Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient

Graphical abstract

[1]  Hiroaki Tanaka,et al.  Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival , 2012, Nature Medicine.

[2]  T. Pawlik,et al.  Treatment and Prognosis for Patients With Intrahepatic Cholangiocarcinoma: Systematic Review and Meta-analysis. , 2014, JAMA surgery.

[3]  Iannis Aifantis,et al.  Oncogenic and tumor suppressor functions of Notch in cancer: it’s NOTCH what you think , 2011, The Journal of experimental medicine.

[4]  Philip J. R. Goulder,et al.  Phenotypic Analysis of Antigen-Specific T Lymphocytes , 1996, Science.

[5]  E. Boerwinkle,et al.  dbNSFP v3.0: A One‐Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice‐Site SNVs , 2016, Human mutation.

[6]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[7]  K. Takasaki,et al.  Extended resection for intrahepatic cholangiocarcinoma in Japan. , 1999, Journal of hepato-biliary-pancreatic surgery.

[8]  B. Neel,et al.  Receptor-Specific Regulation of Phosphatidylinositol 3′-Kinase Activation by the Protein Tyrosine Phosphatase Shp2 , 2002, Molecular and Cellular Biology.

[9]  Wendy S. W. Wong,et al.  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs , 2012, Bioinform..

[10]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[11]  M. Rijn,et al.  Hep Par 1 Antibody Stain for the Differential Diagnosis of Hepatocellular Carcinoma: 676 Tumors Tested Using Tissue Microarrays and Conventional Tissue Sections , 2003, Modern Pathology.

[12]  Heather R. Roberts,et al.  The COX-2/PGE2 pathway: key roles in the hallmarks of cancer and adaptation to the tumour microenvironment. , 2009, Carcinogenesis.

[13]  J. Backer.  The regulation of class IA PI 3-kinases by inter-subunit interactions. , 2010, Current topics in microbiology and immunology.

[14]  Bin Tean Teh,et al.  Exome sequencing of liver fluke–associated cholangiocarcinoma , 2012, Nature Genetics.

[15]  K. Nathanson,et al.  Immunotherapy at Large: The road to personalized cancer vaccines , 2013, Nature Medicine.

[16]  T. Schumacher,et al.  Neoantigens in cancer immunotherapy , 2015, Science.

[17]  H. El‐Serag,et al.  The epidemiology of cholangiocarcinoma. , 2004, Seminars in liver disease.

[18]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[19]  B. Neel,et al.  The 'Shp'ing news: SH2 domain-containing tyrosine phosphatases in cell signaling. , 2003, Trends in biochemical sciences.

[20]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[21]  Pablo Cingolani,et al.  Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift , 2012, Front. Gene..

[22]  E. Lander,et al.  Lessons from the Cancer Genome , 2013, Cell.

[23]  H. Rammensee,et al.  Identification of a naturally processed cyclin D1 T‐helper epitope by a novel combination of HLA class II targeting and differential mass spectrometry , 2004, European journal of immunology.

[24]  T. Pawlik,et al.  Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas , 2013, Nature Genetics.

[25]  H. Rammensee,et al.  Unexpected Abundance of HLA Class II Presented Peptides in Primary Renal Cell Carcinomas , 2006, Clinical Cancer Research.

[26]  S. Stevanović,et al.  Biochemical large-scale identification of MHC class I ligands. , 2013, Methods in molecular biology.

[27]  K. Hess,et al.  Targeted Therapy of Advanced Gallbladder Cancer and Cholangiocarcinoma with Aggressive Biology: Eliciting Early Response Signals from Phase 1 trials , 2013, Oncotarget.

[28]  Simion I. Chiosea,et al.  Frequent mutation of the PI3K pathway in head and neck cancer defines predictive biomarkers. , 2013, Cancer discovery.

[29]  E. J. White,et al.  Inflammatory Adverse Events are Associated with Disease-Free Survival after Vaccine Therapy among Patients with Melanoma , 2014, Annals of Surgical Oncology.

[30]  M. Loh,et al.  PI3K p110δ uniquely promotes gain-of-function Shp2-induced GM-CSF hypersensitivity in a model of JMML. , 2014, Blood.

[31]  E. Kaempgen,et al.  Short Peptide Vaccine Induces CD4+ T Helper Cells in Patients with Different Solid Cancers , 2015, Cancer Immunology Research.

[32]  K. Helin,et al.  The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner , 2014, PloS one.

[33]  G. Mills,et al.  High frequency of PIK3R1 and PIK3R2 mutations in endometrial cancer elucidates a novel mechanism for regulation of PTEN protein stability. , 2011, Cancer discovery.

[34]  Y. Akagi,et al.  Personalized peptide vaccination for advanced colorectal cancer , 2015, Oncoimmunology.

[35]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[36]  N. Yoo,et al.  Mutational analysis of NOTCH1, 2, 3 and 4 genes in common solid cancers and acute leukemias , 2007, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[37]  O. Lund,et al.  NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure , 2010, Immunome research.

[38]  F. Miura,et al.  Aggressive Surgical Resection for Hilar-invasive and Peripheral Intrahepatic Cholangiocarcinoma , 2003, World Journal of Surgery.

[39]  H. Rammensee,et al.  Promiscuous survivin peptide induces robust CD4+ T‐cell responses in the majority of vaccinated cancer patients , 2012, International journal of cancer.

[40]  H. Rammensee,et al.  Identification and Characterization of T-Cell Epitopes Deduced from RGS5, a Novel Broadly Expressed Tumor Antigen , 2007, Clinical Cancer Research.

[41]  T. Han,et al.  Ptpn11/Shp2 acts as a tumor suppressor in hepatocellular carcinogenesis. , 2011, Cancer cell.

[42]  C. Eckert,et al.  Ras pathway mutations are prevalent in relapsed childhood acute lymphoblastic leukemia and confer sensitivity to MEK inhibition. , 2013, Blood.

[43]  W. Birchmeier,et al.  The tyrosine phosphatase Shp2 in development and cancer. , 2010, Advances in cancer research.

[44]  Ira M. Hall,et al.  SAMBLASTER: fast duplicate marking and structural variant read extraction , 2014, Bioinform..

[45]  L. Monasta,et al.  Cytokine Levels in the Serum of Healthy Subjects , 2013, Mediators of inflammation.

[46]  C. Desponts,et al.  Regulation of the Mitogen-activated Protein Kinase Signaling Pathway by SHP2* , 2002, The Journal of Biological Chemistry.

[47]  Morten Nielsen,et al.  Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers , 2008, Bioinform..

[48]  Hans-Georg Rammensee,et al.  HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL) , 2014, Proceedings of the National Academy of Sciences.

[49]  Nansheng Chen,et al.  Mutational landscape of intrahepatic cholangiocarcinoma , 2014, Nature Communications.

[50]  M. Fukayama,et al.  Loss of histone demethylase KDM6B enhances aggressiveness of pancreatic cancer through downregulation of C/EBPα. , 2014, Carcinogenesis.

[51]  Yiling Lu,et al.  Naturally occurring neomorphic PIK3R1 mutations activate the MAPK pathway, dictating therapeutic response to MAPK pathway inhibitors. , 2014, Cancer cell.

[52]  O. Lund,et al.  NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence , 2007, PloS one.

[53]  Benjamin Schubert,et al.  OptiType: precision HLA typing from next-generation sequencing data , 2014, Bioinform..

[54]  Swe Swe Myint,et al.  Exome sequencing identifies distinct mutational patterns in liver fluke–related and non-infection-related bile duct cancers , 2013, Nature Genetics.

[55]  Arul M Chinnaiyan,et al.  Metabolism unhinged: IDH mutations in cancer , 2011, Nature Medicine.

[56]  R. Vermeulen,et al.  Reproducibility and Correlations of Multiplex Cytokine Levels in Asymptomatic Persons , 2008, Cancer Epidemiology Biomarkers & Prevention.

[57]  V. Mazzaferro,et al.  Molecular Pathogenesis and Targeted Therapies for Intrahepatic Cholangiocarcinoma , 2015, Clinical Cancer Research.

[58]  S. H. van der Burg,et al.  Cryopreservation of MHC Multimers: Recommendations for Quality Assurance in Detection of Antigen Specific T Cells , 2014, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[59]  Morten Nielsen,et al.  NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11 , 2008, Nucleic Acids Res..

[60]  Cun-Yu Wang,et al.  Histone Demethylase KDM6B Promotes Epithelial-Mesenchymal Transition* , 2012, The Journal of Biological Chemistry.

[61]  O. Lund,et al.  NetMHCpan, a method for MHC class I binding prediction beyond humans , 2008, Immunogenetics.

[62]  S Brunak,et al.  Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. , 2003, Tissue antigens.

[63]  S. Rosenberg,et al.  Cancer Immunotherapy Based on Mutation-Specific CD4+ T Cells in a Patient with Epithelial Cancer , 2014, Science.

[64]  H. Rammensee,et al.  Matrilysin (MMP-7) Is a Novel Broadly Expressed Tumor Antigen Recognized by Antigen-Specific T Cells , 2008, Clinical Cancer Research.

[65]  H. Rammensee,et al.  SYFPEITHI: database for MHC ligands and peptide motifs , 1999, Immunogenetics.

[66]  O. Lund,et al.  novel sequence representations Reliable prediction of T-cell epitopes using neural networks with , 2003 .

[67]  L. Amon,et al.  Treatment Failure of a TLR-7 Agonist Occurs Due to Self-Regulation of Acute Inflammation and Can Be Overcome by IL-10 Blockade , 2010, The Journal of Immunology.