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Herhaus L, Gestal-Mato U, Eapen VV, Mačinković I, Bailey HJ, Prieto-Garcia C, Misra M, Jacomin AC, Ammanath AV, Bagarić I, Michaelis J, Vollrath J, Bhaskara RM, Bündgen G, Covarrubias-Pinto A, Husnjak K, Zöller J, Gikandi A, Ribičić S, Bopp T, van der Heden van Noort GJ, Langer JD, Weigert A, Harper JW, Mancias JD, Dikic I. IRGQ-mediated autophagy in MHC class I quality control promotes tumor immune evasion. Cell 2024; 187:7285-7302.e29. [PMID: 39481378 DOI: 10.1016/j.cell.2024.09.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 06/24/2024] [Accepted: 09/29/2024] [Indexed: 11/02/2024]
Abstract
The autophagy-lysosome system directs the degradation of a wide variety of cargo and is also involved in tumor progression. Here, we show that the immunity-related GTPase family Q protein (IRGQ), an uncharacterized protein to date, acts in the quality control of major histocompatibility complex class I (MHC class I) molecules. IRGQ directs misfolded MHC class I toward lysosomal degradation through its binding mode to GABARAPL2 and LC3B. In the absence of IRGQ, free MHC class I heavy chains do not only accumulate in the cell but are also transported to the cell surface, thereby promoting an immune response. Mice and human patients suffering from hepatocellular carcinoma show improved survival rates with reduced IRGQ levels due to increased reactivity of CD8+ T cells toward IRGQ knockout tumor cells. Thus, we reveal IRGQ as a regulator of MHC class I quality control, mediating tumor immune evasion.
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Affiliation(s)
- Lina Herhaus
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Uxía Gestal-Mato
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Vinay V Eapen
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Institutes of Medicine, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Igor Mačinković
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Institute of Biochemistry I, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Henry J Bailey
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Cristian Prieto-Garcia
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Mohit Misra
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Anne-Claire Jacomin
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Aparna Viswanathan Ammanath
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ivan Bagarić
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jolina Michaelis
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Joshua Vollrath
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Goethe University Frankfurt, Riedberg Campus, 60438 Frankfurt am Main, Germany
| | - Ramachandra M Bhaskara
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Georg Bündgen
- Institute for Immunology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Adriana Covarrubias-Pinto
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jonathan Zöller
- Max Planck Institute of Biophysics, Goethe University Frankfurt, Riedberg Campus, 60438 Frankfurt am Main, Germany
| | - Ajami Gikandi
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Institutes of Medicine, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Sara Ribičić
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Tobias Bopp
- Institute for Immunology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Julian D Langer
- Max Planck Institute of Biophysics, Goethe University Frankfurt, Riedberg Campus, 60438 Frankfurt am Main, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Institutes of Medicine, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Frankfurt, Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Max Planck Institute of Biophysics, Goethe University Frankfurt, Riedberg Campus, 60438 Frankfurt am Main, Germany.
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Chieochansin T, Sanachai K, Darai N, Chiraphapphaiboon W, Choomee K, Yenchitsomanus PT, Thuwajit C, Rungrotmongkol T. In silico advancements in Peptide-MHC interaction: A molecular dynamics study of predicted glypican-3 peptides and HLA-A*11:01. Heliyon 2024; 10:e36654. [PMID: 39263056 PMCID: PMC11385767 DOI: 10.1016/j.heliyon.2024.e36654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024] Open
Abstract
Our study employed molecular dynamics (MD) simulations to assess the binding affinity between short peptides derived from the tumor-associated antigen glypican 3 (GPC3) and the major histocompatibility complex (MHC) molecule HLA-A*11:01 in hepatocellular carcinoma. We aimed to improve the reliability of in silico predictions of peptide-MHC interactions, which are crucial for developing targeted cancer therapies. We used five algorithms to discover four peptides (TTDHLKFSK, VINTTDHLK, KLIMTQVSK, and STIHDSIQY), demonstrating the substantial potential for HLA-A11:01 presentation. The Anchored Peptide-MHC Ensemble Generator (APE-Gen) was used to create the initial structure of the peptide-MHC complex. This was followed by a 200 ns molecular dynamics (MD) simulation using AMBER22, which verified the precise positioning of the peptides in the binding groove of HLA-A*11:01, specifically at the A and F pockets. Notably, the 2nd residue, which serves as a critical anchor within the 2nd pocket, played a pivotal role in stabilising the binding interactions.VINTTDHLK (ΔG SIE = -14.46 ± 0.53 kcal/mol and ΔG MM/GBSA = -30.79 ± 0.49 kcal/mol) and STIHDSIQY (ΔG SIE and ΔG MM/GBSA = -14.55 ± 0.16 and -23.21 ± 2.23 kcal/mol) exhibited the most effective binding potential among the examined peptides, as indicated by both their binding free energies and its binding affinity on the T2 cell line (VINTTDHLK: IC50 = 0.45 nM; STIHDSIQY: IC50 = 0.35 nM). The remarkable concordance between in silico and in vitro binding affinity results was of particular significance, indicating that MD simulation is a potent instrument capable of bolstering confidence in in silico peptide predictions. By employing MD simulation as a method, our study provides a promising avenue for improving the prediction of potential peptide-MHC interactions, thereby facilitating the development of more effective and targeted cancer therapies.
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Affiliation(s)
- Thaweesak Chieochansin
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Nitchakan Darai
- Futuristic Science Research Center, School of Science, Walailak University, Nakhon Si Thammarat, Thailand
| | - Wannasiri Chiraphapphaiboon
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kornkan Choomee
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Structural and Computational Biology, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
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Ayukawa S, Kamoshita N, Maruyama T. Epithelial recognition and elimination against aberrant cells. Semin Immunopathol 2024; 45:521-532. [PMID: 38411739 DOI: 10.1007/s00281-024-01001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024]
Abstract
Epithelial cells, which are non-immune cells, not only function as a physical defence barrier but also continuously monitor and eliminate aberrant epithelial cells in their vicinity. In other words, it has become evident that epithelial cells possess immune cell-like functions. In fact, recent research has revealed that epithelial cells recognise the Major Histocompatibility Complex I (MHC-I) of aberrant cells as a mechanism for surveillance. This cellular defence mechanism of epithelial cells probably detects aberrant cells more promptly than the conventional immune response, making it a novel and primary biological defence. Furthermore, there is the potential for this new immune-like biological defence mechanism to establish innovative treatment for disease prevention, leading to increasing anticipation for its future medical applications. In this review, we aim to summarise the recognition and attack mechanisms of aberrant cells by epithelial cells in mammals, with a particular focus on the field of cancer. Additionally, we discuss the potential therapeutic applications of epithelial cell-based defence against cancer, including novel prophylactic treatment methods based on molecular mechanisms.
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Affiliation(s)
- Shiyu Ayukawa
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Department of Medical Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Science, Tokyo, Japan
| | - Nagisa Kamoshita
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Waseda Institute for Advanced Study, Waseda University, Tokyo, Japan
| | - Takeshi Maruyama
- Department of Medical Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Science, Tokyo, Japan.
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan.
- Waseda Institute for Advanced Study, Waseda University, Tokyo, Japan.
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Andreescu M, Berbec N, Tanase AD. Assessment of Impact of Human Leukocyte Antigen-Type and Cytokine-Type Responses on Outcomes after Targeted Therapy Currently Used to Treat Chronic Lymphocytic Leukemia. J Clin Med 2023; 12:jcm12072731. [PMID: 37048814 PMCID: PMC10094967 DOI: 10.3390/jcm12072731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
Tumor growth and metastasis are reliant on intricate interactions between the host immune system and various counter-regulatory immune escape mechanisms employed by the tumor. Tumors can resist immune surveillance by modifying the expression of human leukocyte antigen (HLA) molecules, which results in the impaired presentation of tumor-associated antigens, subsequently evading detection and destruction by the immune system. The management of chronic lymphocytic leukemia (CLL) is based on symptom severity and includes various types of targeted therapies, including rituximab, obinutuzumab, ibrutinib, acalabrutinib, zanubrutinib, idelalisib, and venetoclax. These therapies rely on the recognition of specific peptides presented by HLAs on the surface of tumor cells by T cells, leading to an immune response. HLA class I molecules are found in most human cell types and interact with T-cell receptors (TCRs) to activate T cells, which play a vital role in inducing adaptive immune responses. However, tumor cells may evade T-cell attack by downregulating HLA expression, limiting the efficacy of HLA-dependent immunotherapy. The prognosis of CLL largely depends on the presence or absence of genetic abnormalities, such as del(17p), TP53 point mutations, and IGHV somatic hypermutation status. These oral targeted therapies alone or in combination with anti-CD20 antibodies have replaced chemoimmunotherapy as the primary treatment for CLL. In this review, we summarize the current clinical evidence on the impact of HLA- and cytokine-type responses on outcomes after targeted therapies currently used to treat CLL.
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Affiliation(s)
- Mihaela Andreescu
- Department of Clinical Sciences, Hematology, Faculty of Medicine, Titu Maiorescu University of Bucharest, 040051 Bucharest, Romania
- Department of Hematology, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Nicoleta Berbec
- Department of Hematology, Coltea Clinical Hospital, 020125 Bucharest, Romania
- Faculty of Medicine, Carol Davila University of Bucharest, 040051 Bucharest, Romania
| | - Alina Daniela Tanase
- Faculty of Medicine, Carol Davila University of Bucharest, 040051 Bucharest, Romania
- Department of Hematology, Fundeni Clinical Hospital, 020125 Bucharest, Romania
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Li C, Li S, Yang C, Ding Y, Zhang Y, Wang X, Zhou X, Su Z, Ming W, Zeng L, Ma Y, Shi Y, Kang X. Blood transcriptome reveals immune and metabolic-related genes involved in growth of pasteurized colostrum-fed calves. Front Genet 2023; 14:1075950. [PMID: 36814903 PMCID: PMC9939824 DOI: 10.3389/fgene.2023.1075950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
The quality of colostrum is a key factor contributing to healthy calf growth, and pasteurization of colostrum can effectively reduce the counts of pathogenic microorganisms present in the colostrum. Physiological changes in calves fed with pasteurized colostrum have been well characterized, but little is known about the underlying molecular mechanisms. In this study, key genes and functional pathways through which pasteurized colostrum affects calf growth were identified through whole blood RNA sequencing. Our results showed that calves in the pasteurized group (n = 16) had higher body height and daily weight gain than those in the unpasteurized group (n = 16) in all months tested. Importantly, significant differences in body height were observed at 3 and 4 months of age (p < 0.05), and in daily weight gain at 2, 3, and 6 months of age (p < 0.05) between the two groups. Based on whole blood transcriptome data from 6-months old calves, 630 differentially expressed genes (DEGs), of which 235 were upregulated and 395 downregulated, were identified in the pasteurized compared to the unpasteurized colostrum groups. Most of the DEGs have functions in the immune response (e.g., CCL3, CXCL3, and IL1A) and metabolism (e.g., PTX3 and EXTL1). Protein-protein interaction analyses of DEGs revealed three key subnetworks and fifteen core genes, including UBA52 and RPS28, that have roles in protein synthesis, oxidative phosphorylation, and inflammatory responses. Twelve co-expression modules were identified through weighted gene co-expression network analysis. Among them, 17 genes in the two modules that significantly associated with pasteurization were mainly involved in the tricarboxylic acid cycle, NF-kappa B signaling, and NOD-like receptor signaling pathways. Finally, DEGs that underwent alternative splicing in calves fed pasteurized colostrum have roles in the immune response (SLCO4A1, AKR1C4, and MED13L), indicative of potential roles in immune regulation. Results from multiple analytical methods used suggest that differences in calf growth between the pasteurized and unpasteurized groups may be due to differential immune activity. Our data provide new insights into the impact of pasteurization on calf immune and metabolic-related pathways through its effects on gene expression.
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