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Cai X, Li JJ, Liu T, Brian O, Li J. Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design. Brief Funct Genomics 2021; 20:289-303. [PMID: 34089044 PMCID: PMC8194884 DOI: 10.1093/bfgp/elab027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 12/15/2022] Open
Abstract
Messenger RNA (mRNA) vaccines have recently emerged as a new type of vaccine technology, showing strong potential to combat the COVID-19 pandemic. In addition to SARS-CoV-2 which caused the pandemic, mRNA vaccines have been developed and tested to prevent infectious diseases caused by other viruses such as Zika virus, the dengue virus, the respiratory syncytial virus, influenza H7N9 and Flavivirus. Interestingly, mRNA vaccines may also be useful for preventing non-infectious diseases such as diabetes and cancer. This review summarises the current progresses of mRNA vaccines designed for a range of diseases including COVID-19. As epitope study is a primary component in the in silico design of mRNA vaccines, we also survey on advanced bioinformatics and machine learning algorithms which have been used for epitope prediction, and review on user-friendly software tools available for this purpose. Finally, we discuss some of the unanswered concerns about mRNA vaccines, such as unknown long-term side effects, and present with our perspectives on future developments in this exciting area.
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Affiliation(s)
- Xinhui Cai
- Data Science Institute, Faculty of Engineering & IT, University of Technology Sydney, 15 Broadway, Ultimo, 2007, New South Wales, Australia
| | - Jiao Jiao Li
- School of Biomedical Engineering, Faculty of Engineering and IT, University of Technology Sydney, 15 Broadway, Ultimo, 2007, New South Wales, Australia
| | - Tao Liu
- School of Life Sciences, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, 2007, New South Wales, Australia
| | - Oliver Brian
- Children’s Cancer Institute Australia, University of New South Wales Sydney, Children’s Cancer Institute Australia, Randwick, Sydney, 2031, New South Wales, Australia
| | - Jinyan Li
- Data Science Institute, Faculty of Engineering & IT, University of Technology Sydney, 15 Broadway, Ultimo, 2007, New South Wales, Australia
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2
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De Keersmaecker B, Claerhout S, Carrasco J, Bar I, Corthals J, Wilgenhof S, Neyns B, Thielemans K. TriMix and tumor antigen mRNA electroporated dendritic cell vaccination plus ipilimumab: link between T-cell activation and clinical responses in advanced melanoma. J Immunother Cancer 2021; 8:jitc-2019-000329. [PMID: 32114500 PMCID: PMC7057443 DOI: 10.1136/jitc-2019-000329] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2020] [Indexed: 12/31/2022] Open
Abstract
Background We previously reported that dendritic cell-based mRNA vaccination plus ipilimumab (TriMixDC-MEL IPI) results in an encouraging rate of tumor responses in patients with pretreated advanced melanoma. Here, we report the TriMixDC-MEL IPI-induced T-cell responses detected in the peripheral blood. Methods Monocyte-derived dendritic cells electroporated with mRNA encoding CD70, CD40 ligand, and constitutively active TLR4 (TriMix) as well as the tumor-associated antigens tyrosinase, gp100, MAGE-A3, or MAGE-C2 were administered together with IPI for four cycles. For 18/39 patients, an additional vaccine was administered before the first IPI administration. We evaluated tumor-associated antigen specific T-cell responses in previously collected peripheral blood mononuclear cells, available from 15 patients. Results Vaccine-induced enzyme-linked immunospot assay responses detected after in vitro T-cell stimulation were shown in 12/15 patients. Immune responses detected in patients with a complete or partial response were significantly stronger and broader, and exhibited a higher degree of multifunctionality compared with responses in patients with stable or progressive disease. CD8+ T-cell responses from patients with an ongoing clinical response, either elicited by TriMixDC-MEL IPI or on subsequent pembrolizumab treatment, exhibited the highest degree of multifunctionality. Conclusions TriMixDC-MEL IPI treatment results in robust CD8+ T-cell responses in a meaningful portion of stage III or IV melanoma patients, and obviously in patients with a clinical response. The levels of polyfunctional and multiantigen T-cell responses measured in patients with a complete response, particularly in patients evidently cured after 5+ years of follow-up, may provide a benchmark for the level of immune stimulation needed to achieve a durable clinical remission. Trial registration number NCT01302496.
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Affiliation(s)
| | | | - Javier Carrasco
- Laboratory of Translational Oncology, Institute of Pathology and Genetics, Grand Hopital de Charleroi, Charleroi, Hainaut, Belgium
| | - Isabelle Bar
- Laboratory of Translational Oncology, Institute of Pathology and Genetics, Grand Hopital de Charleroi, Charleroi, Hainaut, Belgium
| | - Jurgen Corthals
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussel, Belgium
| | - Sofie Wilgenhof
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Bart Neyns
- Department of Medical Oncology, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussel, Belgium
| | - Kris Thielemans
- Laboratory of Molecular and Cellular Therapy, Department of Biomedical Sciences, Vrije Universiteit Brussel, Brussel, Belgium
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3
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Mathieu M, Odagiu L, Gaudot L, Daudelin JF, Melichar HJ, Lapointe R, Labrecque N. Inflammation enhances the vaccination potential of CD40-activated B cells in mice. Eur J Immunol 2016; 47:269-279. [PMID: 27873323 DOI: 10.1002/eji.201646568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 10/28/2016] [Accepted: 11/17/2016] [Indexed: 12/29/2022]
Abstract
Vaccination with antigen-pulsed CD40-activated B (CD40-B) cells can efficiently lead to the in vivo differentiation of naive CD8+ T cells into fully functional effectors. In contrast to bone marrow-derived dendritic cell (BMDC) vaccination, CD40-B cell priming does not allow for memory CD8+ T-cell generation but the reason for this deficiency is unknown. Here, we show that compared to BMDCs, murine CD40-B cells induce lower expression of several genes regulated by T-cell receptor signaling, costimulation, and inflammation (signals 1-3) in mouse T cells. The reduced provision of signals 1 and 2 by CD40-B cells can be explained by a reduction in the quality and duration of the interactions with naive CD8+ T cells as compared to BMDCs. Furthermore, CD40-B cells produce less inflammatory mediators, such as IL-12 and type I interferon, and increasing inflammation by coadministration of polyriboinosinic-polyribocytidylic acid with CD40-B-cell immunization allowed for the generation of long-lived and functional CD8+ memory T cells. In conclusion, it is possible to manipulate CD40-B-cell vaccination to promote the formation of long-lived functional CD8+ memory T cells, a key step before translating the use of CD40-B cells for therapeutic vaccination.
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Affiliation(s)
- Mélissa Mathieu
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, Québec, Canada.,Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montréal, Québec, Canada
| | - Livia Odagiu
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, Québec, Canada.,Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montréal, Québec, Canada
| | - Léa Gaudot
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, Québec, Canada
| | | | - Heather J Melichar
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, Québec, Canada.,Department of Medicine, University of Montreal, Montréal, Québec, Canada
| | - Réjean Lapointe
- Department of Medicine, University of Montreal, Montréal, Québec, Canada.,Research Centre, Centre Hospitalier de l'Université de Montréal (CRCHUM), University of Montreal and Institut du Cancer de Montréal, Montréal, Québec, Canada
| | - Nathalie Labrecque
- Maisonneuve-Rosemont Hospital Research Centre, Montréal, Québec, Canada.,Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montréal, Québec, Canada.,Department of Medicine, University of Montreal, Montréal, Québec, Canada
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4
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Effective Cytotoxic T Lymphocyte Targeting of Persistent HIV-1 during Antiretroviral Therapy Requires Priming of Naive CD8+ T Cells. mBio 2016; 7:mBio.00473-16. [PMID: 27247230 PMCID: PMC4895106 DOI: 10.1128/mbio.00473-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Curing HIV-1 infection will require elimination of persistent cellular reservoirs that harbor latent virus in the face of combination antiretroviral therapy (cART). Proposed immunotherapeutic strategies to cure HIV-1 infection include enhancing lysis of these infected cells by cytotoxic T lymphocytes (CTL). A major challenge in this strategy is overcoming viral immune escape variants that have evaded host immune control. Here we report that naive CD8+ T cells from chronic HIV-1-infected participants on long-term cART can be primed by dendritic cells (DC). These DC must be mature, produce high levels of interleukin 12p70 (IL-12p70), be responsive to CD40 ligand (CD40L), and be loaded with inactivated, autologous HIV-1. These DC-primed CD8+ T cell responders produced high levels of gamma interferon (IFN-γ) in response to a broad range of both conserved and variable regions of Gag and effectively killed CD4+ T cell targets that were either infected with the autologous latent reservoir-associated virus or loaded with autologous Gag peptides. In contrast, HIV-1-specific memory CD8+ T cells stimulated with autologous HIV-1-loaded DC produced IFN-γ in response to a narrow range of conserved and variable Gag peptides compared to the primed T cells and most notably, displayed significantly lower cytolytic function. Our findings highlight the need to selectively induce new HIV-1-specific CTL from naive precursors while avoiding activation of existing, dysfunctional memory T cells in potential curative immunotherapeutic strategies for HIV-1 infection. Current immunotherapeutic approaches aim to enhance antiviral immunity against the HIV-1 reservoir; however, it has yet to be shown whether T cells from persons on cART can recognize and eliminate virus-infected cells. We show that in persons on cART a personalized medicine approach using their dendritic cells to stimulate their naive T cells induces potent effector CTL in vitro that recognize and eradicate HIV-1-infected CD4+ T cells. Additionally, we show that the same stimulation of existing memory T cells results in cytokine secretion but limited effector function. Our study demonstrates that the naive T cell repertoire can recognize persistent HIV-1 during cART and supports immunotherapy strategies for an HIV-1 cure that targets naive T cells, rather than existing, dysfunctional, memory T cells.
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5
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Gros A, Parkhurst MR, Tran E, Pasetto A, Robbins PF, Ilyas S, Prickett TD, Gartner JJ, Crystal JS, Roberts IM, Trebska-McGowan K, Wunderlich JR, Yang JC, Rosenberg SA. Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. Nat Med 2016; 22:433-8. [PMID: 26901407 PMCID: PMC7446107 DOI: 10.1038/nm.4051] [Citation(s) in RCA: 610] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/26/2016] [Indexed: 01/10/2023]
Abstract
Detection of lymphocytes that target tumor-specific mutant neoantigens--derived from products encoded by mutated genes in the tumor--is mostly limited to tumor-resident lymphocytes, but whether these lymphocytes often occur in the circulation is unclear. We recently reported that intratumoral expression of the programmed cell death 1 (PD-1) receptor can guide the identification of the patient-specific repertoire of tumor-reactive CD8(+) lymphocytes that reside in the tumor. In view of these findings, we investigated whether PD-1 expression on peripheral blood lymphocytes could be used as a biomarker to detect T cells that target neoantigens. By using a high-throughput personalized screening approach, we identified neoantigen-specific lymphocytes in the peripheral blood of three of four melanoma patients. Despite their low frequency in the circulation, we found that CD8(+)PD-1(+), but not CD8(+)PD-1(-), cell populations had lymphocytes that targeted 3, 3 and 1 unique, patient-specific neoantigens, respectively. We show that neoantigen-specific T cells and gene-engineered lymphocytes expressing neoantigen-specific T cell receptors (TCRs) isolated from peripheral blood recognized autologous tumors. Notably, the tumor-antigen specificities and TCR repertoires of the circulating and tumor-infiltrating CD8(+)PD-1(+) cells appeared similar, implying that the circulating CD8(+)PD-1(+) lymphocytes could provide a window into the tumor-resident antitumor lymphocytes. Thus, expression of PD-1 identifies a diverse and patient-specific antitumor T cell response in peripheral blood, providing a novel noninvasive strategy to develop personalized therapies using neoantigen-reactive lymphocytes or TCRs to treat cancer.
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MESH Headings
- Adult
- Aged
- Antigens, Neoplasm/blood
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- CD8-Positive T-Lymphocytes/immunology
- Cell Line, Tumor
- Female
- Humans
- Immunotherapy
- Lymphocytes/immunology
- Lymphocytes/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/pathology
- Male
- Melanoma/blood
- Melanoma/genetics
- Melanoma/immunology
- Melanoma/therapy
- Middle Aged
- Programmed Cell Death 1 Receptor/blood
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/immunology
- Prospective Studies
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
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Affiliation(s)
- Alena Gros
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Maria R Parkhurst
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Eric Tran
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Anna Pasetto
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Sadia Ilyas
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Todd D Prickett
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Jessica S Crystal
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Ilana M Roberts
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Kasia Trebska-McGowan
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - John R Wunderlich
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - James C Yang
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA
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Abstract
Dendritic cells are known to be the most potent antigen presenting cell in the immune system and are used as cellular adjuvants in therapeutic anticancer vaccines using various tumor-associated antigens or their derivatives. One way of loading antigen into the dendritic cells is by mRNA electroporation, ensuring presentation of antigen through major histocompatibility complex I and potentially activating T cells, enabling them to kill the tumor cells. Despite extensive research in the field, only one dendritic cell-based vaccine has been approved. There is therefore a great need to elucidate and understand the immunological impact of dendritic cell vaccination in order to improve clinical benefit. In this chapter, we describe a method for performing immune monitoring using peripheral blood mononuclear cells and autologous dendritic cells transfected with tumor-associated antigen-encoding mRNA.
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7
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Nielsen JS, Sedgwick CG, Shahid A, Zong Z, Brumme ZL, Yu S, Liu L, Kroeger DR, Treon SP, Connors JM, Gascoyne RD, Berry BR, Marra MA, Morin RD, Macpherson N, Nelson BH. Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8+ T Cells. Clin Cancer Res 2015; 22:2226-36. [PMID: 26631611 DOI: 10.1158/1078-0432.ccr-15-2023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE A fundamental challenge in the era of next-generation sequencing (NGS) is to design effective treatments tailored to the mutational profiles of tumors. Many newly discovered cancer mutations are difficult to target pharmacologically; however, T-cell-based therapies may provide a valuable alternative owing to the exquisite sensitivity and specificity of antigen recognition. To explore this concept, we assessed the immunogenicity of a panel of genes that are common sites of driver mutations in follicular lymphoma, an immunologically sensitive yet currently incurable disease. EXPERIMENTAL DESIGN Exon capture and NGS were used to interrogate tumor samples from 53 patients with follicular lymphoma for mutations in 10 frequently mutated genes. For 13 patients, predicted mutant peptides and proteins were evaluated for recognition by autologous peripheral blood T cells after in vitro priming. RESULTS Mutations were identified in 1-5 genes in 81% (43/53) of tumor samples. Autologous, mutation-specific CD8(+) T cells were identified in 23% (3/13) of evaluated cases. T-cell responses were directed toward putative driver mutations in CREBBP and MEF2B. Responding T cells showed exquisite specificity for mutant versus wild-type proteins and recognized lymphoma cells expressing the appropriate mutations. Responding T cells appeared to be from the naïve repertoire, as they were found at low frequencies and only at single time points in each patient. CONCLUSIONS Patients with follicular lymphoma harbor rare yet functionally competent CD8(+) T cells specific for recurrent mutations. Our results support the concept of using NGS to design individualized immunotherapies targeting common driver mutations in follicular lymphoma and other malignancies. Clin Cancer Res; 22(9); 2226-36. ©2015 AACR.
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Affiliation(s)
- Julie S Nielsen
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada.
| | - Colin G Sedgwick
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Zusheng Zong
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Stephen Yu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Lewis Liu
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada
| | - David R Kroeger
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada
| | - Steven P Treon
- Bing Center for Waldenstrom's Macroglobulinemia, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Joseph M Connors
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. University of British Columbia, Vancouver, British Columbia, Canada
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian R Berry
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Nicol Macpherson
- Department of Medical Oncology, British Columbia Cancer Agency, Victoria, British Columbia, Canada
| | - Brad H Nelson
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, British Columbia, Canada. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada. Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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8
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Martin SD, Coukos G, Holt RA, Nelson BH. Targeting the undruggable: immunotherapy meets personalized oncology in the genomic era. Ann Oncol 2015; 26:2367-74. [PMID: 26371284 PMCID: PMC4658541 DOI: 10.1093/annonc/mdv382] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 12/22/2022] Open
Abstract
Owing to recent advances in genomic technologies, personalized oncology is poised to fundamentally alter cancer therapy. In this paradigm, the mutational and transcriptional profiles of tumors are assessed, and personalized treatments are designed based on the specific molecular abnormalities relevant to each patient's cancer. To date, such approaches have yielded impressive clinical responses in some patients. However, a major limitation of this strategy has also been revealed: the vast majority of tumor mutations are not targetable by current pharmacological approaches. Immunotherapy offers a promising alternative to exploit tumor mutations as targets for clinical intervention. Mutated proteins can give rise to novel antigens (called neoantigens) that are recognized with high specificity by patient T cells. Indeed, neoantigen-specific T cells have been shown to underlie clinical responses to many standard treatments and immunotherapeutic interventions. Moreover, studies in mouse models targeting neoantigens, and early results from clinical trials, have established proof of concept for personalized immunotherapies targeting next-generation sequencing identified neoantigens. Here, we review basic immunological principles related to T-cell recognition of neoantigens, and we examine recent studies that use genomic data to design personalized immunotherapies. We discuss the opportunities and challenges that lie ahead on the road to improving patient outcomes by incorporating immunotherapy into the paradigm of personalized oncology.
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Affiliation(s)
- S D Martin
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria Interdisciplinary Oncology Program, University of British Columbia, Vancouver Michael Smith's Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - G Coukos
- Ludwig Center for Cancer Research, University of Lausanne, Lausanne Hospital of the University of Lausanne (CHUV), Lausanne, Switzerland
| | - R A Holt
- Michael Smith's Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada Molecular Biology and Biochemistry, Simon Fraser University, Vancouver Department of Medical Genetics, University of British Columbia, Vancouver
| | - B H Nelson
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria Department of Medical Genetics, University of British Columbia, Vancouver Department of Microbiology and Biochemistry, University of Victoria, Victoria, Canada
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Zaccard CR, Watkins SC, Kalinski P, Fecek RJ, Yates AL, Salter RD, Ayyavoo V, Rinaldo CR, Mailliard RB. CD40L induces functional tunneling nanotube networks exclusively in dendritic cells programmed by mediators of type 1 immunity. THE JOURNAL OF IMMUNOLOGY 2014; 194:1047-56. [PMID: 25548234 DOI: 10.4049/jimmunol.1401832] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ability of dendritic cells (DC) to mediate CD4(+) T cell help for cellular immunity is guided by instructive signals received during DC maturation, as well as the resulting pattern of DC responsiveness to the Th signal, CD40L. Furthermore, the professional transfer of antigenic information from migratory DC to lymph node-residing DC is critical for the effective induction of cellular immune responses. In this study we report that, in addition to their enhanced IL-12p70 producing capacity, human DC matured in the presence of inflammatory mediators of type 1 immunity are uniquely programmed to form networks of tunneling nanotube-like structures in response to CD40L-expressing Th cells or rCD40L. This immunologic process of DC reticulation facilitates intercellular trafficking of endosome-associated vesicles and Ag, but also pathogens such HIV-1, and is regulated by the opposing roles of IFN-γ and IL-4. The initiation of DC reticulation represents a novel helper function of CD40L and a superior mechanism of intercellular communication possessed by type 1 polarized DC, as well as a target for exploitation by pathogens to enhance direct cell-to-cell spread.
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Affiliation(s)
- Colleen R Zaccard
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Simon C Watkins
- Department of Cell Biology and Physiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Pawel Kalinski
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261; Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15261; Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - Ronald J Fecek
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Aarika L Yates
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Russell D Salter
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Velpandi Ayyavoo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Charles R Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261; Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261
| | - Robbie B Mailliard
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261;
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10
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Ye W, Xing Y, Paustian C, van de Ven R, Moudgil T, Hilton TL, Fox BA, Urba WJ, Zhao W, Hu HM. Cross-presentation of viral antigens in dribbles leads to efficient activation of virus-specific human memory T cells. J Transl Med 2014; 12:100. [PMID: 24735498 PMCID: PMC4021424 DOI: 10.1186/1479-5876-12-100] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 04/03/2014] [Indexed: 12/11/2022] Open
Abstract
Background Autophagy regulates innate and adaptive immune responses to pathogens and tumors. We have reported that autophagosomes derived from tumor cells after proteasome inhibition, DRibbles (Defective ribosomal products in blebs), were excellent sources of antigens for efficient cross priming of tumor-specific CD8+ T cells, which mediated regression of established tumors in mice. But the activity of DRibbles in human has not been reported. Methods DRibbles or cell lysates derived from HEK293T or UbiLT3 cell lines expressing cytomegalovirus (CMV) pp65 protein or transfected with a plasmid encoding dominant HLA-A2 restricted CMV, Epstein-Barr virus (EBV), and Influenza (Flu) epitopes (CEF) were loaded onto human monocytes or PBMCs and the response of human CMV pp65 or CEF antigen-specific CD4+ and CD8+ memory T cells was detected by intracellular staining. The effect of cytokines (GM-CSF, IL-4, IL-12, TNF-α, IFN-α and IFN-γ) TLR agonists (Lipopolysaccharide, Polyinosinic-polycytidylic acid (poly(I:C), M52-CpG, R848, TLR2 ligand) and CD40 ligand on the cross-presentation of antigens contained in DRibbles or cell lysates was explored. Results In this study we showed that purified monocytes, or human PBMCs, loaded with DRibbles isolated from cells expressing CMV or CEF epitopes, could activate CMV- or CEF-specific memory T cells. DRibbles were significantly more efficient at stimulating CD8+ memory T cells compared to cell lysates expressing the same antigenic epitopes. We optimized the conditions for T-cell activation and IFN-γ production following direct loading of DRibbles onto PBMCs. We found that the addition of Poly(I:C), CD40 ligand, and GM-CSF to the PBMCs together with DRibbles significantly increased the level of CD8+ T cell responses. Conclusions DRibbles containing specific viral antigens are an efficient ex vivo activator of human antigen-specific memory T cells specific for those antigens. This function could be enhanced by combining with Poly(I:C), CD40 ligand, and GM-CSF. This study provides proof-of-concept for applying this strategy to activate memory T cells against other antigens, including tumor-specific T cells ex vivo for immunological monitoring and adoptive immunotherapy, and in vivo as vaccines for patients with cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wei Zhao
- Medical School, Southeast University, 87 Dingjiaqiao Street, 210009 Nanjing, Jiangsu, PR China.
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Augmentation of epithelial resistance to invading bacteria by using mRNA transfections. Infect Immun 2013; 81:3975-83. [PMID: 23940207 DOI: 10.1128/iai.00539-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
To protect against invading bacteria, oral epithelial cells appear to use two effector antimicrobial peptides (AMPs): calprotectin (S100A8-S100A9 heterodimer [S100A8/A9]) in the cytosol and cathelicidin antimicrobial protein (CAMP) in endosomes. We sought to learn whether innate immunity might be augmented benignly to increase resistance against invasive bacteria. Epithelial cells were transiently transfected with mRNA constructs containing either the CAMP, S100A8, and S100A9 open reading frames, A8-IRES-A9 (fusion sequence), or A8-nIRES-A9 (fusion with native internal ribosome entry site [IRES] sequence). CAMP, S100A8, and S100A9 protein levels generally peaked between 16 and 44 h after mRNA transfection, depending on the construct; CAMP was processed to LL-37 over time. Following transfection with the respective mRNAs, CAMP and S100A8/A9 each independently increased resistance of epithelial cells to invasion by Listeria and Salmonella for up to 48 h; tandem S100A8/A9 constructs were also effective. Cotransfection to express S100A8/A9 and CAMP together augmented resistance, but synergy was not seen. Independent of the new proteins produced, transfection reduced cell viability after 48 h by 20%, with only 2% attributable to apoptosis. Taken together, these results suggest that epithelial cell resistance to invasive pathogens can be augmented by transient transfection of antimicrobial mRNAs into epithelial cells.
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Cancer genome sequencing and its implications for personalized cancer vaccines. Cancers (Basel) 2011; 3:4191-211. [PMID: 24213133 PMCID: PMC3763418 DOI: 10.3390/cancers3044191] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 10/31/2011] [Accepted: 11/09/2011] [Indexed: 12/31/2022] Open
Abstract
New DNA sequencing platforms have revolutionized human genome sequencing. The dramatic advances in genome sequencing technologies predict that the $1,000 genome will become a reality within the next few years. Applied to cancer, the availability of cancer genome sequences permits real-time decision-making with the potential to affect diagnosis, prognosis, and treatment, and has opened the door towards personalized medicine. A promising strategy is the identification of mutated tumor antigens, and the design of personalized cancer vaccines. Supporting this notion are preliminary analyses of the epitope landscape in breast cancer suggesting that individual tumors express significant numbers of novel antigens to the immune system that can be specifically targeted through cancer vaccines.
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Zhang GL, Lin HH, Keskin DB, Reinherz EL, Brusic V. Dana-Farber repository for machine learning in immunology. J Immunol Methods 2011; 374:18-25. [PMID: 21782820 DOI: 10.1016/j.jim.2011.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 07/06/2011] [Indexed: 11/27/2022]
Abstract
The immune system is characterized by high combinatorial complexity that necessitates the use of specialized computational tools for analysis of immunological data. Machine learning (ML) algorithms are used in combination with classical experimentation for the selection of vaccine targets and in computational simulations that reduce the number of necessary experiments. The development of ML algorithms requires standardized data sets, consistent measurement methods, and uniform scales. To bridge the gap between the immunology community and the ML community, we designed a repository for machine learning in immunology named Dana-Farber Repository for Machine Learning in Immunology (DFRMLI). This repository provides standardized data sets of HLA-binding peptides with all binding affinities mapped onto a common scale. It also provides a list of experimentally validated naturally processed T cell epitopes derived from tumor or virus antigens. The DFRMLI data were preprocessed and ensure consistency, comparability, detailed descriptions, and statistically meaningful sample sizes for peptides that bind to various HLA molecules. The repository is accessible at http://bio.dfci.harvard.edu/DFRMLI/.
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Affiliation(s)
- Guang Lan Zhang
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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