دورية أكاديمية

Distinct modulation of cellular immunopeptidome by the allosteric regulatory site of ER aminopeptidase 1.

التفاصيل البيبلوغرافية
العنوان: Distinct modulation of cellular immunopeptidome by the allosteric regulatory site of ER aminopeptidase 1.
المؤلفون: Temponeras I; National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece.; Department of Pharmacy, University of Patras, Patra, Greece., Samiotaki M; Biomedical Sciences Research Center 'Alexander Fleming,', Institute for Bioinnovation, Vari, Greece., Koumantou D; National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece., Nikopaschou M; National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece.; Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Greece., Kuiper JJW; Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands., Panayotou G; Biomedical Sciences Research Center 'Alexander Fleming,', Institute for Bioinnovation, Vari, Greece., Stratikos E; National Centre for Scientific Research Demokritos, Agia Paraskevi, Greece.; Department of Chemistry, National and Kapodistrian University of Athens, Zografou, Greece.
المصدر: European journal of immunology [Eur J Immunol] 2023 Aug; Vol. 53 (8), pp. e2350449. Date of Electronic Publication: 2023 May 15.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 1273201 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1521-4141 (Electronic) Linking ISSN: 00142980 NLM ISO Abbreviation: Eur J Immunol Subsets: MEDLINE
أسماء مطبوعة: Publication: <2005->: Weinheim : Wiley-VCH
Original Publication: Weinheim, Verlag Chemie GmbH.
مواضيع طبية MeSH: Aminopeptidases*/genetics , Peptides*, Humans ; Antigen Presentation ; Antigens ; Minor Histocompatibility Antigens/genetics ; Minor Histocompatibility Antigens/metabolism
مستخلص: ER aminopeptidase 1 (ERAP1) is an ER-resident aminopeptidase that excises N-terminal residues of peptides that then bind onto Major Histocompatibility Complex I molecules (MHC-I) and indirectly modulates adaptive immune responses. ERAP1 contains an allosteric regulatory site that accommodates the C-terminus of at least some peptide substrates, raising questions about its exact influence on antigen presentation and the potential of allosteric inhibition for cancer immunotherapy. We used an inhibitor that targets this regulatory site to study its effect on the immunopeptidome of a human cancer cell line. The immunopeptidomes of allosterically inhibited and ERAP1 KO cells contain high-affinity peptides with sequence motifs consistent with the cellular HLA class I haplotypes but are strikingly different in peptide composition. Compared to KO cells, allosteric inhibition did not affect the length distribution of peptides and skewed the peptide repertoire both in terms of sequence motifs and HLA allele utilization, indicating significant mechanistic differences between the two ways of disrupting ERAP1 function. These findings suggest that the regulatory site of ERAP1 plays distinct roles in antigenic peptide selection, which should be taken into consideration when designing therapeutic interventions targeting the cancer immunopeptidome.
(© 2023 The Authors. European Journal of Immunology published by Wiley-VCH GmbH.)
References: Rock, K. L., Reits, E. and Neefjes, J., Present yourself! By MHC class I and MHC class II molecules. Trends. Immunol. 2016. 0: 1-14.
Weimershaus, M., Evnouchidou, I., Saveanu, L. and van Endert, P., Peptidases trimming MHC class I ligands. Curr. Opin. Immunol. 2013. 25: 90-96.
Admon, A. and Bassani-Sternberg, M., The human immunopeptidome project, a suggestion for yet another postgenome next big thing. Mol. Cell. Proteomics 2011. 10: 1-4.
Atkinson, E. A. and Bleackley, R. C., Mechanisms of lysis by cytotoxic T cells. Crit. Rev. Immunol. 1995. 15: 359-384.
Koumantou, D., Barnea, E., Martin-Esteban, A., Maben, Z., Papakyriakou, A., Mpakali, A., Kokkala, P. et al., Editing the immunopeptidome of melanoma cells using a potent inhibitor of endoplasmic reticulum aminopeptidase 1 (ERAP1). Cancer Immunol. Immunother. 2019. 68: 1245-1261.
Abele, R. and Tampé, R., Moving the cellular peptidome by transporters. Front. Cell Dev. Biol. 2018. 6: 43.
Thomas, C. and Tampe, R., MHC I chaperone complexes shaping immunity. Curr. Opin. Immunol. 2019. 58: 9-15.
Madden, D. R., The three-dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 1995. 13: 587-622.
York, I. A., Chang, S.-C. C., Saric, T., Keys, J. A., Favreau, J. M., Goldberg, A. L. and Rock, K. L., The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues. Nat. Immunol. 2002. 3: 1177-1184.
Lopez de Castro, J. A., How ERAP1 and ERAP2 shape the peptidomes of disease-associated MHC-I proteins. Front. Immunol. 2018. 9: 2463.
Stratikos, E., Stamogiannos, A., Zervoudi, E. and Fruci, D., A role for naturally occurring alleles of endoplasmic reticulum aminopeptidases in tumor immunity and cancer pre-disposition. Front. Oncol. 2014. 4: 363.
Mpakali, A., Maben, Z., Stern, L. J. and Stratikos, E., Molecular pathways for antigenic peptide generation by ER aminopeptidase 1. Mol. Immunol. 2019. 113: 50-57.
Hutchinson, J. P., Temponeras, I., Kuiper, J., Cortes, A., Korczynska, J., Kitchen, S. and Stratikos, E., Common allotypes of ER aminopeptidase 1 have substrate-dependent and highly variable enzymatic properties. J. Biol. Chem. 2021. 296: 100443.
Stamatakis, G., Samiotaki, M., Temponeras, I., Panayotou, G. and Stratikos, E., Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 spike glycoprotein. J. Biol. Chem. 2021. 297: 101329.
Stratikos, E., Regulating adaptive immune responses using small molecule modulators of aminopeptidases that process antigenic peptides. Curr. Opin. Chem. Biol. 2014. 23: 1-7.
Reeves, E., Islam, Y. and James, E., ERAP1: A potential therapeutic target for a myriad of diseases. Expert Opin. Ther. Targets 2020. 24: 535-544.
Georgiadis, D., Mpakali, A., Koumantou, D. and Stratikos, E., Inhibitors of ER aminopeptidase 1 and 2: from design to clinical application. Curr. Med. Chem. 2019. 26: 2715-2729.
Liddle, J., Hutchinson, J. P., Kitchen, S., Rowland, P., Neu, M., Cecconie, T., Holmes, D. S. et al., Targeting the regulatory site of ER aminopeptidase 1 leads to the discovery of a natural product modulator of antigen presentation. J. Med. Chem. 2020. 63: 3348-3358.
Maben, Z., Arya, R., Rane, D., An, W. F., Metkar, S., Hickey, M., Bender, S. et al., Discovery of selective inhibitors of endoplasmic reticulum aminopeptidase 1. J. Med. Chem. 2020. 63: 103-121.
Deddouche-Grass, S., Andouche, C., Bärenz, F., Halter, C., Hohwald, A., Lebrun, L., Membré, N. et al., Discovery and optimization of a series of benzofuran selective ERAP1 inhibitors: biochemical and in silico studies. ACS Med. Chem. Lett. 2021. 12: 1137-1142.
Joyce, P., Quibell, M., Shiers, J., Tong, C., Clark, K., Ternette, N., Anderton, K. et al., 553 First-in-class inhibitors of ERAP1 alter the immunopeptidome of cancer, driving a differentiated T cell response leading to tumor growth inhibition. J. Immunother. Cancer 2021. 9(Suppl): A583.
Papakyriakou, A. and Stratikos, E., The role of conformational dynamics in antigen trimming by intracellular aminopeptidases. Front. Immunol. 2017. 8: 946.
Nguyen, T. T., Chang, S.-C., Evnouchidou, I., York, I. A., Zikos, C., Rock, K. L., Goldberg, A. L. et al., Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1. Nat. Struct. Mol. Biol. 2011. 18: 604-613.
Kochan, G., Krojer, T., Harvey, D., Fischer, R., Chen, L., Vollmar, M., von Delft, F. et al., Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming. Proc. Natl. Acad. Sci. U. S. A. 2011. 108: 7745-7750.
Maben, Z., Arya, R., Georgiadis, D., Stratikos, E. and Stern, L. J., Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nat. Commun. 2021. 12: 5302.
Giastas, P., Mpakali, A., Papakyriakou, A., Lelis, A., Kokkala, P., Neu, M., Rowland, P. et al., Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1. Proc. Natl. Acad. Sci. U. S. A. 2019. 116: 26709-26716.
Bruderer, R., Bernhardt, O. M., Gandhi, T., Miladinović, S. M., Cheng, L.-Y., Messner, S., Ehrenberger, T. et al., Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues. Mol. Cell. Proteomics 2015. 14: 1400-1410.
Alvarez-Navarro, C., Martín-Esteban, A., Barnea, E., Admon, A. and López De Castro, J. A., Endoplasmic reticulum aminopeptidase 1 (ERAP1) polymorphism relevant to inflammatory disease shapes the peptidome of the birdshot chorioretinopathy-associated HLA-A*29:02 antigen. Mol. Cell. Proteomics 2015. 14: 1770-1780.
Barnea, E., Melamed Kadosh, D., Haimovich, Y., Satumtira, N., Dorris, M. L., Nguyen, M. T., Hammer, R. E. et al., The human leukocyte antigen (HLA)-B27 peptidome in vivo, in spondyloarthritis-susceptible HLA-B27 transgenic rats and the effect of Erap1 deletion. Mol. Cell. Proteomics 2017. 16: 642-662.
Guasp, P., Barnea, E., Gonzalez-Escribano, M. F., Jimenez-Reinoso, A., Regueiro, J. R., Admon, A. and Lopez de Castro, J. A., The behcet's disease-associated variant of the aminopeptidase ERAP1 shapes a low-affinity HLA-B*51 peptidome by differential subpeptidome processing. J. Biol. Chem. 2017. 292: 9680-9689.
Patil, I., Visualizations with statistical details: The “ggstatsplot” approach. J. Open Source Softw. 2021. 6: 3167.
Sarkizova, S., Klaeger, S., Le, P. M., Li, L. W., Oliveira, G., Keshishian, H., Hartigan, C. R. et al., A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat. Biotechnol. 2020. 38: 199-209.
Hammer, G. E., Gonzalez, F., James, E., Nolla, H. and Shastri, N., In the absence of aminopeptidase ERAAP, MHC class I molecules present many unstable and highly immunogenic peptides. Nat. Immunol. 2007. 8: 101-108.
Chong, C., Müller, M., Pak, H. S., Harnett, D., Huber, F., Grun, D., Leleu, M. et al., Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Nat. Commun. 2020. 11, https://doi.org/10.1038/s41467-020-14968-9.
Evnouchidou, I., Momburg, F., Papakyriakou, A., Chroni, A., Leondiadis, L., Chang, S.-C., Goldberg, A. L. et al., The internal sequence of the peptide-substrate determines its n-terminus trimming by ERAP1. PLoS One 2008. 3: e3658.
Goslee, S. C. and Urban, D. L., The ecodist package for dissimilarity-based analysis of ecological data. J. Stat. Softw. 2007. 22: 1-19.
Zervoudi, E., Papakyriakou, A., Georgiadou, D., Evnouchidou, I., Gajda, A., Poreba, M., Salvesen, G. S. et al., Probing the S1 specificity pocket of the aminopeptidases that generate antigenic peptides. Biochem. J. 2011. 435: 411-420.
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A. and Zhang, F., Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 2013. 8: 2281-2308.
Temponeras, I., Stamatakis, G., Samiotaki, M., Georgiadis, D., Pratsinis, H., Panayotou, G. and Stratikos, E., ERAP2 inhibition induces cell-surface presentation by MOLT-4 leukemia cancer cells of many novel and potentially antigenic peptides. Int. J. Mol. Sci. 2022. 23: 1913.
Hughes, C. S., Moggridge, S., Müller, T., Sorensen, P. H., Morin, G. B. and Krijgsveld, J., Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nat. Protoc. 2019. 14: 68-85.
Venema, W. J., Hiddingh, S., de Boer, J. H., Claas, F. H. J., Mulder, A., den Hollander, A. I., Stratikos, E. et al., ERAP2 increases the abundance of a peptide submotif highly selective for the birdshot uveitis-associated HLA-A29. Front. Immunol. 2021. 12: 634441.
Hennig, C. Flexible procedures for clustering. 2020.
Hahsler, M., Piekenbrock, M. and Doran, D., Dbscan: fast density-based clustering with R. J. Stat. Softw. 2019. 91: 1-30.
Wagih, O. G. A versatile R package for drawing sequence logos. Bioinforma. Oxf. Engl. 2017. 33: 3645-3647.
Stratikos, E., Modulating antigen processing for cancer immunotherapy. Oncoimmunology 2014. 3: e27568.
Schumacher, T. N. and Schreiber, R. D., Neoantigens in cancer immunotherapy. Science 2015. 348: 69-74.
McGonagle, D., Aydin, S. Z., Gul, A., Mahr, A. and Direskeneli, H. ’MHC-I-Opathy’-unified concept for spondyloarthritis and behcet disease. Nat. Rev. Rheumatol. 2015. 11: 731-740.
Yang, X., Garner, L. I., Zvyagin, I. V., Paley, M. A., Komech, E. A., Jude, K. M., Zhao, X. et al., Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Nature 2022. 612: 771-777.
Arakawa, A., Reeves, E., Vollmer, S., Arakawa, Y., He, M., Galinski, A., Stöhr, J. et al., ERAP1 controls the autoimmune response against melanocytes in psoriasis by generating the melanocyte autoantigen and regulating its amount for HLA-C*06:02 presentation. J. Immunol. Baltim. Md. 1950 2021. 207: 2235-2244.
James, E., Bailey, I., Sugiyarto, G. and Elliott, T. Induction of protective antitumor immunity through attenuation of ERAAP function. J. Immunol. 2013. 190: 5839-5846.
Admon, A., ERAP1 shapes just part of the immunopeptidome. Hum. Immunol. 2019. 80: 296-301.
Hisatsune, C., Ebisui, E., Usui, M., Ogawa, N., Suzuki, A., Mataga, N., Takahashi-Iwanaga, H. et al., ERp44 exerts redox-dependent control of blood pressure at the ER. Mol. Cell 2015. 58: 1015-1027.
Saveanu, L., Carroll, O., Lindo, V., Del Val, M., Lopez, D., Lepelletier, Y., Greer, F. et al., Concerted peptide trimming by human ERAP1 and ERAP2 aminopeptidase complexes in the endoplasmic reticulum. Nat. Immunol. 2005. 6: 689-697.
Papakyriakou, A., Mpakali, A. and Stratikos, E., Can ERAP1 and ERAP2 form functional heterodimers? A structural dynamics investigation. Front. Immunol. 2022. 13: 863529.
Aldhamen, Y. A., Pepelyayeva, Y., Rastall, D. P. W., Seregin, S. S., Zervoudi, E., Koumantou, D., Aylsworth, C. F. et al., Autoimmune disease-associated variants of extracellular endoplasmic reticulum aminopeptidase 1 induce altered innate immune responses by human immune cells. J. Innate Immun. 2015. 7: 275-289.
Schmidt, K., Leisegang, M. and Kloetzel, P.-M., ERAP2 supports TCR recognition of three immunotherapy targeted tumor epitopes. Mol. Immunol. 2023. 154: 61-68.
Perez-Riverol, Y., Csordas, A., Bai, J., Bernal-Llinares, M., Hewapathirana, S., Kundu, D. J., Inuganti, A. et al., The PRIDE database and related tools and resources in 2019: Improving support for quantification data. Nucleic. Acids. Res. 2019. 47: D442-D450.
معلومات مُعتمدة: 954992-CAPSTONE-H2020-MSCA-ITN-2020 United Kingdom MCCC_ Marie Curie
فهرسة مساهمة: Keywords: Major Histocompatibility Molecules class I; allosteric inhibitor; autoimmunity; cancer immunotherapy; immunopeptidome
المشرفين على المادة: EC 3.4.11.- (Aminopeptidases)
0 (Peptides)
0 (Antigens)
0 (Minor Histocompatibility Antigens)
EC 3.4.11.- (ERAP1 protein, human)
تواريخ الأحداث: Date Created: 20230503 Date Completed: 20230814 Latest Revision: 20230815
رمز التحديث: 20231215
DOI: 10.1002/eji.202350449
PMID: 37134263
قاعدة البيانات: MEDLINE
الوصف
تدمد:1521-4141
DOI:10.1002/eji.202350449