Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma

Anagnostou, 2016, Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer, Cancer Discov.

Barretina, 2010, Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy, Nat. Genet., 42, 715, 10.1038/ng.619

Brastianos, 2015, Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets, Cancer Discov., 5, 1164, 10.1158/2159-8290.CD-15-0369

Brennan, 2013, The somatic genomic landscape of glioblastoma, Cell, 155, 462, 10.1016/j.cell.2013.09.034

Carter, 2012, Absolute quantification of somatic DNA alterations in human cancer, Nat. Biotechnol., 30, 413, 10.1038/nbt.2203

Cerami, 2012, The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data, Cancer Discov., 2, 401, 10.1158/2159-8290.CD-12-0095

Fritsch, 2014, HLA-binding properties of tumor neoepitopes in humans, Cancer Immunol. Res., 2, 522, 10.1158/2326-6066.CIR-13-0227

Futreal, 2004, A census of human cancer genes, Nat. Rev. Cancer, 4, 177, 10.1038/nrc1299

Gao, 2013, Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal, Sci. Signal., 6, pl1, 10.1126/scisignal.2004088

Gao, 2017, 3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets, Genome Med., 9, 4, 10.1186/s13073-016-0393-x

Gao, 2016, Loss of IFN-γ pathway genes in tumor cells as a mechanism of resistance to anti-CTLA-4 therapy, Cell, 167, 397, 10.1016/j.cell.2016.08.069

Giannakis, 2016, Genomic correlates of immune-cell infiltrates in colorectal carcinoma, Cell Rep., 15, 857, 10.1016/j.celrep.2016.03.075

Hoof, 2009, NetMHCpan, a method for MHC class I binding prediction beyond humans, Immunogenetics, 61, 1, 10.1007/s00251-008-0341-z

Hugo, 2016, Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma, Cell, 165, 35, 10.1016/j.cell.2016.02.065

Li, 2011, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, 12, 323, 10.1186/1471-2105-12-323

Lin, 2009, Optimization and validation of a robust human T-cell culture method for monitoring phenotypic and polyfunctional antigen-specific CD4 and CD8 T-cell responses, Cytotherapy, 11, 912, 10.3109/14653240903136987

Maeda, 2014, Detection of self-reactive CD8+ T cells with an anergic phenotype in healthy individuals, Science, 346, 1536, 10.1126/science.aaa1292

Maki, 2013, A pilot study of anti-CTLA4 antibody ipilimumab in patients with synovial sarcoma, Sarcoma, 2013, 168145, 10.1155/2013/168145

McGranahan, 2016, Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade, Science, 351, 1463, 10.1126/science.aaf1490

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

Nielsen, 2007, NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence, PLoS ONE, 2, e796, 10.1371/journal.pone.0000796

Peng, 2016, Loss of PTEN promotes resistance to T cell-mediated immunotherapy, Cancer Discov., 6, 202, 10.1158/2159-8290.CD-15-0283

Philips, 2015, Therapeutic uses of anti-PD-1 and anti-PD-L1 antibodies, Int. Immunol., 27, 39, 10.1093/intimm/dxu095

Rizvi, 2016, Immunotherapy and oncogenic pathways: The PTEN connection, Cancer Discov., 6, 128, 10.1158/2159-8290.CD-15-1501

Rizvi, 2015, Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer, Science, 348, 124, 10.1126/science.aaa1348

Robbins, 2013, Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells, Nat. Med., 19, 747, 10.1038/nm.3161

Sharma, 2015, The future of immune checkpoint therapy, Science, 348, 56, 10.1126/science.aaa8172

Shukla, 2015, Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes, Nat. Biotechnol., 33, 1152, 10.1038/nbt.3344

Snyder, 2014, Genetic basis for clinical response to CTLA-4 blockade in melanoma, N. Engl. J. Med., 371, 2189, 10.1056/NEJMoa1406498

Stachler, 2015, Paired exome analysis of Barrett’s esophagus and adenocarcinoma, Nat. Genet., 47, 1047, 10.1038/ng.3343

Thorvaldsdóttir, 2013, Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration, Brief. Bioinform., 14, 178, 10.1093/bib/bbs017

Toso, 2014, Enhancing chemotherapy efficacy in Pten-deficient prostate tumors by activating the senescence-associated antitumor immunity, Cell Rep., 9, 75, 10.1016/j.celrep.2014.08.044

Tran, 2016, T-cell transfer therapy targeting mutant KRAS in cancer, N. Engl. J. Med., 375, 2255, 10.1056/NEJMoa1609279

Van Allen, 2015, Genomic correlates of response to CTLA-4 blockade in metastatic melanoma, Science, 350, 207, 10.1126/science.aad0095

Van Allen, 2014, Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine, Nat. Med., 20, 682, 10.1038/nm.3559

van Rooij, 2013, Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma, J. Clin. Oncol., 31, e439, 10.1200/JCO.2012.47.7521

Verdegaal, 2016, Neoantigen landscape dynamics during human melanoma-T cell interactions, Nature, 536, 91, 10.1038/nature18945

Walter, 2012, Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival, Nat. Med., 18, 1254, 10.1038/nm.2883

Zaretsky, 2016, Mutations associated with acquired resistance to PD-1 blockade in melanoma, N. Engl. J. Med., 375, 819, 10.1056/NEJMoa1604958