. J. Clin. Invest.129(3), 1109–1114 (2019).
   PubMed Web of Science ®Google Scholar
• Bailey MH , TokheimC , Porta-PardoEet al. Comprehensive characterization of cancer driver genes and mutations. Cell173(2), 371–385.e18 (2018).
   PubMed Web of Science ®Google Scholar
• Chang MT , AsthanaS , GaoSPet al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat. Biotechnol.34(2), 155–163 (2016).
   PubMed Web of Science ®Google Scholar
• Rech AJ , VonderheideRH. T-cell transfer therapy targeting mutant KRAS. N. Engl. J. Med.376(7), e11 (2017).
   PubMedGoogle Scholar
• Cao J , TamAJ , DiazLAet al. Generation of MANAbodies specific to HLA-restricted epitopes encoded by somatically mutated genes. Proc. Natl Acad. Sci.112(32), 9967–9972 (2015).
   PubMed Web of Science ®Google Scholar
• Marty R , KaabinejadianS , RossellDet al. MHC-I genotype restricts the oncogenic mutational landscape. Cell171(6), 1272–1283.e15 (2017).
   PubMed Web of Science ®Google Scholar
• Zhang J , FujimotoJ , ZhangJet al. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science346(6206), 256–259 (2014).
   PubMed Web of Science ®Google Scholar
• Zhou Z , WuS , LaiJet al. Identification of trunk mutations in gastric carcinoma: a case study. BMC Med. Genomics10(1), 1–8 (2017).
   PubMedGoogle Scholar