Skip to main content
Top
Published in: BMC Immunology 1/2018

Open Access 01-12-2018 | Review

In silico prediction of cancer immunogens: current state of the art

Authors: Irini A. Doytchinova, Darren R. Flower

Published in: BMC Immunology | Issue 1/2018

Login to get access

Abstract

Cancer kills 8 million annually worldwide. Although survival rates in prevalent cancers continue to increase, many cancers have no effective treatment, prompting the search for new and improved protocols. Immunotherapy is a new and exciting addition to the anti-cancer arsenal. The successful and accurate identification of aberrant host proteins acting as antigens for vaccination and immunotherapy is a key aspiration for both experimental and computational research. Here we describe key elements of in silico prediction, including databases of cancer antigens and bleeding-edge methodology for their prediction. We also highlight the role dendritic cell vaccines can play and how they can act as delivery mechanisms for epitope ensemble vaccines. Immunoinformatics can help streamline the discovery and utility of Cancer Immunogens.
Literature
1.
3.
go back to reference Greenlee RT, Goodman MT, Lynch CF, Platz CE, Havener LA, Howe HL. The occurrence of rare cancers in United States adults, 1995-2004. Public Health Rep. 2010;125(1):28–43.CrossRefPubMedPubMedCentral Greenlee RT, Goodman MT, Lynch CF, Platz CE, Havener LA, Howe HL. The occurrence of rare cancers in United States adults, 1995-2004. Public Health Rep. 2010;125(1):28–43.CrossRefPubMedPubMedCentral
4.
go back to reference Gradishar WJ, Anderson BO, Balassanian R, Blair SL, Burstein HJ, Cyr A, Elias AD, Farrar WB, Forero A, Giordano SH, Goetz MP, Goldstein LJ, Isakoff SJ, Lyons J, Marcom PK, Mayer IA, McCormick B, Moran MS, O'Regan RM, Patel SA, Pierce LJ, Reed EC, Salerno KE, Schwartzberg LS, Sitapati A, Smith KL, Smith ML, Soliman H, Somlo G, Telli M, Ward JH, Shead DA, Kumar R. NCCN Guidelines Insights: Breast Cancer, Version 1.2017. J Natl Compr Canc Netw. 2017;15(4):433-51. Gradishar WJ, Anderson BO, Balassanian R, Blair SL, Burstein HJ, Cyr A, Elias AD, Farrar WB, Forero A, Giordano SH, Goetz MP, Goldstein LJ, Isakoff SJ, Lyons J, Marcom PK, Mayer IA, McCormick B, Moran MS, O'Regan RM, Patel SA, Pierce LJ, Reed EC, Salerno KE, Schwartzberg LS, Sitapati A, Smith KL, Smith ML, Soliman H, Somlo G, Telli M, Ward JH, Shead DA, Kumar R. NCCN Guidelines Insights: Breast Cancer, Version 1.2017. J Natl Compr Canc Netw. 2017;15(4):433-51.
5.
go back to reference Carroll PR, Parsons JK, Andriole G, Bahnson RR, Castle EP, Catalona WJ, Dahl DM, Davis JW, Epstein JI, Etzioni RB, Farrington T, Hemstreet GP 3rd, Kawachi MH, Kim S, Lange PH, Loughlin KR, Lowrance W, Maroni P, Mohler J, Morgan TM, Moses KA, Nadler RB, Poch M, Scales C, Shaneyfelt TM, Smaldone MC, Sonn G, Sprenkle P, Vickers AJ, Wake R, Shead DA, Freedman-Cass DA. NCCN Guidelines Insights: Prostate Cancer Early Detection, Version 2.2016. J Natl Compr Canc Netw. 2016;14(5):509-19. Carroll PR, Parsons JK, Andriole G, Bahnson RR, Castle EP, Catalona WJ, Dahl DM, Davis JW, Epstein JI, Etzioni RB, Farrington T, Hemstreet GP 3rd, Kawachi MH, Kim S, Lange PH, Loughlin KR, Lowrance W, Maroni P, Mohler J, Morgan TM, Moses KA, Nadler RB, Poch M, Scales C, Shaneyfelt TM, Smaldone MC, Sonn G, Sprenkle P, Vickers AJ, Wake R, Shead DA, Freedman-Cass DA. NCCN Guidelines Insights: Prostate Cancer Early Detection, Version 2.2016. J Natl Compr Canc Netw. 2016;14(5):509-19.
6.
go back to reference Siegel RL, Miller KD, Jemal A. Colorectal Cancer mortality rates in adults aged 20 to 54 years in the United States, 1970-2014. JAMA. 2017;318(6):572–4.CrossRefPubMedPubMedCentral Siegel RL, Miller KD, Jemal A. Colorectal Cancer mortality rates in adults aged 20 to 54 years in the United States, 1970-2014. JAMA. 2017;318(6):572–4.CrossRefPubMedPubMedCentral
7.
go back to reference Biermann JS, Chow W, Reed DR, Lucas D, Adkins DR, Agulnik M, Benjamin RS, Brigman B, Budd GT, Curry WT, Didwania A, Fabbri N, Hornicek FJ, Kuechle JB, Lindskog D, Mayerson J, McGarry SV, Million L, Morris CD, Movva S, O'Donnell RJ, Randall RL, Rose P, Santana VM, Satcher RL, Schwartz H, Siegel HJ, Thornton K, Villalobos V, Bergman MA, Scavone JL. NCCN Guidelines Insights: Bone Cancer, Version 2.2017. J Natl Compr Canc Netw. 2017;15(2):155-67. Biermann JS, Chow W, Reed DR, Lucas D, Adkins DR, Agulnik M, Benjamin RS, Brigman B, Budd GT, Curry WT, Didwania A, Fabbri N, Hornicek FJ, Kuechle JB, Lindskog D, Mayerson J, McGarry SV, Million L, Morris CD, Movva S, O'Donnell RJ, Randall RL, Rose P, Santana VM, Satcher RL, Schwartz H, Siegel HJ, Thornton K, Villalobos V, Bergman MA, Scavone JL. NCCN Guidelines Insights: Bone Cancer, Version 2.2017. J Natl Compr Canc Netw. 2017;15(2):155-67.
8.
go back to reference McMaster ML, Goldstein AM, Bromley CM, Ishibe N, Parry DM. Chordoma: incidence and survival patterns in the United States, 1973-1995. Cancer Causes Control. 2001;12:1–11.CrossRefPubMed McMaster ML, Goldstein AM, Bromley CM, Ishibe N, Parry DM. Chordoma: incidence and survival patterns in the United States, 1973-1995. Cancer Causes Control. 2001;12:1–11.CrossRefPubMed
11.
go back to reference Isoldi MC, Visconti MA, Castrucci AM. Anti-cancer drugs: molecular mechanisms of action. Mini Rev Med Chem. 2005;5(7):685–95.CrossRefPubMed Isoldi MC, Visconti MA, Castrucci AM. Anti-cancer drugs: molecular mechanisms of action. Mini Rev Med Chem. 2005;5(7):685–95.CrossRefPubMed
12.
go back to reference Morrow MP, Kraynyak KA, Sylvester AJ, Shen X, Amante D, Sakata L, Parker L, Yan J, Boyer J, Roh C, et al. Augmentation of cellular and humoral immune responses to HPV16 and HPV18 E6 and E7 antigens by VGX-3100. Mol Ther Oncolytics. 2016;3:16025.CrossRefPubMedPubMedCentral Morrow MP, Kraynyak KA, Sylvester AJ, Shen X, Amante D, Sakata L, Parker L, Yan J, Boyer J, Roh C, et al. Augmentation of cellular and humoral immune responses to HPV16 and HPV18 E6 and E7 antigens by VGX-3100. Mol Ther Oncolytics. 2016;3:16025.CrossRefPubMedPubMedCentral
13.
go back to reference Nilsson C, Hejdeman B, Godoy-Ramirez K, Tecleab T, Scarlatti G, Brave A, Earl PL, Stout RR, Robb ML, Shattock RJ, et al. HIV-DNA given with or without intradermal electroporation is safe and highly immunogenic in healthy Swedish HIV-1 DNA/MVA vaccinees: a phase I randomized trial. PLoS One. 2015;10:e0131748.CrossRefPubMedPubMedCentral Nilsson C, Hejdeman B, Godoy-Ramirez K, Tecleab T, Scarlatti G, Brave A, Earl PL, Stout RR, Robb ML, Shattock RJ, et al. HIV-DNA given with or without intradermal electroporation is safe and highly immunogenic in healthy Swedish HIV-1 DNA/MVA vaccinees: a phase I randomized trial. PLoS One. 2015;10:e0131748.CrossRefPubMedPubMedCentral
14.
go back to reference Vormehr M, Schrörs B, Boegel S, Löwer M, Türeci Ö, Sahin U. Mutanome engineered RNA immunotherapy: towards patient-centered tumor vaccination. J Immunol Res. 2015;2015:595363.CrossRefPubMedPubMedCentral Vormehr M, Schrörs B, Boegel S, Löwer M, Türeci Ö, Sahin U. Mutanome engineered RNA immunotherapy: towards patient-centered tumor vaccination. J Immunol Res. 2015;2015:595363.CrossRefPubMedPubMedCentral
15.
go back to reference Rauch S, Lutz J, Kowalczyk A, Schlake T, Heidenreich R. RNActive (R) technology: generation and testing of stable and immunogenic mRNA vaccines. Methods Mol Biol. 2017;1499:89–107.CrossRefPubMed Rauch S, Lutz J, Kowalczyk A, Schlake T, Heidenreich R. RNActive (R) technology: generation and testing of stable and immunogenic mRNA vaccines. Methods Mol Biol. 2017;1499:89–107.CrossRefPubMed
16.
go back to reference Guo C, Manjili MH, Subjeck JR, Sarkar D, Fisher PB, Xiang-Yang Wang XY. Therapeutic Cancer vaccines: past, present and future. Adv Cancer Res. 2013;119:421–75.CrossRefPubMedPubMedCentral Guo C, Manjili MH, Subjeck JR, Sarkar D, Fisher PB, Xiang-Yang Wang XY. Therapeutic Cancer vaccines: past, present and future. Adv Cancer Res. 2013;119:421–75.CrossRefPubMedPubMedCentral
17.
go back to reference Flower DR. Towards the systematic discovery of immunomodulatory adjuvants. In: Flower DR, Perrie Y, editors. Immunomic discovery of adjuvants and candidate subunit vaccines: Springer; 2013. p. 155–80. Flower DR. Towards the systematic discovery of immunomodulatory adjuvants. In: Flower DR, Perrie Y, editors. Immunomic discovery of adjuvants and candidate subunit vaccines: Springer; 2013. p. 155–80.
18.
go back to reference Wood C, Srivastava P, Bukowski R, Lacombe L, Gorelov AI, Gorelov S, et al. An adjuvant autologous therapeutic vaccine (HSPPC-96; vitespen) versus observation alone for patients at high risk of recurrence after nephrectomy for renal cell carcinoma: a multicentre, open-label, randomised phase III trial. Lancet. 2008;372:145–54.CrossRefPubMed Wood C, Srivastava P, Bukowski R, Lacombe L, Gorelov AI, Gorelov S, et al. An adjuvant autologous therapeutic vaccine (HSPPC-96; vitespen) versus observation alone for patients at high risk of recurrence after nephrectomy for renal cell carcinoma: a multicentre, open-label, randomised phase III trial. Lancet. 2008;372:145–54.CrossRefPubMed
19.
go back to reference Wang XY, Sun X, Chen X, Facciponte J, Repasky EA, Kane J, et al. Superior antitumor response induced by large stress protein chaperoned protein antigen compared with peptide antigen. J Immunol. 2010;184:6309–19.CrossRefPubMedPubMedCentral Wang XY, Sun X, Chen X, Facciponte J, Repasky EA, Kane J, et al. Superior antitumor response induced by large stress protein chaperoned protein antigen compared with peptide antigen. J Immunol. 2010;184:6309–19.CrossRefPubMedPubMedCentral
20.
go back to reference Kessler JH, Melief CJM. Identification of T-cell epitopes for cancer immunotherapy. Leukemia. 2007;21:1859–74.CrossRefPubMed Kessler JH, Melief CJM. Identification of T-cell epitopes for cancer immunotherapy. Leukemia. 2007;21:1859–74.CrossRefPubMed
21.
go back to reference Tonecka K, Plich Z, Ramji K, Taclak B, Kiraga L, Krol M, et al. Immune cells as targets and tools for cancer therapy. Immunotherapy. 2017;3:143. Tonecka K, Plich Z, Ramji K, Taclak B, Kiraga L, Krol M, et al. Immune cells as targets and tools for cancer therapy. Immunotherapy. 2017;3:143.
22.
go back to reference Clifton GT, Mittendorf EA, Peoples GE. Adjuvant HER2/neu peptide cancer vaccines in breast cancer. Immunotherapy. 2015;7:1159–68.CrossRefPubMed Clifton GT, Mittendorf EA, Peoples GE. Adjuvant HER2/neu peptide cancer vaccines in breast cancer. Immunotherapy. 2015;7:1159–68.CrossRefPubMed
23.
go back to reference Morello A, Sadelain M, Adusumilli PS. Mesothelin-targeted CARs: driving T cells to solid tumors. Cancer Discov. 2016;6:133–46.CrossRefPubMed Morello A, Sadelain M, Adusumilli PS. Mesothelin-targeted CARs: driving T cells to solid tumors. Cancer Discov. 2016;6:133–46.CrossRefPubMed
25.
go back to reference Kenter GG, Welters MJ, Valentijn AR, Lowik MJ, Berends-van der Meer DM, Vloon AP, Essahsah F, Fathers LM, Offringa R, Drijfhout JW, et al. Vaccination against HPV-16 oncoproteins for vulvar intraepithelial neoplasia. N Engl J Med. 2009;361:1838–47.CrossRefPubMed Kenter GG, Welters MJ, Valentijn AR, Lowik MJ, Berends-van der Meer DM, Vloon AP, Essahsah F, Fathers LM, Offringa R, Drijfhout JW, et al. Vaccination against HPV-16 oncoproteins for vulvar intraepithelial neoplasia. N Engl J Med. 2009;361:1838–47.CrossRefPubMed
26.
27.
go back to reference Jongeneel V. Towards a cancer immunome database. Cancer Immun. 2001;1:3.PubMed Jongeneel V. Towards a cancer immunome database. Cancer Immun. 2001;1:3.PubMed
28.
go back to reference Li H, He Y, Ding G, Wang C, Xie L, Li Y. dbDEPC: a database of differentially expressed proteins in human cancers. Nucleic Acids Res. 2010;38:D658–64.CrossRefPubMed Li H, He Y, Ding G, Wang C, Xie L, Li Y. dbDEPC: a database of differentially expressed proteins in human cancers. Nucleic Acids Res. 2010;38:D658–64.CrossRefPubMed
29.
go back to reference He Y, Zhang M, Ju Y, Yu Z, Lv D, Sun H, et al. dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. Nucleic Acids Res. 2012;40:D964–71.CrossRefPubMed He Y, Zhang M, Ju Y, Yu Z, Lv D, Sun H, et al. dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. Nucleic Acids Res. 2012;40:D964–71.CrossRefPubMed
30.
go back to reference Almeida LG, Sakabe NJ, deOliveira AR, Silva MC, Mundstein AS, Cohen T, et al. CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res. 2009;37:D816–9.CrossRefPubMed Almeida LG, Sakabe NJ, deOliveira AR, Silva MC, Mundstein AS, Cohen T, et al. CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res. 2009;37:D816–9.CrossRefPubMed
31.
go back to reference Olsen LR, Tongchusak S, Lin H, Reinherz EL, Brusic V, Zhang GL. TANTIGEN: a comprehensive database of tumor T cell antigens. Cancer Immunol Immunother. 2017;66:731–5.CrossRefPubMed Olsen LR, Tongchusak S, Lin H, Reinherz EL, Brusic V, Zhang GL. TANTIGEN: a comprehensive database of tumor T cell antigens. Cancer Immunol Immunother. 2017;66:731–5.CrossRefPubMed
34.
go back to reference Flower DR, Macdonald IK, Ramakrishnan K, Davies MN, Doytchinova IA. Computer aided selection of candidate vaccine antigens. Immunome Res. 2010;6(Suppl 2):S1.CrossRefPubMedPubMedCentral Flower DR, Macdonald IK, Ramakrishnan K, Davies MN, Doytchinova IA. Computer aided selection of candidate vaccine antigens. Immunome Res. 2010;6(Suppl 2):S1.CrossRefPubMedPubMedCentral
35.
go back to reference Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics. 2007;8:4.CrossRefPubMedPubMedCentral Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics. 2007;8:4.CrossRefPubMedPubMedCentral
36.
go back to reference Hellberg S, Sjöström M, Skagerberg B, Wold S. Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem. 1987;30:1126–35.CrossRefPubMed Hellberg S, Sjöström M, Skagerberg B, Wold S. Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem. 1987;30:1126–35.CrossRefPubMed
37.
go back to reference Nyström Å, Andersson PM, Lundstedt T. Multivariate data analysis of topographically modified á-melanotropin analoques using auto and cross auto covariances (ACC). Quant Struct Act Relat. 2000;19:264–9.CrossRef Nyström Å, Andersson PM, Lundstedt T. Multivariate data analysis of topographically modified á-melanotropin analoques using auto and cross auto covariances (ACC). Quant Struct Act Relat. 2000;19:264–9.CrossRef
38.
go back to reference Tappeiner E, Finotello F, Charoentong P, Mayer C, Rieder D, Trajanoski Z. TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. Bioinformatics. 2017;33:3140–1.CrossRefPubMed Tappeiner E, Finotello F, Charoentong P, Mayer C, Rieder D, Trajanoski Z. TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. Bioinformatics. 2017;33:3140–1.CrossRefPubMed
39.
go back to reference Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC. MuPeXI: prediction of neo-epitopes from tumor sequencing data. Cancer Immunol Immunother. 2017;66:1123–30.CrossRefPubMed Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC. MuPeXI: prediction of neo-epitopes from tumor sequencing data. Cancer Immunol Immunother. 2017;66:1123–30.CrossRefPubMed
40.
go back to reference Merad M, Sathe P, Helft J, Miller J, Mortha A. The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting. Annu Rev Immunol. 2013;31:563–604.CrossRefPubMed Merad M, Sathe P, Helft J, Miller J, Mortha A. The dendritic cell lineage: ontogeny and function of dendritic cells and their subsets in the steady state and the inflamed setting. Annu Rev Immunol. 2013;31:563–604.CrossRefPubMed
41.
go back to reference Tesfatsion DA. Dendritic cell vaccine against leukemia: advances and perspectives. Immunotherapy. 2014;6(4):485–96.CrossRefPubMed Tesfatsion DA. Dendritic cell vaccine against leukemia: advances and perspectives. Immunotherapy. 2014;6(4):485–96.CrossRefPubMed
42.
go back to reference Datta J, Berk E, Cintolo J, Xu S, Roses R, Czerniecki B. Rationale for a multimodality strategy to enhance the efficacy of dendritic cell-based Cancer immunotherapy. Front Immunol. 2015;6:271.CrossRefPubMedPubMedCentral Datta J, Berk E, Cintolo J, Xu S, Roses R, Czerniecki B. Rationale for a multimodality strategy to enhance the efficacy of dendritic cell-based Cancer immunotherapy. Front Immunol. 2015;6:271.CrossRefPubMedPubMedCentral
43.
go back to reference Rai J, Lok KI, Mok CY, Mann H, Noor M, Patel P, Flower DR. Immunoinformatic evaluation of multiple epitope ensembles as vaccine candidates: E coli 536. Bioinformation. 2012;8(6):272–5.CrossRefPubMedPubMedCentral Rai J, Lok KI, Mok CY, Mann H, Noor M, Patel P, Flower DR. Immunoinformatic evaluation of multiple epitope ensembles as vaccine candidates: E coli 536. Bioinformation. 2012;8(6):272–5.CrossRefPubMedPubMedCentral
44.
go back to reference Molero-Abraham M, Lafuente EM, Flower DR, Reche PA. Selection of conserved epitopes from hepatitis C virus for pan-populational stimulation of T-cell responses. Clin Dev Immunol. 2013;2013:601943.CrossRefPubMedPubMedCentral Molero-Abraham M, Lafuente EM, Flower DR, Reche PA. Selection of conserved epitopes from hepatitis C virus for pan-populational stimulation of T-cell responses. Clin Dev Immunol. 2013;2013:601943.CrossRefPubMedPubMedCentral
45.
go back to reference Sheikh QM, Gatherer D, Reche PA, Flower DR. Towards the knowledge-based design of universal influenza epitope ensemble vaccines. Bioinformatics. 2016;32(21):3233–9.CrossRefPubMedPubMedCentral Sheikh QM, Gatherer D, Reche PA, Flower DR. Towards the knowledge-based design of universal influenza epitope ensemble vaccines. Bioinformatics. 2016;32(21):3233–9.CrossRefPubMedPubMedCentral
46.
go back to reference Dimitrov I, Atanasova M, Patronov A, Flower DR, Doytchinova I. A cohesive and integrated platform for immunogenicity prediction. Methods Mol Biol. 2016;1404:761–70.CrossRefPubMed Dimitrov I, Atanasova M, Patronov A, Flower DR, Doytchinova I. A cohesive and integrated platform for immunogenicity prediction. Methods Mol Biol. 2016;1404:761–70.CrossRefPubMed
48.
go back to reference Dotti G, Gottschalk S, Savoldo B, Brenner MK. Design and development of therapies using chimeric antigen receptor-expressing T cells. Immunol Rev. 2014;257:107–26.CrossRefPubMed Dotti G, Gottschalk S, Savoldo B, Brenner MK. Design and development of therapies using chimeric antigen receptor-expressing T cells. Immunol Rev. 2014;257:107–26.CrossRefPubMed
49.
go back to reference Wurch T, Pierré A, Depil S. Novel protein scaffolds as emerging therapeutic proteins: from discovery to clinical proof-of-concept. Trends Biotechnol. 2012;30:575–82.CrossRefPubMed Wurch T, Pierré A, Depil S. Novel protein scaffolds as emerging therapeutic proteins: from discovery to clinical proof-of-concept. Trends Biotechnol. 2012;30:575–82.CrossRefPubMed
50.
go back to reference Simeon R, Chen Z. In vitro-engineered non-antibody protein therapeutics. Protein Cell. 2018;9:3–14.CrossRefPubMed Simeon R, Chen Z. In vitro-engineered non-antibody protein therapeutics. Protein Cell. 2018;9:3–14.CrossRefPubMed
52.
go back to reference Gebauer M, Skerra A. Engineered protein scaffolds as next-generation antibody therapeutics. Curr Opin Chem Biol. 2009;13:245–55.CrossRefPubMed Gebauer M, Skerra A. Engineered protein scaffolds as next-generation antibody therapeutics. Curr Opin Chem Biol. 2009;13:245–55.CrossRefPubMed
53.
go back to reference Ansari HR, Flower DR, Raghava GP. AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res. 2010;38(Database issue):D847–53.CrossRefPubMed Ansari HR, Flower DR, Raghava GP. AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res. 2010;38(Database issue):D847–53.CrossRefPubMed
54.
go back to reference Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B. The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 2015;43(Database issue):D405–12.CrossRefPubMed Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B. The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 2015;43(Database issue):D405–12.CrossRefPubMed
55.
go back to reference Chattopadhyay AK, Nasiev D, Flower DR. A statistical physics perspective on alignment-independent protein sequence comparison. Bioinformatics. 2015;31(15):2469–74.CrossRefPubMedPubMedCentral Chattopadhyay AK, Nasiev D, Flower DR. A statistical physics perspective on alignment-independent protein sequence comparison. Bioinformatics. 2015;31(15):2469–74.CrossRefPubMedPubMedCentral
56.
go back to reference Akhoon BA, Slathia PS, Sharma P, Gupta SK, Verma V. In silico identification of novel protective VSG antigens expressed by Trypanosoma brucei and an effort for designing a highly immunogenic DNA vaccine using IL-12 as adjuvant. Microb Pathog. 2011;51(1-2):77–87.CrossRefPubMed Akhoon BA, Slathia PS, Sharma P, Gupta SK, Verma V. In silico identification of novel protective VSG antigens expressed by Trypanosoma brucei and an effort for designing a highly immunogenic DNA vaccine using IL-12 as adjuvant. Microb Pathog. 2011;51(1-2):77–87.CrossRefPubMed
57.
go back to reference Gupta A, Chaukiker D, Singh TR. Comparative analysis of epitope predictions: proposed library of putative vaccine candidates for HIV. Bioinformation. 2011;5(9):386–9.CrossRefPubMedPubMedCentral Gupta A, Chaukiker D, Singh TR. Comparative analysis of epitope predictions: proposed library of putative vaccine candidates for HIV. Bioinformation. 2011;5(9):386–9.CrossRefPubMedPubMedCentral
59.
go back to reference Seyed N, Zahedifard F, Safaiyan S, Gholami E, Doustdari F, Azadmanesh K, Mirzaei M, Saeedi Eslami N, Khadem Sadegh A, Eslami Far A, Sharifi I, Rafati S. In silico analysis of six known Leishmania major antigens and in vitro evaluation of specific epitopes eliciting HLA-A2 restricted CD8 T cell response. PLoS Negl Trop Dis. 2011;5(9):e1295.CrossRefPubMedPubMedCentral Seyed N, Zahedifard F, Safaiyan S, Gholami E, Doustdari F, Azadmanesh K, Mirzaei M, Saeedi Eslami N, Khadem Sadegh A, Eslami Far A, Sharifi I, Rafati S. In silico analysis of six known Leishmania major antigens and in vitro evaluation of specific epitopes eliciting HLA-A2 restricted CD8 T cell response. PLoS Negl Trop Dis. 2011;5(9):e1295.CrossRefPubMedPubMedCentral
60.
go back to reference Wieser A, Romann E, Magistro G, Hoffmann C, Nörenberg D, Weinert K, Schubert S. A multiepitope subunit vaccine conveys protection against extraintestinal pathogenic Escherichia coli in mice. Infect Immun. 2010;78(8):3432–42.CrossRefPubMedPubMedCentral Wieser A, Romann E, Magistro G, Hoffmann C, Nörenberg D, Weinert K, Schubert S. A multiepitope subunit vaccine conveys protection against extraintestinal pathogenic Escherichia coli in mice. Infect Immun. 2010;78(8):3432–42.CrossRefPubMedPubMedCentral
Metadata
Title
In silico prediction of cancer immunogens: current state of the art
Authors
Irini A. Doytchinova
Darren R. Flower
Publication date
01-12-2018
Publisher
BioMed Central
Published in
BMC Immunology / Issue 1/2018
Electronic ISSN: 1471-2172
DOI
https://doi.org/10.1186/s12865-018-0248-x

Other articles of this Issue 1/2018

BMC Immunology 1/2018 Go to the issue
Obesity Clinical Trial Summary

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

Highlights from the ACC 2024 Congress

Year in Review: Pediatric cardiology

Watch Dr. Anne Marie Valente present the last year's highlights in pediatric and congenital heart disease in the official ACC.24 Year in Review session.

Year in Review: Pulmonary vascular disease

The last year's highlights in pulmonary vascular disease are presented by Dr. Jane Leopold in this official video from ACC.24.

Year in Review: Valvular heart disease

Watch Prof. William Zoghbi present the last year's highlights in valvular heart disease from the official ACC.24 Year in Review session.

Year in Review: Heart failure and cardiomyopathies

Watch this official video from ACC.24. Dr. Biykem Bozkurt discuss last year's major advances in heart failure and cardiomyopathies.