101
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Scheetz L, Kadiyala P, Sun X, Son S, Hassani Najafabadi A, Aikins M, Lowenstein PR, Schwendeman A, Castro MG, Moon JJ. Synthetic High-density Lipoprotein Nanodiscs for Personalized Immunotherapy Against Gliomas. Clin Cancer Res 2020; 26:4369-4380. [PMID: 32439701 PMCID: PMC7442596 DOI: 10.1158/1078-0432.ccr-20-0341] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/15/2020] [Accepted: 05/15/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE Gliomas are brain tumors with dismal prognoses. The standard-of-care treatments for gliomas include surgical resection, radiation, and temozolomide administration; however, they have been ineffective in providing significant increases in median survival. Antigen-specific cancer vaccines and immune checkpoint blockade may provide promising immunotherapeutic approaches for gliomas. EXPERIMENTAL DESIGN We have developed immunotherapy delivery vehicles based on synthetic high-density lipoprotein (sHDL) loaded with CpG, a Toll-like receptor-9 agonist, and tumor-specific neoantigens to target gliomas and elicit immune-mediated tumor regression. RESULTS We demonstrate that vaccination with neoantigen peptide-sHDL/CpG cocktail in combination with anti-PD-L1 immune checkpoint blocker elicits robust neoantigen-specific T-cell responses against GL261 cells and eliminated established orthotopic GL261 glioma in 33% of mice. Mice remained tumor free upon tumor cell rechallenge in the contralateral hemisphere, indicating the development of immunologic memory. Moreover, in a genetically engineered murine model of orthotopic mutant IDH1 (mIDH1) glioma, sHDL vaccination with mIDH1 neoantigen eliminated glioma in 30% of animals and significantly extended the animal survival, demonstrating the versatility of our approach in multiple glioma models. CONCLUSIONS Overall, our strategy provides a general roadmap for combination immunotherapy against gliomas and other cancer types.
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Affiliation(s)
- Lindsay Scheetz
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan
| | - Padma Kadiyala
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan
| | - Xiaoqi Sun
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan
| | - Sejin Son
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan
| | - Alireza Hassani Najafabadi
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan
| | - Marisa Aikins
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan
| | - Pedro R Lowenstein
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Anna Schwendeman
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan.
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - James J Moon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan.
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
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102
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Abstract
Immunotherapies that harness the immune system to kill cancer cells have showed significant therapeutic efficacy in many human malignancies. A growing number of studies have highlighted the relevance of neoantigens in recognizing cancer cells by intrinsic T cells. Cancer neoantigens are a direct consequence of somatic mutations presenting on the surface of individual cancer cells. Neoantigens are fully cancer-specific and exempt from central tolerance. In addition, neoantigens are important targets for checkpoint blockade therapy. Recently, technological innovations have made neoantigen discovery possible in a variety of malignancies, thus providing an impetus to develop novel immunotherapies that selectively enhance T cell reactivity for the destruction of cancer cells while leaving normal tissues unharmed. In this review, we aim to introduce the methods of the identification of neoantigens, the mutational patterns of human cancers, related clinical trials, neoantigen burden and sensitivity to immune checkpoint blockade. Moreover, we focus on relevant challenges of targeting neoantigens for cancer treatment.
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103
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Muramatsu T, Noguchi T, Sugiyama D, Kanada Y, Fujimaki K, Ito S, Gotoh M, Nishikawa H. Newly emerged immunogenic neoantigens in established tumors enable hosts to regain immunosurveillance in a T-cell-dependent manner. Int Immunol 2020; 33:39-48. [PMID: 32729901 DOI: 10.1093/intimm/dxaa049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022] Open
Abstract
Tumor neoantigens derived from genetic alterations are potential T-cell targets for antitumor immunity. However, tumors develop immune escape mechanisms including loss of preexisting neoantigens and/or impairment of T-cell responses during tumor development and progression. Here, we addressed whether newly emerged immunogenic neoantigens in established tumors enabled hosts to inhibit tumor growth via controlling immune escape mechanisms. Using a doxycycline-driven gene expression system, we generated murine MC38, CT26 (colorectal cancer) and B16 (melanoma) cell lines with inducible expression of model immunogenic neoantigens such as chicken ovalbumin and human NY-ESO-1. A model neoantigen was induced by doxycycline administration in the tumors once tumors became palpable. Tumor growth was significantly inhibited upon induction of the neoantigen and this inhibition was abrogated in nude mice lacking T cells and in mice deprived of CD8+ T cells, indicating the critical role of CD8+ T cells in tumor regression. In addition, PD-1/PD-L1 blockade further augmented the antitumor immune response, resulting in a far stronger inhibition of tumor growth. Accordingly, newly emerged tumor neoantigen-specific CD8+ T cells with enhanced effector functions were significantly increased in mice treated with PD-1/PD-L1 blockade. We propose that a newly emerged neoantigen is sufficient to inhibit tumor growth via preventing immune escape in a T-cell-dependent manner. Our results imply that induction of immunogenic tumor neoantigens is a novel strategy to overcome the resistance to immune checkpoint blockade therapy.
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Affiliation(s)
- Tomoaki Muramatsu
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takuro Noguchi
- Department of Medical Oncology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshie Kanada
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kaori Fujimaki
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sachiko Ito
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Momokazu Gotoh
- Department of Urology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Cancer Immunology, Research Institute, National Cancer Center, Tokyo, Japan.,Division of Cancer Immunology, Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Chiba, Japan
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104
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Wu D, Liu Y, Li X, Liu Y, Yang Q, Liu Y, Wu J, Tian C, Zeng Y, Zhao Z, Xiao Y, Gu F, Zhang K, Hu Y, Liu L. Identification of Clonal Neoantigens Derived From Driver Mutations in an EGFR-Mutated Lung Cancer Patient Benefitting From Anti-PD-1. Front Immunol 2020; 11:1366. [PMID: 32793190 PMCID: PMC7390822 DOI: 10.3389/fimmu.2020.01366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have been recommended as the first-line therapy for non-small cell lung cancer (NSCLC) patients harboring EGFR mutations. However, acquired resistance to EGFR-TKIs is inevitable. Although immune checkpoint blockades (ICBs) targeting the programmed cell death 1 (PD-1)/PD-ligand (L)1 axis have achieved clinical success for many cancer types, the clinical efficacy of anti-PD-1/PD-L1 blockades in EGFR mutated NSCLC patients has been demonstrated to be lower than those without EGFR mutations. Here, we reported an advanced NSCLC patient with EGFR driver mutations benefitting from anti-PD-1 blockade therapy after acquiring resistance to EGFR-TKI. We characterized the mutational landscape of the patient with next-generation sequencing (NGS) and successfully identified specific T-cell responses to clonal neoantigens encoded by EGFR exon 19 deletion, TP53 A116T and DENND6B R398Q mutations. Our findings support the potential application of immune checkpoint blockades in NSCLC patients with acquired resistance to EGFR-TKIs in the context of specific clonal neoantigens with high immunogenicity. Personalized immunomodulatory therapy targeting these neoantigens should be explored for better clinical outcomes in EGFR mutated NSCLC patients.
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Affiliation(s)
- Di Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yangyang Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoting Li
- YuceBio Technology Co., Ltd., Shenzhen, China
| | - Yiying Liu
- YuceBio Technology Co., Ltd., Shenzhen, China
| | - Qifan Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuting Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Tian
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yulan Zeng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhikun Zhao
- YuceBio Technology Co., Ltd., Shenzhen, China
| | - Yajie Xiao
- YuceBio Technology Co., Ltd., Shenzhen, China
| | - Feifei Gu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Hu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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105
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Rus Bakarurraini NAA, Ab Mutalib NS, Jamal R, Abu N. The Landscape of Tumor-Specific Antigens in Colorectal Cancer. Vaccines (Basel) 2020; 8:E371. [PMID: 32664247 PMCID: PMC7565947 DOI: 10.3390/vaccines8030371] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 12/24/2022] Open
Abstract
Over the last few decades, major efforts in cancer research and treatment have intensified. Apart from standard chemotherapy approaches, immunotherapy has gained substantial traction. Personalized immunotherapy has become an important tool for cancer therapy with the discovery of immune checkpoint inhibitors. Traditionally, tumor-associated antigens are used in immunotherapy-based treatments. Nevertheless, these antigens lack specificity and may have increased toxicity. With the advent of next-generation technologies, the identification of new tumor-specific antigens is becoming more important. In colorectal cancer, several tumor-specific antigens were identified and functionally validated. Multiple clinical trials from vaccine-based and adoptive cell therapy utilizing tumor-specific antigens have commenced. Herein, we will summarize the current landscape of tumor-specific antigens particularly in colorectal cancer.
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Affiliation(s)
| | | | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (N.A.A.R.B.); (N.S.A.M.)
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (N.A.A.R.B.); (N.S.A.M.)
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106
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Bianchi V, Harari A, Coukos G. Neoantigen-Specific Adoptive Cell Therapies for Cancer: Making T-Cell Products More Personal. Front Immunol 2020; 11:1215. [PMID: 32695101 PMCID: PMC7333784 DOI: 10.3389/fimmu.2020.01215] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Mutation-derived neoantigens are taking central stage as a determinant in eliciting effective antitumor immune responses following adoptive T-cell therapies. These mutations are patient-specific, and their targeting calls for highly personalized pipelines. The promising clinical outcomes of tumor-infiltrating lymphocyte (TIL) therapy have spurred interest in generating T-cell infusion products that have been selectively enriched in neoantigen (or autologous tumor) reactivity. The implementation of an isolation step, prior to T-cell in vitro expansion and reinfusion, may provide a way to improve the overall response rates achieved to date by adoptive T-cell therapies in metastatic cancer patients. Here we provide an overview of the main technologies [i.e., peptide major histocompatibility complex (pMHC) multimers, cytokine capture, and activation markers] to enrich infiltrating or circulating T-cells in predefined neoantigen specificities (or tumor reactivity). The unique technical and regulatory challenges faced by such highly specialized and patient-specific manufacturing T-cell platforms are also discussed.
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Affiliation(s)
- Valentina Bianchi
- Department of Oncology, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Center of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Center of Experimental Therapeutics, Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
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107
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Salomon N, Vascotto F, Selmi A, Vormehr M, Quinkhardt J, Bukur T, Schrörs B, Löewer M, Diken M, Türeci Ö, Sahin U, Kreiter S. A liposomal RNA vaccine inducing neoantigen-specific CD4 + T cells augments the antitumor activity of local radiotherapy in mice. Oncoimmunology 2020; 9:1771925. [PMID: 32923128 PMCID: PMC7458669 DOI: 10.1080/2162402x.2020.1771925] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antigen-encoding, lipoplex-formulated RNA (RNA-LPX) enables systemic delivery to lymphoid compartments and selective expression in resident antigen-presenting cells. We report here that the rejection of CT26 tumors, mediated by local radiotherapy (LRT), is further augmented in a CD8+ T cell-dependent manner by an RNA-LPX vaccine that encodes CD4+ T cell-recognized neoantigens (CD4 neoantigen vaccine). Whereas CD8+ T cells induced by LRT alone were primarily directed against the immunodominant gp70 antigen, mice treated with LRT plus the CD4 neoantigen vaccine rejected gp70-negative tumors and were protected from rechallenge with these tumors, indicating a potent poly-antigenic CD8+ T cell response and T cell memory. In the spleens of CD4 neoantigen-vaccinated mice, we found a high number of activated, poly-functional, Th1-like CD4+ T cells against ME1, the immunodominant CD4 neoantigen within the poly-neoantigen vaccine. LRT itself strongly increased CD8+ T cell numbers and clonal expansion. However, tumor infiltrates of mice treated with CD4 neoantigen vaccine/LRT, as compared to LRT alone, displayed a higher fraction of activated gp70-specific CD8+ T cells, lower PD-1/LAG-3 expression and contained ME1-specific IFNγ+ CD4+ T cells capable of providing cognate help. CD4 neoantigen vaccine/LRT treatment followed by anti-CTLA-4 antibody therapy further enhanced the efficacy with complete remission of gp70-negative CT26 tumors and survival of all mice. Our data highlight the power of combining synergistic modes of action and warrants further exploration of the presented treatment schema.
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Affiliation(s)
- Nadja Salomon
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University gGmbH, 55131 Mainz, Germany
| | - Fulvia Vascotto
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University gGmbH, 55131 Mainz, Germany
| | - Abderaouf Selmi
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University gGmbH, 55131 Mainz, Germany
| | | | | | - Thomas Bukur
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University gGmbH, 55131 Mainz, Germany
| | - Barbara Schrörs
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University gGmbH, 55131 Mainz, Germany
| | - Martin Löewer
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University gGmbH, 55131 Mainz, Germany
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University gGmbH, 55131 Mainz, Germany
| | | | - Ugur Sahin
- BioNTech SE, 55131 Mainz, Germany.,Research Center for Immunotherapy (FZI) of the University Medical Center of the Johannes Gutenberg-University Mainz, 55131 Mainz, Germany
| | - Sebastian Kreiter
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg-University gGmbH, 55131 Mainz, Germany
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108
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Podaza E, Carri I, Aris M, von Euw E, Bravo AI, Blanco P, Ortiz Wilczyñski JM, Koile D, Yankilevich P, Nielsen M, Mordoh J, Barrio MM. Evaluation of T-Cell Responses Against Shared Melanoma Associated Antigens and Predicted Neoantigens in Cutaneous Melanoma Patients Treated With the CSF-470 Allogeneic Cell Vaccine Plus BCG and GM-CSF. Front Immunol 2020; 11:1147. [PMID: 32582212 PMCID: PMC7290006 DOI: 10.3389/fimmu.2020.01147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/11/2020] [Indexed: 01/30/2023] Open
Abstract
The CSF-470 vaccine consists of lethally-irradiated allogeneic cells derived from four cutaneous melanoma cell lines administered plus BCG and GM-CSF as adjuvants. In an adjuvant phase II study vs. IFN-α2b, the vaccine significantly prolonged the distant metastasis-free survival (DMFS) of stages IIB-IIC-III melanoma patients with evidence of the induction of immune responses against vaccine cells. Purpose: The aim of this study was to analyze the antigens against which the immune response was induced, as well as the T-helper profile and lytic ability of immune cells after CSF-470 treatment. Methods: HLA-restricted peptides from tumor-associated antigens (TAAs) were selected from TANTIGEN database for 13 evaluable vaccinated patients. In addition, for patient #006 (pt#006), tumor somatic variants were identified by NGS and candidate neoAgs were selected by predicted HLA binding affinity and similarity between wild type (wt) and mutant peptides. The patient's PBMC reactivity against selected peptides was detected by IFNγ-ELISPOT. T-helper transcriptional profile was determined by quantifying GATA-3, T-bet, and FOXP3 mRNA by RT-PCR, and intracellular cytokines were analyzed by flow cytometry. Autologous tumor cell lysis by PBMC was assessed in an in vitro calcein release assay. Results: Vaccinated patient's PBMC reactivity against selected TAAs derived peptides showed a progressive increase in the number of IFNγ-producing cells throughout the 2-yr vaccination protocol. ELISPOT response correlated with delayed type hypersensitivity (DTH) reaction to CSF-470 vaccine cells. Early upregulation of GATA-3 and Foxp3 mRNA, as well as an increase in CD4+IL4+cells, was associated with a low DMFS. Also, IFNγ response against 9/73 predicted neoAgs was evidenced in the case of pt#006; 7/9 emerged after vaccination. We verified in pt# 006 that post-vaccination PBMC boosted in vitro with the vaccine lysate were able to lyse autologous tumor cells. Conclusions: A progressive increase in the immune response against TAAs expressed in the vaccine and in the patient's tumor was induced by CSF-470 vaccination. In pt#006, we demonstrated immune recognition of patient's specific neoAgs, which emerged after vaccination. These results suggest that an initial response against shared TAAs could further stimulate an immune response against autologous tumor neoAgs.
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Affiliation(s)
- Enrique Podaza
- Centro de Investigaciones Oncológicas, Fundación Cáncer, Buenos Aires, Argentina
| | - Ibel Carri
- IIBIO, UNSAM, San Martín, Buenos Aires, Argentina
| | - Mariana Aris
- Centro de Investigaciones Oncológicas, Fundación Cáncer, Buenos Aires, Argentina
| | - Erika von Euw
- UCLA JCCC-Translational Oncology Research Labs, Los Angeles, CA, United States
- T-Cure Bioscience Inc., Los Angeles, CA, United States
| | - Alicia Inés Bravo
- Centro de Excelencia en Medicina Translacional, Hospital El Cruce, Buenos Aires, Argentina
| | - Paula Blanco
- Centro de Investigaciones Oncológicas, Fundación Cáncer, Buenos Aires, Argentina
| | | | - Daniel Koile
- Plataforma Bioinformática, INBioBA-MPSP, Buenos Aires, Argentina
| | | | - Morten Nielsen
- IIBIO, UNSAM, San Martín, Buenos Aires, Argentina
- Department of Health Technology, The Technical University of Denmark, Lyngby, Denmark
| | - José Mordoh
- Centro de Investigaciones Oncológicas, Fundación Cáncer, Buenos Aires, Argentina
- IIBBA-CONICET, Fundación Instituto Leloir, Buenos Aires, Argentina
- Instituto Alexander Fleming, Buenos Aires, Argentina
| | - María Marcela Barrio
- Centro de Investigaciones Oncológicas, Fundación Cáncer, Buenos Aires, Argentina
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109
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Capietto AH, Jhunjhunwala S, Delamarre L. Cancer neoantigens and immunogenicity: mutation position matters. Mol Cell Oncol 2020; 7:1740071. [PMID: 32391432 PMCID: PMC7199756 DOI: 10.1080/23723556.2020.1740071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 11/29/2022]
Abstract
Cancer mutations can elicit protective immunity. Computational methods are critical for selecting these neoantigens for immunotherapy. While significant progress has been made in the field in predicting peptide presentation, our understanding of which mutated peptide is recognized as foreign by T cells remains limited. We used mouse vaccination studies to examine the features of immunogenic neoantigens and demonstrated that the mutation position is an important criterion for predicting neoantigens.
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Affiliation(s)
| | | | - Lélia Delamarre
- cancer Immunology Department, Genentech, South San Francisco, CA, USA
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110
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Jia Q, Chiu L, Wu S, Bai J, Peng L, Zheng L, Zang R, Li X, Yuan B, Gao Y, Wu D, Li X, Wu L, Sun J, He J, Robinson BWS, Zhu B. Tracking Neoantigens by Personalized Circulating Tumor DNA Sequencing during Checkpoint Blockade Immunotherapy in Non-Small Cell Lung Cancer. Adv Sci (Weinh) 2020; 7:1903410. [PMID: 32382482 PMCID: PMC7201246 DOI: 10.1002/advs.201903410] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/24/2020] [Accepted: 03/04/2020] [Indexed: 05/10/2023]
Abstract
The evolutionary dynamics of tumor-associated neoantigens carry information about drug sensitivity and resistance to the immune checkpoint blockade (ICB). However, the spectrum of somatic mutations is highly heterogeneous among patients, making it difficult to track neoantigens by circulating tumor DNA (ctDNA) sequencing using "one size fits all" commercial gene panels. Thus, individually customized panels (ICPs) are needed to track neoantigen evolution comprehensively during ICB treatment. Dominant neoantigens are predicted from whole exome sequencing data for treatment-naïve tumor tissues. Panels targeting predicted neoantigens are used for personalized ctDNA sequencing. Analyzing ten patients with non-small cell lung cancer, ICPs are effective for tracking most predicted dominant neoantigens (80-100%) in serial peripheral blood samples, and to detect substantially more genes (18-30) than the capacity of current commercial gene panels. A more than 50% decrease in ctDNA concentration after eight weeks of ICB administration is associated with favorable progression-free survival. Furthermore, at the individual level, the magnitude of the early ctDNA response is correlated with the subsequent change in tumor burden. The application of ICP-based ctDNA sequencing is expected to improve the understanding of ICB-driven tumor evolution and to provide personalized management strategies that optimize the clinical benefits of immunotherapies.
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Affiliation(s)
- Qingzhu Jia
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
- Chongqing Key Laboratory of ImmunotherapyXinqiao Main StreetChongqing400037China
| | - Luting Chiu
- Berry Oncology CorporationNO. 4 Science Park Road, Changping DistrictBeijing102206China
| | - Shuangxiu Wu
- Berry Oncology CorporationNO. 4 Science Park Road, Changping DistrictBeijing102206China
| | - Jian Bai
- Berry Oncology CorporationNO. 4 Science Park Road, Changping DistrictBeijing102206China
| | - Lina Peng
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
- Chongqing Key Laboratory of ImmunotherapyXinqiao Main StreetChongqing400037China
| | - Linpeng Zheng
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
- Chongqing Key Laboratory of ImmunotherapyXinqiao Main StreetChongqing400037China
| | - Rui Zang
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
| | - Xueqin Li
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
| | - Bibo Yuan
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
| | - Yixing Gao
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
- Chongqing Key Laboratory of ImmunotherapyXinqiao Main StreetChongqing400037China
| | - Dingyong Wu
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
| | - Xiaohong Li
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
| | - Lin Wu
- Berry Oncology CorporationNO. 4 Science Park Road, Changping DistrictBeijing102206China
| | - Jianguo Sun
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
- Chongqing Key Laboratory of ImmunotherapyXinqiao Main StreetChongqing400037China
| | - Ji He
- GeneCast Biotechnology Co., Ltd.35 Huayuan North Road, HealthWork Suite 901Beijing100191China
| | - Bruce W. S. Robinson
- School of Medicine and PharmacologyUniversity of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
- National Centre for Asbestos Related DiseasesGPO Box U1908PerthWestern Australia6845Australia
| | - Bo Zhu
- Institute of CancerXinqiao HospitalThe Army Medical UniversityXinqiao Main StreetChongqing400037China
- Chongqing Key Laboratory of ImmunotherapyXinqiao Main StreetChongqing400037China
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111
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Abstract
INTRODUCTION Glioblastoma multiforme (GBM) is the most prevalent primary brain tumor. In spite of the rigorous multimodal treatment involving surgery and radiochemotherapy, GBM has a dismal prognosis and rapid relapsing potential. Hence, search for novel therapeutic agents still continues. Neoantigens are the tumor-specific antigens which arise due to somatic mutations in the tumor genome. In recent years, personalized vaccine approach targeting neoantigens has been explored widely in cancer immunotherapy and several efforts have also been made to revolutionize the immunotherapy of cold tumors such as GBM using neoantigen targeted vaccines. AREAS COVERED In this review, we discuss the clinical application of personalized neoantigen targeted vaccine strategy in GBM immunotherapy. While discussing this strategy, we brief about the current challenges faced in GBM treatment by the novel immunotherapeutics. EXPERT OPINION To date, very few vaccines developed for GBM have reached till phase III clinical development. Early-phase clinical trials of GBM neoantigen vaccines have shown promising clinical outcomes and therefore, its rapid clinical development is warranted. Advent of newer and faster techniques such as next-generation sequencing will drive the faster clinical development of multiplex neoantigen vaccines and hence, increase in the clinical trials is expected.
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Affiliation(s)
- Vaishali Y Londhe
- Shobhaben Pratapbhai Patel School of Pharmacy &, Technology Management, SVKM's NMIMS University , Mumbai, India
| | - Varada Date
- Shobhaben Pratapbhai Patel School of Pharmacy &, Technology Management, SVKM's NMIMS University , Mumbai, India
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112
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De Mattos-Arruda L, Blanco-Heredia J, Aguilar-Gurrieri C, Carrillo J, Blanco J. New emerging targets in cancer immunotherapy: the role of neoantigens. ESMO Open 2020; 4:e000684. [PMID: 32269031 PMCID: PMC7326255 DOI: 10.1136/esmoopen-2020-000684] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/24/2022] Open
Abstract
The success of cancer therapies with immune checkpoint inhibitors is transforming the treatment of patients with cancer and fostering cancer research. Therapies that target immune checkpoint inhibitors have shown unprecedented rates of durable long-lasting responses in patients with various cancer types, but only in a fraction of patients. Thus, novel approaches are needed to make immunotherapy more precise and also less toxic. The advances of next-generation sequencing technologies have allowed fast detection of somatic mutations in genes present in the exome of an individual tumour. Targeting neoantigens, the mutated peptides expressed only by tumour cells, may enable antitumour T-cell responses and tumour destruction without causing harm to healthy tissues. Currently, neoantigens can be identified in tumour clinical samples by using genomic-based computational tools. The two main treatment modalities targeting neoantigens that have been investigated in clinical trials are personalised vaccines and tumour infiltrating lymphocytes-based adoptive T-cell therapy. In this mini review, we discuss the promises and challenges for using neoantigens as emergent targets to personalise and guide cancer immunotherapy in a broader set of cancers.
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Affiliation(s)
- Leticia De Mattos-Arruda
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Juan Blanco-Heredia
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Carmen Aguilar-Gurrieri
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol University Hospital, Badalona, Spain; Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain; Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Vic, Spain
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113
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Brightman SE, Naradikian MS, Miller AM, Schoenberger SP. Harnessing neoantigen specific CD4 T cells for cancer immunotherapy. J Leukoc Biol 2020; 107:625-633. [PMID: 32170883 PMCID: PMC7793607 DOI: 10.1002/jlb.5ri0220-603rr] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/22/2022] Open
Abstract
The goal of precision immunotherapy is to direct a patient's T cell response against the immunogenic mutations expressed on their tumors. Most immunotherapy approaches to-date have focused on MHC class I-restricted peptide epitopes by which cytotoxic CD8+ T lymphocytes (CTL) can directly recognize tumor cells. This strategy largely overlooks the critical role of MHC class II-restricted CD4+ T cells as both positive regulators of CTL and other effector cell types, and as direct effectors of antitumor immunity. In this review, we will discuss the role of neoantigen specific CD4+ T cells in cancer immunotherapy and how existing treatment modalities may be leveraged to engage this important T cell subset.
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Affiliation(s)
- Spencer E. Brightman
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Martin S. Naradikian
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Aaron M. Miller
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA 92037
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114
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Chruściel E, Urban-Wójciuk Z, Arcimowicz Ł, Kurkowiak M, Kowalski J, Gliwiński M, Marjański T, Rzyman W, Biernat W, Dziadziuszko R, Montesano C, Bernardini R, Marek-Trzonkowska N. Adoptive Cell Therapy-Harnessing Antigen-Specific T Cells to Target Solid Tumours. Cancers (Basel) 2020; 12:E683. [PMID: 32183246 DOI: 10.3390/cancers12030683] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, much research has been focused on the field of adoptive cell therapies (ACT) that use native or genetically modified T cells as therapeutic tools. Immunotherapy with T cells expressing chimeric antigen receptors (CARs) demonstrated great success in the treatment of haematologic malignancies, whereas adoptive transfer of autologous tumour infiltrating lymphocytes (TILs) proved to be highly effective in metastatic melanoma. These encouraging results initiated many studies where ACT was tested as a treatment for various solid tumours. In this review, we provide an overview of the challenges of T cell-based immunotherapies of solid tumours. We describe alternative approaches for choosing the most efficient T cells for cancer treatment in terms of their tumour-specificity and phenotype. Finally, we present strategies for improvement of anti-tumour potential of T cells, including combination therapies.
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115
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Hansen UK, Ramskov S, Bjerregaard AM, Borch A, Andersen R, Draghi A, Donia M, Bentzen AK, Marquard AM, Szallasi Z, Eklund AC, Svane IM, Hadrup SR. Tumor-Infiltrating T Cells From Clear Cell Renal Cell Carcinoma Patients Recognize Neoepitopes Derived From Point and Frameshift Mutations. Front Immunol 2020; 11:373. [PMID: 32226429 PMCID: PMC7080703 DOI: 10.3389/fimmu.2020.00373] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Mutation-derived neoantigens are important targets for T cell-mediated reactivity toward tumors and, due to their unique tumor expression, an attractive target for immunotherapy. Neoepitope-specific T cells have been detected across a number of solid cancers with high mutational burden tumors, but neoepitopes have been mostly selected from single nucleotide variations (SNVs), and little focus has been given to neoepitopes derived from in-frame and frameshift indels, which might be equally important and potentially highly immunogenic. Clear cell renal cell carcinomas (ccRCCs) are medium-range mutational burden tumors with a high pan-cancer proportion of frameshift mutations. In this study, the mutational landscape of tumors from six RCC patients was analyzed by whole-exome sequencing (WES) of DNA from tumor fragments (TFs), autologous tumor cell lines (TCLs), and tumor-infiltrating lymphocytes (TILs, germline reference). Neopeptides were predicted using MuPeXI, and patient-specific peptide–MHC (pMHC) libraries were created for all neopeptides with a rank score < 2 for binding to the patient's HLAs. T cell recognition toward neoepitopes in TILs was evaluated using the high-throughput technology of DNA barcode-labeled pMHC multimers. The patient-specific libraries consisted of, on average, 258 putative neopeptides (range, 103–397, n = 6). In four patients, WES was performed on two different sources (TF and TCL), whereas in two patients, WES was performed only on TF. Most of the peptides were predicted from both sources. However, a fraction was predicted from one source only. Among the total predicted neopeptides, 16% were derived from frameshift indels. T cell recognition of 52 neoepitopes was detected across all patients (range, 4–18, n = 6) and spanning two to five HLA restrictions per patient. On average, 21% of the recognized neoepitopes were derived from frameshift indels (range, 0–43%, n = 6). Thus, frameshift indels are equally represented in the pool of immunogenic neoepitopes as SNV-derived neoepitopes. This suggests the importance of a broad neopeptide prediction strategy covering multiple sources of tumor material, and including different genetic alterations. This study, for the first time, describes the T cell recognition of frameshift-derived neoepitopes in RCC and determines their immunogenic profile.
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Affiliation(s)
- Ulla Kring Hansen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sofie Ramskov
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Annie Borch
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Rikke Andersen
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Copenhagen, Denmark
| | - Arianna Draghi
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marco Donia
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Copenhagen, Denmark
| | - Amalie Kai Bentzen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Aron Charles Eklund
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Clinical Microbiomics A/S, Copenhagen, Denmark
| | - Inge Marie Svane
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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116
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Yarmarkovich M, Farrel A, Sison A, di Marco M, Raman P, Parris JL, Monos D, Lee H, Stevanovic S, Maris JM. Immunogenicity and Immune Silence in Human Cancer. Front Immunol 2020; 11:69. [PMID: 32256484 PMCID: PMC7092187 DOI: 10.3389/fimmu.2020.00069] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Despite recent advances in cancer immunotherapy, the process of immunoediting early in tumorigenesis remains obscure. Here, we employ a mathematical model that utilizes the Cancer Genome Atlas (TCGA) data to elucidate the contribution of individual mutations and HLA alleles to the immunoediting process. We find that common cancer mutations including BRAF-V600E and KRAS-G12D are predicted to bind none of the common HLA alleles, and are thus “immunogenically silent” in the human population. We identify regions of proteins that are not presented by HLA at a population scale, coinciding with frequently mutated hotspots in cancer, and other protein regions broadly presented across the population in which few mutations occur. We also find that 9/29 common HLA alleles contribute disproportionately to the immunoediting of early oncogenic mutations. These data provide insights into immune evasion of common driver mutations and a molecular basis for the association of particular HLA genotypes with cancer susceptibility.
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Affiliation(s)
- Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Artemio Sison
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Moreno di Marco
- Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Pichai Raman
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,The Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Joshua L Parris
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Dimitrios Monos
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States.,Department of Pathology and Lab Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hongzhe Lee
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | | | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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117
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Picard E, Verschoor CP, Ma GW, Pawelec G. Relationships Between Immune Landscapes, Genetic Subtypes and Responses to Immunotherapy in Colorectal Cancer. Front Immunol 2020; 11:369. [PMID: 32210966 PMCID: PMC7068608 DOI: 10.3389/fimmu.2020.00369] [Citation(s) in RCA: 251] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is highly heterogeneous at the genetic and molecular level, which has major repercussions on the efficacy of immunotherapy. A small subset of CRCs exhibit microsatellite instability (MSI), a molecular indicator of defective DNA mismatch repair (MMR), but the majority are microsatellite-stable (MSS). The high tumor mutational burden (TMB) and neoantigen load in MSI tumors favors the infiltration of immune effector cells, and antitumor immune responses within these tumors are strong relative to their MSS counterparts. MSI has emerged as a major predictive marker for the efficacy of immune checkpoint blockade over the last few years and nivolumab or pembrolizumab targeting PD-1 has been approved for patients with MSI refractory or metastatic CRC. However, some MSS tumors show DNA polymerase epsilon (POLE) mutations that also confer a very high TMB and may also be heavily infiltrated by immune cells making them amenable to respond to immune checkpoint inhibitors (ICI). In this review we discuss the role of the different immune landscapes in CRC and their relationships with defined CRC genetic subtypes. We discuss potential reasons why immune checkpoint blockade has met with limited success for the majority of CRC patients, despite the finding that immune cell infiltration of primary non-metastatic tumors is a strong predictive, and prognostic factor for relapse and survival. We then consider in which ways CRC cells develop mechanisms to resist ICI. Finally, we address the latest advances in CRC vaccination and how a personalized neoantigen vaccine strategy might overcome the resistance of MSI and MSS tumors in patients for whom immune checkpoint blockade is not a treatment option.
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Affiliation(s)
- Emilie Picard
- Health Sciences North Research Institute, Sudbury, ON, Canada
| | | | - Grace W Ma
- Department of Surgery, Health Sciences North, Sudbury, ON, Canada
| | - Graham Pawelec
- Health Sciences North Research Institute, Sudbury, ON, Canada.,Department of Immunology, University of Tübingen, Tübingen, Germany
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118
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Accolla RS, Buonaguro L, Melief C, Rammensee HG, Bassani-Sternberg M. Editorial: Novel Strategies for Anti-Tumor Vaccines. Front Immunol 2020; 10:3117. [PMID: 32010150 PMCID: PMC6979277 DOI: 10.3389/fimmu.2019.03117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Roberto S Accolla
- Department of Medicine and Surgery, School of Medicine, University of Insubria, Varese, Italy
| | - Luigi Buonaguro
- Cancer Immunoregulation Unit, Istituto Nazionale Tumori, IRCCS, "Fond G. Pascale", Naples, Italy
| | - Cornelis Melief
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands.,ISA Pharmaceuticals, Leiden, Netherlands
| | - Hans-George Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
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119
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Crowley SJ, Bruck PT, Bhuiyan MA, Mitchell-Gears A, Walsh MJ, Zhangxu K, Ali LR, Jeong HJ, Ingram JR, Knipe DM, Ploegh HL, Dougan M, Dougan SK. Neoleukin-2 enhances anti-tumour immunity downstream of peptide vaccination targeted by an anti-MHC class II VHH. Open Biol 2020; 10:190235. [PMID: 32019478 PMCID: PMC7058936 DOI: 10.1098/rsob.190235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer-specific mutations can lead to peptides of unique sequence presented on MHC class I to CD8 T cells. These neoantigens can be potent tumour-rejection antigens, appear to be the driving force behind responsiveness to anti-CTLA-4 and anti-PD1/L1-based therapies and have been used to develop personalized vaccines. The platform for delivering neoantigen-based vaccines has varied, and further optimization of both platform and adjuvant will be necessary to achieve scalable vaccine products that are therapeutically effective at a reasonable cost. Here, we developed a platform for testing potential CD8 T cell tumour vaccine candidates. We used a high-affinity alpaca-derived VHH against MHC class II to deliver peptides to professional antigen-presenting cells. We show in vitro and in vivo that peptides derived from the model antigen ovalbumin are better able to activate naive ovalbumin-specific CD8 T cells when conjugated to an MHC class II-specific VHH when compared with an irrelevant control VHH. We then used the VHH-peptide platform to evaluate a panel of candidate neoantigens in vivo in a mouse model of pancreatic cancer. None of the candidate neoantigens tested led to protection from tumour challenge; however, we were able to show vaccine-induced CD8 T cell responses to a melanoma self-antigen that was augmented by combination therapy with the synthetic cytokine mimetic Neo2/15.
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Affiliation(s)
- Stephanie J. Crowley
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick T. Bruck
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Md Aladdin Bhuiyan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Amelia Mitchell-Gears
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- University of Leeds, Leeds, West Yorkshire, UK
| | - Michael J. Walsh
- Program in Virology and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Kevin Zhangxu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lestat R. Ali
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hee-Jin Jeong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological and Chemical Engineering, Hongik University, Mapo-gu, Seoul, Korea
| | - Jessica R. Ingram
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David M. Knipe
- Program in Virology and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Hidde L. Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Michael Dougan
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie K. Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
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120
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Abstract
Chromosomal rearrangements are a defining molecular feature of mesothelioma that are not readily detected by standard DNA sequencing approaches but could be detected by whole genome sequencing methods such as mate-pair sequencing. These chromosomal rearrangements result in novel, unique gene junctions that can be expressed and potentially result in the presentation of several neoantigens. These predicted neoantigens can be presented by tumors on major histocompatibility complex (MHC) proteins and are correlated with clonal expansion of tumor infiltrating T cells. T cells responsive to these neoantigens have been identified in the circulation of a patient. The predictive values of next generation sequencing-based tumor mutation burden measurements may be significantly enhanced by the addition of techniques such as mate-pair sequencing that can detect chromosomal rearrangements. Furthermore, rearrangement associated neo-antigens may also represent valuable targets for future anti-tumor vaccine strategies. Finally, chromosomal rearrangements are now recognized as a mutation signature in cancer and these events are likely to be important in the oncogenesis and immune recognition of not only in mesothelioma but multiple malignancies including non-small cell lung cancer.
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Affiliation(s)
- Aaron Scott Mansfield
- Division of Medical Oncology, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Tobias Peikert
- Division of Pulmonary and Critical Care Medicine, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - George Vasmatzis
- Biomarker Discovery Group, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
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121
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Wang Y, Zhang H, Jiao B, Nie J, Li X, Wang W, Wang H. The Roles of Alternative Splicing in Tumor-immune Cell Interactions. Anticancer Agents Med Chem 2020; 20:729-740. [PMID: 32560607 PMCID: PMC8388066 DOI: 10.2174/1568009620666200619123725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022]
Abstract
Alternative splicing (AS) plays a significant role in the hallmarks of cancer and can provide neoantigens for immunotherapy. Here, we summarize recent advances in immune system associated tumor specific-antigens (TSAs) produced by AS. We further discuss the regulating mechanisms involved in AS-mediated innate and adaptive immune responses and the anti-tumoral and protumoral roles in different types of cancer. For example, ULBP1_RI, MLL5Δ21spe, NKp44-1Δ5, MHC-IΔ7, CD200SΔ1, 2, PVR α/β/γ/δ and IL-33 variants 1/2/3 act as regulators in solid tumors and IPAK4-L and, FOXP1ΔN100 exhibit functions in hematological cancers.
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Affiliation(s)
| | - Honglei Zhang
- Address correspondence to these authors at Kunming Institute of Zoology, Chinese Academy of Sciences; 32 Jiaochang E. Road, Kunming, Yunnan, China; Tel: +86-871-68191706; E-mail: ; and Department of Breast Cancer, Third Affiliated Hospital, Kunming Medical University, 519 Kunzhou Road, Kunming, Yunnan, China; Tel: +86-13608815577; E-mail:
| | - Baowei Jiao
- Address correspondence to these authors at Kunming Institute of Zoology, Chinese Academy of Sciences; 32 Jiaochang E. Road, Kunming, Yunnan, China; Tel: +86-871-68191706; E-mail: ; and Department of Breast Cancer, Third Affiliated Hospital, Kunming Medical University, 519 Kunzhou Road, Kunming, Yunnan, China; Tel: +86-13608815577; E-mail:
| | - Jianyun Nie
- Address correspondence to these authors at Kunming Institute of Zoology, Chinese Academy of Sciences; 32 Jiaochang E. Road, Kunming, Yunnan, China; Tel: +86-871-68191706; E-mail: ; and Department of Breast Cancer, Third Affiliated Hospital, Kunming Medical University, 519 Kunzhou Road, Kunming, Yunnan, China; Tel: +86-13608815577; E-mail:
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122
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Abstract
Neoantigens derive from non-synonymous somatic mutations in malignant cells. Recognition of neoantigens presented via human leukocyte antigen (HLA) molecules on the tumor cell surface by T cells holds promise to enable highly specific and effective anti-cancer immune responses and thus neoantigens provide an exceptionally attractive target for immunotherapy. While genome sequencing approaches already enable the reliable identification of somatic mutations in tumor samples, the identification of mutation-derived, naturally HLA-presented neoepitopes as targets for immunotherapy remains challenging, particularly in low mutational burden cancer entities, including hematological malignancies. Several approaches have been utilized to identify neoepitopes from primary tumor samples. Besides whole genome sequencing with subsequent in silico prediction of potential mutation-derived HLA ligands, mass spectrometry (MS) allows for the only unbiased identification of naturally presented mutation-derived HLA ligands. The feasibility of characterizing and targeting these novel antigens has recently been demonstrated in acute myeloid leukemia (AML). Several immunogenic, HLA-presented peptides derived from mutated Nucleophosmin 1 (NPM1) were identified, allowing for the generation of T-cell receptor-transduced NPM1mut-specific T cells with anti-leukemic activity in a xenograft mouse model. Neoantigen-specific T-cell responses have also been identified for peptides derived from mutated isocitrate dehydrogenase (IDHmut), and specific T-cell responses could be induced by IDHmut peptide vaccination. In this review, we give a comprehensive overview on known neoantigens in hematological malignancies, present possible prediction and discovery tools and discuss their role as targets for immunotherapy approaches.
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Affiliation(s)
- Malte Roerden
- Department of Hematology, Oncology, Rheumatology and Clinical Immunology, University Hospital Tübingen, Tübingen, Germany
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany
| | - Juliane S. Walz
- Department of Hematology, Oncology, Rheumatology and Clinical Immunology, University Hospital Tübingen, Tübingen, Germany
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany
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123
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Cannon MJ, Block MS, Morehead LC, Knutson KL. The evolving clinical landscape for dendritic cell vaccines and cancer immunotherapy. Immunotherapy 2019; 11:75-79. [PMID: 30730268 DOI: 10.2217/imt-2018-0129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Martin J Cannon
- Department of Microbiology & Immunology, University of Arkansas for Medical Sciences, 4301 West Markham, Little Rock, AR 72205, USA
| | - Matthew S Block
- Department of Oncology, & Department of Immunology, Mayo Clinic, 200 First St, SW Rochester, MN 55905, USA
| | - Lauren C Morehead
- Department of Microbiology & Immunology, University of Arkansas for Medical Sciences, 4301 West Markham, Little Rock, AR 72205, USA
| | - Keith L Knutson
- Department of Immunology, Mayo Clinic Florida, 4500 San Pablo Road S, Jacksonville, FL 32224, USA
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124
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Oh CY, Klatt MG, Bourne C, Dao T, Dacek MM, Brea EJ, Mun SS, Chang AY, Korontsvit T, Scheinberg DA. ALK and RET Inhibitors Promote HLA Class I Antigen Presentation and Unmask New Antigens within the Tumor Immunopeptidome. Cancer Immunol Res 2019; 7:1984-1997. [PMID: 31540894 PMCID: PMC6891198 DOI: 10.1158/2326-6066.cir-19-0056] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/18/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022]
Abstract
T-cell immunotherapies are often thwarted by the limited presentation of tumor-specific antigens abetted by the downregulation of human leukocyte antigen (HLA). We showed that drugs inhibiting ALK and RET produced dose-related increases in cell-surface HLA in tumor cells bearing these mutated kinases in vitro and in vivo, as well as elevated transcript and protein expression of HLA and other antigen-processing machinery. Subsequent analysis of HLA-presented peptides after ALK and RET inhibitor treatment identified large changes in the immunopeptidome with the appearance of hundreds of new antigens, including T-cell epitopes associated with impaired peptide processing (TEIPP) peptides. ALK inhibition additionally decreased PD-L1 levels by 75%. Therefore, these oncogenes may enhance cancer formation by allowing tumors to evade the immune system by downregulating HLA expression. Altogether, RET and ALK inhibitors could enhance T-cell-based immunotherapies by upregulating HLA, decreasing checkpoint blockade ligands, and revealing new, immunogenic, cancer-associated antigens.
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Affiliation(s)
- Claire Y Oh
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medicine, New York, New York
| | - Martin G Klatt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher Bourne
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medicine, New York, New York
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Megan M Dacek
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medicine, New York, New York
| | - Elliott J Brea
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medicine, New York, New York
| | - Sung Soo Mun
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aaron Y Chang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medicine, New York, New York
| | - Tatyana Korontsvit
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David A Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Weill Cornell Medicine, New York, New York
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125
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Affiliation(s)
- Ariana Nicole Renrick
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN, USA.,Department of Microbiology, Immunology & Physiology, School of Medicine, Meharry Medical College, Nashville, TN, USA.,School of Graduate Studies & Research, Meharry Medical College, Nashville, TN, USA
| | - Zerick Terrell Dunbar
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN, USA.,Department of Microbiology, Immunology & Physiology, School of Medicine, Meharry Medical College, Nashville, TN, USA.,School of Graduate Studies & Research, Meharry Medical College, Nashville, TN, USA
| | - Anil Shanker
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN, USA.,School of Graduate Studies & Research, Meharry Medical College, Nashville, TN, USA.,Host-Tumor Interactions Research Program, Vanderbilt-Ingram Comprehensive Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.,Vanderbilt Institute for Infection, Immunology & Inflammation, Vanderbilt University School of Medicine, Nashville, TN, USA
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126
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Mauriello A, Zeuli R, Cavalluzzo B, Petrizzo A, Tornesello ML, Buonaguro FM, Ceccarelli M, Tagliamonte M, Buonaguro L. High Somatic Mutation and Neoantigen Burden Do Not Correlate with Decreased Progression-Free Survival in HCC Patients not Undergoing Immunotherapy. Cancers (Basel) 2019; 11:cancers11121824. [PMID: 31756926 PMCID: PMC6966682 DOI: 10.3390/cancers11121824] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 12/17/2022] Open
Abstract
Cancer genome instability leads to accumulation of mutations which may result into tumor-specific mutated “neoantigens”, not be affected by central T-cell tolerance. Such neoantigens are considered the optimal target for the patient’s anti-tumor T cell immunity as well as for personalized cancer immunotherapy strategies. However, only a minor fraction of predicted neoantigens are relevant to the clinical outcome. In the present study, a prediction algorithm was applied using datasets of RNA sequencing from all 377 Hepatocellular carcinoma (HCC) patients available at The Cancer Genome Atlas (TCGA), to predict neoantigens to be presented by each patient’s autologous HLA molecules. Correlation with patients’ survival was performed on the 115 samples for whom the exact date of death was known. A total of 30 samples were used for the training set, and 85 samples were used for the validation sets. Neither the somatic mutations nor the number nor the quality of the predicted neoantigens correlate as single parameter with survival of HCC patients who do not undergo immunotherapy treatment. Furthermore, the preferential presentation of such neoantigens in the context of one of the major histocompatibility complex MHC class I molecules does not have an impact on the survival. On the contrary, the expression of Granzyme A (GZMA) is significantly correlated with survival and, in the context of high GZMA, a direct correlation between number and quality of neoantigens with survival is observed. This is in striking contrast to results described in cancer patients undergoing immunotherapy, in which a strong correlation between Tumor Mutational Burden (TMB), number of predicted neoantigens and survival has been reported.
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Affiliation(s)
- Angela Mauriello
- Laboratory of Cancer Immunoregulation, Istituto Nazionale per lo Studio e la Cura dei Tumori IRCCS, “Fondazione Pascale”, 80131 Naples, Italy; (A.M.); (B.C.); (A.P.)
| | - Roberta Zeuli
- Science and Technology Dept, University del Sannio, 82100 Benevento, Italy; (R.Z.); (M.C.)
- BIOGEM S.c.a.r.l., 83031 Ariano Iprino, Italy
| | - Beatrice Cavalluzzo
- Laboratory of Cancer Immunoregulation, Istituto Nazionale per lo Studio e la Cura dei Tumori IRCCS, “Fondazione Pascale”, 80131 Naples, Italy; (A.M.); (B.C.); (A.P.)
| | - Annacarmen Petrizzo
- Laboratory of Cancer Immunoregulation, Istituto Nazionale per lo Studio e la Cura dei Tumori IRCCS, “Fondazione Pascale”, 80131 Naples, Italy; (A.M.); (B.C.); (A.P.)
| | - Maria Lina Tornesello
- Laboratory of Molecular Biology and Viral Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, “Fondazione Pascale”-IRCCS, 80131 Naples, Italy; (M.L.T.); (F.M.B.)
| | - Franco M. Buonaguro
- Laboratory of Molecular Biology and Viral Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, “Fondazione Pascale”-IRCCS, 80131 Naples, Italy; (M.L.T.); (F.M.B.)
| | - Michele Ceccarelli
- Science and Technology Dept, University del Sannio, 82100 Benevento, Italy; (R.Z.); (M.C.)
- BIOGEM S.c.a.r.l., 83031 Ariano Iprino, Italy
| | - Maria Tagliamonte
- Laboratory of Cancer Immunoregulation, Istituto Nazionale per lo Studio e la Cura dei Tumori IRCCS, “Fondazione Pascale”, 80131 Naples, Italy; (A.M.); (B.C.); (A.P.)
- Correspondence: (M.T.); (L.B.); Tel.: +39-081-5903-624 (M.T.); +39-081-5903-296 (L.B.); Fax: +39-081-5451-276 (L.B.)
| | - Luigi Buonaguro
- Laboratory of Cancer Immunoregulation, Istituto Nazionale per lo Studio e la Cura dei Tumori IRCCS, “Fondazione Pascale”, 80131 Naples, Italy; (A.M.); (B.C.); (A.P.)
- Correspondence: (M.T.); (L.B.); Tel.: +39-081-5903-624 (M.T.); +39-081-5903-296 (L.B.); Fax: +39-081-5451-276 (L.B.)
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127
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Peng S, Zaretsky JM, Ng AHC, Chour W, Bethune MT, Choi J, Hsu A, Holman E, Ding X, Guo K, Kim J, Xu AM, Heath JE, Noh WJ, Zhou J, Su Y, Lu Y, McLaughlin J, Cheng D, Witte ON, Baltimore D, Ribas A, Heath JR. Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood. Cell Rep 2019; 28:2728-2738.e7. [PMID: 31484081 PMCID: PMC6774618 DOI: 10.1016/j.celrep.2019.07.106] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 05/04/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.
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Affiliation(s)
- Songming Peng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jesse M Zaretsky
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Alphonsus H C Ng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael T Bethune
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Alice Hsu
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Elizabeth Holman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Xiaozhe Ding
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katherine Guo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jungwoo Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Alexander M Xu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - John E Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Won Jun Noh
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jing Zhou
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Yapeng Su
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yue Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jami McLaughlin
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Owen N Witte
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Antoni Ribas
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA.
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128
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Tondini E, Arakelian T, Oosterhuis K, Camps M, van Duikeren S, Han W, Arens R, Zondag G, van Bergen J, Ossendorp F. A poly-neoantigen DNA vaccine synergizes with PD-1 blockade to induce T cell-mediated tumor control. Oncoimmunology 2019; 8:1652539. [PMID: 31646082 PMCID: PMC6791440 DOI: 10.1080/2162402x.2019.1652539] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/23/2019] [Accepted: 07/31/2019] [Indexed: 12/20/2022] Open
Abstract
The combination of immune-stimulating strategies has the potency to improve immunotherapy of cancer. Vaccination against neoepitopes derived from patient tumor material can generate tumor-specific T cell immunity, which could reinforce the efficacy of checkpoint inhibitor therapies such as anti-PD-1 treatment. DNA vaccination is a versatile platform that allows the inclusion of multiple neoantigen-coding sequences in a single formulation and therefore represents an ideal platform for neoantigen vaccination. We developed an anti-tumor vaccine based on a synthetic DNA vector designed to contain multiple cancer-specific epitopes in tandem. The DNA vector encoded a fusion gene consisting of three neoepitopes derived from the mouse colorectal tumor MC38 and their natural flanking sequences as 40 amino acid stretches. In addition, we incorporated as reporter epitopes the helper and CTL epitope sequences of ovalbumin. The poly-neoantigen DNA vaccine elicited T cell responses to all three neoantigens and induced functional CD8 and CD4 T cell responses to the reporter antigen ovalbumin after intradermal injection in mice. The DNA vaccine was effective in preventing outgrowth of B16 melanoma expressing ovalbumin in a prophylactic setting. Moreover, the combination of therapeutic DNA vaccination and anti-PD-1 treatment was synergistic in controlling MC38 tumor growth whereas individual treatments did not succeed. These data demonstrate the potential of DNA vaccination to target multiple neoepitopes in a single formulation and highlight the cooperation between vaccine-based and checkpoint blockade immunotherapies for the successful eradication of established tumors.
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Affiliation(s)
- Elena Tondini
- Dept. Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Tsolere Arakelian
- Dept. Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Marcel Camps
- Dept. Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Suzanne van Duikeren
- Dept. Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Wanda Han
- Immunetune BV, Leiden, The Netherlands
| | - Ramon Arens
- Dept. Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Ferry Ossendorp
- Dept. Immunohematology and Blood transfusion, Leiden University Medical Center, Leiden, The Netherlands
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129
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Abstract
Mutation-derived neoantigens distinguish tumor from normal cells. T cells can sense the HLA-presented mutations, recognize tumor cells as non-self and destroy them. Therapeutically, immunotherapy antibodies can increase the virulence of the immune system by increasing T-cell cytotoxicity targeted toward neoantigens. Neoantigen vaccines act through antigen-presenting cells, such as dendritic cells, to activate patient-endogenous T cells that recognize vaccine-encoded mutations. Infusion of mutation-targeting T cells by adoptive cell therapy (ACT) directly increases the number and frequency of cytotoxic T cells recognizing and killing tumor cells. At the same time, publicly-funded consortia have profiled tumor genomes across many indications, identifying mutations in each tumor. For example, we find basal and HER2 positive tumors contain more mutated proteins and more TP53 mutations than luminal A/B breast tumors. HPV negative tumors have more mutated proteins than HPV positive head and neck tumors and in agreement with the hypothesis that HPV activity interferes with p53 activity, only 14% of the HPV positive mutations have TP53 mutations vs. 86% of the HPV negative tumors. Lung adenocarcinomas in smokers have over four times more mutated proteins relative to those in never smokers (median 248 vs. 61, respectively). With an eye toward immunotherapy applications, we review the spectrum of mutations in multiple indications, show variations in indication sub-types, and examine intra- and inter-indication prevalence of re-occurring mutation neoantigens that could be used for warehouse vaccines and ACT.
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130
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Atif SM, Gibbings SL, Redente EF, Camp FA, Torres RM, Kedl RM, Henson PM, Jakubzick CV. Immune Surveillance by Natural IgM Is Required for Early Neoantigen Recognition and Initiation of Adaptive Immunity. Am J Respir Cell Mol Biol 2019; 59:580-591. [PMID: 29953261 DOI: 10.1165/rcmb.2018-0159oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Early recognition of neoantigen-expressing cells is complex, involving multiple immune cell types. In this study, in vivo, we examined how antigen-presenting cell subtypes coordinate and induce an immunological response against neoantigen-expressing cells, particularly in the absence of a pathogen-associated molecular pattern, which is normally required to license antigen-presenting cells to present foreign or self-antigens as immunogens. Using two reductionist models of neoantigen-expressing cells and two cancer models, we demonstrated that natural IgM is essential for the recognition and initiation of adaptive immunity against neoantigen-expressing cells. Natural IgM antibodies form a cellular immune complex with the neoantigen-expressing cells. This immune complex licenses surveying monocytes to present neoantigens as immunogens to CD4+ T cells. CD4+ T helper cells, in turn, use CD40L to license cross-presenting CD40+ Batf3+ dendritic cells to elicit a cytotoxic T cell response against neoantigen-expressing cells. Any break along this immunological chain reaction results in the escape of neoantigen-expressing cells. This study demonstrates the surprising, essential role of natural IgM as the initiator of a sequential signaling cascade involving multiple immune cell subtypes. This sequence is required to coordinate an adaptive immune response against neoantigen-expressing cells.
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Affiliation(s)
- Shaikh M Atif
- 1 Department of Pediatrics, National Jewish Health, Denver, Colorado; and
| | - Sophie L Gibbings
- 1 Department of Pediatrics, National Jewish Health, Denver, Colorado; and
| | | | - Faye A Camp
- 2 Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado
| | - Raul M Torres
- 2 Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado
| | - Ross M Kedl
- 2 Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado
| | - Peter M Henson
- 1 Department of Pediatrics, National Jewish Health, Denver, Colorado; and.,2 Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado
| | - Claudia V Jakubzick
- 1 Department of Pediatrics, National Jewish Health, Denver, Colorado; and.,2 Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado
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131
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Otoshi T, Nagano T, Tachihara M, Nishimura Y. Possible Biomarkers for Cancer Immunotherapy. Cancers (Basel) 2019; 11:cancers11070935. [PMID: 31277279 PMCID: PMC6678720 DOI: 10.3390/cancers11070935] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/18/2019] [Accepted: 06/30/2019] [Indexed: 01/05/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) have drastically changed the clinical care of cancer. Although cancer immunotherapy has shown promise in various types of malignancies, thus far, the proportion of patients who can benefit from ICIs is relatively small. Immune-related adverse events and high cost are unavoidable problems. Therefore, biomarkers defining patients that are most likely to benefit from ICIs are urgently needed. The expression of programmed cell death-ligand 1 (PD-L1) is a logical biomarker for the prediction of response to anti-PD1/PD-L1 immunotherapies. However, its usefulness is currently debatable because of its varied definition, threshold, and spatial/temporal heterogeneity. Recently, it was reported that the tumor mutational burden, expression of neoantigens, mismatch repair status, and specific gene mutations may be markers for the success of treatment with ICIs. Moreover, it was suggested that the fecal microbiota prior to immunotherapy may play an important role in predicting the efficacy of ICIs. In this review, we focused on these potential biomarkers for cancer immunotherapy reported in recent clinical articles. Further studies are warranted to develop a predictive model using these biomarkers, with the aim of practicing precision medicine in cancer immunotherapy.
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Affiliation(s)
- Takehiro Otoshi
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Tatsuya Nagano
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
| | - Motoko Tachihara
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Yoshihiro Nishimura
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
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132
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Nakayasu ES, Qian WJ, Evans-Molina C, Mirmira RG, Eizirik DL, Metz TO. The role of proteomics in assessing beta-cell dysfunction and death in type 1 diabetes. Expert Rev Proteomics 2019; 16:569-582. [PMID: 31232620 PMCID: PMC6628911 DOI: 10.1080/14789450.2019.1634548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/18/2019] [Indexed: 12/17/2022]
Abstract
Introduction: Type 1 diabetes (T1D) is characterized by autoimmune-induced dysfunction and destruction of the pancreatic beta cells. Unfortunately, this process is poorly understood, and the current best treatment for type 1 diabetes is the administration of exogenous insulin. To better understand these mechanisms and to develop new therapies, there is an urgent need for biomarkers that can reliably predict disease stage. Areas covered: Mass spectrometry (MS)-based proteomics and complementary techniques play an important role in understanding the autoimmune response, inflammation and beta-cell death. MS is also a leading technology for the identification of biomarkers. This, and the technical difficulties and new technologies that provide opportunities to characterize small amounts of sample in great depth and to analyze large sample cohorts will be discussed in this review. Expert opinion: Understanding disease mechanisms and the discovery of disease-associated biomarkers are highly interconnected goals. Ideal biomarkers would be molecules specific to the different stages of the disease process that are released from beta cells to the bloodstream. However, such molecules are likely to be present in trace amounts in the blood due to the small number of pancreatic beta cells in the human body and the heterogeneity of the target organ and disease process.
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Affiliation(s)
- Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Raghavendra G. Mirmira
- Center for Diabetes and Metabolic Diseases, Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Decio L. Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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133
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Fennemann FL, de Vries IJM, Figdor CG, Verdoes M. Attacking Tumors From All Sides: Personalized Multiplex Vaccines to Tackle Intratumor Heterogeneity. Front Immunol 2019; 10:824. [PMID: 31040852 PMCID: PMC6476980 DOI: 10.3389/fimmu.2019.00824] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/28/2019] [Indexed: 12/23/2022] Open
Abstract
Tumor vaccines are an important asset in the field of cancer immunotherapy. Whether prophylactic or therapeutic, these vaccines aim to enhance the T cell-mediated anti-tumor immune response that is orchestrated by dendritic cells. Although promising preclinical and early-stage clinical results have been obtained, large-scale clinical implementation of cancer vaccination is stagnating due to poor clinical response. The challenges of clinical efficacy of tumor vaccines can be mainly attributed to tumor induced immunosuppression and poor immunogenicity of the chosen tumor antigens. Recently, intratumor heterogeneity and the relation with tumor-specific neoantigen clonality were put in the equation.In this perspective we provide an overview of recent studies showing how personalized tumor vaccines containing multiple neoantigens can broaden and enhance the anti-tumor immune response. Furthermore, we summarize advances in the understanding of the intratumor mutational landscape containing different tumor cell subclones and the temporal and spatial diversity of neoantigen presentation and burden, and the relation between these factors with respect to tumor immunogenicity. Together, the presented knowledge calls for the investment in the characterization of neoantigens in the context of intratumor heterogeneity to improve clinical efficacy of personalized tumor vaccines.
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Affiliation(s)
- Felix L Fennemann
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - I Jolanda M de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Medical Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Division of Immunotherapy, Oncode Institute, Radboud University Medical Center, Nijmegen, Netherlands.,Institute for Chemical Immunology, Nijmegen, Netherlands
| | - Martijn Verdoes
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Institute for Chemical Immunology, Nijmegen, Netherlands
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134
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Abstract
The recent successful use of the immune checkpoint inhibitors (CPIs) anti-programmed death receptor-1 (PD-1)/PD-1 ligand 1 in clinical trials indicates their crucial role in obtaining an effective cancer immune therapy. These CPIs have been identified to have an effective therapeutic response, particularly in tumors with high tumor mutation burden. Targeting private somatic mutations encoding immunogenic neoantigens (neo-Ags) has been developed as an autologous gene therapy. T-cell receptor-engineered T cells targeting neo-Ags are a novel option for adoptive cell therapy used for the treatment of lung cancer. However, not all patients experience an effective response from immunotherapy. Although the resistance mechanism of CPIs has been reported, its association with other treatment methods during systemic anticancer therapy remains unclear, particularly the treatment options following the emergence of drug resistance in lung cancer. The potential biomarkers used for liquid biopsy may assist in the identification of patients who would benefit the most from immunotherapy. Attempts to identify potential biomarkers for predicting clinical response to immunotherapy are underway. With regard to liquid biopsy, the present review summarizes and discusses the lung cancer management of immunotherapy for precision medicine by reviewing recent literature and associated clinical trials.
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Affiliation(s)
- Liang-Liang Cai
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
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135
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Wu YM, Cieślik M, Lonigro RJ, Vats P, Reimers MA, Cao X, Ning Y, Wang L, Kunju LP, de Sarkar N, Heath EI, Chou J, Feng FY, Nelson PS, de Bono JS, Zou W, Montgomery B, Alva A, Robinson DR, Chinnaiyan AM. Inactivation of CDK12 Delineates a Distinct Immunogenic Class of Advanced Prostate Cancer. Cell 2019; 173:1770-1782.e14. [PMID: 29906450 DOI: 10.1016/j.cell.2018.04.034] [Citation(s) in RCA: 360] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/23/2018] [Accepted: 04/24/2018] [Indexed: 12/15/2022]
Abstract
Using integrative genomic analysis of 360 metastatic castration-resistant prostate cancer (mCRPC) samples, we identified a novel subtype of prostate cancer typified by biallelic loss of CDK12 that is mutually exclusive with tumors driven by DNA repair deficiency, ETS fusions, and SPOP mutations. CDK12 loss is enriched in mCRPC relative to clinically localized disease and characterized by focal tandem duplications (FTDs) that lead to increased gene fusions and marked differential gene expression. FTDs associated with CDK12 loss result in highly recurrent gains at loci of genes involved in the cell cycle and DNA replication. CDK12 mutant cases are baseline diploid and do not exhibit DNA mutational signatures linked to defects in homologous recombination. CDK12 mutant cases are associated with elevated neoantigen burden ensuing from fusion-induced chimeric open reading frames and increased tumor T cell infiltration/clonal expansion. CDK12 inactivation thereby defines a distinct class of mCRPC that may benefit from immune checkpoint immunotherapy.
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Affiliation(s)
- Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Melissa A Reimers
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu Ning
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lisha Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Navonil de Sarkar
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Elisabeth I Heath
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201, USA
| | - Jonathan Chou
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Felix Y Feng
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA; Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Johann S de Bono
- Cancer Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK; Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London SM2 5NG, UK
| | - Weiping Zou
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA 98109, USA; Veterans Affairs Puget Sound Health Care System, University of Washington, Seattle, WA 98109, USA
| | - Ajjai Alva
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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136
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Stenzinger A, Allen JD, Maas J, Stewart MD, Merino DM, Wempe MM, Dietel M. Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions. Genes Chromosomes Cancer 2019; 58:578-588. [PMID: 30664300 PMCID: PMC6618007 DOI: 10.1002/gcc.22733] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 01/10/2023] Open
Abstract
Characterization of tumors utilizing next‐generation sequencing methods, including assessment of the number of somatic mutations (tumor mutational burden [TMB]), is currently at the forefront of the field of personalized medicine. Recent clinical studies have associated high TMB with improved patient response rates and survival benefit from immune checkpoint inhibitors; hence, TMB is emerging as a biomarker of response for these immunotherapy agents. However, variability in current methods for TMB estimation and reporting is evident, demonstrating a need for standardization and harmonization of TMB assessment methodology across assays and centers. Two uniquely placed organizations, Friends of Cancer Research (Friends) and the Quality Assurance Initiative Pathology (QuIP), have collaborated to coordinate efforts for international multistakeholder initiatives to address this need. Friends and QuIP, who have partnered with several academic centers, pharmaceutical organizations, and diagnostic companies, have adopted complementary, multidisciplinary approaches toward the goal of proposing evidence‐based recommendations for achieving consistent TMB estimation and reporting in clinical samples across assays and centers. Many factors influence TMB assessment, including preanalytical factors, choice of assay, and methods of reporting. Preliminary analyses highlight the importance of targeted gene panel size and composition, and bioinformatic parameters for reliable TMB estimation. Herein, Friends and QuIP propose recommendations toward consistent TMB estimation and reporting methods in clinical samples across assays and centers. These recommendations should be followed to minimize variability in TMB estimation and reporting, which will ensure reliable and reproducible identification of patients who are likely to benefit from immune checkpoint inhibitors.
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Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg (on behalf of QuIP® GmbH, Berlin, Germany), Heidelberg, Germany
| | - Jeffrey D Allen
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Jörg Maas
- Management Department, QuIP® GmbH, Berlin, Germany
| | - Mark D Stewart
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Diana M Merino
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Madison M Wempe
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Manfred Dietel
- Institute of Pathology, Charité Berlin (on behalf of QuIP® GmbH, Berlin, Germany), Berlin, Germany
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137
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Zeneyedpour L, Dekker LJM, van Sten‐van`t Hoff JJM, Burgers PC, ten Hacken NHT, Luider TM. Neoantigens in Chronic Obstructive Pulmonary Disease and Lung Cancer: A Point of View. Proteomics Clin Appl 2019; 13:e1800093. [PMID: 30706659 PMCID: PMC6593722 DOI: 10.1002/prca.201800093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/21/2019] [Indexed: 12/20/2022]
Abstract
The goal of this manuscript is to explore the role of clinical proteomics for detecting mutations in chronic obstructive pulmonary disease (COPD) and lung cancer by mass spectrometry-based technology. COPD and lung cancer caused by smoke inhalation are most likely linked by challenging the immune system via partly shared pathways. Genome-wide association studies have identified several single nucleotide polymorphisms which predispose an increased susceptibility to COPD and lung cancer. In lung cancer, this leads to coding mutations in the affected tissues, development of neoantigens, and different functionality and abundance of proteins in specific pathways. If a similar reasoning can also be applied in COPD will be discussed. The technology of mass spectrometry has developed into an advanced technology for proteome research detecting mutated peptides or proteins and finding relevant molecular mechanisms that will enable predicting the response to immunotherapy in COPD and lung cancer patients.
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Affiliation(s)
| | | | | | | | - Nick H. T. ten Hacken
- Department of PulmonologyUniversity Medical Center Groningen/University of Groningen9713 GroningenNetherlands
| | - Theo M. Luider
- Department of NeurologyErasmus MCRotterdam3015 GENetherlands
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138
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Kanygina AV, Sharova EI, Sultanov RI, Schelygin YA, Doludin YV, Kostryukova ES, Generozov EV. [Targeted gene sequencing panels: applicability for neoantigen profiling of colon and rectal adenocarcinoma]. Biomed Khim 2019; 64:517-524. [PMID: 30632980 DOI: 10.18097/pbmc20186406517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cancer immunotherapy represents a promising and rapidly developing approach for the treatment of oncological diseases. Among the methods of personalized adjuvant immunotherapy, neoantigenic peptide-based drugs have demonstrated substantial efficiency. These drugs are designed to target mutant proteins arising from somatic alterations in the genome of tumor cells and thus stimulate immune response against tumor tissues. The methods of individual screening for potentially immunogenic mutations are mostly based on next-generation exome sequencing of tumor samples, which is a complex and costly procedure for clinical application. Targeted gene sequencing panels limited to a certain set of genes represent a reasonable alternative to WES. Targeted sequencing is also more efficient when there is a low amount of the sample DNA available. We have estimated the potential efficiency of targeted oncological panels in terms of somatic neoantigen profiling in colorectal cancer (colon and rectal adenocarcinoma). The clinical practice of identification of frequent somatic variants does not provide enough data for designing an efficient personalized drug when applied to low and medium mutated cancers such as colorectal cancer. Our analysis of 11 commercially available panels containing different number of genes has shown that neither the larger size of a panel nor its initial customization for colorectal cancer provides a significantly better estimation of an individual somatic mutation profile. The optimal approach is to use the general-purpose medium-sized cancer panels (2300-11200 amplicons and/or 150-600 genes). These panels allow to detect a sufficient number of immunogenic epitopes (>3) per patient for over 30-50% of patients.
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Affiliation(s)
- A V Kanygina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - E I Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - R I Sultanov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Y A Schelygin
- State Scientific Center of Coloproctology, Moscow, Russia
| | - Y V Doludin
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - E S Kostryukova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - E V Generozov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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139
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Ye L, Ma S, Robinson BW, Creaney J. Immunotherapy strategies for mesothelioma - the role of tumor specific neoantigens in a new era of precision medicine. Expert Rev Respir Med 2018; 13:181-192. [PMID: 30596292 DOI: 10.1080/17476348.2019.1563488] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Immunotherapy has long been considered a potential therapy for malignant mesothelioma and is currently being pursued as such. Some of the early phase clinical trials involving immunomodulators have demonstrated encouraging results and numerous clinical trials are underway to further investigate this treatment approach in various treatment settings and larger patient cohorts. Areas covered: This review summarizes the current and emerging clinical evidence for checkpoint blockade and other immunotherapeutic strategies in mesothelioma. The mesothelioma tumor immune microenvironment and mutational landscape are also discussed, including their impact on treatment strategies. We also provide an evaluation of the current evidence for neoantigen targeted personalized immunotherapy. Expert opinion: Immune checkpoint inhibitors work by unleashing the host immune response against probable neoantigens. Despite impressive activity in a small subset of patients and the potential for prolonged responses, most patients experience treatment failure. Neoantigen vaccines provide a potential complementary therapeutic strategy by increasing the immunogenic antigen load, which can lead to an increased tumor specific immune response. Further research is needed explore this treatment option in mesothelioma and technological advances are required to translate this concept into clinical practice.
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Affiliation(s)
- Linda Ye
- a Department of Medical Oncology , Sir Charles Gairdner Hospital , Nedlands , Australia
| | - Shaokang Ma
- b National Centre for Asbestos Related Disease , University of Western Australia , Nedlands , Australia
| | - Bruce W Robinson
- b National Centre for Asbestos Related Disease , University of Western Australia , Nedlands , Australia.,c Department of Respiratory Medicine , Sir Charles Gairdner Hospital , Nedlands , Australia
| | - Jenette Creaney
- b National Centre for Asbestos Related Disease , University of Western Australia , Nedlands , Australia.,c Department of Respiratory Medicine , Sir Charles Gairdner Hospital , Nedlands , Australia.,d Institute of Respiratory Health , University of Western Australia , Nedlands , Australia
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140
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Abstract
Malignant transformation of cells depends on accumulation of DNA damage. Over the past years we have learned that the T cell-based immune system frequently responds to the neoantigens that arise as a consequence of this DNA damage. Furthermore, recognition of neoantigens appears an important driver of the clinical activity of both T cell checkpoint blockade and adoptive T cell therapy as cancer immunotherapies. Here we review the evidence for the relevance of cancer neoantigens in tumor control and the biological properties of these antigens. We discuss recent technological advances utilized to identify neoantigens, and the T cells that recognize them, in individual patients. Finally, we discuss strategies that can be employed to exploit cancer neoantigens in clinical interventions.
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Affiliation(s)
- Ton N Schumacher
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; , .,Oncode Institute, 3521AL Utrecht, The Netherlands
| | - Wouter Scheper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; , .,Oncode Institute, 3521AL Utrecht, The Netherlands
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; ,
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141
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Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 2018; 34:211-224.e6. [PMID: 30078747 PMCID: PMC9844097 DOI: 10.1016/j.ccell.2018.07.001] [Citation(s) in RCA: 483] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/30/2018] [Accepted: 07/02/2018] [Indexed: 01/19/2023]
Abstract
Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects alternative splicing events and tumor variants by reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more alternative splicing events than normal samples. Association analysis of somatic variants with alternative splicing events confirmed known trans associations with variants in SF3B1 and U2AF1 and identified additional trans-acting variants (e.g., TADA1, PPP2R1A). Many tumors have thousands of alternative splicing events not detectable in normal samples; on average, we identified ≈930 exon-exon junctions ("neojunctions") in tumors not typically found in GTEx normals. From Clinical Proteomic Tumor Analysis Consortium data available for breast and ovarian tumor samples, we confirmed ≈1.7 neojunction- and ≈0.6 single nucleotide variant-derived peptides per tumor sample that are also predicted major histocompatibility complex-I binders ("putative neoantigens").
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Affiliation(s)
- André Kahles
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Kjong-Van Lehmann
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Nora C Toussaint
- ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Matthias Hüser
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Stefan G Stark
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Timo Sachsenberg
- University of Tübingen, Department of Computer Science, Tübingen, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Oliver Kohlbacher
- University of Tübingen, Department of Computer Science, Tübingen, Germany; Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Quantitative Biology Center, University of Tübingen, Tübingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; Institute for Translational Bioinformatics, University Medical Center, Tübingen, Germany
| | - Chris Sander
- Dana-Farber Cancer Institute, cBio Center, Department of Biostatistics and Computational Biology, Boston, MA, USA; Harvard Medical School, CompBio Collaboratory, Department of Cell Biology, Boston, USA
| | | | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; ETH Zurich, Department of Biology, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.
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142
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Abstract
Dramatic success in cancer immunotherapy has been achieved over the last decade with the introduction of checkpoint inhibitors, leading to response rates higher than with chemotherapy in certain cancer types. These responses are often restricted to cancers that have a high mutational burden and show pre-existing T-cell infiltrates. Despite extensive efforts, therapeutic vaccines have been mostly unsuccessful in the clinic. With the introduction of next generation sequencing, the identification of individual mutations is possible, enabling the production of personalized cancer vaccines. Combining immune check point inhibitors to overcome the immunosuppressive microenvironment and personalized cancer vaccines for directing the host immune system against the chosen antigens might be a promising treatment strategy.
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143
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Inamura K, Shigematsu Y, Ninomiya H, Nakashima Y, Kobayashi M, Saito H, Takahashi K, Futaya E, Okumura S, Ishikawa Y, Kanda H. CSF1R-Expressing Tumor-Associated Macrophages, Smoking and Survival in Lung Adenocarcinoma: Analyses Using Quantitative Phosphor-Integrated Dot Staining. Cancers (Basel) 2018; 10:cancers10080252. [PMID: 30065206 PMCID: PMC6115958 DOI: 10.3390/cancers10080252] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/16/2018] [Accepted: 07/27/2018] [Indexed: 12/12/2022] Open
Abstract
CSF1R-expressing tumor-associated macrophages (TAMs) induce a tumor-promoting microenvironment by regulating immunity. Evidence demonstrates that the expression and single nucleotide polymorphisms of CSF1R relate with survival and risk of lung cancer in never smokers. However, no previous studies have examined the association of CSF1R expression in TAMs with mortality or whether the prognostic association differs according to smoking status in lung adenocarcinoma. Quantitative phosphor-integrated dot staining was used to precisely assess CSF1R expression in TAMs. Using 195 consecutive cases of lung adenocarcinoma, we examined the association of CSF1R expression with mortality and whether the prognostic association differs according to smoking status. We observed high expression levels of CSF1R in TAMs in 65 of 195 (33%) cases of lung adenocarcinoma. High expression levels of CSF1R were associated with high lung cancer-specific mortality (log-rank p = 0.037; hazard ratio (HR) = 1.61, 95% confidence interval (CI) = 1.02−2.52, p = 0.043). This prognostic association differed according to smoking status (p for interaction = 0.049, between never-smoking and ever-smoking patients). The association between high expression levels of CSF1R and lung cancer-specific mortality was stronger in never-smoking patients (log-rank p = 0.0027; HR = 2.90, 95% CI = 1.41−6.11, p = 0.0041) than in ever-smoking patients (log-rank p = 0.73; HR = 1.11, 95% CI = 0.59−2.00, p = 0.73). The findings suggest that CSF1R-expressing TAMs may exert stronger tumor-promoting immunity in never-smoking patients with lung adenocarcinoma and serve as a therapeutic target in precision immunotherapies.
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Affiliation(s)
- Kentaro Inamura
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Yasuyuki Shigematsu
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Hironori Ninomiya
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Yasuhiro Nakashima
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Maki Kobayashi
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Haruyuki Saito
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc., 1 Sakura-machi, Hino, Tokyo 191-8511, Japan.
| | - Katsuhiro Takahashi
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc., 1 Sakura-machi, Hino, Tokyo 191-8511, Japan.
| | - Etsuko Futaya
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc., 1 Sakura-machi, Hino, Tokyo 191-8511, Japan.
| | - Sakae Okumura
- Department of Thoracic Surgical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Yuichi Ishikawa
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
| | - Hiroaki Kanda
- Division of Pathology, The Cancer Institute, Department of Pathology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan.
- Department of Pathology, Saitama Cancer Center, 780 Komuro, Ina, Kitaadachi-gun, Saitama 362-0806, Japan.
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Abstract
INTRODUCTION Cancer vaccines represent one of the oldest immunotherapy strategies. A variety of tumor-associated antigens have been exploited to investigate their immunogenicity as well as multiple strategies for vaccine administration. These efforts have led to the development of several clinical trials in tumors with different histological origins to test the clinical efficacy of cancer vaccines. However, suboptimal clinical results have been reported mainly due to the lack of optimized strategies to induce strong and sustained systemic tumor antigen-specific immune responses. AREAS COVERED We provide an overview of different types of cancer vaccines that have been developed and used in the context of clinical studies. Moreover, we review different preclinical and clinical strategies pursued to enhance the immunogenicity, stability, and targeting at tumor site of cancer vaccines. EXPERT OPINION Additional and appropriate preclinical studies are warranted to optimize the immunogenicity and delivery of cancer vaccines. The appropriate choice of target antigens is challenging; however, the exploitation of neoantigens generated from somatic mutations of tumor cells represents a promising approach to target highly immunogenic tumor-specific antigens. Remarkably, the investigation of the combination of cancer vaccines with immunomodulating agents able to skew the tumor microenvironment from immunosuppressive to immunostimulating will dramatically improve their clinical efficacy.
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Affiliation(s)
- Lorenzo Pilla
- a Medical Oncology Unit , San Gerardo Hospital , Monza , Italy
| | - Soldano Ferrone
- b Department of Surgery , Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - Cristina Maccalli
- c Clinical Research Center, Division of Translational Medicine , Sidra Medicine , Doha , Qatar
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Creech AL, Ting YS, Goulding SP, Sauld JF, Barthelme D, Rooney MS, Addona TA, Abelin JG. The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction. Proteomics 2018; 18:e1700259. [PMID: 29314742 PMCID: PMC6033110 DOI: 10.1002/pmic.201700259] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/12/2017] [Indexed: 12/30/2022]
Abstract
A challenge in developing personalized cancer immunotherapies is the prediction of putative cancer-specific antigens. Currently, predictive algorithms are used to infer binding of peptides to human leukocyte antigen (HLA) heterodimers to aid in the selection of putative epitope targets. One drawback of current epitope prediction algorithms is that they are trained on datasets containing biochemical HLA-peptide binding data that may not completely capture the rules associated with endogenous processing and presentation. The field of MS has made great improvements in instrumentation speed and sensitivity, chromatographic resolution, and proteogenomic database search strategies to facilitate the identification of HLA-ligands from a variety of cell types and tumor tissues. As such, these advances have enabled MS profiling of HLA-binding peptides to be a tractable, orthogonal approach to lower throughput biochemical assays for generating comprehensive datasets to train epitope prediction algorithms. In this review, we will highlight the progress made in the field of HLA-ligand profiling enabled by MS and its impact on current and future epitope prediction strategies.
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146
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Bjerregaard AM, Nielsen M, Jurtz V, Barra CM, Hadrup SR, Szallasi Z, Eklund AC. Corrigendum: An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes. Front Immunol 2018; 9:1007. [PMID: 29795801 PMCID: PMC5961322 DOI: 10.3389/fimmu.2018.01007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/23/2018] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article on p. 1566 in vol. 8, PMID: 29187854.].
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Affiliation(s)
- Anne-Mette Bjerregaard
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Vanessa Jurtz
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carolina M Barra
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Sine Reker Hadrup
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Zoltan Szallasi
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.,Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Aron Charles Eklund
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
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147
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Brown JS, Sundar R, Lopez J. Combining DNA damaging therapeutics with immunotherapy: more haste, less speed. Br J Cancer 2018; 118:312-324. [PMID: 29123260 PMCID: PMC5808021 DOI: 10.1038/bjc.2017.376] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 09/04/2017] [Accepted: 09/04/2017] [Indexed: 12/14/2022] Open
Abstract
The idea that chemotherapy can be used in combination with immunotherapy may seem somewhat counterproductive, as it can theoretically eliminate the immune cells needed for antitumour immunity. However, much preclinical work has now demonstrated that in addition to direct cytotoxic effects on cancer cells, a proportion of DNA damaging agents may actually promote immunogenic cell death, alter the inflammatory milieu of the tumour microenvironment and/or stimulate neoantigen production, thereby activating an antitumour immune response. Some notable combinations have now moved forward into the clinic, showing promise in phase I-III trials, whereas others have proven toxic, and challenging to deliver. In this review, we discuss the emerging data of how DNA damaging agents can enhance the immunogenic properties of malignant cells, focussing especially on immunogenic cell death, and the expansion of neoantigen repertoires. We discuss how best to strategically combine DNA damaging therapeutics with immunotherapy, and the challenges of successfully delivering these combination regimens to patients. With an overwhelming number of chemotherapy/immunotherapy combination trials in process, clear hypothesis-driven trials are needed to refine the choice of combinations, and determine the timing and sequencing of agents in order to stimulate antitumour immunological memory and improve maintained durable response rates, with minimal toxicity.
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Affiliation(s)
- Jessica S Brown
- Royal Marsden NHS Foundation Trust, Downs Road, London SM2 5PT, UK
| | - Raghav Sundar
- Royal Marsden NHS Foundation Trust, Downs Road, London SM2 5PT, UK
- Department of Haematology-Oncology, National University Health System, Singapore
| | - Juanita Lopez
- Royal Marsden NHS Foundation Trust, Downs Road, London SM2 5PT, UK
- The Institute of Cancer Research, London SM2 5NG, UK
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148
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Furness AJ, Quezada SA, Peggs KS. Neoantigen heterogeneity: a key driver of immune response and sensitivity to immune checkpoint blockade? Immunotherapy 2018; 8:763-6. [PMID: 27349975 DOI: 10.2217/imt-2016-0064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Andrew Js Furness
- Cancer Immunology Unit, University College London Cancer Institute, London, UK.,The Royal Marsden NHS Foundation Trust, London, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Cancer Immunology Unit, University College London Cancer Institute, London, UK
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149
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Marty R, de Prisco N, Carter H, Font-Burgada J. MHC-I genotype drives early immune selection of oncogenic mutations. Mol Cell Oncol 2018; 5:e1409863. [PMID: 29487895 PMCID: PMC5821412 DOI: 10.1080/23723556.2017.1409863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 11/24/2022]
Abstract
MHC-I exposes the intracellular contents to immune cells for surveillance of cellular health. Due to high genomic variation, individuals' immune systems differ in their ability to expose and eliminate cancer-causing mutations. These personalized immune blind spots create specific oncogenic mutation predispositions within patients and influence their prevalence across populations.
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Affiliation(s)
- Rachel Marty
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Nicola de Prisco
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.,Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Cancer Cell Map Initiative (CCMI), University of California San Diego, La Jolla, CA, USA
| | - Joan Font-Burgada
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, USA
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150
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Tan Q, Ku W, Zhang C, Heyilimu P, Tian Y, Ke Y, Lu Z. Mutation analysis of the EBV-lymphoblastoid cell line cautions their use as antigen-presenting cells. Immunol Cell Biol 2018; 96:204-211. [PMID: 29363169 DOI: 10.1111/imcb.1030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 12/13/2022]
Abstract
Lymphoblastoid cell lines (LCLs) have been widely used as professional antigen-presenting cells (APCs). However, neoantigen-loaded LCLs could induce nonspecific T-cell response, which could be due to expression of both Epstein-Barr virus (EBV) antigens and nonsynonymous mutations arising in LCLs. Since the number of passages could influence mutational characteristics of LCLs, and moreover extensive proliferation of LCLs in vitro is necessary to activate T cells for immunotherapy, we comprehensively profiled mutational characteristics by comparing eight sets of B cells and matched high-passage LCLs using whole-exome sequencing in order to assess the effect of nonsynonymous mutations arising in LCLs on nonspecific T-cell response. We found 315 nongermline mutations (approximately 40mut/subject) randomly distributed across all chromosomes including 18 mutations in immunoglobulin V and J genes in eight LCLs, of which 137 candidate neoantigens (approximately 17mut/subject) were identified. The underlying mutational processes linked to EBV-transformed LCLs could be attributed to activation induced cytidine deaminase gene expression which contributes to cytosine mutation clusters in LCLs through cytosine deamination. Pathways significantly enriched by nonsilent mutations of each LCL were totally different among all LCLs. In conclusion, high-passage LCLs may not be suitable to serve as APCs due to random nonsilent mutations, particularly for presentation of neoantigens of low immunogenicity, although further experimental proofs are needed.
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Affiliation(s)
- Qin Tan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wenjing Ku
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Chaoting Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Palashati Heyilimu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuan Tian
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zheming Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
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