Tumor Cell-Intrinsic Factors Underlie Heterogeneity of Immune Cell Infiltration and Response to Immunotherapy

Ahmadzadeh, 2009, Tumor antigen-specific CD8 T cells infiltrating the tumor express high levels of PD-1 and are functionally impaired, Blood, 114, 1537, 10.1182/blood-2008-12-195792

Bailey, 2016, Exploiting the neoantigen landscape for immunotherapy of pancreatic ductal adenocarcinoma, Sci. Rep., 6, 35848, 10.1038/srep35848

Balachandran, 2017, Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer, Nature, 551, 512, 10.1038/nature24462

Balli, 2017, Immune Cytolytic Activity Stratifies Molecular Subsets of Human Pancreatic Cancer, Clin. Cancer Res., 23, 3129, 10.1158/1078-0432.CCR-16-2128

Baslan, 2012, Genome-wide copy number analysis of single cells, Nature Protocols 2012 7:6, 7, 1024

Baslan, 2015, Optimizing sparse sequencing of single cells for highly multiplex copy number profiling, Genome Res., 25, 714, 10.1101/gr.188060.114

Bayne, 2012, Tumor-derived granulocyte-macrophage colony-stimulating factor regulates myeloid inflammation and T cell immunity in pancreatic cancer, Cancer Cell, 21, 822, 10.1016/j.ccr.2012.04.025

Buenrostro, 2013, Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position, Nat. Methods, 10, 1213, 10.1038/nmeth.2688

Burrell, 2013, The causes and consequences of genetic heterogeneity in cancer evolution, Nature, 501, 338, 10.1038/nature12625

Byrne, 2016, CD40 Stimulation Obviates Innate Sensors and Drives T Cell Immunity in Cancer, Cell Rep., 15, 2719, 10.1016/j.celrep.2016.05.058

Callari, 2017, Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers, Genome Med., 9, 35, 10.1186/s13073-017-0425-1

Casey, 2016, MYC regulates the antitumor immune response through CD47 and PD-L1, Science, 352, 227, 10.1126/science.aac9935

Chao, 2016, CXCR2-Dependent Accumulation of Tumor-Associated Neutrophils Regulates T-cell Immunity in Pancreatic Ductal Adenocarcinoma, Cancer Immunol. Res., 4, 968, 10.1158/2326-6066.CIR-16-0188

Chen, 2016, Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade, Cancer Discov., 6, 827, 10.1158/2159-8290.CD-15-1545

Daud, 2016, Tumor immune profiling predicts response to anti-PD-1 therapy in human melanoma, J. Clin. Invest., 126, 3447, 10.1172/JCI87324

Delmore, 2011, BET bromodomain inhibition as a therapeutic strategy to target c-Myc, Cell, 146, 904, 10.1016/j.cell.2011.08.017

Desch, 2011, CD103+ pulmonary dendritic cells preferentially acquire and present apoptotic cell–associated antigen, Journal of Experimental Medicine, 208, 10.1084/jem.20110538

Evans, 2016, Lack of immunoediting in murine pancreatic cancer reversed with neoantigen, JCI Insight, 1, 10.1172/jci.insight.88328

Fourcade, 2010, Upregulation of Tim-3 and PD-1 expression is associated with tumor antigen-specific CD8+ T cell dysfunction in melanoma patients, J. Exp. Med., 207, 2175, 10.1084/jem.20100637

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

Goel, 2017, CDK4/6 inhibition triggers anti-tumour immunity, Nature, 548, 471, 10.1038/nature23465

Gunderson, 2016, Bruton Tyrosine Kinase-Dependent Immune Cell Cross-talk Drives Pancreas Cancer, Cancer Discov., 6, 270, 10.1158/2159-8290.CD-15-0827

Hildner, 2008, Batf3 deficiency reveals a critical role for CD8α+ dendritic cells in cytotoxic T cell immunity, Science, 322, 1097, 10.1126/science.1164206

Hingorani, 2005, Trp53R172H and KrasG12D cooperate to promote chromosomal instability and widely metastatic pancreatic ductal adenocarcinoma in mice, Cancer Cell, 7, 469, 10.1016/j.ccr.2005.04.023

Hodi, 2010, Improved survival with ipilimumab in patients with metastatic melanoma, N. Engl. J. Med., 363, 711, 10.1056/NEJMoa1003466

Ji, 2012, An immune-active tumor microenvironment favors clinical response to ipilimumab, Cancer Immunol. Immunother., 61, 1019, 10.1007/s00262-011-1172-6

Kim, 2017, Strelka2: Fast and accurate variant calling for clinical sequencing applications, bioRxiv, 192872, 192872

Kortlever, 2017, Myc Cooperates with Ras by Programming Inflammation and Immune Suppression, Cell, 171, 1301, 10.1016/j.cell.2017.11.013

Kumar, 2017, Cancer-Associated Fibroblasts Neutralize the Anti-tumor Effect of CSF1 Receptor Blockade by Inducing PMN-MDSC Infiltration of Tumors, Cancer Cell, 32, 654, 10.1016/j.ccell.2017.10.005

Larkin, 2015, Combined Nivolumab and Ipilimumab or Monotherapy in Untreated Melanoma, N. Engl. J. Med., 373, 1270, 10.1056/NEJMoa1504030

Le, 2017, Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade, Science, 357, 409, 10.1126/science.aan6733

Li, 2010, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, 26, 589, 10.1093/bioinformatics/btp698

Liao, 2014, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656

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

Natale, 2018, Activation of G protein-coupled estrogen receptor signaling inhibits melanoma and improves response to immune checkpoint blockade, eLife, 7, 116, 10.7554/eLife.31770

Pauken, 2016, Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade, Science, 354, 1160, 10.1126/science.aaf2807

Paul, 2013, HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity, J. Immunol., 191, 5831, 10.4049/jimmunol.1302101

Peng, 2015, Epigenetic silencing of TH1-type chemokines shapes tumour immunity and immunotherapy, Nature, 527, 249, 10.1038/nature15520

Pylayeva-Gupta, 2012, Oncogenic Kras-induced GM-CSF production promotes the development of pancreatic neoplasia, Cancer Cell, 21, 836, 10.1016/j.ccr.2012.04.024

Quail, 2013, Microenvironmental regulation of tumor progression and metastasis, Nat. Med., 19, 1423, 10.1038/nm.3394

Rahib, 2014, Projecting cancer incidence and deaths to 2030: the unexpected burden of thyroid, liver, and pancreas cancers in the United States, Cancer Res., 74, 2913, 10.1158/0008-5472.CAN-14-0155

Rech, 2018, Tumor immunity and survival as a function of alternative neopeptides in human cancer, Cancer Immunol. Res., 6, 276, 10.1158/2326-6066.CIR-17-0559

Rhim, 2012, EMT and dissemination precede pancreatic tumor formation, Cell, 148, 349, 10.1016/j.cell.2011.11.025

Roberts, 2016, Critical Role for CD103(+)/CD141(+) Dendritic Cells Bearing CCR7 for Tumor Antigen Trafficking and Priming of T Cell Immunity in Melanoma, Cancer Cell, 30, 324, 10.1016/j.ccell.2016.06.003

Sanjana, 2014, Improved vectors and genome-wide libraries for CRISPR screening, Nat. Methods, 11, 783, 10.1038/nmeth.3047

Sedlazeck, 2013, NextGenMap: fast and accurate read mapping in highly polymorphic genomes, Bioinformatics, 29, 2790, 10.1093/bioinformatics/btt468

Spranger, 2015, Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity, Nature, 523, 231, 10.1038/nature14404

Spranger, 2016, Density of immunogenic antigens does not explain the presence or absence of the T-cell-inflamed tumor microenvironment in melanoma, Proc. Natl. Acad. Sci. USA, 113, E7759, 10.1073/pnas.1609376113

Spranger, 2017, Tumor-Residing Batf3 Dendritic Cells Are Required for Effector T Cell Trafficking and Adoptive T Cell Therapy, Cancer Cell, 31, 711, 10.1016/j.ccell.2017.04.003

Steele, 2016, CXCR2 Inhibition Profoundly Suppresses Metastases and Augments Immunotherapy in Pancreatic Ductal Adenocarcinoma, Cancer Cell, 29, 832, 10.1016/j.ccell.2016.04.014

Stromnes, 2017, T-cell Localization, Activation, and Clonal Expansion in Human Pancreatic Ductal Adenocarcinoma, Cancer Immunol. Res., 5, 978, 10.1158/2326-6066.CIR-16-0322

Topalian, 2012, Safety, activity, and immune correlates of anti-PD-1 antibody in cancer, N. Engl. J. Med., 366, 2443, 10.1056/NEJMoa1200690

Tseng, 2014, PVT1 dependence in cancer with MYC copy-number increase, Nature, 512, 82, 10.1038/nature13311

Tumeh, 2014, PD-1 blockade induces responses by inhibiting adaptive immune resistance, Nature, 515, 568, 10.1038/nature13954

Wang, 2016, Targeting YAP-Dependent MDSC Infiltration Impairs Tumor Progression, Cancer Discov., 6, 80, 10.1158/2159-8290.CD-15-0224

Wculek, 2015, Neutrophils support lung colonization of metastasis-initiating breast cancer cells, Nature, 528, 413, 10.1038/nature16140

Welte, 2016, Oncogenic mTOR signalling recruits myeloid-derived suppressor cells to promote tumour initiation, Nat. Cell Biol., 18, 632, 10.1038/ncb3355

Winograd, 2015, Induction of T-cell Immunity Overcomes Complete Resistance to PD-1 and CTLA-4 Blockade and Improves Survival in Pancreatic Carcinoma, Cancer Immunol. Res., 3, 399, 10.1158/2326-6066.CIR-14-0215

Yousefzadeh, 2014, Mechanism of suppression of chromosomal instability by DNA polymerase POLQ, PLoS Genet., 10, e1004654, 10.1371/journal.pgen.1004654