Promising New Tools for Targeting P53 Mutant Cancers: Humoral and Cell-Based Immunotherapies
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Tumor Neoantigens: from Basic Research to Clinical Applications
Jiang et al. Journal of Hematology & Oncology (2019) 12:93 https://doi.org/10.1186/s13045-019-0787-5 REVIEW Open Access Tumor neoantigens: from basic research to clinical applications Tao Jiang1,4†, Tao Shi2†, Henghui Zhang3†,JieHu1, Yuanlin Song1, Jia Wei2*, Shengxiang Ren4* and Caicun Zhou4* Abstract Tumor neoantigen is the truly foreign protein and entirely absent from normal human organs/tissues. It could be specifically recognized by neoantigen-specific T cell receptors (TCRs) in the context of major histocompatibility complexes (MHCs) molecules. Emerging evidence has suggested that neoantigens play a critical role in tumor- specific T cell-mediated antitumor immune response and successful cancer immunotherapies. From a theoretical perspective, neoantigen is an ideal immunotherapy target because they are distinguished from germline and could be recognized as non-self by the host immune system. Neoantigen-based therapeutic personalized vaccines and adoptive T cell transfer have shown promising preliminary results. Furthermore, recent studies suggested the significant role of neoantigen in immune escape, immunoediting, and sensitivity to immune checkpoint inhibitors. In this review, we systematically summarize the recent advances of understanding and identification of tumor- specific neoantigens and its role on current cancer immunotherapies. We also discuss the ongoing development of strategies based on neoantigens and its future clinical applications. Keywords: Neoantigen, Immunotherapy, Immune escape, Immune checkpoint, Resistance Introduction polyomavirus (MCPyV)–related Merkel cell carcinoma Tumor neoantigen, or tumor-specific antigen (TSA), (MCC) and Epstein-Barr virus (EBV)–relatedheadandneck is the repertoire of peptides that displays on the cancers, any epitopes derive from open reading frames tumor cell surface and could be specifically recog- (ORFs) in the viral genome also contribute to the potential nized by neoantigen-specific T cell receptors (TCRs) source of neoantigens [6–8]. -
Pioneering Individualized Cancer Therapies
PLATFORMS Pharmacologically optimized protein coding RNA for targeted in vivo delivery mRNA Technology • Cancer immunotherapies • Prophylactic vaccines • Protein replacement Immunotherapy with genetically engineered T cells, adoptive T cell transfer Cell Therapy • T cell receptor therapies • CAR-T therapies Engineered nanoparticles for cancer immunotherapy • Bispecific antibodies Protein Therapeutics • Microbodies • Virus-like particles Small molecule drug discovery • TLR7-agonists Small Molecules • Immuno-modulating small molecules • Drug discovery services FIRST INDIVIDUALIZED CLINICAL CANCER TRIALS WORLDWIDE WITH • An mRNA-based individualized cancer vaccine targeting neo-antigens • An intravenous formulation of an mRNA vaccine • An mRNA-based individualized vaccine drawn from a warehouse of mRNAs encoding cancer-selective antigens • A genomics-driven GMP-approved manufacturing process for individual patient-specific therapies PIONEERING INDIVIDUALIZED BioNTech SE An der Goldgrube 12 CANCER THERAPIES 55131 Mainz Germany +49 6131 – 9084 – 0 [email protected] www.biontech.de/de COMPANY OVERVIEW INDIVIDUALIZED MRNA IMMUNOLOGY BioNTech is the largest privately held biopharmaceutical company in Europe. CONCEPTS – A BIONTECH PLATFORM We develop truly individualized and patient-tailored treatments against cancer. Our objective is to transform cancer into a manageable and non-lethal disease by BioNTech’s initial product candidates for individualized cancer treatments providing treatments from a suite of therapeutic platforms and offering lifelong are developed using the company’s mRNA technology platform. The IVAC® patient support. We currently have several product candidates in clinical develop- (Individualized Vaccines Against Cancer) platform has enabled the design ment and have established all of the building blocks necessary in an effort to bring of immunotherapies targeting cancer mutations and therefore has the highly potent, tailor-made and individualized cancer therapies to patients. -
Chapter 1 Introduction
REDIRECTED T CELL ACTIVITY BY HIGH AFFINITY TCR-ANTI-CD3 BISPECIFIC CANDIDATE THERAPEUTICS A Thesis submitted in requirement of Cardiff University for the Degree of Doctor of Philosophy ***** Katherine Jane Adams 2013 School of Medicine 1 ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor, Professor Andrew Sewell, and to Dr. Bent Jakobsen of Immunocore Ltd, who have given me the opportunity to undertake this long held ambition. I would like to thank my co-workers at Immunocore Ltd who have been so supportive and helpful throughout this endeavour. Special thanks goes to Dr. Giovanna Bossi who has provided excellent scientific advice and opportunities for many fruitful discussions. Huge thanks also goes to Dr. Andrew Knox for his Microsoft Word troubleshooting skills. This journey would not have been possible without the love and support of my family so I would like to thank my father, and my brother, Paul, for being there for me. Finally I would like to acknowledge my late mother who sadly died of cancer in 2009. She has been a true inspiration to me. 2 DECLARATION This work has not been submitted in substance for any other degree or award at this or any other university or place of learning, nor is being submitted concurrently in candidature for any degree or other award. Signed ………………………………………… (candidate) Date ………………… STATEMENT 1 This thesis is being submitted in partial fulfillment of the requirements for the degree of …………………………(insert MCh, MD, MPhil, PhD etc, as appropriate) Signed ………………………………………… (candidate) Date ………………… STATEMENT 2 This thesis is the result of my own independent work/investigation, except where otherwise stated. -
Multi-Step Screening of Neoantigens'
www.nature.com/scientificreports OPEN Multi‑step screening of neoantigens’ HLA‑ and TCR‑interfaces improves prediction of survival Guilhem Richard1*, Anne S. De Groot2,3, Gary D. Steinberg4, Tzintzuni I. Garcia5, Alec Kacew5, Matthew Ardito2, William D. Martin2, Gad Berdugo1,6, Michael F. Princiotta1, Arjun V. Balar4 & Randy F. Sweis5* Improvement of risk stratifcation through prognostic biomarkers may enhance the personalization of cancer patient monitoring and treatment. We used Ancer, an immunoinformatic CD8, CD4, and regulatory T cell neoepitope screening system, to perform an advanced neoantigen analysis of genomic data derived from the urothelial cancer cohort of The Cancer Genome Atlas. Ancer demonstrated improved prognostic stratifcation and fve‑year survival prediction compared to standard analyses using tumor mutational burden or neoepitope identifcation using NetMHCpan and NetMHCIIpan. The superiority of Ancer, shown in both univariate and multivariate survival analyses, is attributed to the removal of neoepitopes that do not contribute to tumor immunogenicity based on their homology with self‑epitopes. This analysis suggests that the presence of a higher number of unique, non‑self CD8‑ and CD4‑neoepitopes contributes to cancer survival, and that prospectively defning these neoepitopes using Ancer is a novel prognostic or predictive biomarker. Understanding mechanisms of cancer progression and identifying patients at high risk for recurrence are pivotal to the personalization of cancer care. Improvements in DNA sequencing techniques combined with cost reduc- tions have enabled the routine mapping of the tumor genome and improved our mechanistic understanding of cancer progression and patients’ survival. Tumor mutational burden (TMB) has arisen as a potential cancer prognosis biomarker in numerous tumor types 1,2. -
Identification of the Core Regulators of the HLA I-Peptide Binding Process
www.nature.com/scientificreports OPEN Identification of the core regulators of the HLA I-peptide binding process Received: 01 November 2016 Yu-Hang Zhang1,*, Zhihao Xing1,*, Chenglin Liu2, ShaoPeng Wang3, Tao Huang1, Yu-Dong Cai3 Accepted: 13 January 2017 & Xiangyin Kong1 Published: 17 February 2017 During the display of peptide/human leukocyte antigen (HLA) -I complex for further immune recognition, the cleaved and transported antigenic peptides have to bind to HLA-I protein and the binding affinity between peptide epitopes and HLA proteins directly influences the immune recognition ability in human beings. Key factors affecting the binding affinity during the generation, selection and presentation processes of HLA-I complex have not yet been fully discovered. In this study, a new method describing the HLA class I-peptide interactions was proposed. Three hundred and forty features of HLA I proteins and peptide sequences were utilized for analysis by four candidate algorithms, screening the optimal classifier. Features derived from the optimal classifier were further selected and systematically analyzed, revealing the core regulators. The results validated the hypothesis that features of HLA I proteins and related peptides simultaneously affect the binding process, though with discrepant redundancy. Besides, the high relative ratio (16/20) of the amino acid composition features suggests the unique role of sequence signatures for the binding processes. Integrating biological, evolutionary and chemical features of both HLA I molecules and peptides, this study may provide a new perspective of the underlying mechanisms of HLA I-mediated immune reactions. Human leukocyte antigen (HLA), which refers in particular to the major histocompatibility complex (MHC) in humans, is a group of cell surface proteins that is essential for the recognition of self-cells and non-self-cells and activation of the acquired immune system to eliminate the non-self-components1,2. -
Peptide Libraries for the Comprehensive Coverage of The
von Hoegen et al. Journal for ImmunoTherapy of Cancer 2015, 3(Suppl 2):P265 http://www.immunotherapyofcancer.org/content/3/S2/P265 POSTERPRESENTATION Open Access Peptide libraries for the comprehensive coverage of the tumor mutanome for immune monitoring and immuno therapy Paul von Hoegen1*, Tobias Knaute2, Holger Wenschuh3, Ulf Reimer2 From 30th Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2015) National Harbor, MD, USA. 4-8 November 2015 Many cancers are associated with functional mutations different tumor-specific and ideally functionally relevant which now can be readily identified using new DNA mutations. sequencing methods. Sequence information is now used Our aim is to generate peptide libraries for specific for the generation of personalized cancer vaccines with antigens which represent a generic cancer mutanome promising clinical benefit [1]. Intelligent ways to select applicable to a large number of individual patients based the relevant, tumor-specific protein-coding mutations on available databases as the catalogue of somatic muta- are applied to filter the large number of identified muta- tions in cancer and epitope information from the tion to a manageable number. Besides, there is an immune epitope database and prediction algorithms. increasing data pool of mutations, both germline and One library type can contain the full length sequence somatic, the latter frequently even with attached addi- of the antigen enriched by peptides representing over- tional information on the tissue and histology. lapping scans for relevant mutations. Alternatively, Even though the use of actual sequence of an indivi- known or predicted epitopes can be selected and the dual patient is the optimal basis for treatment and mutated epitopes can be included. -
Neoepitope Targets of Tumour-Infiltrating Lymphocytes From
www.nature.com/bjc ARTICLE Immunotherapy Neoepitope targets of tumour-infiltrating lymphocytes from patients with pancreatic cancer Qingda Meng1, Davide Valentini1,2, Martin Rao1, Carlos Fernández Moro3, Georgia Paraschoudi1,2, Elke Jäger4, Ernest Dodoo1, Elena Rangelova5, Marco del Chiaro5 and Markus Maeurer1,2,6 BACKGROUND: Pancreatic cancer exhibits a poor prognosis and often presents with metastasis at diagnosis. Immunotherapeutic approaches targeting private cancer mutations (neoantigens) are a clinically viable option to improve clinical outcomes. METHODS: 3/40 TIL lines (PanTT26, PanTT39, PanTT77) were more closely examined for neoantigen recognition. Whole-exome sequencing was performed to identify non-synonymous somatic mutations. Mutant peptides were synthesised and assessed for antigen-specific IFN-γ production and specific tumour killing in a standard Cr51 assay. TIL phenotype was tested by flow cytometry. Lymphocytes and HLA molecules in tumour tissue were visualised by immunohistochemistry. RESULTS: PanTT26 and PanTT39 TILs recognised and killed the autologous tumour cells. PanTT26 TIL recognised the KRASG12v mutation, while a PanTT39 CD4+ TIL clone recognised the neoepitope (GLLRYWRTERLF) from an aquaporin 1-like protein (gene: K7N7A8). Repeated stimulation of TILs with the autologous tumour cells line lead to focused recognition of several mutated targets, based on IFN-γ production. TILs and corresponding PBMCs from PanTT77 showed shared as well as mutually exclusively tumour epitope recognition (TIL-responsive or PBMC-responsive). -
Specificity of Bispecific T Cell Receptors and Antibodies Targeting Peptide-HLA
Supplemental Materials (JCI130562DS1) Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA Christopher J. Holland*1, Rory M. Crean*2,3, Johanne M. Pentier*1, Ben de Wet*1, Angharad Lloyd1*, Velupillai Srikannathasan1, Nikolai Lissin1, Katy A. Lloyd1, Thomas H. Blicher1, Paul J. Conroy1, Miriam Hock1, Robert J. Pengelly1, Thomas E. Spinner1, Brian Cameron1, Elizabeth A. Potter1, Anitha Jeyanthan1, Peter E. Molloy1, Malkit Sami1, Milos Aleksic1, Nathaniel Liddy1, Ross A. Robinson1, Stephen Harper1, Marco Lepore1, Chris R. Pudney2, Marc W. van der Kamp4, Pierre J. Rizkallah5, Bent K. Jakobsen1, Annelise Vuidepot1 and David K. Cole1 1Immunocore Ltd., Milton Park, Abingdon, UK. 2Department of Biology and Biochemistry, University of Bath, Bath, UK. 3Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, Bath, UK. 4School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, UK. 5Cardiff University School of Medicine, Heath Park, Cardiff, UK. *These authors contributed equally to this study. Supplemental Methods Analysis of on-target and off-target T cell reactivity via re-direction using anti-pHLA/anti-CD3 bispecific reagents The activity of the ImmTAC molecules (TCR-CD3 scFv fusions) and the TCR-mimic scFv-CD3 scFv fusions was tested through their ability to redirect T cells against a range of antigen-positive and antigen-negative cell lines (tumour and healthy cells). Incucyte killing assays were performed according to the manufacturer’s instructions (Sartorius, UK). Briefly, 100,000 PBMCs per well were added to 10,000 target cells per well. Target cells included HLA-A*02:01 and HLA-A*01:01 positive tumour cell lines, which were positive or negative for expression of target protein, as well as a panel of healthy cell lines. -
MHC Class I Deficiency in Solid Tumors and Therapeutic Strategies
International Journal of Molecular Sciences Review MHC Class I Deficiency in Solid Tumors and Therapeutic Strategies to Overcome It Elena Shklovskaya * and Helen Rizos Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; [email protected] * Correspondence: [email protected]; Tel.: +61-2-9850-2790 Abstract: It is now well accepted that the immune system can control cancer growth. However, tumors escape immune-mediated control through multiple mechanisms and the downregulation or loss of major histocompatibility class (MHC)-I molecules is a common immune escape mechanism in many cancers. MHC-I molecules present antigenic peptides to cytotoxic T cells, and MHC-I loss can render tumor cells invisible to the immune system. In this review, we examine the dysregulation of MHC-I expression in cancer, explore the nature of MHC-I-bound antigenic peptides recognized by immune cells, and discuss therapeutic strategies that can be used to overcome MHC-I deficiency in solid tumors, with a focus on the role of natural killer (NK) cells and CD4 T cells. Keywords: major histocompatibility complex (MHC); MHC-I; tumor antigens; tumor antigen pre- sentation; immunotherapy; immune checkpoint blockade; NK cells; T-cell subsets 1. Introduction Citation: Shklovskaya, E.; Rizos, H. The immune system plays a critical role in preventing and controlling cancer growth. MHC Class I Deficiency in Solid Anti-tumor immunity relies largely on CD8 T cell-mediated recognition of tumor antigens. Tumors and Therapeutic Strategies to Cancers have developed sophisticated strategies to escape immune-mediated control and Overcome It. Int. J. Mol. -
Radiation Therapy and Anti-Tumor Immunity: Exposing Immunogenic
Lhuillier et al. Genome Medicine (2019) 11:40 https://doi.org/10.1186/s13073-019-0653-7 OPINION Open Access Radiation therapy and anti-tumor immunity: exposing immunogenic mutations to the immune system Claire Lhuillier1†, Nils-Petter Rudqvist1†, Olivier Elemento2,3,4, Silvia C. Formenti1,3 and Sandra Demaria1,3,5* Abstract The expression of antigens that are recognized by self-reactive T cells is essential for immune-mediated tumor rejection by immune checkpoint blockade (ICB) therapy. Growing evidence suggests that mutation-associated neoantigens drive ICB responses in tumors with high mutational burden. In most patients, only a few of the mutations in the cancer exome that are predicted to be immunogenic are recognized by T cells. One factor that limits this recognition is the level of expression of the mutated gene product in cancer cells. Substantial preclinical data show that radiation can convert the irradiated tumor into a site for priming of tumor-specific T cells, that is, an in situ vaccine, and can induce responses in otherwise ICB-resistant tumors. Critical for radiation-elicited T-cell activation is the induction of viral mimicry, which is mediated by the accumulation of cytosolic DNA in the irradiated cells, with consequent activation of the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon (IFN) genes (STING) pathway and downstream production of type I IFN and other pro-inflammatory cytokines. Recent data suggest that radiation can also enhance cancer cell antigenicity by upregulating the expression of a large number of genes that are involved in the response to DNA damage and cellular stress, thus potentially exposing immunogenic mutations to the immune system. -
Press Release July 5, 2017
Press Release July 5, 2017 Nature Publication Reports Favorable Clinical Trial Results of BioNTech's Individualized Cancer Vaccine IVAC® MUTANOME - First-ever clinical study demonstrates personalized RNA-based vaccine using mutant neo-epitopes as antigens activates immune system against individual mutations and exerts anti-cancer activity - Mainz, Germany, July 5, 2017 – BioNTech AG, a fully-integrated biotechnology company pioneering individualized cancer immunotherapy, today announced Phase I trial results demonstrating its IVAC® MUTANOME, an individualized RNA vaccine based on patient-specific mutations, induces strong immunogenicity as well as promising anti-tumor activity in high-risk patients with late-stage melanoma. Additionally, in this early trial, a majority of patients showed prolonged progression-free survival in comparison to historical controls. The first-in-human study applied a process covering the comprehensive identification of individual mutations from routine tumor biopsies to next generation sequencing, the computational prediction of potential neo-epitopes as vaccine targets, and the design and manufacturing of an RNA vaccine encoding multiple neo-epitopes unique for each patient. The data, published today online in Nature, were obtained from research conducted in collaboration with clinical partners and the translational research institute, TRON. In the first-in-human application of a personalized RNA-based vaccine approach, 13 patients with melanoma were treated. The vaccine boosted immunity against multiple tumor antigens in all patients, and infiltration of vaccine-induced T-cells into tumors was observed in two patients. Eight of the 13 patients remained tumor-free at 23 months; five patients had tumor relapses before starting neo-epitope vaccination. Two of these patients experienced objective responses after neo-epitope vaccination and one patient had a complete response after sequential administration of neo-epitope vaccination and anti-PD-1 therapy. -
Overcoming Challenges for CD3-Bispecific Antibody Therapy In
cancers Review Overcoming Challenges for CD3-Bispecific Antibody Therapy in Solid Tumors Jim Middelburg 1 , Kristel Kemper 2, Patrick Engelberts 2 , Aran F. Labrijn 2 , Janine Schuurman 2 and Thorbald van Hall 1,* 1 Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; [email protected] 2 Genmab, 3584 CT Utrecht, The Netherlands; [email protected] (K.K.); [email protected] (P.E.); [email protected] (A.F.L.); [email protected] (J.S.) * Correspondence: [email protected]; Tel.: +31-71-5266945 Simple Summary: CD3-bispecific antibody therapy is a form of immunotherapy that enables soldier cells of the immune system to recognize and kill tumor cells. This type of therapy is currently successfully used in the clinic to treat tumors in the blood and is under investigation for tumors in our organs. The treatment of these solid tumors faces more pronounced hurdles, which affect the safety and efficacy of CD3-bispecific antibody therapy. In this review, we provide a brief status update of this field and identify intrinsic hurdles for solid cancers. Furthermore, we describe potential solutions and combinatorial approaches to overcome these challenges in order to generate safer and more effective therapies. Abstract: Immunotherapy of cancer with CD3-bispecific antibodies is an approved therapeutic option for some hematological malignancies and is under clinical investigation for solid cancers. However, the treatment of solid tumors faces more pronounced hurdles, such as increased on-target off-tumor toxicities, sparse T-cell infiltration and impaired T-cell quality due to the presence of an Citation: Middelburg, J.; Kemper, K.; immunosuppressive tumor microenvironment, which affect the safety and limit efficacy of CD3- Engelberts, P.; Labrijn, A.F.; bispecific antibody therapy.