Machine-Learning Prediction of Tumor Antigen Immunogenicity in the Selection of Therapeutic Epitopes
Tóm tắt
Từ khóa
Tài liệu tham khảo
Gubin, 2015, Tumor neoantigens: building a framework for personalized cancer immunotherapy, J Clin Invest, 125, 3413, 10.1172/JCI80008
Castle, 2012, Exploiting the mutanome for tumor vaccination, Cancer Res, 72, 1081, 10.1158/0008-5472.CAN-11-3722
Kreiter, 2015, Mutant MHC class II epitopes drive therapeutic immune responses to cancer, Nature, 520, 692, 10.1038/nature14426
Kranz, 2016, Systemic RNA delivery to dendritic cells exploits antiviral defence for cancer immunotherapy, Nature, 534, 396, 10.1038/nature18300
Sahin, 2017, Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer, Nature, 547, 222, 10.1038/nature23003
Ott, 2017, An immunogenic personal neoantigen vaccine for patients with melanoma, Nature, 547, 217, 10.1038/nature22991
Hoof, 2009, NetMHCpan, a method for MHC class i binding prediction beyond humans, Immunogenetics, 61, 1, 10.1007/s00251-008-0341-z
Nielsen, 2016, NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets, Genome Med, 8, 33, 10.1186/s13073-016-0288-x
Jurtz, 2017, NetMHCpan-4.0: improved peptide–MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data, J Immunol, 199, 3360, 10.4049/jimmunol.1700893
Andreatta, 2015, Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification, Immunogenetics, 67, 641, 10.1007/s00251-015-0873-y
Zhang, 2008, Immune epitope database analysis resource (IEDB-AR), Nucleic Acids Res, 36, W513, 10.1093/nar/gkn254
Kim, 2012, Immune epitope database analysis resource, Nucleic Acids Res, 40, W525, 10.1093/nar/gks438
O'Donnell, 2018, MHCflurry: open-source class I MHC binding affinity prediction, Cell Syst, 7, 129, 10.1016/j.cels.2018.05.014
Karosiene, 2012, NetMHCcons: a consensus method for the major histocompatibility complex class I predictions, Immunogenetics, 64, 177, 10.1007/s00251-011-0579-8
Saito, 2018, Molecular subtype-specific immunocompetent models of high-grade urothelial carcinoma reveal differential neoantigen expression and response to immunotherapy, Cancer Res, 78, 3954, 10.1158/0008-5472.CAN-18-0173
Colli, 2016, Burden of nonsynonymous mutations among TCGA cancers and candidate immune checkpoint inhibitor responses, Cancer Res, 76, 3767, 10.1158/0008-5472.CAN-16-0170
Jayasinghe, 2018, Systematic analysis of splice-site-creating mutations in cancer, Cell Rep, 23, 270, 10.1016/j.celrep.2018.03.052
Kahles, 2018, Comprehensive analysis of alternative splicing across tumors from 8,705 patients, Cancer Cell, 34, 211, 10.1016/j.ccell.2018.07.001
Laumont, 2018, Noncoding regions are the main source of targetable tumor-specific antigens, Sci Transl Med, 10, eaau5516, 10.1126/scitranslmed.aau5516
Weiss, 1987, Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting, Cold Spring Harb Symp Quant Biol, 52, 687, 10.1101/SQB.1987.052.01.078
Saulquin, 2002, +1 Frameshifting as a novel mechanism to generate a cryptic cytotoxic T lymphocyte epitope derived from human interleukin 10, J Exp Med, 195, 353, 10.1084/jem.20011399
Macejak, 1991, Internal initiation of translation mediated by the 5′ leader of a cellular mRNA, Nature, 353, 90, 10.1038/353090a0
Bullock, 1997, Initiation codon scanthrough versus termination codon readthrough demonstrates strong potential for major histocompatibility complex class I–restricted cryptic epitope expression, J Exp Med, 186, 1051, 10.1084/jem.186.7.1051
Bullock, 1996, Ribosomal scanning past the primary initiation codon as a mechanism for expression of CTL epitopes encoded in alternative reading frames, J Exp Med, 184, 1319, 10.1084/jem.184.4.1319
Malarkannan, 1999, Presentation of out-of-frame peptide/MHC class I complexes by a novel translation initiation mechanism, Immunity, 10, 681, 10.1016/S1074-7613(00)80067-9
Van Den Eynde, 1999, A new antigen recognized by cytolytic T lymphocytes on a human kidney tumor results from reverse strand transcription, J Exp Med, 190, 1793, 10.1084/jem.190.12.1793
Bruce, 1986, tRNA anticodon replacement experiments show that ribosomal frameshifting can be caused by doublet decoding, Proc Natl Acad Sci U S A, 83, 5062, 10.1073/pnas.83.14.5062
Bruce, 2017, Type 2 innate lymphoid cells treat and prevent acute gastrointestinal graft-versus-host disease, J Clin Invest, 127, 1813, 10.1172/JCI91816
Roberts, 2012, Combined PI3K/mTOR and MEK inhibition provides broad antitumor activity in faithful murine cancer models, Clin Cancer Res, 18, 5290, 10.1158/1078-0432.CCR-12-0563
Cooke, 1996, An experimental model of idiopathic pneumonia syndrome after bone marrow transplantation: I. The roles of minor H antigens and endotoxin, Blood, 88, 3230, 10.1182/blood.V88.8.3230.bloodjournal8883230
Wilkerson, 2014, Integrated RNA and DNA sequencing improves mutation detection in low purity tumors, Nucleic Acids Res, 42, e107, 10.1093/nar/gku489
Rajasagi, 2014, Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia, Blood, 124, 453, 10.1182/blood-2014-04-567933
Pertea, 2015, StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nat Biotechnol, 33, 290, 10.1038/nbt.3122
Haas, 2013, De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat Protoc, 8, 1494, 10.1038/nprot.2013.084
Coghill, 2010, Separation of graft-versus-host disease from graft-versus-leukemia responses by targeting CC-chemokine receptor 7 on donor T cells, Blood, 115, 4914, 10.1182/blood-2009-08-239848
Dolton, 2015, More tricks with tetramers: a practical guide to staining T cells with peptide-MHC multimers, Immunology, 146, 11, 10.1111/imm.12499
Wölfl, 2014, Antigen-specific activation and cytokine-facilitated expansion of naive, human CD8+T cells, Nat Protoc, 9, 950, 10.1038/nprot.2014.064
Quintarelli, 2008, Cytotoxic T lymphocytes directed to the preferentially expressed antigen of melanoma (PRAME) target chronic myeloid leukemia, Blood, 112, 1876, 10.1182/blood-2008-04-150045
Chan, 2009, Identification, molecular characterization, clinical prognosis, and therapeutic targeting of human bladder tumor-initiating cells, Proc Natl Acad Sci U S A, 106, 14016, 10.1073/pnas.0906549106
Prat, 2010, Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer, Breast Cancer Res, 12, R68, 10.1186/bcr2635
Iglesia, 2014, Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer, Clin Cancer Res, 20, 3818, 10.1158/1078-0432.CCR-13-3368
Kardos, 2016, Claudin-low bladder tumors are immune infiltrated and actively immune suppressed, JCI Insight, 1, e85902, 10.1172/jci.insight.85902
Bindea, 2013, Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer, Immunity, 39, 782, 10.1016/j.immuni.2013.10.003
Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, 15, 550, 10.1186/s13059-014-0550-8
Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc Natl Acad Sci U S A, 102, 15545, 10.1073/pnas.0506580102
Ingenuity Systems, 2013, Ingenuity Pathway Analysis, 5020
Huang, 2007, The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists, Genome Biol, 8, R183, 10.1186/gb-2007-8-9-r183
Bolotin, 2015, MiXCR: software for comprehensive adaptive immunity profiling, Nat Methods, 12, 380, 10.1038/nmeth.3364
Kim, 2018, Neopepsee: accurate genome-level prediction of neoantigens by harnessing sequence and amino acid immunogenicity information, Ann Oncol, 29, 1030, 10.1093/annonc/mdy022
Smith, 2018, Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma, J Clin Invest, 128, 4804, 10.1172/JCI121476
Irvine, 2015, Synthetic nanoparticles for vaccines and immunotherapy, Chem Rev, 115, 11109, 10.1021/acs.chemrev.5b00109