Journal Articles

Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States

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Wei and Sharma et al. investigated the role of negative costimulation on T cell differentiation and found that, in addition to their effects on activation, during peripheral proliferation CTLA-4 significantly imposes phenotypic boundaries on CD4+ T cell phenotypes and PD-1 subtly imposes phenotypic boundaries on CD8+ T cells. T cells engineered to lack these molecules are able to differentiate further down active pathways, leading to the acquisition of phenotypes not observed under natural circumstances. Antibody blockade of these molecules may similarly reduce some of the limitations on T cell differentiation.

Wei and Sharma et al. investigated the role of negative costimulation on T cell differentiation and found that, in addition to their effects on activation, during peripheral proliferation CTLA-4 significantly imposes phenotypic boundaries on CD4+ T cell phenotypes and PD-1 subtly imposes phenotypic boundaries on CD8+ T cells. T cells engineered to lack these molecules are able to differentiate further down active pathways, leading to the acquisition of phenotypes not observed under natural circumstances. Antibody blockade of these molecules may similarly reduce some of the limitations on T cell differentiation.

Co-stimulation regulates T cell activation, but it remains unclear whether co-stimulatory pathways also control T cell differentiation. We used mass cytometry to profile T cells generated in the genetic absence of the negative co-stimulatory molecules CTLA-4 and PD-1. Our data indicate that negative co-stimulation constrains the possible cell states that peripheral T cells can acquire. CTLA-4 imposes major boundaries on CD4(+) T cell phenotypes, whereas PD-1 subtly limits CD8(+) T cell phenotypes. By computationally reconstructing T cell differentiation paths, we identified protein expression changes that underlied the abnormal phenotypic expansion and pinpointed when lineage choice events occurred during differentiation. Similar alterations in T cell phenotypes were observed after anti-CTLA-4 and anti-PD-1 antibody blockade. These findings implicate negative co-stimulation as a key regulator and determinant of T cell differentiation and suggest that checkpoint blockade might work in part by altering the limits of T cell phenotypes.

Author Info: (1) Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (2) Computational and Systems Biology Program, Sloan Kettering Institute, N

Author Info: (1) Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (2) Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY 10065, USA; Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA. (3) Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (4) Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY 10065, USA. (5) Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (6) Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (7) Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY 10065, USA. (8) Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (9) Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. (10) Computational and Systems Biology Program, Sloan Kettering Institute, New York, NY 10065, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (11) Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: jallison@mdanderson.org.

Genetic diversity of tumors with mismatch repair deficiency influences anti-PD-1 immunotherapy response

Tumors with mismatch repair deficiency (MMR-d) are characterized by sequence alterations in microsatellites and can accumulate thousands of mutations. This high mutational burden renders tumors immunogenic and sensitive to programmed cell death-1 (PD-1) immune checkpoint inhibitors. Yet, despite their tumor immunogenicity, patients with MMR-deficient tumors experience highly variable responses, and roughly half are refractory to treatment. We present experimental and clinical evidence showing that the degree of microsatellite instability (MSI) and resultant mutational load, in part, underlies the variable response to PD-1 blockade immunotherapy in MMR-d human and mouse tumors. The extent of response is particularly associated with the accumulation of insertion-deletion (indel) mutational load. This study provides a rationale for the genome-wide characterization of MSI intensity and mutational load to better profile responses to anti-PD-1 immunotherapy across MMR-deficient human cancers.

Author Info: (1) Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD 21287, USA. Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Ba

Author Info: (1) Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD 21287, USA. Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (2) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (3) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (4) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (5) Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA. (6) Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (7) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (8) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (9) Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (10) Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (11) Department of Otolaryngology-Head and Neck Surgery, Weill Cornell New York Presbyterian Hospital, New York, NY 10065, USA. (12) Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA. Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA. Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA. (13) Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA. (14) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (15) Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (16) Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (17) Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (18) Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (19) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (20) Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (21) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (22) Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA. Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA. Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA. (23) Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. (24) Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. chant@mskcc.org. Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

CD8(+) T cells regulate tumour ferroptosis during cancer immunotherapy

Cancer immunotherapy restores or enhances the effector function of CD8(+) T cells in the tumour microenvironment(1,2). CD8(+) T cells activated by cancer immunotherapy clear tumours mainly by inducing cell death through perforin-granzyme and Fas-Fas ligand pathways(3,4). Ferroptosis is a form of cell death that differs from apoptosis and results from iron-dependent accumulation of lipid peroxide(5,6). Although it has been investigated in vitro(7,8), there is emerging evidence that ferroptosis might be implicated in a variety of pathological scenarios(9,10). It is unclear whether, and how, ferroptosis is involved in T cell immunity and cancer immunotherapy. Here we show that immunotherapy-activated CD8(+) T cells enhance ferroptosis-specific lipid peroxidation in tumour cells, and that increased ferroptosis contributes to the anti-tumour efficacy of immunotherapy. Mechanistically, interferon gamma (IFNgamma) released from CD8(+) T cells downregulates the expression of SLC3A2 and SLC7A11, two subunits of the glutamate-cystine antiporter system xc(-), impairs the uptake of cystine by tumour cells, and as a consequence, promotes tumour cell lipid peroxidation and ferroptosis. In mouse models, depletion of cystine or cysteine by cyst(e)inase (an engineered enzyme that degrades both cystine and cysteine) in combination with checkpoint blockade synergistically enhanced T cell-mediated anti-tumour immunity and induced ferroptosis in tumour cells. Expression of system xc(-) was negatively associated, in cancer patients, with CD8(+) T cell signature, IFNgamma expression, and patient outcome. Analyses of human transcriptomes before and during nivolumab therapy revealed that clinical benefits correlate with reduced expression of SLC3A2 and increased IFNgamma and CD8. Thus, T cell-promoted tumour ferroptosis is an anti-tumour mechanism, and targeting this pathway in combination with checkpoint blockade is a potential therapeutic approach.

Author Info: (1) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel

Author Info: (1) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (2) Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, MI, USA. (3) Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA. Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA. (4) Cayman Chemical Company, Ann Arbor, MI, USA. (5) Cayman Chemical Company, Ann Arbor, MI, USA. (6) Cayman Chemical Company, Ann Arbor, MI, USA. (7) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (8) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, MI, USA. (9) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (10) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (11) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (12) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (13) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (14) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (15) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (16) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (17) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (18) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (19) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. (20) Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA. (21) Department of Obstetrics and Gynecology, University of Michigan School of Medicine, Ann Arbor, MI, USA. (22) Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, MI, USA. (23) Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA. Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. (24) Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA. Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. (25) Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA. Department of Computational Medicine & Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI, USA. (26) Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA. Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. (27) Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA. Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA. (28) Immunogenomics and Precision Oncology Platform, Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. (29) Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA. Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA. Howard Hughes Medical Institute, University of Michigan School of Medicine, Ann Arbor, MI, USA. (30) Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, USA. wzou@med.umich.edu. Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, MI, USA. wzou@med.umich.edu. Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA. wzou@med.umich.edu. Graduate Program in Immunology, University of Michigan School of Medicine, Ann Arbor, MI, USA. wzou@med.umich.edu. Graduate Program in Cancer Biology, University of Michigan School of Medicine, Ann Arbor, MI, USA. wzou@med.umich.edu.

Reprogramming the microenvironment with tumor-selective angiotensin blockers enhances cancer immunotherapy

Cancer-associated fibroblasts (CAFs) can either suppress or support T lymphocyte activity, suggesting that CAFs may be reprogrammable to an immunosupportive state. Angiotensin receptor blockers (ARBs) convert myofibroblast CAFs to a quiescent state, but whether ARBs can reprogram CAFs to promote T lymphocyte activity and enhance immunotherapy is unknown. Moreover, ARB doses are limited by systemic adverse effects such as hypotension due to the importance of angiotensin signaling outside tumors. To enhance the efficacy and specificity of ARBs in cancer with the goal of revealing their effects on antitumor immunity, we developed ARB nanoconjugates that preferentially accumulate and act in tumors. We created a diverse library of hundreds of acid-degradable polymers and chemically linked ARBs to the polymer most sensitive to tumor pH. These tumor microenvironment-activated ARBs (TMA-ARBs) remain intact and inactive in circulation while achieving high concentrations in tumors, wherein they break down to active ARBs. This tumor-preferential activity enhances the CAF-reprogramming effects of ARBs while eliminating blood pressure-lowering effects. Notably, TMA-ARBs alleviate immunosuppression and improve T lymphocyte activity, enabling dramatically improved responses to immune-checkpoint blockers in mice with primary as well as metastatic breast cancer.

Author Info: (1) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. Koch Institute for Integrative Cancer

Author Info: (1) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139. Harvard School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138. (2) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139. Harvard School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138. (3) Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139. Laboratory for Biomaterials and Drug Delivery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115. Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115. Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115. (4) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. (5) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139. (6) Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. (7) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. (8) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. (9) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114. (10) Laboratory for Biomaterials and Drug Delivery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115. Department of Anesthesiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115. Division of Critical Care Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115. (11) Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 ; rlanger@mit.edu jain@steele.mgh.harvard.edu. Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139. (12) Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; rlanger@mit.edu jain@steele.mgh.harvard.edu.

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

BACKGROUND: Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs. METHODS: In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data. RESULTS: The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations. CONCLUSIONS: This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden.

Author Info: (1) Department of General, Visceral and Transplant Surgery, University Hospital Tubingen, Hoppe-Seyler-Str. 3, D-72076, Tubingen, Germany. Markus.Loeffler@uni-tuebingen.de. Interfa

Author Info: (1) Department of General, Visceral and Transplant Surgery, University Hospital Tubingen, Hoppe-Seyler-Str. 3, D-72076, Tubingen, Germany. Markus.Loeffler@uni-tuebingen.de. Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. Markus.Loeffler@uni-tuebingen.de. German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tubingen, Tubingen, Germany. Markus.Loeffler@uni-tuebingen.de. Department of Clinical Pharmacology, University Hospital Tubingen, Auf der Morgenstelle 8, D-72076, Tubingen, Germany. Markus.Loeffler@uni-tuebingen.de. (2) Institute for Translational Bioinformatics, University Hospital Tubingen, Tubingen, Germany. Quantitative Biology Center (QBiC), University of Tubingen, Auf der Morgenstelle 10, D-72076, Tubingen, Germany. (3) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. Center for Bioinformatics, University of Tubingen, Sand 14, D-72076, Tubingen, Germany. Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076, Tubingen, Germany. (4) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tubingen, Tubingen, Germany. (5) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. Center for Bioinformatics, University of Tubingen, Sand 14, D-72076, Tubingen, Germany. Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076, Tubingen, Germany. Present address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD,, United Kingdom. (6) Institute of Medical Genetics and Applied Genomics, University Hospital Tubingen, Calwerstr. 7, D-72076, Tubingen, Germany. (7) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. (8) Institute of Medical Genetics and Applied Genomics, University Hospital Tubingen, Calwerstr. 7, D-72076, Tubingen, Germany. (9) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. (10) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. (11) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. Present address: Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15, D-72076, Tubingen, Germany. (12) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. Present address: Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15, D-72076, Tubingen, Germany. (13) Institute of Medical Genetics and Applied Genomics, University Hospital Tubingen, Calwerstr. 7, D-72076, Tubingen, Germany. (14) Institute of Medical Genetics and Applied Genomics, University Hospital Tubingen, Calwerstr. 7, D-72076, Tubingen, Germany. (15) Institute of Medical Genetics and Applied Genomics, University Hospital Tubingen, Calwerstr. 7, D-72076, Tubingen, Germany. NGS Competence Center Tubingen (NCCT), University of Tubingen, Tubingen, Germany. (16) Quantitative Biology Center (QBiC), University of Tubingen, Auf der Morgenstelle 10, D-72076, Tubingen, Germany. (17) Quantitative Biology Center (QBiC), University of Tubingen, Auf der Morgenstelle 10, D-72076, Tubingen, Germany. (18) Department of General, Visceral and Transplant Surgery, University Hospital Tubingen, Hoppe-Seyler-Str. 3, D-72076, Tubingen, Germany. (19) Department of General, Visceral and Transplant Surgery, University Hospital Tubingen, Hoppe-Seyler-Str. 3, D-72076, Tubingen, Germany. (20) Department of General, Visceral and Transplant Surgery, University Hospital Tubingen, Hoppe-Seyler-Str. 3, D-72076, Tubingen, Germany. (21) Department of General, Visceral and Transplant Surgery, University Hospital Tubingen, Hoppe-Seyler-Str. 3, D-72076, Tubingen, Germany. Present address: Department of General and Visceral Surgery, Schwarzwald-Baar Hospital, Klinikstr. 11, D-78052, Villingen-Schwenningen, Germany. (22) Institute of Pathology and Neuropathology, University Hospital Tubingen, Liebermeisterstr. 8, D-72076, Tubingen, Germany. (23) Institute of Pathology and Neuropathology, University Hospital Tubingen, Liebermeisterstr. 8, D-72076, Tubingen, Germany. (24) Interfaculty Institute for Cell Biology, Proteome Center Tubingen (PCT), University of Tubingen, Auf der Morgenstelle 15, 72076, Tubingen, Germany. (25) Interfaculty Institute for Cell Biology, Proteome Center Tubingen (PCT), University of Tubingen, Auf der Morgenstelle 15, 72076, Tubingen, Germany. (26) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tubingen, Tubingen, Germany. Internal Medicine, Department for Oncology, Hematology, Immunology, Rheumatology and Pulmonology, University of Tubingen, Otfried-Muller-Str. 10, D-72076, Tubingen, Germany. (27) Cancer Immunoregulation Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, "Fondazione Pascale" - IRCCS, 80131, Naples, Italy. (28) German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tubingen, Tubingen, Germany. Institute for Translational Bioinformatics, University Hospital Tubingen, Tubingen, Germany. Quantitative Biology Center (QBiC), University of Tubingen, Auf der Morgenstelle 10, D-72076, Tubingen, Germany. Center for Bioinformatics, University of Tubingen, Sand 14, D-72076, Tubingen, Germany. Department of Computer Science, Applied Bioinformatics, Sand 14, D-72076, Tubingen, Germany. NGS Competence Center Tubingen (NCCT), University of Tubingen, Tubingen, Germany. Max Planck Institute for Developmental Biology, Biomolecular Interactions, Spemannstr. 35, D-72076, Tubingen, Germany. (29) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tubingen, Tubingen, Germany. (30) Department of General, Visceral and Transplant Surgery, University Hospital Tubingen, Hoppe-Seyler-Str. 3, D-72076, Tubingen, Germany. German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tubingen, Tubingen, Germany. (31) Interfaculty Institute for Cell Biology, Department of Immunology, University of Tubingen, Auf der Morgenstelle 15, D-72076, Tubingen, Germany. German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tubingen, Tubingen, Germany.

A library of Neo Open Reading Frame peptides (NOPs) as a sustainable resource of common neoantigens in up to 50% of cancer patients

Somatic mutations in cancer can result in neoantigens against which patients can be vaccinated. The quest for tumor specific neoantigens has yielded no targets that are common to all tumors, yet foreign to healthy cells. Single base pair substitutions (SNVs) at best can alter 1 amino acid which can result in a neoantigen; with the exception of rare site-specific oncogenic driver mutations (such as RAS) such mutations are private. Here, we describe a source of common neoantigens induced by frame shift mutations, based on analysis of 10,186 TCGA tumor samples. We find that these frame shift mutations can produce long neoantigens. These are completely new to the body, and indeed recent evidence suggests that frame shifts can be highly immunogenic. We report that many different frame shift mutations converge to the same small set of 3' neo open reading frame peptides (NOPs), all encoded by the Neo-ORFeome. We find that a fixed set of only 1,244 neo-peptides in as much as 30% of all TCGA cancer patients. For some tumor classes this is higher; e.g. for colon and cervical cancer, peptides derived from only ten genes (saturated at 90 peptides) can be applied to 39% of all patients. 50% of all TCGA patients can be achieved at saturation (using all those peptides in the library found more than once). A pre-fabricated library of vaccines (peptide, RNA or DNA) based on this set can provide off the shelf, quality certified, 'personalized' vaccines within hours, saving months of vaccine preparation. This is crucial for critically ill cancer patients with short average survival expectancy after diagnosis.

Author Info: (1) Amsterdam UMC, University of Amsterdam, Department of Oncogenomics, Meibergdreef 9, Amsterdam, The Netherlands. jankoster@amc.uva.nl. (2) myTomorrows, Antoni Fokkerweg 61, Amst

Author Info: (1) Amsterdam UMC, University of Amsterdam, Department of Oncogenomics, Meibergdreef 9, Amsterdam, The Netherlands. jankoster@amc.uva.nl. (2) myTomorrows, Antoni Fokkerweg 61, Amsterdam, The Netherlands. ronald.plasterk@frametherapeutics.com. Founder/CEO, Frame Cancer Therapeutics, Science Park 106, Amsterdam, 1098 XG, The Netherlands. ronald.plasterk@frametherapeutics.com. Amsterdam UMC, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam, The Netherlands. ronald.plasterk@frametherapeutics.com.

Identification of Neoantigen-Reactive Tumor-Infiltrating Lymphocytes in Primary Bladder Cancer

Immune checkpoint inhibitors are effective in treating a variety of malignancies, including metastatic bladder cancer. A generally accepted hypothesis suggests that immune checkpoint inhibitors induce tumor regressions by reactivating a population of endogenous tumor-infiltrating lymphocytes (TILs) that recognize cancer neoantigens. Although previous studies have identified neoantigen-reactive TILs from several types of cancer, no study to date has shown whether neoantigen-reactive TILs can be found in bladder tumors. To address this, we generated TIL cultures from patients with primary bladder cancer and tested their ability to recognize tumor-specific mutations. We found that CD4(+) TILs from one patient recognized mutated C-terminal binding protein 1 in an MHC class II-restricted manner. This finding suggests that neoantigen-reactive TILs reside in bladder cancer, which may help explain the effectiveness of immune checkpoint blockade in this disease and also provides a rationale for the future use of adoptive T cell therapy targeting neoantigens in bladder cancer.

Author Info: (1) Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. Hematology Branch, National Heart, Lung and Blood Institute, National Institutes o

Author Info: (1) Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20982. (2) Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. (3) Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. (4) Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. (5) Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. (6) Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and. (7) Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. (8) Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892. (9) Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; Yong-Chen.Lu@nih.gov.

Complementing the Cancer-Immunity Cycle

Reactivation of cytotoxic CD8(+) T-cell responses has set a new direction for cancer immunotherapy. Neutralizing antibodies targeting immune checkpoint programmed cell death protein 1 (PD-1) or its ligand (PD-L1) have been particularly successful for tumor types with limited therapeutic options such as melanoma and lung cancer. However, reactivation of T cells is only one step toward tumor elimination, and a substantial fraction of patients fails to respond to these therapies. In this context, combination therapies targeting more than one of the steps of the cancer-immune cycle may provide significant benefits. To find the best combinations, it is of upmost importance to understand the interplay between cancer cells and all the components of the immune response. This review focuses on the elements of the complement system that come into play in the cancer-immunity cycle. The complement system, an essential part of innate immunity, has emerged as a major regulator of cancer immunity. Complement effectors such as C1q, anaphylatoxins C3a and C5a, and their receptors C3aR and C5aR1, have been associated with tolerogenic cell death and inhibition of antitumor T-cell responses through the recruitment and/or activation of immunosuppressive cell subpopulations such as myeloid-derived suppressor cells (MDSCs), regulatory T cells (Tregs), or M2 tumor-associated macrophages (TAMs). Evidence is provided to support the idea that complement blocks many of the effector routes associated with the cancer-immunity cycle, providing the rationale for new therapeutic combinations aimed to enhance the antitumor efficacy of anti-PD-1/PD-L1 checkpoint inhibitors.

Author Info: (1) Program in Solid Tumors (CIMA) and Department of Biochemistry and Genetics (School of Medicine), University of Navarra, Pamplona, Spain. Navarra Institute for Health Research (

Author Info: (1) Program in Solid Tumors (CIMA) and Department of Biochemistry and Genetics (School of Medicine), University of Navarra, Pamplona, Spain. Navarra Institute for Health Research (IDISNA), Pamplona, Spain. Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain. (2) Program in Solid Tumors (CIMA) and Department of Biochemistry and Genetics (School of Medicine), University of Navarra, Pamplona, Spain. Navarra Institute for Health Research (IDISNA), Pamplona, Spain. Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain. (3) Program in Solid Tumors (CIMA) and Department of Biochemistry and Genetics (School of Medicine), University of Navarra, Pamplona, Spain. (4) Humanitas Clinical and Research Center, Humanitas University, Milan, Italy. William Harvey Research Institute, Queen Mary University of London, London, United Kingdom. (5) Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States.

Modulating inflammation for cancer therapy

A link between chronic inflammation and development of tumors is well established. Moreover, it has become evident that tumorigenesis is not a cell autonomous disease, and an inflammatory microenvironment is a prerequisite of basically all tumors, including those that emerge in the absence of overt inflammation. This knowledge has led to the development of anti-inflammatory concepts to treat and prevent cancer. In contrast, immunotherapies, in particular checkpoint inhibitors, representing the most significant progress in the therapy of several malignancies depend on the presence of a pro-inflammatory "hot" environment. Here, we discuss pro- and anti-inflammatory concepts for the treatment of cancer.

Author Info: (1) Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt/Main, Germany. (2) Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, F

Author Info: (1) Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt/Main, Germany. (2) Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt/Main, Germany greten@gsh.uni-frankfurt.de. Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany. German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany.

Differential effects of depleting versus programming tumor-associated macrophages on engineered T cells in pancreatic ductal adenocarcinoma

Spotlight 

Stromnes et al. combined mesothelin-specific CD8+ T cell (TCRMSLN) transfer with two tumor-associated macrophage (TAM)-targeting strategies in murine pancreatic ductal adenocarcinoma (PDA). TCRMSLN cells alone increased intratumoral M1 TAMs and survival. Anti-CSF1R decreased M2 TAMs and improved intratumoral endogenous CD8+ T cell numbers but had minimal impact on TCRMSLN cells. Agonist-CD40 boosted TCRMSLN cell persistence and Ki67/GzmB levels, reduced PD-1 expression, and supported remodeling of the tumor stroma, but did not rescue IFNγ production. In human PDA, M2 TAMs correlated with CSF1/CSF1R expression.

Contributed by Alex Najibi

Stromnes et al. combined mesothelin-specific CD8+ T cell (TCRMSLN) transfer with two tumor-associated macrophage (TAM)-targeting strategies in murine pancreatic ductal adenocarcinoma (PDA). TCRMSLN cells alone increased intratumoral M1 TAMs and survival. Anti-CSF1R decreased M2 TAMs and improved intratumoral endogenous CD8+ T cell numbers but had minimal impact on TCRMSLN cells. Agonist-CD40 boosted TCRMSLN cell persistence and Ki67/GzmB levels, reduced PD-1 expression, and supported remodeling of the tumor stroma, but did not rescue IFNγ production. In human PDA, M2 TAMs correlated with CSF1/CSF1R expression.

Contributed by Alex Najibi

Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy resistant to therapies, including immune checkpoint blockade. We investigated two distinct strategies to modulate tumor-associated macrophages (TAMs) to enhance cellular therapy targeting mesothelin in an autochthonous PDA mouse model. Administration of an antibody to colony-stimulating factor (anti-Csf1R) depleted Ly6Clow pro-tumorigenic TAMs and significantly enhanced endogenous T-cell intratumoral accumulation. Despite increasing the number of endogenous T cells at the tumor site, as previously reported, TAM depletion had only minimal impact on intratumoral accumulation and persistence of T cells engineered to express a murine mesothelin-specific T-cell receptor (TCR). TAM depletion interfered with the antitumor activity of the infused T cells in PDA, evidenced by reduced tumor cell apoptosis. In contrast, TAM programming with agonistic anti-CD40 increased both Ly6Chigh TAMs and the intratumoral accumulation and longevity of TCR-engineered T cells. Anti-CD40 significantly increased the frequency and number of proliferating and granzyme B+ engineered T cells, and increased tumor cell apoptosis. However, anti-CD40 failed to rescue intratumoral engineered T-cell IFNgamma production. Thus, although functional modulation, rather than TAM depletion, enhanced the longevity of engineered T cells and increased tumor cell apoptosis, ultimately, anti-CD40 modulation was insufficient to rescue key effector defects in tumor-reactive T cells. This study highlights critical distinctions between how endogenous T cells that evolve in vivo, and engineered T cells with previously acquired effector activity, respond to modifications of the tumor microenvironment.

Author Info: (1) Microbiology and Immunology, University of Minnesota Medical School ingunn@umn.edu. (2) Microbiology and Immunology, University of Minnesota Medical School. (3) University of W

Author Info: (1) Microbiology and Immunology, University of Minnesota Medical School ingunn@umn.edu. (2) Microbiology and Immunology, University of Minnesota Medical School. (3) University of Washington. (4) Fred Hutchinson Cancer Research Center. (5) Immunology, Fred Hutchinson Cancer Research Center. (6) Cancer Biology, Fred Hutchinson Cancer Research Center. (7) Microbiology and Immunology, University of Minnesota Medical School. (8) Department of Microbiology and Immunology, University of Minnesota Medical Center. (9) Experimental Pathology, Program in Immunology, Fred Hutchinson Cancer Research Center. (10) Immunology, Fred Hutchinson Cancer Research Center. (11) Fred Hutchinson Cancer Research Center.