PMID- 26681737 OWN - NLM STAT- MEDLINE DCOM- 20170707 LR - 20181113 IS - 1468-3288 (Electronic) IS - 0017-5749 (Print) IS - 0017-5749 (Linking) VI - 66 IP - 3 DP - 2017 Mar TI - T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes. PG - 454-463 LID - 10.1136/gutjnl-2015-309453 [doi] AB - OBJECTIVE: Patient-specific (unique) tumour antigens, encoded by somatically mutated cancer genes, generate neoepitopes that are implicated in the induction of tumour-controlling T cell responses. Recent advancements in massive DNA sequencing combined with robust T cell epitope predictions have allowed their systematic identification in several malignancies. DESIGN: We undertook the identification of unique neoepitopes in colorectal cancers (CRCs) by using high-throughput sequencing of cDNAs expressed by standard cancer cell cultures, and by related cancer stem/initiating cells (CSCs) cultures, coupled with a reverse immunology approach not requiring human leukocyte antigen (HLA) allele-specific epitope predictions. RESULTS: Several unique mutated antigens of CRC, shared by standard cancer and related CSC cultures, were identified by this strategy. CD8(+) and CD4(+) T cells, either autologous to the patient or derived from HLA-matched healthy donors, were readily expanded in vitro by peptides spanning different cancer mutations and specifically recognised differentiated cancer cells and CSC cultures, expressing the mutations. Neoepitope-specific CD8(+) T cell frequency was also increased in a patient, compared with healthy donors, supporting the occurrence of clonal expansion in vivo. CONCLUSIONS: These results provide a proof-of-concept approach for the identification of unique neoepitopes that are immunogenic in patients with CRC and can also target T cells against the most aggressive CSC component. CI - Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/. FAU - Mennonna, Daniele AU - Mennonna D AD - Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy. FAU - Maccalli, Cristina AU - Maccalli C AD - Division of Experimental Oncology, San Raffaele Scientific Institute, Milan, Italy. FAU - Romano, Michele C AU - Romano MC AD - Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy. FAU - Garavaglia, Claudio AU - Garavaglia C AD - Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy. FAU - Capocefalo, Filippo AU - Capocefalo F AD - Division of Experimental Oncology, San Raffaele Scientific Institute, Milan, Italy. FAU - Bordoni, Roberta AU - Bordoni R AD - Institute for Biomedical Technologies, National Research Council, Segrate, Italy. FAU - Severgnini, Marco AU - Severgnini M AD - Institute for Biomedical Technologies, National Research Council, Segrate, Italy. FAU - De Bellis, Gianluca AU - De Bellis G AD - Institute for Biomedical Technologies, National Research Council, Segrate, Italy. FAU - Sidney, John AU - Sidney J AD - La Jolla Institute for Allergy & Immunology, La Jolla, California, USA. FAU - Sette, Alessandro AU - Sette A AD - La Jolla Institute for Allergy & Immunology, La Jolla, California, USA. FAU - Gori, Alessandro AU - Gori A AD - Institute of Molecular Recognition Chemistry, National Research Council, Milan, Italy. FAU - Longhi, Renato AU - Longhi R AD - Institute of Molecular Recognition Chemistry, National Research Council, Milan, Italy. FAU - Braga, Marco AU - Braga M AD - Department of Surgery, San Raffaele Scientific Institute, Milan, Italy. FAU - Ghirardelli, Luca AU - Ghirardelli L AD - Department of Surgery, San Raffaele Scientific Institute, Milan, Italy. FAU - Baldari, Ludovica AU - Baldari L AD - Department of Surgery, San Raffaele Scientific Institute, Milan, Italy. FAU - Orsenigo, Elena AU - Orsenigo E AD - Department of Surgery, San Raffaele Scientific Institute, Milan, Italy. FAU - Albarello, Luca AU - Albarello L AD - Department of Pathology, San Raffaele Scientific Institute, Milano, Italy. FAU - Zino, Elisabetta AU - Zino E AD - Unit of Molecular and Functional Immunogenetics, San Raffaele Scientific Institute, Milan, Italy. FAU - Fleischhauer, Katharina AU - Fleischhauer K AD - Unit of Molecular and Functional Immunogenetics, San Raffaele Scientific Institute, Milan, Italy. AD - Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany. FAU - Mazzola, Gina AU - Mazzola G AD - Department of Medical Sciences, Center for Transplantation Biology and Immunogenetics, University of Turin, Turin, Italy. FAU - Ferrero, Norma AU - Ferrero N AD - Department of Medical Sciences, Center for Transplantation Biology and Immunogenetics, University of Turin, Turin, Italy. FAU - Amoroso, Antonio AU - Amoroso A AD - Department of Medical Sciences, Center for Transplantation Biology and Immunogenetics, University of Turin, Turin, Italy. FAU - Casorati, Giulia AU - Casorati G AD - Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy. FAU - Parmiani, Giorgio AU - Parmiani G AD - Division of Experimental Oncology, San Raffaele Scientific Institute, Milan, Italy. FAU - Dellabona, Paolo AU - Dellabona P AD - Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20151217 PL - England TA - Gut JT - Gut JID - 2985108R RN - 0 (APC protein, human) RN - 0 (Adenomatous Polyposis Coli Protein) RN - 0 (Cell Cycle Proteins) RN - 0 (DNA, Complementary) RN - 0 (Epitopes, T-Lymphocyte) RN - 0 (F-Box Proteins) RN - 0 (F-Box-WD Repeat-Containing Protein 7) RN - 0 (FBXW7 protein, human) RN - 0 (HLA Antigens) RN - 0 (KRAS protein, human) RN - 0 (SMAD4 protein, human) RN - 0 (Smad4 Protein) RN - 0 (Tumor Suppressor Protein p53) RN - EC 2.3.2.27 (Ubiquitin-Protein Ligases) RN - EC 2.7.1.- (Phosphatidylinositol 3-Kinases) RN - EC 2.7.1.137 (Class I Phosphatidylinositol 3-Kinases) RN - EC 2.7.1.137 (PIK3CA protein, human) RN - EC 3.6.5.2 (Proto-Oncogene Proteins p21(ras)) SB - IM MH - Adenomatous Polyposis Coli Protein/genetics MH - CD4-Positive T-Lymphocytes/*immunology MH - CD8-Positive T-Lymphocytes/*immunology MH - Cell Cycle Proteins/genetics MH - Class I Phosphatidylinositol 3-Kinases MH - Colorectal Neoplasms/*genetics/*immunology MH - DNA Mutational Analysis MH - DNA, Complementary/*analysis MH - Epitopes, T-Lymphocyte/*genetics/immunology MH - F-Box Proteins/genetics MH - F-Box-WD Repeat-Containing Protein 7 MH - Gene Expression MH - HLA Antigens/genetics/immunology MH - High-Throughput Screening Assays MH - Humans MH - Neoplastic Stem Cells/immunology MH - Phosphatidylinositol 3-Kinases/genetics MH - Proto-Oncogene Proteins p21(ras)/genetics MH - Smad4 Protein/genetics/immunology MH - Tumor Cells, Cultured MH - Tumor Suppressor Protein p53/genetics MH - Ubiquitin-Protein Ligases/genetics PMC - PMC5534766 OTO - NOTNLM OT - ANTIGENS OT - CANCER IMMUNOBIOLOGY OT - COLORECTAL CANCER OT - GENE MUTATION OT - IMMUNE RESPONSE COIS- Competing interests: None declared. EDAT- 2015/12/19 06:00 MHDA- 2017/07/08 06:00 PMCR- 2017/07/31 CRDT- 2015/12/19 06:00 PHST- 2015/02/24 00:00 [received] PHST- 2015/11/04 00:00 [revised] PHST- 2015/11/06 00:00 [accepted] PHST- 2015/12/19 06:00 [pubmed] PHST- 2017/07/08 06:00 [medline] PHST- 2015/12/19 06:00 [entrez] PHST- 2017/07/31 00:00 [pmc-release] AID - gutjnl-2015-309453 [pii] AID - 10.1136/gutjnl-2015-309453 [doi] PST - ppublish SO - Gut. 2017 Mar;66(3):454-463. doi: 10.1136/gutjnl-2015-309453. Epub 2015 Dec 17.