Organoid Modeling of the Tumor Immune Microenvironment

Anagnostou, 2017, Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer, Cancer Discov., 7, 264, 10.1158/2159-8290.CD-16-0828 Azizi, 2018, Single-cell map of diverse immune phenotypes in the breast tumor microenvironment, Cell, 174, 1293, 10.1016/j.cell.2018.05.060 Bailey, 2016, Genomic analyses identify molecular subtypes of pancreatic cancer, Nature, 531, 47, 10.1038/nature16965 Barretina, 2012, The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity, Nature, 483, 603, 10.1038/nature11003 Boj, 2015, Organoid models of human and mouse ductal pancreatic cancer, Cell, 160, 324, 10.1016/j.cell.2014.12.021 Borghaei, 2015, Nivolumab versus docetaxel in advanced nonsquamous non-small-cell lung cancer, N. Engl. J. Med., 373, 1627, 10.1056/NEJMoa1507643 Brahmer, 2015, Nivolumab versus docetaxel in advanced squamous-cell non-small-cell lung cancer, N. Engl. J. Med., 373, 123, 10.1056/NEJMoa1504627 Cancer Genome Atlas, 2012, Comprehensive molecular characterization of human colon and rectal cancer, Nature, 487, 330, 10.1038/nature11252 Carbognin, 2015, Differential activity of nivolumab, pembrolizumab and MPDL3280A according to the tumor expression of programmed death-ligand-1 (PD-L1): sensitivity analysis of trials in melanoma, lung and genitourinary cancers, PLoS ONE, 10, e0130142, 10.1371/journal.pone.0130142 Chen, 2018, Single-cell transcriptome analysis identifies distinct cell types and intercellular niche signaling in a primary gastric organoid model, bioRxiv Chevrier, 2017, An immune atlas of clear cell renal cell carcinoma, Cell, 169, 736, 10.1016/j.cell.2017.04.016 Cibulskis, 2013, Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples, Nat. Biotechnol., 31, 213, 10.1038/nbt.2514 Croce, 1985, Gene for alpha-chain of human T-cell receptor: location on chromosome 14 region involved in T-cell neoplasms, Science, 227, 1044, 10.1126/science.3919442 Deng, 2018, CDK4/6 inhibition augments antitumor immunity by enhancing T-cell activation, Cancer Discov., 8, 216, 10.1158/2159-8290.CD-17-0915 Dijkstra, 2018, Generation of tumor-reactive T cells by co-culture of peripheral blood lymphocytes and tumor organoids, Cell, 174, 1586, 10.1016/j.cell.2018.07.009 DiMarco, 2014, Engineering of three-dimensional microenvironments to promote contractile behavior in primary intestinal organoids, Integr. Biol., 6, 127, 10.1039/C3IB40188J Feder-Mengus, 2008, New dimensions in tumor immunology: what does 3D culture reveal?, Trends Mol. Med., 14, 333, 10.1016/j.molmed.2008.06.001 Feldman, 2015, Adoptive cell therapy--tumor-infiltrating lymphocytes, T-cell receptors, and chimeric antigen receptors, Semin. Oncol., 42, 626, 10.1053/j.seminoncol.2015.05.005 Finnberg, 2017, Application of 3D tumoroid systems to define immune and cytotoxic therapeutic responses based on tumoroid and tissue slice culture molecular signatures, Oncotarget, 8, 66747, 10.18632/oncotarget.19965 Forget, 2017, A novel method to generate and expand clinical-grade, genetically modified, tumor-infiltrating lymphocytes, Front. Immunol., 8, 908, 10.3389/fimmu.2017.00908 Fujii, 2016, A colorectal tumor organoid library demonstrates progressive loss of niche factor requirements during tumorigenesis, Cell Stem Cell, 18, 827, 10.1016/j.stem.2016.04.003 Gandini, 2016, PD-L1 expression in cancer patients receiving anti PD-1/PD-L1 antibodies: A systematic review and meta-analysis, Crit. Rev. Oncol. Hematol., 100, 88, 10.1016/j.critrevonc.2016.02.001 Garon, 2015, Pembrolizumab for the treatment of non-small-cell lung cancer, N. Engl. J. Med., 372, 2018, 10.1056/NEJMoa1501824 Gordon, 2017, PD-1 expression by tumour-associated macrophages inhibits phagocytosis and tumour immunity, Nature, 545, 495, 10.1038/nature22396 Han, 2014, Linking T-cell receptor sequence to functional phenotype at the single-cell level, Nat. Biotechnol., 32, 684, 10.1038/nbt.2938 Herbst, 2014, Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients, Nature, 515, 563, 10.1038/nature14011 Herbst, 2016, Pembrolizumab versus docetaxel for previously treated, PD-L1-positive, advanced non-small-cell lung cancer (KEYNOTE-010): a randomised controlled trial, Lancet, 387, 1540, 10.1016/S0140-6736(15)01281-7 Hirt, 2014, “In vitro” 3D models of tumor-immune system interaction, Adv. Drug Deliv. Rev., 79-80, 145, 10.1016/j.addr.2014.05.003 Huang, 2017, T-cell invigoration to tumour burden ratio associated with anti-PD-1 response, Nature, 545, 60, 10.1038/nature22079 Jenkins, 2018, Ex vivo profiling of PD-1 blockade using organotypic tumor spheroids, Cancer Discov., 8, 196, 10.1158/2159-8290.CD-17-0833 Junttila, 2013, Influence of tumour micro-environment heterogeneity on therapeutic response, Nature, 501, 346, 10.1038/nature12626 Kamphorst, 2017, Proliferation of PD-1+ CD8 T cells in peripheral blood after PD-1-targeted therapy in lung cancer patients, Proc. Natl. Acad. Sci. USA, 114, 4993, 10.1073/pnas.1705327114 Klemm, 2015, Microenvironmental regulation of therapeutic response in cancer, Trends Cell Biol., 25, 198, 10.1016/j.tcb.2014.11.006 Krieg, 2018, High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy, Nat. Med., 24, 144, 10.1038/nm.4466 Lavin, 2017, Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses, Cell, 169, 750, 10.1016/j.cell.2017.04.014 Li, 2014, Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture, Nat. Med., 20, 769, 10.1038/nm.3585 Motzer, 2015, Nivolumab versus everolimus in advanced renal-cell carcinoma, N. Engl. J. Med., 373, 1803, 10.1056/NEJMoa1510665 Neal, 2016, Organoids as models for neoplastic transformation, Annu. Rev. Pathol., 11, 199, 10.1146/annurev-pathol-012615-044249 Ootani, 2009, Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche, Nat. Med., 15, 701, 10.1038/nm.1951 Palucka, 2016, The basis of oncoimmunology, Cell, 164, 1233, 10.1016/j.cell.2016.01.049 Pardoll, 2012, The blockade of immune checkpoints in cancer immunotherapy, Nat. Rev. Cancer, 12, 252, 10.1038/nrc3239 Picelli, 2014, Full-length RNA-seq from single cells using Smart-seq2, Nat. Protoc., 9, 171, 10.1038/nprot.2014.006 Ribas, 2015, Pembrolizumab versus investigator-choice chemotherapy for ipilimumab-refractory melanoma (KEYNOTE-002): a randomised, controlled, phase 2 trial, Lancet Oncol., 16, 908, 10.1016/S1470-2045(15)00083-2 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 Robert, 2015, Nivolumab in previously untreated melanoma without BRAF mutation, N. Engl. J. Med., 372, 320, 10.1056/NEJMoa1412082 Satija, 2015, Spatial reconstruction of single-cell gene expression data, Nat. Biotechnol., 33, 495, 10.1038/nbt.3192 Sato, 2011, Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium, Gastroenterology, 141, 1762, 10.1053/j.gastro.2011.07.050 Sivan, 2015, Commensal bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy, Science, 350, 1084, 10.1126/science.aac4255 Spence, 2011, Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro, Nature, 470, 105, 10.1038/nature09691 Spitzer, 2017, Systemic immunity is required for effective cancer immunotherapy, Cell, 168, 487, 10.1016/j.cell.2016.12.022 Topalian, 2012, Safety, activity, and immune correlates of anti-PD-1 antibody in cancer, N. Engl. J. Med., 366, 2443, 10.1056/NEJMoa1200690 Topalian, 2016, Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy, Nat. Rev. Cancer, 16, 275, 10.1038/nrc.2016.36 Tran, 2016, T-cell transfer therapy targeting mutant KRAS in cancer, N. Engl. J. Med., 375, 2255, 10.1056/NEJMoa1609279 van de Wetering, 2015, Prospective derivation of a living organoid biobank of colorectal cancer patients, Cell, 161, 933, 10.1016/j.cell.2015.03.053 Vlachogiannis, 2018, Patient-derived organoids model treatment response of metastatic gastrointestinal cancers, Science, 359, 920, 10.1126/science.aao2774 Weber, 2015, Nivolumab versus chemotherapy in patients with advanced melanoma who progressed after anti-CTLA-4 treatment (CheckMate 037): a randomised, controlled, open-label, phase 3 trial, Lancet Oncol., 16, 375, 10.1016/S1470-2045(15)70076-8 Wei, 2017, Distinct cellular mechanisms underlie anti-CTLA-4 and anti-PD-1 checkpoint blockade, Cell, 170, 1120, 10.1016/j.cell.2017.07.024 Yan, 2017, Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem-cell self-renewal, Nature, 545, 238, 10.1038/nature22313 Zheng, 2017, Massively parallel digital transcriptional profiling of single cells, Nat. Commun., 8, 14049, 10.1038/ncomms14049