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IntroSpect: Motif-Guided Immunopeptidome Database Building Tool to Improve the Sensitivity of HLA I Binding Peptide Identification by Mass Spectrometry. Biomolecules 2022; 12:biom12040579. [PMID: 35454168 PMCID: PMC9025654 DOI: 10.3390/biom12040579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 01/02/2023] Open
Abstract
Although database search tools originally developed for shotgun proteome have been widely used in immunopeptidomic mass spectrometry identifications, they have been reported to achieve undesirably low sensitivities or high false positive rates as a result of the hugely inflated search space caused by the lack of specific enzymic digestions in immunopeptidome. To overcome such a problem, we developed a motif-guided immunopeptidome database building tool named IntroSpect, which is designed to first learn the peptide motifs from high confidence hits in the initial search, and then build a targeted database for refined search. Evaluated on 18 representative HLA class I datasets, IntroSpect can improve the sensitivity by an average of 76%, compared to conventional searches with unspecific digestions, while maintaining a very high level of accuracy (~96%), as confirmed by synthetic validation experiments. A distinct advantage of IntroSpect is that it does not depend on any external HLA data, so that it performs equally well on both well-studied and poorly-studied HLA types, unlike the previously developed method SpectMHC. We have also designed IntroSpect to keep a global FDR that can be conveniently controlled, similar to a conventional database search. Finally, we demonstrate the practical value of IntroSpect by discovering neoepitopes from MS data directly, an important application in cancer immunotherapies. IntroSpect is freely available to download and use.
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Sauerer T, Lischer C, Weich A, Berking C, Vera J, Dörrie J. Single-Molecule RNA Sequencing Reveals IFNγ-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus-Positive MCC Cell Lines. Front Microbiol 2021; 12:785662. [PMID: 35003017 PMCID: PMC8727593 DOI: 10.3389/fmicb.2021.785662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a rare and highly aggressive cancer, which is mainly caused by genomic integration of the Merkel cell polyomavirus and subsequent expression of a truncated form of its large T antigen. The resulting primary tumor is known to be immunogenic and under constant pressure to escape immune surveillance. Because interferon gamma (IFNγ), a key player of immune response, is secreted by many immune effector cells and has been shown to exert both anti-tumoral and pro-tumoral effects, we studied the transcriptomic response of MCC cells to IFNγ. In particular, immune modulatory effects that may help the tumor evade immune surveillance were of high interest to our investigation. The effect of IFNγ treatment on the transcriptomic program of three MCC cell lines (WaGa, MKL-1, and MKL-2) was analyzed using single-molecule sequencing via the Oxford Nanopore platform. A significant differential expression of several genes was detected across all three cell lines. Subsequent pathway analysis and manual annotation showed a clear upregulation of genes involved in the immune escape of tumor due to IFNγ treatment. The analysis of selected genes on protein level underlined our sequencing results. These findings contribute to a better understanding of immune escape of MCC and may help in clinical treatment of MCC patients. Furthermore, we demonstrate that single-molecule sequencing can be used to assess characteristics of large eukaryotic transcriptomes and thus contribute to a broader access to sequencing data in the community due to its low cost of entry.
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Affiliation(s)
- Tatjana Sauerer
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christopher Lischer
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Adrian Weich
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Carola Berking
- Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Julio Vera
- Systems Tumor Immunology, Hautklinik, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Erlangen, Germany
| | - Jan Dörrie
- RNA-based Immunotherapy, Hautklinik, Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg, Deutsches Zentrum Immuntherapie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Vanajothi R, Srikanth N, Vijayakumar R, Palanisamy M, Bhavaniramya S, Premkumar K. HPV-mediated Cervical Cancer: A Systematic review on Immunological Basis, Molecular Biology and Immune evasion mechanisms. Curr Drug Targets 2021; 23:782-801. [PMID: 34939539 DOI: 10.2174/1389450123666211221160632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Human papillomavirus (HPV), one of the most frequently transmitted viruses globally, causing several malignancies including cervical cancer. AIM Owing to their unique pathogenicity HPV viruses can persist in the host organism for a longer duration than other virus types, to complete their lifecycle. During its association with the host, HPV causes various pathological conditions affecting the immune system by evading the host immune- mechanisms leading to the progression of various diseases, including cancer. METHOD To date, ~ 150 serotypes were identified, and certain high-risk HPV types are known to be associated with genital warts and cervical cancer. As of now, two prophylactic vaccines are in use for the treatment of HPV infection, however, no effective antiviral drug is available for HPV-associated disease/infections. Numerous clinical and laboratory studies are being investigated to formulate an effective and specific vaccine again HPV infections and associated diseases. RESULT As the immunological basis of HPV infection and associated disease progress persist indistinctly, deeper insights on immune evasion mechanism and molecular biology of disease would aid in developing an effective vaccine. CONCLUSION Thus this review focuses, aiming a systematic review on the immunological aspects of HPV-associated cervical cancer by uncovering immune evasion strategies adapted by HPV.
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Affiliation(s)
- Ramar Vanajothi
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli-620024. India
| | - Natarajan Srikanth
- Department of Integrative Biology, Vellore Institute of Technology, Vellore. India
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah 11952. Saudi Arabia
| | - Manikandan Palanisamy
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952. Saudi Arabia
| | - Sundaresan Bhavaniramya
- College of Food and Dairy Technology, Tamil Nadu Veterinary and Animal Sciences, University, Chennai-600052, Tamil Nadu. India
| | - Kumpati Premkumar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli-620024. India
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Jiang P, Veenstra RN, Seitz A, Nolte IM, Hepkema BG, Visser L, van den Berg A, Diepstra A. Interaction between ERAP Alleles and HLA Class I Types Support a Role of Antigen Presentation in Hodgkin Lymphoma Development. Cancers (Basel) 2021; 13:cancers13030414. [PMID: 33499248 PMCID: PMC7865538 DOI: 10.3390/cancers13030414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Hodgkin lymphoma (HL) is a common lymphoma in young adults derived from B cells. Emerging evidence suggests that antigen presentation by the malignant B cells is critically involved in HL pathogenesis. In fact, genetic variants of the antigen presenting Human Leukocyte Antigens (HLA) are strongly associated with HL susceptibility. Interestingly, the endoplasmic reticulum aminopeptidase (ERAP)1 and ERAP2 genes, that code for enzymes that process antigens, also appear to be associated. In this study, we show that genetic variants of ERAP genes strongly affect expression levels of ERAP1 and ERAP2. In addition, we find that certain ERAP variants interact with specific HLA class I types in HL patients. This suggests that mechanisms that determine the repertoire of antigens that are presented to the immune system, affect the chance of developing HL. Our findings therefore support a prominent role of antigen presentation in HL susceptibility. Abstract Genetic variants in the HLA region are the strongest risk factors for developing Hodgkin lymphoma (HL), suggesting an important role for antigen presentation. This is supported by another HL-associated genomic region which contains the loci of two enzymes that process endogenous proteins to peptides to be presented by HLA class I, i.e., endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2. We hypothesized that ERAP and HLA class I type interact in HL susceptibility, as shown previously for several autoimmune diseases. We detected ERAP1 and ERAP2 expression in tumor cells and cells in the microenvironment in primary HL tissue samples. Seven ERAP SNPs and ERAP1 haplotypes showed strong associations with RNA and protein levels of ERAP1 and ERAP2 in LCLs and HL cell lines. Analysis of HLA class I types, ERAP SNPs and ERAP haplotypes by direct genotyping or imputation from genome-wide association data in 390 HL patients revealed significant interactions between HLA-A11, rs27038 and the rs27038 associated ERAP haplotype, as well as between HLA-Cw2 and rs26618. In conclusion, our results show that ERAP and HLA class I interact in genetic susceptibility to HL, providing further evidence that antigen presentation is an important process in HL susceptibility and pathogenesis.
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Affiliation(s)
- Peijia Jiang
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
- Department of Laboratory Medicine, Shenyang Huanggu National Defense Hospital, Shenyang 110032, China
| | - Rianne N. Veenstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands;
| | - Bouke G. Hepkema
- Department of Laboratory Medicine, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands;
| | - Lydia Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands; (P.J.); (R.N.V.); (A.S.); (L.V.); (A.v.d.B.)
- Correspondence:
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Jee B, Yadav R, Pankaj S, Shahi SK. Immunology of HPV-mediated cervical cancer: current understanding. Int Rev Immunol 2020; 40:359-378. [PMID: 32853049 DOI: 10.1080/08830185.2020.1811859] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human papilloma virus (HPV) has emerged as a primary cause of cervical cancer worldwide. HPV is a relatively small (55 nm in diameter) and non-enveloped virus containing approximately 8 kb long double stranded circular DNA genome. To date, 228 genotypes of HPV have been identified. Although all HPV infections do not lead to the development of malignancy of cervix, only persistent infection of high-risk types of HPV (mainly with HPV16 and HPV18) results in the disease. In addition, the immunity of the patients also acts as a key determinant in the carcinogenesis. Since, no HPV type specific medication is available for the patient suffering with cervical cancer, hence, a deep understanding of the disease etiology may be vital for developing an effective strategy for its prevention and management. From the immunological perspectives, the entire mechanisms of disease progression still remain unclear despite continuous efforts. In the present review, the recent developments in immunology of HPV-mediated cervix carcinoma were discussed. At the end, the prevention of disease using HPV type specific recombinant vaccines was also highlighted.
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Affiliation(s)
- Babban Jee
- Department of Health Research, Ministry of Health and Family Welfare, Government of India, New Delhi, India
| | - Renu Yadav
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Sangeeta Pankaj
- Department of Gynecological Oncology, Regional Cancer Centre, Indira Gandhi Institute of Medical Sciences, Patna, India
| | - Shivendra Kumar Shahi
- Department of Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, India
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Li C, Li Y, Yan Z, Dai S, Liu S, Wang X, Wang J, Zhang X, Shi L, Yao Y. Polymorphisms in endoplasmic reticulum aminopeptidase genes are associated with cervical cancer risk in a Chinese Han population. BMC Cancer 2020; 20:341. [PMID: 32321463 PMCID: PMC7178719 DOI: 10.1186/s12885-020-06832-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
Background Antigen-processing machinery molecules play crucial roles in infectious diseases and cancers. Studies have shown that polymorphisms in endoplasmic reticulum aminopeptidase (ERAP) genes can influence the enzymatic activity of ERAP proteins and are associated with the risk of diseases. In the current study, we evaluated the influence of ERAP gene (ERAP1 and ERAP2) polymorphisms on susceptibility to cervical intraepithelial neoplasia (CIN) and cervical cancer. Methods Six single nucleotide polymorphisms (SNPs) in ERAP1 and 5 SNPs in ERAP2 were selected and genotyped in 556 CIN patients, 1072 cervical cancer patients, and 1262 healthy control individuals. Candidate SNPs were genotyped using SNaPshot assay. And the association of these SNPs with CIN and cervical cancer was analysed. Results The results showed that allelic and genotypic frequencies of rs26653 in ERAP1 were significantly different between cervical cancer and control groups (P = 0.001 and 0.004). The allelic frequencies of rs27044 in ERAP1 and rs2287988 in ERAP2 were significantly different between control and cervical cancer groups (P = 0.003 and 0.004). Inheritance model analysis showed that genotypes of rs27044, rs26618, rs26653 and rs2287988 SNPs may be associated with the risk of cervical cancer (P = 0.003, 0.004, 0.001 and 0.002). Additionally, haplotype analysis results showed that the ERAP1 haplotype, rs27044C-rs30187T-rs26618T-rs26653G-rs3734016C, was associated with a lower risk of cervical cancer (P = 0.001). The ERAP2 haplotypes rs2549782G- rs2548538A-rs2248374A-rs2287988G-rs1056893T (P = 0.009 and 0.006) and rs2549782T-rs2548538T-rs2248374G-rs2287988A-rs1056893T (P = 0.003 and 0.009) might be associated with cervical cancer and the development from CIN to cervical cancer. Conclusion Our results indicated that rs27044, rs26618 and rs26653 in ERAP1 and rs2287988 in ERAP2 influenced susceptibility to cervical cancer.
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Affiliation(s)
- Chuanyin Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
| | - Yaheng Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
| | - Zhiling Yan
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Shuying Dai
- School of Basic Medical Science, Kunming Medical University, Kunming, 650500, China
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
| | - Xia Wang
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Jun Wang
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Xinwen Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China.
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China.
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Reeves E, Islam Y, James E. ERAP1: a potential therapeutic target for a myriad of diseases. Expert Opin Ther Targets 2020; 24:535-544. [PMID: 32249641 DOI: 10.1080/14728222.2020.1751821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) is a key regulator of the peptide repertoire displayed by Major Histocompatibility Complex I (MHC I) to circulating CD8 + T cells and NK cells. Studies have highlighted the essential requirement for the generation of stable peptide MHC I in regulating both innate and adaptive immune responses in health and disease.Areas covered: We review the role of ERAP1 in peptide trimming of N-terminally extended precursors that enter the ER, before loading on to MHC I, and the consequence of loss or downregulation of this activity. Polymorphisms in ERAP1 form multiple combinations (allotypes) within the population, and we discuss the contribution of this ERAP1 variation, and expression, on disease pathogenesis, including the resulting effect on both innate and adaptive immunity. We consider the current efforts to design inhibitors based on approaches using rational design and small molecule screening, and the potential effect of pharmacological modulation on the treatment of autoimmunity and cancer.Expert opinion: ERAP1 is fundamental for the regulation of immune responses, through generation of the presented peptide repertoire at the cell surface. Modulation of ERAP1 function, through design of inhibitors, may serve as a vital tool for changing immune responses in disease.
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Affiliation(s)
- Emma Reeves
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Yasmin Islam
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK
| | - Edward James
- Centre for Cancer Immunology, Faculty of Medicine, University Hospital Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
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Saulle I, Vicentini C, Clerici M, Biasin M. An Overview on ERAP Roles in Infectious Diseases. Cells 2020; 9:E720. [PMID: 32183384 PMCID: PMC7140696 DOI: 10.3390/cells9030720] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/12/2022] Open
Abstract
Endoplasmic reticulum (ER) aminopeptidases ERAP1 and ERAP2 (ERAPs) are crucial enzymes shaping the major histocompatibility complex I (MHC I) immunopeptidome. In the ER, these enzymes cooperate in trimming the N-terminal residues from precursors peptides, so as to generate optimal-length antigens to fit into the MHC class I groove. Alteration or loss of ERAPs function significantly modify the repertoire of antigens presented by MHC I molecules, severely affecting the activation of both NK and CD8+ T cells. It is, therefore, conceivable that variations affecting the presentation of pathogen-derived antigens might result in an inadequate immune response and onset of disease. After the first evidence showing that ERAP1-deficient mice are not able to control Toxoplasma gondii infection, a number of studies have demonstrated that ERAPs are control factors for several infectious organisms. In this review we describe how susceptibility, development, and progression of some infectious diseases may be affected by different ERAPs variants, whose mechanism of action could be exploited for the setting of specific therapeutic approaches.
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Affiliation(s)
- Irma Saulle
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
- Cattedra di Immunologia, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti Università degli Studi di Milano, 20122 Milan, Italy;
| | - Chiara Vicentini
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
| | - Mario Clerici
- Cattedra di Immunologia, Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti Università degli Studi di Milano, 20122 Milan, Italy;
- IRCCS Fondazione Don Carlo Gnocchi, 20157 Milan, Italy
| | - Mara Biasin
- Cattedra di Immunologia, Dipartimento di Scienze Biomediche e Cliniche L. Sacco”, Università degli Studi di Milano, 20157 Milan, Italy; (C.V.); (M.B.)
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Ferreira AR, Ramalho AC, Marques M, Ribeiro D. The Interplay between Antiviral Signalling and Carcinogenesis in Human Papillomavirus Infections. Cancers (Basel) 2020; 12:cancers12030646. [PMID: 32164347 PMCID: PMC7139948 DOI: 10.3390/cancers12030646] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Human papillomaviruses (HPV) are the causative agents of the most common sexually transmitted infection worldwide. While infection is generally asymptomatic and can be cleared by the host immune system, when persistence occurs, HPV can become a risk factor for malignant transformation. Progression to cancer is actually an unintended consequence of the complex HPV life cycle. Different antiviral defence mechanisms recognize HPV early in infection, leading to the activation of the innate immune response. However, the virus has evolved several specific strategies to efficiently evade the antiviral immune signalling. Here, we review and discuss the interplay between HPV and the host cell innate immunity. We further highlight the evasion strategies developed by different HPV to escape this cellular response and focus on the correlation with HPV-induced persistence and tumorigenesis.
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Affiliation(s)
| | | | | | - Daniela Ribeiro
- Correspondence: ; Tel.: +351-234-247 014; Fax: +351-234-372-587
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Georgiadis D, Mpakali A, Koumantou D, Stratikos E. Inhibitors of ER Aminopeptidase 1 and 2: From Design to Clinical Application. Curr Med Chem 2019; 26:2715-2729. [PMID: 29446724 DOI: 10.2174/0929867325666180214111849] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/04/2018] [Accepted: 01/31/2018] [Indexed: 12/19/2022]
Abstract
Endoplasmic Reticulum aminopeptidase 1 and 2 are two homologous enzymes that help generate peptide ligands for presentation by Major Histocompatibility Class I molecules. Their enzymatic activity influences the antigenic peptide repertoire and indirectly controls adaptive immune responses. Accumulating evidence suggests that these two enzymes are tractable targets for the regulation of immune responses with possible applications ranging from cancer immunotherapy to treating inflammatory autoimmune diseases. Here, we review the state-of-the-art in the development of inhibitors of ERAP1 and ERAP2 as well as their potential and limitations for clinical applications.
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Affiliation(s)
- Dimitris Georgiadis
- Department of Chemistry, National and Kapodistrian University of Athens, Zografou, 15771, Athens, Greece
| | - Anastasia Mpakali
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
| | - Despoina Koumantou
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
| | - Efstratios Stratikos
- National Center for Scientific Research Demokritos, Agia Paraskevi, 15341, Greece
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Reeves E, Wood O, Ottensmeier CH, King EV, Thomas GJ, Elliott T, James E. HPV Epitope Processing Differences Correlate with ERAP1 Allotype and Extent of CD8 + T-cell Tumor Infiltration in OPSCC. Cancer Immunol Res 2019; 7:1202-1213. [PMID: 31151965 PMCID: PMC6640044 DOI: 10.1158/2326-6066.cir-18-0498] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 02/15/2019] [Accepted: 05/09/2019] [Indexed: 12/11/2022]
Abstract
Presence of tumor-infiltrating lymphocytes (TIL) predicts survival in many cancer types. In HPV-driven cancers, cervical and oropharyngeal squamous cell carcinomas (CSCC and OPSCC, respectively), numbers of infiltrating T cells, particularly CD8+ T cells, and presentation of HPV E6/E7 epitopes are associated with improved prognosis. Endoplasmic reticulum aminopeptidase 1 (ERAP1) regulates the presented peptide repertoire, trimming peptide precursors prior to MHC I loading. ERAP1 is polymorphic, and allotypic variation of ERAP1 enzyme activity has an impact on the presented peptide repertoire. Individual SNPs are associated with incidence and outcome in a number of diseases, including CSCC. Here, we highlight the requirement for ERAP1 in the generation of HPV E6/E7 epitopes and show that the functional activity of ERAP1 allotype combinations identified in OPSCC correlate with tumor-infiltrating CD8+ T-cell (CD8)/TIL (CD8/TIL) status of the tumor. Functional analyses revealed that ERAP1 allotype combinations associated with CD8/TILlow tumors have a reduced capacity to generate both a model antigen SIINFEHL and the HPV-16 E782-90 epitope LLMGTLGIV from N-terminally extended precursor peptides. In contrast, ERAP1 allotypes from CD8/TILhigh tumors generated the epitopes efficiently. These data reveal that ERAP1 function correlates with CD8/TIL numbers and, by implication, prognosis, suggesting that the presentation of HPV-16 epitopes at the cell surface, resulting in an anti-HPV T-cell response, may depend on the ERAP1 allotype combinations expressed within an individual.
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Affiliation(s)
- Emma Reeves
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Oliver Wood
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Christian H Ottensmeier
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Emma V King
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Gareth J Thomas
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Tim Elliott
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Edward James
- Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton, United Kingdom.
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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12
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Jabbar B, Rafique S, Salo-Ahen OMH, Ali A, Munir M, Idrees M, Mirza MU, Vanmeert M, Shah SZ, Jabbar I, Rana MA. Antigenic Peptide Prediction From E6 and E7 Oncoproteins of HPV Types 16 and 18 for Therapeutic Vaccine Design Using Immunoinformatics and MD Simulation Analysis. Front Immunol 2018; 9:3000. [PMID: 30619353 PMCID: PMC6305797 DOI: 10.3389/fimmu.2018.03000] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022] Open
Abstract
Human papillomavirus (HPV) induced cervical cancer is the second most common cause of death, after breast cancer, in females. Three prophylactic vaccines by Merck Sharp & Dohme (MSD) and GlaxoSmithKline (GSK) have been confirmed to prevent high-risk HPV strains but these vaccines have been shown to be effective only in girls who have not been exposed to HPV previously. The constitutively expressed HPV oncoproteins E6 and E7 are usually used as target antigens for HPV therapeutic vaccines. These early (E) proteins are involved, for example, in maintaining the malignant phenotype of the cells. In this study, we predicted antigenic peptides of HPV types 16 and 18, encoded by E6 and E7 genes, using an immunoinformatics approach. To further evaluate the immunogenic potential of the predicted peptides, we studied their ability to bind to class I major histocompatibility complex (MHC-I) molecules in a computational docking study that was supported by molecular dynamics (MD) simulations and estimation of the free energies of binding of the peptides at the MHC-I binding cleft. Some of the predicted peptides exhibited comparable binding free energies and/or pattern of binding to experimentally verified MHC-I-binding epitopes that we used as references in MD simulations. Such peptides with good predicted affinity may serve as candidate epitopes for the development of therapeutic HPV peptide vaccines.
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Affiliation(s)
- Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Outi M H Salo-Ahen
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku, Finland.,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, Finland
| | - Amjad Ali
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Mobeen Munir
- Division of Science and Technology, University of Education Lahore, Lahore, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Michiel Vanmeert
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, Leuven, Belgium
| | - Syed Zawar Shah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Iqra Jabbar
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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13
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Kruse S, Büchler M, Uhl P, Sauter M, Scherer P, Lan TCT, Zottnick S, Klevenz A, Yang R, Rösl F, Mier W, Riemer AB. Therapeutic vaccination using minimal HPV16 epitopes in a novel MHC-humanized murine HPV tumor model. Oncoimmunology 2018; 8:e1524694. [PMID: 30546964 DOI: 10.1080/2162402x.2018.1524694] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/21/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022] Open
Abstract
Therapeutic vaccination as a treatment option for HPV-induced cancers is actively pursued because the two HPV proteins E6 and E7 represent ideal targets for immunotherapy, as they are non-self and expressed in all tumor stages. MHC-humanized mice are valuable tools for the study of therapeutic cancer vaccines - given the availability of a suitable tumor model. Here, we present for the first time an HPV16 tumor model suitable for fully MHC-humanized A2.DR1 mice, PAP-A2 cells, which in contrast to existing HPV16 tumor models allows the exclusive study of HLA-A2- and DR1-mediated immune responses, without any interfering murine MHC-presented epitopes. We used several HPV16 epitopes that were shown to be presented on human cervical cancer cells by mass spectrometry for therapeutic anti-tumor vaccination in the new tumor model. All epitopes were immunogenic when rendered amphiphilic by incorporation into a molecule containing stearic acids. Prophylactic and therapeutic vaccination experiments with the epitope E7/11-19 demonstrated that effective immune responses could be induced with these vaccination approaches in A2.DR1 mice. Interestingly, the combination of E7/11-19 with other immunogenic HPV16 E6/E7 epitopes caused a reduction of vaccine efficacy, although all tested combinations resulted in a survival benefit. In summary, we present the first HPV16 tumor model for exclusive studies of HLA-A2-mediated anti-HPV tumor immune responses and show anti-tumor efficacy of minimal epitope vaccines.
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Affiliation(s)
- Sebastian Kruse
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Marleen Büchler
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Philipp Uhl
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Max Sauter
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Scherer
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tammy C T Lan
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Samantha Zottnick
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alexandra Klevenz
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ruwen Yang
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Rösl
- Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Angelika B Riemer
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
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14
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Fu Y, Li X, Chen Y, Liu R, Wang R, Bai N. Association of ERAP1 gene polymorphisms with the susceptibility to psoriasis vulgaris: A case-control study. Medicine (Baltimore) 2018; 97:e12828. [PMID: 30313118 PMCID: PMC6203476 DOI: 10.1097/md.0000000000012828] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Psoriasis vulgaris (PsV), also known as plaque psoriasis, is a life-threatening autoimmune skin disease. Inflammatory factors may contribute to the development of PsV. Present study aimed to explore the association of endoplasmic reticulum aminopeptidase 1 (ERAP1) gene polymorphisms (rs26653 and rs27524) with PsV susceptibility in a Chinese Han population. Subgroup analysis was also performed based on the onset of PsV.Present case-control study included 143 patients with PsV and 149 healthy controls. Direct sequencing method was used for genotyping ERAP1 polymorphisms. Chi-squared test was used to estimate the association between ERAP1 polymorphisms and PsV susceptibility. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess association strength.The polymorphism rs26653 was positively correlated with PsV susceptibility (CC vs GG, P = .047, OR = 1.964, 95% CI = 1.006-3.834; C vs G, P = .042, OR = 1.403, 95% CI = 1.011-1.946). Meanwhile, its CC genotype and C allele were positively associated with the early onset of PsV (P = .036, OR = 2.080, 95% CI = 1.044-4.145; P = .034, OR = 1.443, 95% CI = 1.028-2.024) and increased PsV risk in the subgroup with family history (P = .029, OR = 2.149, 95% CI = 1.075-4.296; P = .027, OR = 1.466, 95% CI = 1.044-2.059).ERAP1 gene rs26653 polymorphism may increase the risk of PsV in Chinese Han population.
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Affiliation(s)
- Yanjie Fu
- Department of Burn and Plastic Surgery, Linyi People's Hospital, Linyi City
| | - Xiuyan Li
- Department of Surgery, Tancheng People's Hospital, Tancheng City
| | - Yuanzheng Chen
- Department of Burn and Plastic Surgery, Linyi People's Hospital, Linyi City
| | - Rongpeng Liu
- Department of Burn and Plastic Surgery, Linyi People's Hospital, Linyi City
| | - Renheng Wang
- Department of Burn and Plastic Surgery, Linyi People's Hospital, Linyi City
| | - Nan Bai
- Department of Plastic and Cosmetic Surgery, Linyi People's Hospital, Linyi City, Shandong Province, China
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15
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Blatnik R, Mohan N, Bonsack M, Falkenby LG, Hoppe S, Josef K, Steinbach A, Becker S, Nadler WM, Rucevic M, Larsen MR, Salek M, Riemer AB. A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes. Proteomics 2018; 18:e1700390. [PMID: 29603667 PMCID: PMC6033010 DOI: 10.1002/pmic.201700390] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 03/16/2018] [Indexed: 12/12/2022]
Abstract
For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3 -based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711-19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.
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Affiliation(s)
- Renata Blatnik
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Nitya Mohan
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Maria Bonsack
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Lasse G. Falkenby
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Stephanie Hoppe
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Kathrin Josef
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Alina Steinbach
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Sara Becker
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Wiebke M. Nadler
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ) and Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM)HeidelbergGermany
| | - Marijana Rucevic
- Massachusetts General HospitalCenter for Cancer ResearchCharlestownMAUSA
| | - Martin R. Larsen
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Mogjiborahman Salek
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Angelika B. Riemer
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
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16
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Steinbach A, Riemer AB. Immune evasion mechanisms of human papillomavirus: An update. Int J Cancer 2017; 142:224-229. [PMID: 28865151 DOI: 10.1002/ijc.31027] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/04/2017] [Indexed: 12/16/2022]
Abstract
Human papillomavirus (HPV) is the most frequently sexually transmitted agent in the world. It can cause cervical and other anogenital malignancies, and oropharyngeal cancer. HPV has the unique ability to persist in the host's epithelium for a long time-longer than most viruses do-which is necessary to complete its replication cycle. To this end, HPV has developed a variety of immune evasion mechanisms, which unfortunately also favor the progression of the disease from infection to chronic dysplasia and eventually to cancer. This article summarizes the current knowledge about HPV immune evasion strategies. A special emphasis lies in HPV-mediated changes of the antigen processing machinery, which is generating epitopes for T cells and contributes to the detectability of infected cells.
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Affiliation(s)
- Alina Steinbach
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research, Partner Site Heidelberg, Heidelberg, Germany
| | - Angelika B Riemer
- Immunotherapy & Immunoprevention, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Vaccine Design, German Center for Infection Research, Partner Site Heidelberg, Heidelberg, Germany
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17
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Analysis of Class I Major Histocompatibility Complex Gene Transcription in Human Tumors Caused by Human Papillomavirus Infection. Viruses 2017; 9:v9090252. [PMID: 28891951 PMCID: PMC5618018 DOI: 10.3390/v9090252] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/31/2017] [Accepted: 09/02/2017] [Indexed: 12/25/2022] Open
Abstract
Oncoproteins from high-risk human papillomaviruses (HPV) downregulate the transcription of the class I major histocompatibility complex (MHC-I) antigen presentation apparatus in tissue culture model systems. This could allow infected or transformed cells to evade the adaptive immune response. Using data from over 800 human cervical and head & neck tumors from The Cancer Genome Atlas (TCGA), we determined the impact of HPV status on the mRNA expression of all six MHC-I heavy chain genes, and the β2 microglobulin light chain. Unexpectedly, these genes were all expressed at high levels in HPV positive (HPV+) cancers compared with normal control tissues. Indeed, many of these genes were expressed at significantly enhanced levels in HPV+ tumors. Similarly, the transcript levels of several other components of the MHC-I peptide-loading complex were also high in HPV+ cancers. The coordinated expression of high mRNA levels of the MHC-I antigen presentation apparatus could be a consequence of the higher intratumoral levels of interferon γ in HPV+ carcinomas, which correlate with signatures of increased infiltration by T- and NK-cells. These data, which were obtained from both cervical and oral tumors in large human cohorts, indicates that HPV oncoproteins do not efficiently suppress the transcription of the antigen presentation apparatus in human tumors.
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