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Martin KE, Hammer Q, Perica K, Sadelain M, Malmberg KJ. Engineering immune-evasive allogeneic cellular immunotherapies. Nat Rev Immunol 2024:10.1038/s41577-024-01022-8. [PMID: 38658708 DOI: 10.1038/s41577-024-01022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2024] [Indexed: 04/26/2024]
Abstract
Allogeneic cellular immunotherapies hold a great promise for cancer treatment owing to their potential cost-effectiveness, scalability and on-demand availability. However, immune rejection of adoptively transferred allogeneic T and natural killer (NK) cells is a substantial obstacle to achieving clinical responses that are comparable to responses obtained with current autologous chimeric antigen receptor T cell therapies. In this Perspective, we discuss strategies to confer cell-intrinsic, immune-evasive properties to allogeneic T cells and NK cells in order to prevent or delay their immune rejection, thereby widening the therapeutic window. We discuss how common viral and cancer immune escape mechanisms can serve as a blueprint for improving the persistence of off-the-shelf allogeneic cell therapies. The prospects of harnessing genome editing and synthetic biology to design cell-based precision immunotherapies extend beyond programming target specificities and require careful consideration of innate and adaptive responses in the recipient that may curtail the biodistribution, in vivo expansion and persistence of cellular therapeutics.
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Affiliation(s)
- Karen E Martin
- Precision Immunotherapy Alliance, The University of Oslo, Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research Oslo, Oslo University Hospital, Oslo, Norway
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Karlo Perica
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karl-Johan Malmberg
- Precision Immunotherapy Alliance, The University of Oslo, Oslo, Norway.
- Department of Cancer Immunology, Institute for Cancer Research Oslo, Oslo University Hospital, Oslo, Norway.
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
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2
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Zhu B, Ouda R, Kasuga Y, de Figueiredo P, Kobayashi KS. NLRC5/MHC class I transactivator: A key target for immune escape by SARS-CoV-2. Bioessays 2024; 46:e2300109. [PMID: 38461519 DOI: 10.1002/bies.202300109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/11/2023] [Accepted: 02/01/2024] [Indexed: 03/12/2024]
Abstract
Antigen presentation to CD8+ T cells by MHC class I molecules is essential for host defense against viral infections. Various mechanisms have evolved in multiple viruses to escape immune surveillance and defense to support viral proliferation in host cells. Through in vitro SARS-CoV-2 infection studies and analysis of COVID-19 patient samples, we found that SARS-CoV-2 suppresses the induction of the MHC class I pathway by inhibiting the expression and function of NLRC5, a major transcriptional regulator of MHC class I genes. In this review, we discuss the molecular mechanisms for suppression of the MHC class I pathway and clinical implications for COVID-19.
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Affiliation(s)
- Baohui Zhu
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
| | - Ryota Ouda
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
| | - Yusuke Kasuga
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
| | - Paul de Figueiredo
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA
| | - Koichi S Kobayashi
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Hokkaido, Japan
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, Texas, USA
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3
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Yeo YY, Qiu H, Bai Y, Zhu B, Chang Y, Yeung J, Michel HA, Wright K, Shaban M, Sadigh S, Nkosi D, Shanmugam V, Rock P, Tung Yiu SP, Cramer P, Paczkowska J, Stephan P, Liao G, Huang AY, Wang H, Chen H, Frauenfeld L, Mitra B, Gewurz BE, Schürch CM, Zhao B, Nolan GP, Zhang B, Shalek AK, Angelo M, Mahmood F, Ma Q, Burack WR, Shipp MA, Rodig SJ, Jiang S. Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583586. [PMID: 38496566 PMCID: PMC10942289 DOI: 10.1101/2024.03.05.583586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is associated with Epstein-Barr Virus (EBV) in 25% of cases. The specific contributions of EBV to the pathogenesis of cHL remain largely unknown, in part due to technical barriers in dissecting the tumor microenvironment (TME) in high detail. Herein, we applied multiplexed ion beam imaging (MIBI) spatial pro-teomics on 6 EBV-positive and 14 EBV-negative cHL samples. We identify key TME features that distinguish between EBV-positive and EBV-negative cHL, including the relative predominance of memory CD8 T cells and increased T-cell dysfunction as a function of spatial proximity to HRS cells. Building upon a larger multi-institutional cohort of 22 EBV-positive and 24 EBV-negative cHL samples, we orthogonally validated our findings through a spatial multi-omics approach, coupling whole transcriptome capture with antibody-defined cell types for tu-mor and T-cell populations within the cHL TME. We delineate contrasting transcriptomic immunological signatures between EBV-positive and EBV-negative cases that differently impact HRS cell proliferation, tumor-immune interactions, and mecha-nisms of T-cell dysregulation and dysfunction. Our multi-modal framework enabled a comprehensive dissection of EBV-linked reorganization and immune evasion within the cHL TME, and highlighted the need to elucidate the cellular and molecular fac-tors of virus-associated tumors, with potential for targeted therapeutic strategies.
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4
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Ware BC, Parks MG, da Silva MOL, Morrison TE. Chikungunya virus infection disrupts MHC-I antigen presentation via nonstructural protein 2. PLoS Pathog 2024; 20:e1011794. [PMID: 38483968 DOI: 10.1371/journal.ppat.1011794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/26/2024] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Infection by chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes severe polyarthralgia and polymyalgia, which can last in some people for months to years. Chronic CHIKV disease signs and symptoms are associated with the persistence of viral nucleic acid and antigen in tissues. Like humans and nonhuman primates, CHIKV infection in mice results in the development of robust adaptive antiviral immune responses. Despite this, joint tissue fibroblasts survive CHIKV infection and can support persistent viral replication, suggesting that they escape immune surveillance. Here, using a recombinant CHIKV strain encoding the fluorescent protein VENUS with an embedded CD8+ T cell epitope, SIINFEKL, we observed a marked loss of both MHC class I (MHC-I) surface expression and antigen presentation by CHIKV-infected joint tissue fibroblasts. Both in vivo and ex vivo infected joint tissue fibroblasts displayed reduced cell surface levels of H2-Kb and H2-Db MHC-I proteins while maintaining similar levels of other cell surface proteins. Mutations within the methyl transferase-like domain of the CHIKV nonstructural protein 2 (nsP2) increased MHC-I cell surface expression and antigen presentation efficiency by CHIKV-infected cells. Moreover, expression of WT nsP2 alone, but not nsP2 with mutations in the methyltransferase-like domain, resulted in decreased MHC-I antigen presentation efficiency. MHC-I surface expression and antigen presentation was rescued by replacing VENUS-SIINFEKL with SIINFEKL tethered to β2-microglobulin in the CHIKV genome, which bypasses the requirement for peptide processing and TAP-mediated peptide transport into the endoplasmic reticulum. Collectively, this work suggests that CHIKV escapes the surveillance of antiviral CD8+ T cells, in part, by nsP2-mediated disruption of MHC-I antigen presentation.
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Affiliation(s)
- Brian C Ware
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - M Guston Parks
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Mariana O L da Silva
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thomas E Morrison
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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5
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Ware BC, Parks MG, Morrison TE. Chikungunya virus infection disrupts MHC-I antigen presentation via nonstructural protein 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565436. [PMID: 37961400 PMCID: PMC10635105 DOI: 10.1101/2023.11.03.565436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Infection by chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes severe polyarthralgia and polymyalgia, which can last in some people for months to years. Chronic CHIKV disease signs and symptoms are associated with the persistence of viral nucleic acid and antigen in tissues. Like humans and nonhuman primates, CHIKV infection in mice results in the development of robust adaptive antiviral immune responses. Despite this, joint tissue fibroblasts survive CHIKV infection and can support persistent viral replication, suggesting that they escape immune surveillance. Here, using a recombinant CHIKV strain encoding a chimeric protein of VENUS fused to a CD8+ T cell epitope, SIINFEKL, we observed a marked loss of both MHC class I (MHC-I) surface expression and antigen presentation by CHIKV-infected joint tissue fibroblasts. Both in vivo and ex vivo infected joint tissue fibroblasts displayed reduced cell surface levels of H2-Kb and H2-Db MHC proteins while maintaining similar levels of other cell surface proteins. Mutations within the methyl transferase-like domain of the CHIKV nonstructural protein 2 (nsP2) increased MHC-I cell surface expression and antigen presentation efficiency by CHIKV-infected cells. Moreover, expression of WT nsP2 alone, but not nsP2 with mutations in the methyltransferase-like domain, resulted in decreased MHC-I antigen presentation efficiency. MHC-I surface expression and antigen presentation could be rescued by replacing VENUS-SIINFEKL with SIINFEKL tethered to β2-microglobulin in the CHIKV genome, which bypasses the need for peptide processing and TAP-mediated peptide transport into the endoplasmic reticulum. Collectively, this work suggests that CHIKV escapes the surveillance of antiviral CD8+ T cells, in part, by nsP2-mediated disruption of MHC-I antigen presentation.
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Affiliation(s)
- Brian C. Ware
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - M. Guston Parks
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Thomas E. Morrison
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Diao H, Xue WQ, Wang TM, Yang DW, Deng CM, Li DH, Zhang WL, Liao Y, Wu YX, Chen XY, Zhou T, Li XZ, Zhang PF, Zheng XH, Zhang SD, Hu YZ, Cao SM, Liu Q, Ye WM, He YQ, Jia WH. The interaction and mediation effects between the host genetic factors and Epstein-Barr virus VCA-IgA in the risk of nasopharyngeal carcinoma. J Med Virol 2023; 95:e29224. [PMID: 37970759 DOI: 10.1002/jmv.29224] [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: 07/16/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/17/2023]
Abstract
Previous studies have demonstrated strong associations between host genetic factors and Epstein-Barr virus (EBV) VCA-IgA with the risk of nasopharyngeal carcinoma (NPC). However, the specific interplay between host genetics and EBV VCA-IgA on NPC risk is not well understood. In this two-stage case-control study (N = 4804), we utilized interaction and mediation analysis to investigate the interplay between host genetics (genome-wide association study-derived polygenic risk score [PRS]) and EBV VCA-IgA antibody level in the NPC risk. We employed a four-way decomposition analysis to assess the extent to which the genetic effect on NPC risk is mediated by or interacts with EBV VCA-IgA. We consistently found a significant interaction between the PRS and EBV VCA-IgA on NPC risk (discovery population: synergy index [SI] = 2.39, 95% confidence interval [CI] = 1.85-3.10; replication population: SI = 3.10, 95% CI = 2.17-4.44; all pinteraction < 0.001). Moreover, the genetic variants included in the PRS demonstrated similar interactions with EBV VCA-IgA antibody. We also observed an obvious dose-response relationship between the PRS and EBV VCA-IgA antibody on NPC risk (all ptrend < 0.001). Furthermore, our decomposition analysis revealed that a substantial proportion (approximately 90%) of the genetic effects on NPC risk could be attributed to host genetic-EBV interaction, while the risk effects mediated by EBV VCA-IgA antibody were weak and statistically insignificant. Our study provides compelling evidence for an interaction between host genetics and EBV VCA-IgA antibody in the development of NPC. These findings emphasize the importance of implementing measures to control EBV infection as a crucial strategy for effectively preventing NPC, particularly in individuals at high genetic risk.
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Affiliation(s)
- Hua Diao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dan-Hua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xue-Yin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shao-Dan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ye-Zhu Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Su-Mei Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Cancer Prevention Center, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Qing Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
- Department of Cancer Prevention Center, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wei-Min Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology and Health Statistics and Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
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7
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Mogahadam HK, Røsaeg MV. From viral load to survival: Unveiling new genetic links for resistance against PMCV in Atlantic Salmon (Salmo salar). JOURNAL OF FISH DISEASES 2023; 46:1285-1294. [PMID: 37579006 DOI: 10.1111/jfd.13847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
The infectious agent piscine myocarditis virus (PMCV) causes cardiomyopathy syndrome (CMS) and is responsible for substantial mortality and economic losses in the Atlantic salmon (Salmo salar) farming industry. Previous research has demonstrated that breeding for resistance against PMCV is an effective approach to mitigate the disease's impact. In this study, a new quantitative trait locus (QTL) is described on chromosome 23, together with previously described QTLs on chromosomes 12 and 27. The findings are based on two genome-wide association studies conducted on two different year-classes of Atlantic salmon of the Rauma strain. In this study, we utilized data from an experimental challenge trial with the viral load as the phenotype and a field outbreak of CMS with survival data as the phenotype. The estimated SNP-based heritability was 0.55 and 0.44 in the two studies, respectively. In the infection trial, the top associated SNP on chromosome 23 accounted for approximately 46% of the genetic and 25.53% of the phenotypic variations in the viral load. In the field outbreak, we identified a QTL on the same genomic region of chromosome 23. The most significantly associated marker on this chromosome explained 13.57% and 5.97% of the genetic and phenotypic variations. The QTL on chromosome 23 is in proximity to delta-5 fatty acyl desaturase and fatty acid desaturase 2 genes, both of which play a role in the production of polyunsaturated fatty acids. This proximity is particularly interesting as it offers valuable insights into enhancing our understanding of resistance against PMCV.
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Fillion AJ, Bricco AR, Lee HD, Korenchan D, Farrar CT, Gilad AA. Development of a synthetic biosensor for chemical exchange MRI utilizing in silico optimized peptides. NMR IN BIOMEDICINE 2023; 36:e5007. [PMID: 37469121 PMCID: PMC11075521 DOI: 10.1002/nbm.5007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/21/2023]
Abstract
Chemical exchange saturation transfer (CEST) MRI has been identified as a novel alternative to classical diagnostic imaging. Over the last several decades, many studies have been conducted to determine possible CEST agents, such as endogenously expressed compounds or proteins, that can be utilized to produce contrast with minimally invasive procedures and reduced or non-existent levels of toxicity. In recent years there has been an increased interest in the generation of genetically engineered CEST contrast agents, typically based on existing proteins with CEST contrast or modified to produce CEST contrast. We have developed an in silico method for the evolution of peptide sequences to optimize CEST contrast and showed that these peptides could be combined to create de novo biosensors for CEST MRI. A single protein, superCESTide, was designed to be 198 amino acids. SuperCESTide was expressed in E. coli and purified with size exclusion chromatography. The magnetic transfer ratio asymmetry generated by superCESTide was comparable to levels seen in previous CEST reporters, such as protamine sulfate (salmon protamine) and human protamine. These data show that novel peptides with sequences optimized in silico for CEST contrast that utilize a more comprehensive range of amino acids can still produce contrast when assembled into protein units expressed in complex living environments.
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Affiliation(s)
- Adam J. Fillion
- Department of Chemical Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Alexander R. Bricco
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Harvey D. Lee
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, USA
| | - David Korenchan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, MA, USA
| | - Christian T. Farrar
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, MA, USA
| | - Assaf A. Gilad
- Department of Chemical Engineering, Michigan State University, East Lansing, Michigan, USA
- Department of Radiology, Michigan State University, East Lansing, Michigan, USA
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9
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Eberhardt N, Noval MG, Kaur R, Amadori L, Gildea M, Sajja S, Das D, Cilhoroz B, Stewart O, Fernandez DM, Shamailova R, Guillen AV, Jangra S, Schotsaert M, Newman JD, Faries P, Maldonado T, Rockman C, Rapkiewicz A, Stapleford KA, Narula N, Moore KJ, Giannarelli C. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. NATURE CARDIOVASCULAR RESEARCH 2023; 2:899-916. [PMID: 38076343 PMCID: PMC10702930 DOI: 10.1038/s44161-023-00336-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/23/2023] [Indexed: 12/19/2023]
Abstract
Patients with coronavirus disease 2019 (COVID-19) present increased risk for ischemic cardiovascular complications up to 1 year after infection. Although the systemic inflammatory response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection likely contributes to this increased cardiovascular risk, whether SARS-CoV-2 directly infects the coronary vasculature and attendant atherosclerotic plaques remains unknown. Here we report that SARS-CoV-2 viral RNA is detectable and replicates in coronary lesions taken at autopsy from severe COVID-19 cases. SARS-CoV-2 targeted plaque macrophages and exhibited a stronger tropism for arterial lesions than adjacent perivascular fat, correlating with macrophage infiltration levels. SARS-CoV-2 entry was increased in cholesterol-loaded primary macrophages and dependent, in part, on neuropilin-1. SARS-CoV-2 induced a robust inflammatory response in cultured macrophages and human atherosclerotic vascular explants with secretion of cytokines known to trigger cardiovascular events. Our data establish that SARS-CoV-2 infects coronary vessels, inducing plaque inflammation that could trigger acute cardiovascular complications and increase the long-term cardiovascular risk.
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Affiliation(s)
- Natalia Eberhardt
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Maria Gabriela Noval
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Ravneet Kaur
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Letizia Amadori
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Michael Gildea
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Swathy Sajja
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Dayasagar Das
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Burak Cilhoroz
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - O’Jay Stewart
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawn M. Fernandez
- Department of Medicine, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roza Shamailova
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Andrea Vasquez Guillen
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan D. Newman
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Peter Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Maldonado
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Caron Rockman
- Department of Surgery, Vascular Division, New York University Langone Health, New York, NY, USA
| | - Amy Rapkiewicz
- Department of Pathology, NYU Winthrop Hospital, Long Island School of Medicine, New York, NY, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Navneet Narula
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Kathryn J. Moore
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York University School of Medicine, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
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10
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He X, Wang J, Tang Y, Chiang ST, Han T, Chen Q, Qian C, Shen X, Li R, Ai X. Recent Advances of Emerging Spleen-Targeting Nanovaccines for Immunotherapy. Adv Healthc Mater 2023; 12:e2300351. [PMID: 37289567 DOI: 10.1002/adhm.202300351] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Vaccines provide a powerful tool to modulate the immune system for human disease prevention and treatment. Classical vaccines mainly initiate immune responses in the lymph nodes (LNs) after subcutaneous injection. However, some vaccines suffer from inefficient delivery of antigens to LNs, undesired inflammation, and slow immune induction when encountering the rapid proliferation of tumors. Alternatively, the spleen, as the largest secondary lymphoid organ with a high density of antigen-presenting cells (APCs) and lymphocytes, acts as an emerging target organ for vaccinations in the body. Upon intravenous administration, the rationally designed spleen-targeting nanovaccines can be internalized by the APCs in the spleen to induce selective antigen presentation to T and B cells in their specific sub-regions, thereby rapidly boosting durable cellular and humoral immunity. Herein, the recent advances of spleen-targeting nanovaccines for immunotherapy based on the anatomical architectures and functional zones of the spleen, as well as their limitations and perspectives for clinical applications are systematically summarized. The aim is to emphasize the design of innovative nanovaccines for enhanced immunotherapy of intractable diseases in the future.
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Affiliation(s)
- Xuanyi He
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Jing Wang
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Yuqing Tang
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Seok Theng Chiang
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Tianzhen Han
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Qi Chen
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Chunxi Qian
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiaoshuai Shen
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Rongxiu Li
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiangzhao Ai
- Department of Bioengineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
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11
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Sandberg JK, Leeansyah E, Eller MA, Shacklett BL, Paquin-Proulx D. The Emerging Role of MAIT Cell Responses in Viral Infections. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:511-517. [PMID: 37549397 PMCID: PMC10421619 DOI: 10.4049/jimmunol.2300147] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/08/2023] [Indexed: 08/09/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells are unconventional T cells with innate-like antimicrobial responsiveness. MAIT cells are known for MR1 (MHC class I-related protein 1)-restricted recognition of microbial riboflavin metabolites giving them the capacity to respond to a broad range of microbes. However, recent progress has shown that MAIT cells can also respond to several viral infections in humans and in mouse models, ranging from HIV-1 and hepatitis viruses to influenza virus and SARS-CoV-2, in a primarily cognate Ag-independent manner. Depending on the disease context MAIT cells can provide direct or indirect antiviral protection for the host and may help recruit other immune cells, but they may also in some circumstances amplify inflammation and aggravate immunopathology. Furthermore, chronic viral infections are associated with varying degrees of functional and numerical MAIT cell impairment, suggesting secondary consequences for host defense. In this review, we summarize recent progress and highlight outstanding questions regarding the emerging role of MAIT cells in antiviral immunity.
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Affiliation(s)
- Johan K. Sandberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edwin Leeansyah
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Precision Medicine and Healthcare Research Centre, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Michael A. Eller
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Barbara L. Shacklett
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA
| | - Dominic Paquin-Proulx
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD
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12
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Eberhardt N, Noval MG, Kaur R, Sajja S, Amadori L, Das D, Cilhoroz B, Stewart O, Fernandez DM, Shamailova R, Guillen AV, Jangra S, Schotsaert M, Gildea M, Newman JD, Faries P, Maldonado T, Rockman C, Rapkiewicz A, Stapleford KA, Narula N, Moore KJ, Giannarelli C. SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553245. [PMID: 37645908 PMCID: PMC10461985 DOI: 10.1101/2023.08.14.553245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
COVID-19 patients present higher risk for myocardial infarction (MI), acute coronary syndrome, and stroke for up to 1 year after SARS-CoV-2 infection. While the systemic inflammatory response to SARS-CoV-2 infection likely contributes to this increased cardiovascular risk, whether SARS-CoV-2 directly infects the coronary vasculature and attendant atherosclerotic plaques to locally promote inflammation remains unknown. Here, we report that SARS-CoV-2 viral RNA (vRNA) is detectable and replicates in coronary atherosclerotic lesions taken at autopsy from patients with severe COVID-19. SARS-CoV-2 localizes to plaque macrophages and shows a stronger tropism for arterial lesions compared to corresponding perivascular fat, correlating with the degree of macrophage infiltration. In vitro infection of human primary macrophages highlights that SARS-CoV-2 entry is increased in cholesterol-loaded macrophages (foam cells) and is dependent, in part, on neuropilin-1 (NRP-1). Furthermore, although viral replication is abortive, SARS-CoV-2 induces a robust inflammatory response that includes interleukins IL-6 and IL-1β, key cytokines known to trigger ischemic cardiovascular events. SARS-CoV-2 infection of human atherosclerotic vascular explants recapitulates the immune response seen in cultured macrophages, including pro-atherogenic cytokine secretion. Collectively, our data establish that SARS-CoV-2 infects macrophages in coronary atherosclerotic lesions, resulting in plaque inflammation that may promote acute CV complications and long-term risk for CV events.
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13
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He W, Gea-Mallorquí E, Colin-York H, Fritzsche M, Gillespie GM, Brackenridge S, Borrow P, McMichael AJ. Intracellular trafficking of HLA-E and its regulation. J Exp Med 2023; 220:214089. [PMID: 37140910 PMCID: PMC10165540 DOI: 10.1084/jem.20221941] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/13/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Interest in MHC-E-restricted CD8+ T cell responses has been aroused by the discovery of their efficacy in controlling simian immunodeficiency virus (SIV) infection in a vaccine model. The development of vaccines and immunotherapies utilizing human MHC-E (HLA-E)-restricted CD8+ T cell response requires an understanding of the pathway(s) of HLA-E transport and antigen presentation, which have not been clearly defined previously. We show here that, unlike classical HLA class I, which rapidly exits the endoplasmic reticulum (ER) after synthesis, HLA-E is largely retained because of a limited supply of high-affinity peptides, with further fine-tuning by its cytoplasmic tail. Once at the cell surface, HLA-E is unstable and is rapidly internalized. The cytoplasmic tail plays a crucial role in facilitating HLA-E internalization, which results in its enrichment in late and recycling endosomes. Our data reveal distinctive transport patterns and delicate regulatory mechanisms of HLA-E, which help to explain its unusual immunological functions.
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Affiliation(s)
- Wanlin He
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Ester Gea-Mallorquí
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Huw Colin-York
- Kennedy Institute of Rheumatology, University of Oxford , Oxford, UK
| | - Marco Fritzsche
- Kennedy Institute of Rheumatology, University of Oxford , Oxford, UK
| | - Geraldine M Gillespie
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Simon Brackenridge
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Persephone Borrow
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine, Center for Immuno-Oncology, University of Oxford, Oxford, UK
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14
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Kim IJ, Lee YH, Khalid MM, Chen IP, Zhang Y, Ott M, Verdin E. SARS-CoV-2 protein ORF8 limits expression levels of Spike antigen and facilitates immune evasion of infected host cells. J Biol Chem 2023; 299:104955. [PMID: 37354973 PMCID: PMC10289268 DOI: 10.1016/j.jbc.2023.104955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
Recovery from COVID-19 depends on the ability of the host to effectively neutralize virions and infected cells, a process largely driven by antibody-mediated immunity. However, with the newly emerging variants that evade Spike-targeting antibodies, re-infections and breakthrough infections are increasingly common. A full characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mechanisms counteracting antibody-mediated immunity is therefore needed. Here, we report that ORF8 is a virally encoded SARS-CoV-2 factor that controls cellular Spike antigen levels. We show that ORF8 limits the availability of mature Spike by inhibiting host protein synthesis and retaining Spike at the endoplasmic reticulum, reducing cell-surface Spike levels and recognition by anti-SARS-CoV-2 antibodies. In conditions of limited Spike availability, we found ORF8 restricts Spike incorporation during viral assembly, reducing Spike levels in virions. Cell entry of these virions then leaves fewer Spike molecules at the cell surface, limiting antibody recognition of infected cells. Based on these findings, we propose that SARS-CoV-2 variants may adopt an ORF8-dependent strategy that facilitates immune evasion of infected cells for extended viral production.
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Affiliation(s)
- Ik-Jung Kim
- Buck Institute for Research on Aging, Novato, California, United States.
| | - Yong-Ho Lee
- Buck Institute for Research on Aging, Novato, California, United States; Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Irene P Chen
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Yini Zhang
- Buck Institute for Research on Aging, Novato, California, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States; Department of Medicine, University of California, San Francisco, San Francisco, California, United States; Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, United States.
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15
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Palmer WH, Norman PJ. The impact of HLA polymorphism on herpesvirus infection and disease. Immunogenetics 2023; 75:231-247. [PMID: 36595060 PMCID: PMC10205880 DOI: 10.1007/s00251-022-01288-z] [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: 08/18/2022] [Accepted: 11/24/2022] [Indexed: 01/04/2023]
Abstract
Human Leukocyte Antigens (HLA) are cell surface molecules, central in coordinating innate and adaptive immune responses, that are targets of strong diversifying natural selection by pathogens. Of these pathogens, human herpesviruses have a uniquely ancient relationship with our species, where coevolution likely has reciprocating impact on HLA and viral genomic diversity. Consistent with this notion, genetic variation at multiple HLA loci is strongly associated with modulating immunity to herpesvirus infection. Here, we synthesize published genetic associations of HLA with herpesvirus infection and disease, both from case/control and genome-wide association studies. We analyze genetic associations across the eight human herpesviruses and identify HLA alleles that are associated with diverse herpesvirus-related phenotypes. We find that whereas most HLA genetic associations are virus- or disease-specific, HLA-A*01 and HLA-A*02 allotypes may be more generally associated with immune susceptibility and control, respectively, across multiple herpesviruses. Connecting genetic association data with functional corroboration, we discuss mechanisms by which diverse HLA and cognate receptor allotypes direct variable immune responses during herpesvirus infection and pathogenesis. Together, this review examines the complexity of HLA-herpesvirus interactions driven by differential T cell and Natural Killer cell immune responses.
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Affiliation(s)
- William H. Palmer
- Department of Biomedical Informatics, University of Colorado, Aurora, CO USA
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO USA
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado, Aurora, CO USA
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO USA
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16
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Kakavandi S, Zare I, VaezJalali M, Dadashi M, Azarian M, Akbari A, Ramezani Farani M, Zalpoor H, Hajikhani B. Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases. Cell Commun Signal 2023; 21:110. [PMID: 37189112 DOI: 10.1186/s12964-023-01104-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/15/2023] [Indexed: 05/17/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.
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Affiliation(s)
- Sareh Kakavandi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz, 7178795844, Iran
| | - Maryam VaezJalali
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Azarian
- Department of Radiology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Abdullatif Akbari
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, Incheon, 22212, Republic of Korea
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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17
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Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
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Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
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18
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Moriyama M, Lucas C, Monteiro V, Iwasaki A. Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants. Proc Natl Acad Sci U S A 2023; 120:e2221652120. [PMID: 37036977 PMCID: PMC10120007 DOI: 10.1073/pnas.2221652120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/09/2023] [Indexed: 04/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress major histocompatibility complex class I (MHC-I) expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 but not influenza virus infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC-I, the Omicron subvariants exhibited a greater ability to suppress surface MHC-I expression. We identified a common mutation in the E protein of Omicron that further suppressed MHC-I expression. Collectively, our data suggest that in addition to escaping from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.
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Affiliation(s)
- Miyu Moriyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | | | | | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Cellular and Developmental Biology, Yale University, New HavenCT06520
- HHMI, Chevy Chase, MD20815
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19
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Uribe-Herranz M, Beghi S, Ruella M, Parvathaneni K, Salaris S, Kostopoulos N, George SS, Pierini S, Krimitza E, Costabile F, Ghilardi G, Amelsberg KV, Lee YG, Pajarillo R, Markmann C, McGettigan-Croce B, Agarwal D, Frey N, Lacey SF, Scholler J, Gabunia K, Wu G, Chong E, Porter DL, June CH, Schuster SJ, Bhoj V, Facciabene A. Modulation of the gut microbiota engages antigen cross-presentation to enhance antitumor effects of CAR T cell immunotherapy. Mol Ther 2023; 31:686-700. [PMID: 36641624 PMCID: PMC10014349 DOI: 10.1016/j.ymthe.2023.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/20/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Several studies have shown the influence of commensal microbes on T cell function, specifically in the setting of checkpoint immunotherapy for cancer. In this study, we investigated how vancomycin-induced gut microbiota dysbiosis affects chimeric antigen receptor (CAR) T immunotherapy using multiple preclinical models as well as clinical correlates. In two murine tumor models, hematopoietic CD19+-A20 lymphoma and CD19+-B16 melanoma, mice receiving vancomycin in combination with CD19-directed CAR T cell (CART-19) therapy displayed increased tumor control and tumor-associated antigens (TAAs) cross-presentation compared with CART-19 alone. Fecal microbiota transplant from human healthy donors to pre-conditioned mice recapitulated the results obtained in naive gut microbiota mice. Last, B cell acute lymphoblastic leukemia patients treated with CART-19 and exposed to oral vancomycin showed higher CART-19 peak expansion compared with unexposed patients. These results substantiate the role of the gut microbiota on CAR T cell therapy and suggest that modulation of the gut microbiota using vancomycin may improve outcomes after CAR T cell therapy across tumor types.
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Affiliation(s)
- Mireia Uribe-Herranz
- Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Immunology Department, Hospital Clínic of Barcelona, Barcelona 08036, Spain
| | - Silvia Beghi
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco Ruella
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kalpana Parvathaneni
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Silvano Salaris
- Unit of Biostatistics, Epidemiology and Public Health, University of Padova, Padova, Italy
| | - Nektarios Kostopoulos
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Subin S George
- Bioinformatics Core, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stefano Pierini
- Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; The Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elisavet Krimitza
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francesca Costabile
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guido Ghilardi
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kimberly V Amelsberg
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yong Gu Lee
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymone Pajarillo
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caroline Markmann
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bevin McGettigan-Croce
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Divyansh Agarwal
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Noelle Frey
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Simon F Lacey
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Scholler
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Khatuna Gabunia
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Gary Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elise Chong
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - David L Porter
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carl H June
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Stephen J Schuster
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vijay Bhoj
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrea Facciabene
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; The Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Lu H, Liu Z, Deng X, Chen S, Zhou R, Zhao R, Parandaman R, Thind A, Henley J, Tian L, Yu J, Comai L, Feng P, Yuan W. Potent NKT cell ligands overcome SARS-CoV-2 immune evasion to mitigate viral pathogenesis in mouse models. PLoS Pathog 2023; 19:e1011240. [PMID: 36961850 PMCID: PMC10128965 DOI: 10.1371/journal.ppat.1011240] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 04/25/2023] [Accepted: 02/24/2023] [Indexed: 03/25/2023] Open
Abstract
One of the major pathogenesis mechanisms of SARS-CoV-2 is its potent suppression of innate immunity, including blocking the production of type I interferons. However, it is unknown whether and how the virus interacts with different innate-like T cells, including NKT, MAIT and γδ T cells. Here we reported that upon SARS-CoV-2 infection, invariant NKT (iNKT) cells rapidly trafficked to infected lung tissues from the periphery. We discovered that the envelope (E) protein of SARS-CoV-2 efficiently down-regulated the cell surface expression of the antigen-presenting molecule, CD1d, to suppress the function of iNKT cells. E protein is a small membrane protein and a viroporin that plays important roles in virion packaging and envelopment during viral morphogenesis. We showed that the transmembrane domain of E protein was responsible for suppressing CD1d expression by specifically reducing the level of mature, post-ER forms of CD1d, suggesting that it suppressed the trafficking of CD1d proteins and led to their degradation. Point mutations demonstrated that the putative ion channel function was required for suppression of CD1d expression and inhibition of the ion channel function using small chemicals rescued the CD1d expression. Importantly, we discovered that among seven human coronaviruses, only E proteins from highly pathogenic coronaviruses including SARS-CoV-2, SARS-CoV and MERS suppressed CD1d expression, whereas the E proteins of human common cold coronaviruses, HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1, did not. These results suggested that E protein-mediated evasion of NKT cell function was likely an important pathogenesis factor, enhancing the virulence of these highly pathogenic coronaviruses. Remarkably, activation of iNKT cells with their glycolipid ligands, both prophylactically and therapeutically, overcame the putative viral immune evasion, significantly mitigated viral pathogenesis and improved host survival in mice. Our results suggested a novel NKT cell-based anti-SARS-CoV-2 therapeutic approach.
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Affiliation(s)
- Hongjia Lu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Graduate Programs in Biomedical and Biological Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Zhewei Liu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Xiangxue Deng
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Siyang Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Ruiting Zhou
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Rongqi Zhao
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Ramya Parandaman
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amarjot Thind
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jill Henley
- The Hastings and Wright Laboratories, Keck School of Medicine, University Southern California, California, United States of America
| | - Lei Tian
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, California, United States of America
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, California, United States of America
| | - Lucio Comai
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- The Hastings and Wright Laboratories, Keck School of Medicine, University Southern California, California, United States of America
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, United States of America
| | - Weiming Yuan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
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21
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Abd El-Baky N, Amara AA, Redwan EM. HLA-I and HLA-II Peptidomes of SARS-CoV-2: A Review. Vaccines (Basel) 2023; 11:548. [PMID: 36992131 PMCID: PMC10058130 DOI: 10.3390/vaccines11030548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
The adaptive (T-cell-mediated) immune response is a key player in determining the clinical outcome, in addition to neutralizing antibodies, after SARS-CoV-2 infection, as well as supporting the efficacy of vaccines. T cells recognize viral-derived peptides bound to major histocompatibility complexes (MHCs) so that they initiate cell-mediated immunity against SARS-CoV-2 infection or can support developing a high-affinity antibody response. SARS-CoV-2-derived peptides bound to MHCs are characterized via bioinformatics or mass spectrometry on the whole proteome scale, named immunopeptidomics. They can identify potential vaccine targets or therapeutic approaches for SARS-CoV-2 or else may reveal the heterogeneity of clinical outcomes. SARS-CoV-2 epitopes that are naturally processed and presented on the human leukocyte antigen class I (HLA-I) and class II (HLA-II) were identified for immunopeptidomics. Most of the identified SARS-CoV-2 epitopes were canonical and out-of-frame peptides derived from spike and nucleocapsid proteins, followed by membrane proteins, whereby many of which are not caught by existing vaccines and could elicit effective responses of T cells in vivo. This review addresses the detection of SARS-CoV-2 viral epitopes on HLA-I and HLA-II using bioinformatics prediction and mass spectrometry (HLA peptidomics). Profiling the HLA-I and HLA-II peptidomes of SARS-CoV-2 is also detailed.
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Affiliation(s)
- Nawal Abd El-Baky
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Amro A. Amara
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Elrashdy M. Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah P.O. Box 80203, Saudi Arabia
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22
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Lin F, Lin X, Fu B, Xiong Y, Zaky MY, Wu H. Functional studies of HLA and its role in SARS-CoV-2: Stimulating T cell response and vaccine development. Life Sci 2023; 315:121374. [PMID: 36621539 PMCID: PMC9815883 DOI: 10.1016/j.lfs.2023.121374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
In the biological immune process, the major histocompatibility complex (MHC) plays an indispensable role in the expression of HLA molecules in the human body when viral infection activates the T-cell response to remove the virus. Since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2019, how to address and prevent SARS-CoV-2 has become a common problem facing all mankind. The T-cell immune response activated by MHC peptides is a way to construct a defense line and reduce the transmission and harm of the virus. Presentation of SARS-CoV-2 antigen is associated with different types of HLA phenotypes, and different HLA phenotypes induce different immune responses. The prediction of SARS-CoV-2 mutation information and the design of vaccines based on HLAs can effectively activate autoimmunity and cope with virus mutations, which can provide some references for the prevention and treatment of SARS-CoV-2.
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Affiliation(s)
- Feng Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Xiaoyuan Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Mohamed Y Zaky
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, P.O. Box 62521, Beni-Suef, Egypt; Department of Oncology and Department of Biomedical and Clinical Science, Faculty of Medicine, Linköping University, Sweden
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
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23
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Harrison CM, Doster JM, Landwehr EH, Kumar NP, White EJ, Beachboard DC, Stobart CC. Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era. Microorganisms 2023; 11:microorganisms11020445. [PMID: 36838410 PMCID: PMC9961755 DOI: 10.3390/microorganisms11020445] [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: 12/31/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Approximately 15-30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses.
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Affiliation(s)
- Cameron M. Harrison
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Jayden M. Doster
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Emily H. Landwehr
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Nidhi P. Kumar
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Ethan J. White
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Dia C. Beachboard
- Department of Biology, DeSales University, Central Valley, PA 18034, USA
| | - Christopher C. Stobart
- Department of Biological Sciences, Butler University, Indianapolis, IN 46208, USA
- Correspondence:
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24
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Olson E, Ceccarelli T, Raghavan M. Endo-lysosomal assembly variations among human leukocyte antigen class I (HLA class I) allotypes. eLife 2023; 12:e79144. [PMID: 36722462 PMCID: PMC9917446 DOI: 10.7554/elife.79144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 01/13/2023] [Indexed: 02/02/2023] Open
Abstract
The extreme polymorphisms of human leukocyte antigen class I (HLA class I) proteins enable the presentation of diverse peptides to cytotoxic T lymphocytes. The canonical endoplasmic reticulum (ER) HLA class I assembly pathway enables presentation of cytosolic peptides, but effective intracellular surveillance requires multi-compartmental antigen sampling. Endo-lysosomes are generally sites of HLA class II assembly, but human monocytes and monocyte-derived dendritic cells (moDCs) also contain significant reserves of endo-lysosomal HLA class I molecules. We hypothesized variable influences of HLA class I polymorphisms upon outcomes of endo-lysosomal trafficking, as the stabilities and peptide occupancies of cell surface HLA class I molecules are variable. Consistent with this model, when the endo-lysosomal pH of moDCs is disrupted, HLA-B allotypes display varying propensities for reductions in surface expression, with HLA-B*08:01 or HLA-B*35:01 being among the most resistant or sensitive, respectively, among eight tested HLA-B allotypes. Perturbations of moDC endo-lysosomal pH result in accumulation of HLA-B*35:01 in LAMP1+ compartments and increase HLA-B*35:01 peptide receptivity. These findings reveal the intersection of the vacuolar cross-presentation pathway with a constitutive assembly pathway for some HLA-B allotypes. Notably, cross-presentation of epitopes derived from two soluble antigens was also more efficient for B*35:01 compared to B*08:01, even when matched for T cell response sensitivity, and more affected by cathepsin inhibition. Thus, HLA class I polymorphisms dictate the degree of endo-lysosomal assembly, which can supplement ER assembly for constitutive HLA class I expression and increase the efficiency of cross-presentation.
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Affiliation(s)
- Eli Olson
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
- Graduate Program in Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
| | - Theadora Ceccarelli
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
| | - Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
- Graduate Program in Immunology, Michigan Medicine, University of Michigan-Ann ArborAnn ArborUnited States
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25
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Moriyama M, Lucas C, Monteiro VS, Iwasaki A. SARS-CoV-2 Omicron subvariants evolved to promote further escape from MHC-I recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.04.490614. [PMID: 35547852 PMCID: PMC9094094 DOI: 10.1101/2022.05.04.490614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
SARS-CoV-2 variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress MHC I expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC I, Omicron subvariants exhibit a greater ability to suppress surface MHC-I expressions. Collectively, our data suggest that, in addition to escape from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.
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26
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Ye K, Li F, Wang R, Cen T, Liu S, Zhao Z, Li R, Xu L, Zhang G, Xu Z, Deng L, Li L, Wang W, Stepanov A, Wan Y, Guo Y, Li Y, Wang Y, Tian Y, Gabibov AG, Yan Y, Zhang H. An armed oncolytic virus enhances the efficacy of tumor-infiltrating lymphocyte therapy by converting tumors to artificial antigen-presenting cells in situ. Mol Ther 2022; 30:3658-3676. [PMID: 35715953 PMCID: PMC9734027 DOI: 10.1016/j.ymthe.2022.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/20/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
The full potential of tumor-infiltrating lymphocyte (TIL) therapy has been hampered by the inadequate activation and low persistence of TILs, as well as inefficient neoantigen presentation by tumors. We transformed tumor cells into artificial antigen-presenting cells (aAPCs) by infecting them with a herpes simplex virus 1 (HSV-1)-based oncolytic virus encoding OX40L and IL12 (OV-OX40L/IL12) to provide local signals for optimum T cell activation. The infected tumor cells displayed increased expression of antigen-presenting cell-related markers and induced enhanced T cell activation and killing in coculture with TILs. Combining OV-OX40L/IL12 and TIL therapy induced complete tumor regression in patient-derived xenograft and syngeneic mouse tumor models and elicited an antitumor immunological memory. In addition, the combination therapy produced aAPC properties in tumor cells, activated T cells, and reprogrammed macrophages to a more M1-like phenotype in the tumor microenvironment. This combination strategy unleashes the full potential of TIL therapy and warrants further evaluation in clinical studies.
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Affiliation(s)
- Kai Ye
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Fan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Ruikun Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Tianyi Cen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Shiyu Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Zhuoqian Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Ruonan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Lili Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Guanmeng Zhang
- Department of Oromaxillofacial-Head and Neck Surgery, Tianjin Stomatological Hospital, Tianjin 300041, PR China
| | - Zhaoyuan Xu
- Department of Oromaxillofacial-Head and Neck Surgery, Tianjin Stomatological Hospital, Tianjin 300041, PR China
| | - Li Deng
- CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Beijing Institute of Biological Products, Beijing 100176, PR China
| | - Lili Li
- CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Beijing Institute of Biological Products, Beijing 100176, PR China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, PR China
| | - Alexey Stepanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Yajuan Wan
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Yuanke Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Yuan Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Yujie Tian
- CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China
| | - Alexander G Gabibov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Yingbin Yan
- Department of Oromaxillofacial-Head and Neck Surgery, Tianjin Stomatological Hospital, Tianjin 300041, PR China.
| | - Hongkai Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, PR China; CNBG-Nankai University Joint Research and Development Center, Nankai University, Tianjin 300350, PR China; Frontiers Science Center for Cell Responses, Nankai University, Tianjin 300350, PR China.
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27
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Reduced MHC Class I and II Expression in HPV-Negative vs. HPV-Positive Cervical Cancers. Cells 2022; 11:cells11233911. [PMID: 36497170 PMCID: PMC9741043 DOI: 10.3390/cells11233911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Cervical cancer (CC) is the second most common cancer in women worldwide and the fourth leading cause of cancer-associated death in women. Although human papillomavirus (HPV) infection is associated with nearly all CC, it has recently become clear that HPV-negative (HPV-) CC represents a distinct disease phenotype with increased mortality. HPV-positive (HPV+) and HPV- CC demonstrate different molecular pathology, prognosis, and response to treatment. Furthermore, CC caused by HPV α9 types (HPV16-like) often have better outcomes than those caused by HPV α7 types (HPV18-like). This study systematically and comprehensively compared the expression of genes involved in major histocompatibility complex (MHC) class I and II presentation within CC caused by HPV α9 types, HPV α7 types, and HPV- CC. We observed increased expression of MHC class I and II classical and non-classical genes in HPV+ CC and overall higher expression of genes involved in their antigen loading and presentation apparatus as well as transcriptional regulation. Increased expression of MHC I-related genes differs from previous studies using cell culture models. These findings identify crucial differences between antigen presentation within the tumor immune microenvironments of HPV+ and HPV- CC, as well as modest differences between HPV α9 and α7 CC. These differences may contribute to the altered patient outcomes and responses to immunotherapy observed between these distinct cancers.
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28
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Vargas-Zapata V, Geiger KM, Tran D, Ma J, Mao X, Puschnik AS, Coscoy L. SARS-CoV-2 Envelope-mediated Golgi pH dysregulation interferes with ERAAP retention in cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.11.29.518257. [PMID: 36482965 PMCID: PMC9727756 DOI: 10.1101/2022.11.29.518257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Endoplasmic reticulum (ER) aminopeptidase associated with antigen processing (ERAAP) trims peptide precursors in the ER for presentation by major histocompatibility (MHC)-I molecules to surveying CD8+ T-cells. This function allows ERAAP to regulate the nature and quality of the peptide repertoire and, accordingly, the resulting immune responses. We recently showed that infection with murine cytomegalovirus leads to a dramatic loss of ERAAP levels in infected cells. In mice, this loss is associated with the activation of QFL T-cells, a subset of T-cells that monitor ERAAP integrity and eliminate cells experiencing ERAAP dysfunction. In this study, we aimed to identify host factors that regulate ERAAP expression level and determine whether these could be manipulated during viral infections. We performed a CRISPR knockout screen and identified ERp44 as a factor promoting ERAAP retention in the ER. ERp44's interaction with ERAAP is dependent on the pH gradient between the ER and Golgi. We hypothesized that viruses that disrupt the pH of the secretory pathway interfere with ERAAP retention. Here, we demonstrate that expression of the Envelope (E) protein from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) leads to Golgi pH neutralization and consequently decrease of ERAAP intracellular levels. Furthermore, SARS-CoV-2-induced ERAAP loss correlates with its release into the extracellular environment. ERAAP's reliance on ERp44 and a functioning ER/Golgi pH gradient for proper localization and function led us to propose that ERAAP serves as a sensor of disturbances in the secretory pathway during infection and disease.
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Affiliation(s)
- Valerie Vargas-Zapata
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kristina M Geiger
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dan Tran
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jessica Ma
- Division of Microbial Biology, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaowen Mao
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Laurent Coscoy
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
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IFITM proteins: Understanding their diverse roles in viral infection, cancer, and immunity. J Biol Chem 2022; 299:102741. [PMID: 36435199 PMCID: PMC9800550 DOI: 10.1016/j.jbc.2022.102741] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/27/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022] Open
Abstract
Interferon-induced transmembrane proteins (IFITMs) are broad spectrum antiviral factors that inhibit the entry of a wide range of clinically important pathogens including influenza A virus, HIV-1, and Dengue virus. IFITMs are thought to act primarily by antagonizing virus-cell membrane fusion in this regard. However, recent work on these proteins has uncovered novel post-entry viral restriction mechanisms. IFITMs are also increasingly thought to have a role regulating immune responses, including innate antiviral and inflammatory responses as well as adaptive T-cell and B-cell responses. Further, IFITMs may have pathological activities in cancer, wherein IFITM expression can be a marker of therapeutically resistant and aggressive disease courses. In this review, we summarize the respective literatures concerning these apparently diverse functions with a view to identifying common themes and potentially yielding a more unified understanding of IFITM biology.
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Vinjamuri S, Li L, Bouvier M. SARS-CoV-2 ORF8: One protein, seemingly one structure, and many functions. Front Immunol 2022; 13:1035559. [PMID: 36353628 PMCID: PMC9637571 DOI: 10.3389/fimmu.2022.1035559] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/10/2022] [Indexed: 07/30/2023] Open
Abstract
SARS-CoV-2 is the virus responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 encodes nine accessory proteins that are involved in host-pathogen interaction. ORF8 is unique among these accessory proteins. SARS-CoV-2 ORF8 shares a surprisingly low amino acid sequence similarity with SARS-COV ORF8 (30%), and it is presumed to have originated from bat. Studies have shown that ORF8 exerts multiple different functions that interfere with host immune responses, including the downregulation of MHC class I molecules. These functions may represent strategies of host immune evasion. The x-ray crystal structure of ORF8 revealed an immunoglobulin-like domain with several distinguishing features. To date, there are numerous unanswered questions about SARS-CoV-2 ORF8 protein and its structure-function relationship that we discuss in this mini-review. A better understanding of how ORF8 interacts with components of the immune system is needed for elucidating COVID-19 pathogenesis and to develop new avenues for the treatment of the disease.
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Affiliation(s)
| | | | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois at Chicago, College of Medicine, Chicago, IL, United States
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31
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Inhibition of major histocompatibility complex-I antigen presentation by sarbecovirus ORF7a proteins. Proc Natl Acad Sci U S A 2022; 119:e2209042119. [PMID: 36136978 PMCID: PMC9573092 DOI: 10.1073/pnas.2209042119] [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] [Indexed: 11/18/2022] Open
Abstract
Viruses employ a variety of strategies to escape or counteract immune responses, including depletion of cell surface major histocompatibility complex class I (MHC-I), that would ordinarily present viral peptides to CD8+ cytotoxic T cells. As part of a screen to elucidate biological activities associated with individual severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) viral proteins, we found that ORF7a reduced cell surface MHC-I levels by approximately fivefold. Nevertheless, in cells infected with SARS-CoV-2, surface MHC-I levels were reduced even in the absence of ORF7a, suggesting additional mechanisms of MHC-I down-regulation. ORF7a proteins from a sample of sarbecoviruses varied in their ability to induce MHC-I down-regulation and, unlike SARS-CoV-2, the ORF7a protein from SARS-CoV lacked MHC-I downregulating activity. A single amino acid at position 59 (T/F) that is variable among sarbecovirus ORF7a proteins governed the difference in MHC-I downregulating activity. SARS-CoV-2 ORF7a physically associated with the MHC-I heavy chain and inhibited the presentation of expressed antigen to CD8+ T cells. Specifically, ORF7a prevented the assembly of the MHC-I peptide loading complex and caused retention of MHC-I in the endoplasmic reticulum. The differential ability of ORF7a proteins to function in this way might affect sarbecovirus dissemination and persistence in human populations, particularly those with infection- or vaccine-elicited immunity.
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32
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Martins CF, Ribeiro DM, Matzapetakis M, Pinho MA, Kuleš J, Horvatić A, Guillemin N, Eckersall PD, Freire JPB, de Almeida AM, Prates JAM. Effect of dietary Spirulina (Arthrospira platensis) on the intestinal function of post-weaned piglet: An approach combining proteomics, metabolomics and histological studies. J Proteomics 2022; 269:104726. [PMID: 36096433 DOI: 10.1016/j.jprot.2022.104726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/25/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022]
Abstract
The effect of dietary Spirulina (Arthrospira platensis) and CAZyme supplementation was assessed on the gut of weaned piglets, using an integrated NMR-metabolomics approach combined with Tandem Mass Tag labelled proteomics. Thirty weaned male piglets were assigned to one of the three following diets (n = 10): cereal and soybean meal basal diet (Control), basal diet with 10% Spirulina inclusion (SP) and SP diet supplemented with 0.01% lysozyme (SP + L). The experiment lasted 4 weeks and, upon slaughter, small intestine samples were collected for histological, metabolomic and proteomic analysis. No significant differences were found for the histology and metabolomics analysis between the three experimental groups. Lactate, glutamate, glycine and myo-inositol were the most abundant metabolites. Proteomics results showed 1502 proteins identified in the intestine tissue. A total of 23, 78, 27 differentially abundant proteins were detected respectively for the SP vs. Control, SP + L vs. Control and SP + L vs. SP comparisons. The incorporation of Spirulina and supplementation of lysozyme in the piglet's diets is associated to intestinal proteomic changes. These include increased protein synthesis and abundance of contractile apparatus proteins, related with increased nutrient availability, which has beneficial (increased glucose uptake) and detrimental (increased digesta viscosity) metabolic effects. SIGNIFICANCE: The use of conventional feedstuffs becomes increasingly prohibitive due to its environmental toll. To increase the sustainability of the livestock sector, novel feedstuffs such as microalgae need to be considered. However, its recalcitrant cell wall has antinutritional effects that can inhibit high dietary inclusion levels. The supplementation with CAZymes is a possible solution to this issue. The small intestine is a central piece in monogastric digestion and of particular importance for the weaned piglet. Studying the effect of dietary Spirulina and CAZyme supplementation on its histomorphology, metabolome and proteome allows studying relevant physiological adaptations to these diets.
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Affiliation(s)
- Cátia F Martins
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal; LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - David M Ribeiro
- LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal; Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vas. Constantinou Av., 11635 Athens, Greece
| | - Mário A Pinho
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
| | - Josipa Kuleš
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia
| | - Anita Horvatić
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia; Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottieva 6, 10 000 Zagreb, Croatia
| | - Nicolas Guillemin
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia
| | - Peter David Eckersall
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia; Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Rd, Glasgow G61 1QH, UK
| | - João P B Freire
- LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - André M de Almeida
- LEAF - Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal.
| | - José A M Prates
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal
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33
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Rastogi I, Jeon D, Moseman JE, Muralidhar A, Potluri HK, McNeel DG. Role of B cells as antigen presenting cells. Front Immunol 2022; 13:954936. [PMID: 36159874 PMCID: PMC9493130 DOI: 10.3389/fimmu.2022.954936] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/19/2022] [Indexed: 01/27/2023] Open
Abstract
B cells have been long studied for their role and function in the humoral immune system. Apart from generating antibodies and an antibody-mediated memory response against pathogens, B cells are also capable of generating cell-mediated immunity. It has been demonstrated by several groups that B cells can activate antigen-specific CD4 and CD8 T cells, and can have regulatory and cytotoxic effects. The function of B cells as professional antigen presenting cells (APCs) to activate T cells has been largely understudied. This, however, requires attention as several recent reports have demonstrated the importance of B cells within the tumor microenvironment, and B cells are increasingly being evaluated as cellular therapies. Antigen presentation through B cells can be through antigen-specific (B cell receptor (BCR) dependent) or antigen non-specific (BCR independent) mechanisms and can be modulated by a variety of intrinsic and external factors. This review will discuss the pathways and mechanisms by which B cells present antigens, and how B cells differ from other professional APCs.
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34
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Zarkoob H, Allué-Guardia A, Chen YC, Garcia-Vilanova A, Jung O, Coon S, Song MJ, Park JG, Oladunni F, Miller J, Tung YT, Kosik I, Schultz D, Iben J, Li T, Fu J, Porter FD, Yewdell J, Martinez-Sobrido L, Cherry S, Torrelles JB, Ferrer M, Lee EM. Modeling SARS-CoV-2 and influenza infections and antiviral treatments in human lung epithelial tissue equivalents. Commun Biol 2022; 5:810. [PMID: 35962146 PMCID: PMC9373898 DOI: 10.1038/s42003-022-03753-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
There is a critical need for physiologically relevant, robust, and ready-to-use in vitro cellular assay platforms to rapidly model the infectivity of emerging viruses and develop new antiviral treatments. Here we describe the cellular complexity of human alveolar and tracheobronchial air liquid interface (ALI) tissue models during SARS-CoV-2 and influenza A virus (IAV) infections. Our results showed that both SARS-CoV-2 and IAV effectively infect these ALI tissues, with SARS-CoV-2 exhibiting a slower replication peaking at later time-points compared to IAV. We detected tissue-specific chemokine and cytokine storms in response to viral infection, including well-defined biomarkers in severe SARS-CoV-2 and IAV infections such as CXCL10, IL-6, and IL-10. Our single-cell RNA sequencing analysis showed similar findings to that found in vivo for SARS-CoV-2 infection, including dampened IFN response, increased chemokine induction, and inhibition of MHC Class I presentation not observed for IAV infected tissues. Finally, we demonstrate the pharmacological validity of these ALI tissue models as antiviral drug screening assay platforms, with the potential to be easily adapted to include other cell types and increase the throughput to test relevant pathogens.
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Affiliation(s)
- Hoda Zarkoob
- 3D Tissue Bioprinting Lab, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Anna Allué-Guardia
- Host-Pathogen Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Yu-Chi Chen
- 3D Tissue Bioprinting Lab, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Andreu Garcia-Vilanova
- Host-Pathogen Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Olive Jung
- 3D Tissue Bioprinting Lab, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.,Biomedical Ultrasonics & Biotherapy Laboratory, Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Headington, UK
| | - Steven Coon
- Molecular Genomics Core, National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD, USA
| | - Min Jae Song
- 3D Tissue Bioprinting Lab, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jun-Gyu Park
- Host-Pathogen Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Fatai Oladunni
- Host-Pathogen Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Jesse Miller
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yen-Ting Tung
- 3D Tissue Bioprinting Lab, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Ivan Kosik
- National Institute for Allergies and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,High Throughput Screening Core, University of Pennsylvania, Philadelphia, PA, USA
| | - James Iben
- Molecular Genomics Core, National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD, USA
| | - Tianwei Li
- Molecular Genomics Core, National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD, USA
| | - Jiaqi Fu
- 3D Tissue Bioprinting Lab, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Forbes D Porter
- Section on Molecular Dysmorphology, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Jonathan Yewdell
- National Institute for Allergies and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis Martinez-Sobrido
- Host-Pathogen Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sara Cherry
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jordi B Torrelles
- Host-Pathogen Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Marc Ferrer
- 3D Tissue Bioprinting Lab, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
| | - Emily M Lee
- 3D Tissue Bioprinting Lab, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
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Walker-Sperling V, Digitale JC, Viard M, Martin MP, Bashirova A, Yuki Y, Ramsuran V, Kulkarni S, Naranbhai V, Li H, Anderson SK, Yum L, Clifford R, Kibuuka H, Ake J, Thomas R, Rowland-Jones S, Rek J, Arinaitwe E, Kamya M, Rodriguez-Barraquer I, Feeney ME, Carrington M. Genetic variation that determines TAPBP expression levels associates with the course of malaria in an HLA allotype-dependent manner. Proc Natl Acad Sci U S A 2022; 119:e2205498119. [PMID: 35858344 PMCID: PMC9303992 DOI: 10.1073/pnas.2205498119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022] Open
Abstract
HLA class I (HLA-I) allotypes vary widely in their dependence on tapasin (TAPBP), an integral component of the peptide-loading complex, to present peptides on the cell surface. We identified two single-nucleotide polymorphisms that regulate TAPBP messenger RNA (mRNA) expression in Africans, rs111686073 (G/C) and rs59097151 (A/G), located in an AP-2α transcription factor binding site and a microRNA (miR)-4486 binding site, respectively. rs111686073G and rs59097151A induced significantly higher TAPBP mRNA expression relative to the alternative alleles due to higher affinity for AP-2α and abrogation of miR-4486 binding, respectively. These variants associated with lower Plasmodium falciparum parasite prevalence and lower incidence of clinical malaria specifically among individuals carrying tapasin-dependent HLA-I allotypes, presumably by augmenting peptide loading, whereas tapasin-independent allotypes associated with relative protection, regardless of imputed TAPBP mRNA expression levels. Thus, an attenuated course of malaria may occur through enhanced breadth and/or magnitude of antigen presentation, an important consideration when evaluating vaccine efficacy.
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Affiliation(s)
- Victoria Walker-Sperling
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
| | - Jean C. Digitale
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, 94143
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Maureen P. Martin
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Arman Bashirova
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Yuko Yuki
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Smita Kulkarni
- Texas Biomedical Research Institute, Host Pathogen Interaction Program, San Antonio, Texas, 78227
| | - Vivek Naranbhai
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
- Dana Farber Cancer Institute, Department of Medical Oncology, Boston, Massachusetts, 02215
- MGH Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, 02114
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, 4041, South Africa
| | - Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Stephen K. Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
| | - Lauren Yum
- U.S. Military HIV Research Program,, Walter Reed Army Institute of Research, Silver Spring, Maryland, 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, 20817
| | - Robert Clifford
- U.S. Military HIV Research Program,, Walter Reed Army Institute of Research, Silver Spring, Maryland, 20910
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, 20817
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Julie Ake
- U.S. Military HIV Research Program,, Walter Reed Army Institute of Research, Silver Spring, Maryland, 20910
| | - Rasmi Thomas
- U.S. Military HIV Research Program,, Walter Reed Army Institute of Research, Silver Spring, Maryland, 20910
| | - Sarah Rowland-Jones
- Viral Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University, Kampala, Uganda
| | | | - Margaret E. Feeney
- Department of Medicine, University of California San Francisco, San Francisco, California, 94158
- Department of Pediatrics, University of California San Francisco, San Francisco, California, 94158
| | - Mary Carrington
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, 20892
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, 02139
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Zhang L, Li Z, Tang Z, Han L, Wei X, Xie X, Ren S, Meng K, Liu Y, Xu M, Qi L, Chen H, Wu J, Zhang N. Efficient Identification of Tembusu Virus CTL Epitopes in Inbred HBW/B4 Ducks Using a Novel MHC Class I-Restricted Epitope Screening Scheme. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:145-156. [PMID: 35623661 DOI: 10.4049/jimmunol.2100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
The identification of MHC class I-restricted CTL epitopes in certain species, particularly nonmammals, remains a challenge. In this study, we developed a four-step identification scheme and confirmed its efficiency by identifying the Anpl-UAA*76-restricted CTL epitopes of Tembusu virus (TMUV) in inbred haplotype ducks HBW/B4. First, the peptide binding motif of Anpl-UAA*76 was determined by random peptide library in de novo liquid chromatography-tandem mass spectrometry, a novel nonbiased, data-independent acquisition method that we previously established. Second, a total of 38 TMUV peptides matching the motif were screened from the viral proteome, among which 11 peptides were conserved across the different TMUV strains. Third, the conserved TMUV peptides were refolded in vitro with Anpl-UAA*76 and Anpl-β2-microglobulin to verify the results from the previous two steps. To clarify the structural basis of the obtained motif, we resolved the crystal structure of Anpl-UAA*76 with the TMUV NS3 peptide LRKRQLTVL and found that Asp34 is critical for the preferential binding of the B pocket to bind the second residue to arginine as an anchor residue. Fourth, the immunogenicity of the conserved TMUV peptides was tested in vivo using specific pathogen-free HBW/B4 ducks immunized with the attenuated TMUV vaccine. All 11 conserved TMUV epitopes could bind stably to Anpl-UAA*76 in vitro and stimulate the secretion of IFN-γ and lymphocyte proliferation, and three conserved and one nonconserved peptides were selected to evaluate the CTL responses in vivo by flow cytometry and their tetramers. We believe that this new scheme could improve the identification of MHC class I-restricted CTL epitopes, and our data provide a foundation for further study on duck anti-TMUV CTL immunity.
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Affiliation(s)
- Lin Zhang
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhuolin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ziche Tang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lingxia Han
- Division of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaoli Xie
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shuaimeng Ren
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Kai Meng
- Shandong Key Laboratory of Poultry Diseases Diagnosis and Immunology, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yueyue Liu
- Shandong Key Laboratory of Poultry Diseases Diagnosis and Immunology, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Minli Xu
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lihong Qi
- Shandong Key Laboratory of Poultry Diseases Diagnosis and Immunology, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hongyan Chen
- Division of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Jiaqiang Wu
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China;
- Shandong Key Laboratory of Poultry Diseases Diagnosis and Immunology, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China; and
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China;
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing, China
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37
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Zhang F, Zang T, Stevenson EM, Lei X, Copertino DC, Mota TM, Boucau J, Garcia-Beltran WF, Jones RB, Bieniasz PD. Inhibition of major histocompatibility complex-I antigen presentation by sarbecovirus ORF7a proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35665005 PMCID: PMC9164438 DOI: 10.1101/2022.05.25.493467] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Viruses employ a variety of strategies to escape or counteract immune responses, including depletion of cell surface major histocompatibility complex class I (MHC-I), that would ordinarily present viral peptides to CD8+ cytotoxic T cells. As part of a screen to elucidate biological activities associated with individual SARS-CoV-2 viral proteins, we found that ORF7a reduced cell surface MHC-I levels by approximately 5-fold. Nevertheless, in cells infected with SARS-CoV-2, surface MHC-I levels were reduced even in the absence of ORF7a, suggesting additional mechanisms of MHC-I downregulation. ORF7a proteins from a sample of sarbecoviruses varied in their ability to induce MHC-I downregulation and, unlike SARS-CoV-2, the ORF7a protein from SARS-CoV lacked MHC-I downregulating activity. A single-amino acid at position 59 (T/F) that is variable among sarbecovirus ORF7a proteins governed the difference in MHC-I downregulating activity. SARS-CoV-2 ORF7a physically associated with the MHC-I heavy chain and inhibited the presentation of expressed antigen to CD8+ T-cells. Speficially, ORF7a prevented the assembly of the MHC-I peptide loading complex and causing retention of MHC-I in the endoplasmic reticulum. The differential ability of ORF7a proteins to function in this way might affect sarbecovirus dissemination and persistence in human populations, particularly those with infection- or vaccine-elicited immunity.
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38
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Dominant epitopes presented by prevalent HLA alleles permit wide use of banked CMVpp65 T-cells in adoptive therapy. Blood Adv 2022; 6:4859-4872. [PMID: 35605246 DOI: 10.1182/bloodadvances.2022007005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/15/2022] [Indexed: 11/20/2022] Open
Abstract
We established and characterized a bank of 138 CMVpp65 peptide-specific T-cell lines (CMVpp65CTLs) from healthy marrow transplant donors who consented to their use for treatment of individuals other than their transplant recipient. CMVpp65CTL lines included 131 containing predominantly CD8+ T-cells and 7 CD4+ T-cell. CD8+ CMVpp65CTLs were specific for 1-3 epitopes each presented by one of only 34 of the 148 class I alleles in the bank. Similarly, the 7 predominantly CD4+ CMVpp65CTL lines were each specific for epitopes presented by 14 of 40 HLA DR alleles in the bank. Although the number of HLA alleles presenting CMV epitopes is low, their prevalence is high, permitting selection of CMVpp65CTLs restricted by an HLA allele shared by transplant recipient and HCT donor for >90% of an ethnogeographically diverse population of HCT recipients. Within individuals, responses to CMVpp65 peptides presented by different HLA alleles are hierarchical. Furthermore, within groups, epitopes presented by HLA B*07:02 and HLA A*02:01 consistently elicit immunodominant CMVpp65 CTLs, irrespective of other HLA alleles inherited. All dominant CMVpp65CTLs exhibited HLA-restricted cytotoxicity against epitope loaded targets, and usually cleared CMV infections. However, immunodominant CMVpp65 CTL responding to epitopes presented by certain HLA B*35 alleles were ineffective in lysing CMV infected cells in vitro or controlling CMV infections post adoptive therapy. Analysis of the hierarchy of T-cell responses to CMVpp65, the HLA alleles presenting immunodominant CMVpp65 epitopes, and the responses they induce, may lead to detailed algorithms for optimal choice of 3rd party CMVpp65CTLs for effective adoptive therapy.
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39
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Burassakarn A, Phusingha P, Yugawa T, Noguchi K, Ekalaksananan T, Vatanasapt P, Kiyono T, Pientong C. Human Papillomavirus 16 E6 Suppresses Transporter Associated with Antigen-Processing Complex in Human Tongue Keratinocyte Cells by Activating Lymphotoxin Pathway. Cancers (Basel) 2022; 14:cancers14081944. [PMID: 35454851 PMCID: PMC9028769 DOI: 10.3390/cancers14081944] [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: 03/14/2022] [Revised: 04/10/2022] [Accepted: 04/10/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary There is still limited knowledge of the critical pathogenic processes by which HPV16 induces oral carcinogenesis. Therefore, we aimed to illuminate the oncogenic role of HPV16 in the context of oral squamous cell carcinomas (OSCCs). Using human tongue keratinocyte cells, we demonstrated that HPV16 E6 promotes LTα1β2 and LTβR expression, thus promoting the lymphotoxin signaling pathway and leading to suppression of the transporter associated with the antigen-processing complex (TAPs; TAP1 and TAP2). Additionally, in vitro, we also demonstrated regulation of the antigenic peptide-loaded machinery in HPV-infected OSCC tissues through analysis of the transcriptomic profiles of the head and neck squamous cell carcinoma (HNSCC) cohort from the TCGA database, which was validated using fresh biopsied specimens. Thus, our study enhances the proposed functional role of HPV16 E6-associated immune-evasive properties in oral epithelial cells, revealing a possible mechanism underlying the development of HPV-mediated OSCCs. Abstract Infection by high-risk human papillomaviruses (hrHPVs), including HPV type 16 (HPV16), is a major risk factor for oral squamous cell carcinomas (OSCCs). However, the pathogenic mechanism by which hrHPVs promote oral carcinogenesis remains to be elucidated. Here, we demonstrated that the suppression of a transporter associated with the antigen-processing complex (TAPs; TAP1 and TAP2), which is a key molecule in the transportation of viral antigenic peptides into MHC class-I cells, is affected by the E6 protein of HPV16. Mechanistically, HPV-mediated immune evasion is principally mediated via the signal-transduction network of a lymphotoxin (LT) pathway, in particular LTα1β2 and LTβR. Our analysis of transcriptomic data from an HNSCC cohort from the Cancer Genome Atlas (TCGA) indicated that expression of TAP genes, particularly TAP2, was downregulated in HPV-infected cases. We further demonstrated that LTα1β2 and LTβR were upregulated, which was negatively correlated with TAP1 and TAP2 expression in HPV-positive clinical OSCC samples. Taken together, our findings imply that HPV16 E6 regulates the machinery of the antigenic peptide-loading system and helps to clarify the role of oncogenic viruses in the context of oral carcinoma.
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Affiliation(s)
- Ati Burassakarn
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (A.B.); (T.E.)
- HPV & EBV and Carcinogenesis Research Group, Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Pensiri Phusingha
- Center of Excellence for Antibody Research (CEAR), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Takashi Yugawa
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tokyo 104-0045, Japan;
| | - Kazuma Noguchi
- Department of Oral and Maxillofacial Surgery, Hyogo Medical University, Mukogawa-Cho 1-1, Nishinomiya 663-8501, Japan;
| | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (A.B.); (T.E.)
- HPV & EBV and Carcinogenesis Research Group, Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Patravoot Vatanasapt
- HPV & EBV and Carcinogenesis Research Group, Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
- Department of Otorhinolaryngology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Tohru Kiyono
- Project for Prevention of HPV-Related Cancer, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
- Correspondence: (T.K.); (C.P.); Tel./Fax: +66-4334-8385 (C.P.)
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (A.B.); (T.E.)
- HPV & EBV and Carcinogenesis Research Group, Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
- Correspondence: (T.K.); (C.P.); Tel./Fax: +66-4334-8385 (C.P.)
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40
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Fahrner JE, Lahmar I, Goubet AG, Haddad Y, Carrier A, Mazzenga M, Drubay D, Alves Costa Silva C, de Sousa E, Thelemaque C, Melenotte C, Dubuisson A, Geraud A, Ferrere G, Birebent R, Bigenwald C, Picard M, Cerbone L, Lérias JR, Laparra A, Bernard-Tessier A, Kloeckner B, Gazzano M, Danlos FX, Terrisse S, Pizzato E, Flament C, Ly P, Tartour E, Benhamouda N, Meziani L, Ahmed-Belkacem A, Miyara M, Gorochov G, Barlesi F, Trubert A, Ungar B, Estrada Y, Pradon C, Gallois E, Pommeret F, Colomba E, Lavaud P, Deloger M, Droin N, Deutsch E, Gachot B, Spano JP, Merad M, Scotté F, Marabelle A, Griscelli F, Blay JY, Soria JC, Merad M, André F, Villemonteix J, Chevalier MF, Caillat-Zucman S, Fenollar F, Guttman-Yassky E, Launay O, Kroemer G, La Scola B, Maeurer M, Derosa L, Zitvogel L. The Polarity and Specificity of Antiviral T Lymphocyte Responses Determine Susceptibility to SARS-CoV-2 Infection in Patients with Cancer and Healthy Individuals. Cancer Discov 2022; 12:958-983. [PMID: 35179201 PMCID: PMC9394394 DOI: 10.1158/2159-8290.cd-21-1441] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
Abstract
Vaccination against coronavirus disease 2019 (COVID-19) relies on the in-depth understanding of protective immune responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). We characterized the polarity and specificity of memory T cells directed against SARS-CoV-2 viral lysates and peptides to determine correlates with spontaneous, virus-elicited, or vaccine-induced protection against COVID-19 in disease-free and cancer-bearing individuals. A disbalance between type 1 and 2 cytokine release was associated with high susceptibility to COVID-19. Individuals susceptible to infection exhibited a specific deficit in the T helper 1/T cytotoxic 1 (Th1/Tc1) peptide repertoire affecting the receptor binding domain of the spike protein (S1-RBD), a hotspot of viral mutations. Current vaccines triggered Th1/Tc1 responses in only a fraction of all subject categories, more effectively against the original sequence of S1-RBD than that from viral variants. We speculate that the next generation of vaccines should elicit Th1/Tc1 T-cell responses against the S1-RBD domain of emerging viral variants. SIGNIFICANCE This study prospectively analyzed virus-specific T-cell correlates of protection against COVID-19 in healthy and cancer-bearing individuals. A disbalance between Th1/Th2 recall responses conferred susceptibility to COVID-19 in both populations, coinciding with selective defects in Th1 recognition of the receptor binding domain of spike. See related commentary by McGary and Vardhana, p. 892. This article is highlighted in the In This Issue feature, p. 873.
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Affiliation(s)
- Jean-Eudes Fahrner
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Transgene S.A., Illkirch-Graffenstaden, France
| | - Imran Lahmar
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Anne-Gaëlle Goubet
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Yacine Haddad
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Agathe Carrier
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Marine Mazzenga
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Damien Drubay
- Gustave Roussy, Villejuif, France.,Département de Biostatistique et d'Epidémiologie, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Carolina Alves Costa Silva
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Lyon COVID Study Group
- Open Innovation & Partnerships (OIP), bioMérieux S.A., Marcy l'Etoile, France. R&D – Immunoassay, bioMérieux S.A., Marcy l'Etoile, France.,Joint Research Unit Hospices Civils de Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, France.,International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France.,Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France
| | - Eric de Sousa
- ImmunoTherapy/ImmunoSurgery, Champalimaud Centre for the Unknown, Lisboa, Portugal
| | - Cassandra Thelemaque
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Cléa Melenotte
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Aix-Marseille Université, Institut Hospitalo-Universitaire, Institut de Recherche pour le Développement, Assistance Publique – Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Marseille, France
| | - Agathe Dubuisson
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Arthur Geraud
- Gustave Roussy, Villejuif, France.,Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP), Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Gladys Ferrere
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Roxanne Birebent
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Camille Bigenwald
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Marion Picard
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Luigi Cerbone
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Joana R. Lérias
- ImmunoTherapy/ImmunoSurgery, Champalimaud Centre for the Unknown, Lisboa, Portugal
| | - Ariane Laparra
- Gustave Roussy, Villejuif, France.,Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP), Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Alice Bernard-Tessier
- Gustave Roussy, Villejuif, France.,Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP), Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Benoît Kloeckner
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Marianne Gazzano
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - François-Xavier Danlos
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Safae Terrisse
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Eugenie Pizzato
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Caroline Flament
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Pierre Ly
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Eric Tartour
- Center of clinical investigations BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France.,Department of Immunology, Hôpital Européen Georges Pompidou, APHP, Paris, France
| | - Nadine Benhamouda
- Center of clinical investigations BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France.,Department of Immunology, Hôpital Européen Georges Pompidou, APHP, Paris, France
| | | | | | - Makoto Miyara
- Univ Paris Est Créteil, INSERM U955, IMRB, Créteil, France
| | - Guy Gorochov
- Univ Paris Est Créteil, INSERM U955, IMRB, Créteil, France
| | - Fabrice Barlesi
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France.,Sorbonne Université/Institut National de la Santé et de la Recherche Médicale, U1135, Centre d'Immunologie et des Maladies Infectieuses, Hôpital Pitié-Salpêtrière, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Alexandre Trubert
- Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Benjamin Ungar
- Aix Marseille University, CNRS, INSERM, CRCM, Marseille, France
| | - Yeriel Estrada
- Department of Dermatology, Center of Excellence in Eczema Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Caroline Pradon
- Gustave Roussy, Villejuif, France.,Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, New York.,Centre de Ressources Biologiques, ET-EXTRA, Gustave Roussy, Villejuif, France
| | - Emmanuelle Gallois
- Gustave Roussy, Villejuif, France.,Département de Biologie Médicale et Pathologie Médicales, Service de Biochimie, Gustave Roussy, Villejuif, France
| | - Fanny Pommeret
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Emeline Colomba
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Pernelle Lavaud
- Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Marc Deloger
- Département de Biologie Médicale et Pathologie Médicales, Service de Microbiologie, Gustave Roussy, Villejuif, France
| | - Nathalie Droin
- Gustave Roussy, Plateforme de Bioinformatique, Université Paris-Saclay, INSERM US23, CNRS UMS, Villejuif, France
| | - Eric Deutsch
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Gustave Roussy, Plateforme de génomique, Université Paris-Saclay, INSERM US23, CNRS UMS, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1030, Gustave Roussy, Villejuif, France
| | - Bertrand Gachot
- Gustave Roussy, Villejuif, France.,Département de Radiothérapie, Gustave Roussy, Villejuif, France
| | | | - Mansouria Merad
- Gustave Roussy, Villejuif, France.,Department of Medical Oncology, Pitié-Salpétrière Hospital, APHP, Sorbonne Université, Paris, France
| | - Florian Scotté
- Gustave Roussy, Villejuif, France.,Service de Médecine aigue d’Urgence en Cancérologie, Gustave Roussy, Villejuif, France
| | - Aurélien Marabelle
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Département d'Innovation Thérapeutique et d'Essais Précoces (DITEP), Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France.,Département Interdisciplinaire d'Organisation des Parcours Patients, Gustave Roussy, Villejuif, France
| | - Frank Griscelli
- Gustave Roussy, Villejuif, France.,Département de Biologie Médicale et Pathologie Médicales, Service de Biochimie, Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale – UMR935/UA9, Université Paris-Saclay, Villejuif, France.,INGESTEM National IPSC Infrastructure, Université de Paris-Saclay, Villejuif, France.,Université de Paris, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France
| | - Jean-Yves Blay
- Centre Léon Bérard, Lyon, France.,Université Claude Bernard, Lyon, France.,Unicancer, Paris, France
| | - Jean-Charles Soria
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Oncological Science, Icahn School of Medicine at Mount Sinai, New York, New York.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Fabrice André
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U981, Gustave Roussy, Villejuif, France
| | - Juliette Villemonteix
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint-Louis, APHP, Université de Paris, Paris, France
| | - Mathieu F. Chevalier
- INSERM UMR 976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Sophie Caillat-Zucman
- Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint-Louis, APHP, Université de Paris, Paris, France.,INSERM UMR 976, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Florence Fenollar
- IHU Méditérranée Infection, VITROME, IRD, AP-HM, SSA, Aix-Marseille University, Marseille, France
| | - Emma Guttman-Yassky
- Department of Dermatology, Center of Excellence in Eczema Laboratory of Inflammatory Skin Diseases, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Odile Launay
- Université de Paris, Inserm CIC 1417, I-Reivac, APHP, Hopital Cochin, Paris, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France.,Pôle de Biologie, Hôpital Européen George Pompidou, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Bernard La Scola
- Institut Hospitalo-Universitaire, Méditerranée Infection, Marseille, France
| | - Markus Maeurer
- ImmunoTherapy/ImmunoSurgery, Champalimaud Centre for the Unknown, Lisboa, Portugal.,Medizinische Klinik, Johannes Gutenberg University Mainz, Germany
| | - Lisa Derosa
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Laurence Zitvogel
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France.,Gustave Roussy, Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.,Center of clinical investigations BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France.,Corresponding Author: Laurence Zitvogel, University Paris-Saclay, Gustave Roussy Cancer Center, 114 rue Edouard Vaillant, Villejuif Cedex 94805, France. Phone: 331-4211-5041; E-mail:
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Coronavirus Porcine Deltacoronavirus Upregulates MHC Class I Expression through RIG-I/IRF1-Mediated NLRC5 Induction. J Virol 2022; 96:e0015822. [PMID: 35311551 DOI: 10.1128/jvi.00158-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Major histocompatibility complex class I (MHC-I) and MHC-II molecules, mainly being responsible for the processing and presentation of intracellular or extracellular antigen, respectively, are critical for antiviral immunity. Here, we reported that porcine deltacoronavirus (PDCoV) with the zoonotic potential and potential spillover from pigs to humans, upregulated the expressions of porcine MHC-I (swine leukocyte antigen class I, SLA-I) molecules and SLA-I antigen presentation associated genes instead of porcine MHC-II (SLA-II) molecules both in primary porcine enteroids and swine testicular (ST) cells at the late stage of infection, and this finding was verified in vivo. Moreover, the induction of SLA-I molecules by PDCoV infection was mediated through enhancing the expression of NOD-like receptor (NLR) family caspase recruitment domain-containing 5 (NLRC5). Mechanistic studies demonstrated that PDCoV infection robustly elevated retinoic acid-inducible gene I (RIG-I) expression, and further initiated the downstream type I interferon beta (IFN-β) production, which led to the upregulation of NLRC5 and SLA-I genes. Likewise, interferon regulatory factor 1 (IRF1) elicited by PDCoV infection directly activated the promoter activity of NLRC5, resulting in an increased expression of NLRC5 and SLA-I upregulation. Taken together, our findings advance our understanding of how PDCoV manipulates MHC molecules, and knowledge that could help inform the development of therapies and vaccines against PDCoV. IMPORTANCE MHC-I molecules play a crucial role in antiviral immunity by presenting intracellular antigens to CD8+T lymphocytes and eliminating virus-infected cells by natural killer cells' "missing-self recognition." However, the manipulation of MHC molecules by coronaviruses remains poorly understood. Here, we demonstrated that PDCoV, a zoonotic potential coronavirus efficiently infecting cells from broad species, greatly increased the expressions of porcine MHC-I (SLA-I) molecules and MHC-I antigen presentation associated genes but not porcine MHC-II (SLA-II) molecules both in vitro and in vivo. Mechanistically, the upregulation of MHC-I molecules by PDCoV infection required the master transactivator of MHC-I, NLRC5, which was mediated not only by RIG-I-initiated type I IFN signaling pathway but also by IRF1 induced by PDCoV as it could activate NLRC5 promoter activity. These results provide significant insights into the modification of the MHC class I pathway and may provide a potential therapeutic intervention for PDCoV.
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Eslamloo K, Kumar S, Xue X, Parrish KS, Purcell SL, Fast MD, Rise ML. Global gene expression responses of Atlantic salmon skin to Moritella viscosa. Sci Rep 2022; 12:4622. [PMID: 35301338 PMCID: PMC8931016 DOI: 10.1038/s41598-022-08341-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 03/03/2022] [Indexed: 12/19/2022] Open
Abstract
Moritella viscosa is a Gram-negative pathogen that causes large, chronic ulcers, known as winter-ulcer disease, in the skin of several fish species including Atlantic salmon. We used a bath challenge approach to profile the transcriptome responses of M. viscosa-infected Atlantic salmon skin at the lesion (Mv-At) and away from the lesion (Mv-Aw) sites. M. viscosa infection was confirmed through RNA-based qPCR assays. RNA-Seq identified 5212 and 2911 transcripts differentially expressed in the Mv-At compared to no-infection control and Mv-Aw groups, respectively. Also, there were 563 differentially expressed transcripts when comparing the Mv-Aw to control samples. Our results suggest that M. viscosa caused massive and strong, but largely infection site-focused, transcriptome dysregulations in Atlantic salmon skin, and its effects beyond the skin lesion site were comparably subtle. The M. viscosa-induced transcripts of Atlantic salmon were mainly involved in innate and adaptive immune response-related pathways, whereas the suppressed transcripts by this pathogen were largely connected to developmental and cellular processes. As validated by qPCR, M. viscosa dysregulated transcripts encoding receptors, signal transducers, transcription factors and immune effectors playing roles in TLR- and IFN-dependent pathways as well as immunoregulation, antigen presentation and T-cell development. This study broadened the current understanding of molecular pathways underlying M. viscosa-triggered responses of Atlantic salmon, and identified biomarkers that may assist to diagnose and combat this pathogen.
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Affiliation(s)
- Khalil Eslamloo
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada. .,Hoplite Laboratory, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada.
| | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Kathleen S Parrish
- Hoplite Laboratory, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - Sara L Purcell
- Hoplite Laboratory, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - Mark D Fast
- Hoplite Laboratory, Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
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43
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Liu Y, Sun B, Wang J, Sun H, Lu Z, Chen L, Lan M, Xu J, Pan J, Shi J, Sun Y, Zhang X, Wang J, Jiang D, Yang K. In silico analyses and experimental validation of the MHC class-I restricted epitopes of Ebolavirus GP. Int Immunol 2022; 34:313-325. [PMID: 35192720 DOI: 10.1093/intimm/dxac006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Ebolavirus (EBOV) causes an extremely high mortality and prevalence disease called Ebola virus disease (EVD). There is only one glycoprotein (GP) on the virus particle surface, which mediates entry into the host cell. MHC class-I restricted CD8 + T cell responses are important antiviral immune responses. Therefore, it is of great importance to understand EBOV GP-specific MHC class-I restricted epitopes within immunogenicity. In this study, computational approaches were employed to predict the dominant MHC class-I molecule epitopes of EBOV GP for mouse H2 and major alleles of HLA class-I supertypes. Our results yielded 42 dominant epitopes in H2 haplotypes and 301 dominant epitopes in HLA class-I haplotypes. After validation by ELISpot assay, in-depth analyses to ascertain their nature of conservation, immunogenicity, and docking with the corresponding MHC class-I molecules were undertaken. Our study predicted MHC class-I restricted epitopes that may aid the advancement of anti-EBOV immune responses. And the integrated strategy of epitope prediction, validation, and comparative analyses were postulated, promising for epitope-based immunotherapy development and application to viral epidemics.
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Affiliation(s)
- Yang Liu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China.,Shaanxi Provincial Center for Disease Control and Prevention, Xi'an, Shaanxi, P.R. China
| | - Baozeng Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jiawei Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Hao Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China.,Tangshan Sannvhe Airport, Tangshan, Hebei, P.R. China
| | - Zhenhua Lu
- Department of Epidemiology, Public Health School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Longyu Chen
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Mingfu Lan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jiahao Xu
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jingyu Pan
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jingqi Shi
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Yuanjie Sun
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Xiyang Zhang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Jing Wang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Dongbo Jiang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
| | - Kun Yang
- Department of Immunology, Basic Medicine School, Air-Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, P.R. China
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Liu Z, Chen L, Gao X, Zou R, Meng Q, Fu Q, Xie Y, Miao Q, Chen L, Tang X, Zhang S, Zhang H, Schroyen M. Quantitative proteomics reveals tissue-specific toxic mechanisms for acute hydrogen sulfide-induced injury of diverse organs in pig. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150365. [PMID: 34555611 DOI: 10.1016/j.scitotenv.2021.150365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Hydrogen sulfide (H2S) is a highly toxic gas in many environmental and occupational places. It can induce multiple organ injuries particularly in lung, trachea and liver, but the relevant mechanisms remain poorly understood. In this study, we used a TMT-based discovery proteomics to identify key proteins and correlated molecular pathways involved in the pathogenesis of acute H2S-induced toxicity in porcine lung, trachea and liver tissues. Pigs were subjected to acute inhalation exposure of up to 250 ppm of H2S for 5 h for the first time. Changes in hematology and biochemical indexes, serum inflammatory cytokines and histopathology demonstrated that acute H2S exposure induced organs inflammatory injury and dysfunction in the porcine lung, trachea and liver. The proteomic data showed 51, 99 and 84 proteins that were significantly altered in lung, trachea and liver, respectively. Gene ontology (GO) annotation, KEGG pathway and protein-protein interaction (PPI) network analysis revealed that acute H2S exposure affected the three organs via different mechanisms that were relatively similar between lung and trachea. Further analysis showed that acute H2S exposure caused inflammatory damages in the porcine lung and trachea through activating complement and coagulation cascades, and regulating the hyaluronan metabolic process. Whereas antigen presentation was found in the lung but oxidative stress and cell apoptosis was observed exclusively in the trachea. In the liver, an induced dysfunction was associated with protein processing in the endoplasmic reticulum and lipid metabolism. Further validation of some H2S responsive proteins using western blotting indicated that our proteomics data were highly reliable. Collectively, these findings provide insight into toxic molecular mechanisms that could potentially be targeted for therapeutic intervention for acute H2S intoxication.
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Affiliation(s)
- Zhen Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Passage des Déportés 2, Gembloux 5030, Belgium
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Gao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Ruixia Zou
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qin Fu
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Yanjiao Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qixiang Miao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lei Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Martine Schroyen
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Passage des Déportés 2, Gembloux 5030, Belgium
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45
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Roetman JJ, Apostolova MKI, Philip M. Viral and cellular oncogenes promote immune evasion. Oncogene 2022; 41:921-929. [PMID: 35022539 PMCID: PMC8851748 DOI: 10.1038/s41388-021-02145-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022]
Abstract
Thirteen percent of cancers worldwide are associated with viral infections. While many human oncogenic viruses are widely endemic, very few infected individuals develop cancer. This raises the question why oncogenic viruses encode viral oncogenes if they can replicate and spread between human hosts without causing cancer. Interestingly, viral infection triggers innate immune signaling pathways that in turn activate tumor suppressors such as p53, suggesting that tumor suppressors may have evolved not primarily to prevent cancer, but to thwart viral infection. Here, we summarize and compare several major immune evasion strategies used by viral and non-viral cancers, with a focus on oncogenes that play dual roles in promoting tumorigenicity and immune evasion. By highlighting important and illustrative examples of how oncogenic viruses evade the immune system, we aim to shed light on how non-viral cancers avoid immune detection. Further study and understanding of how viral and non-viral oncogenes impact immune function could lead to improved strategies to combine molecular therapies targeting oncoproteins in combination with immunomodulators.
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Affiliation(s)
| | - Minna K. I. Apostolova
- Department of Biochemistry and Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - Mary Philip
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA. .,Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
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46
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Viral immune evasins impact antigen presentation by allele-specific trapping of MHC I at the peptide-loading complex. Sci Rep 2022; 12:1516. [PMID: 35087068 PMCID: PMC8795405 DOI: 10.1038/s41598-022-05000-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/30/2021] [Indexed: 11/30/2022] Open
Abstract
Major histocompatibility complex class I (MHC I) molecules present antigenic peptides to cytotoxic T cells to eliminate infected or cancerous cells. The transporter associated with antigen processing (TAP) shuttles proteasomally generated peptides into the ER for MHC I loading. As central part of the peptide-loading complex (PLC), TAP is targeted by viral factors, which inhibit peptide supply and thereby impact MHC I-mediated immune responses. However, it is still poorly understood how antigen presentation via different MHC I allotypes is affected by TAP inhibition. Here, we show that conditional expression of herpes simplex viral ICP47 suppresses surface presentation of HLA-A and HLA-C, but not of HLA-B, while the human cytomegaloviral US6 reduces surface levels of all MHC I allotypes. This marked difference in HLA-B antigen presentation is echoed by an enrichment of HLA-B allomorphs at US6-arrested PLC in comparison to ICP47-PLC. Although both viral factors prevent TAP-mediated peptide supply, our data imply that MHC I allomorphs favor different conformationally arrested states of the PLC, leading to differential downregulation of MHC I surface presentation. These findings will help understand MHC I biology in general and will even advance the targeted treatment of infections depending on patients’ allotypes.
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47
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Yin L, Liu X, Hu D, Luo Y, Zhang G, Liu P. Swine Enteric Coronaviruses (PEDV, TGEV, and PDCoV) Induce Divergent Interferon-Stimulated Gene Responses and Antigen Presentation in Porcine Intestinal Enteroids. Front Immunol 2022; 12:826882. [PMID: 35126380 PMCID: PMC8810500 DOI: 10.3389/fimmu.2021.826882] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/27/2021] [Indexed: 02/02/2023] Open
Abstract
Swine enteric coronaviruses (SECoVs) including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV), account for the majority of lethal watery diarrhea in neonatal pigs and pose significant economic and public health burdens in the world. While the three SECoVs primarily infect intestinal epithelia in vivo and cause similar clinical signs, there are evident discrepancies in their cellular tropism and pathogenicity. However, the underlying mechanisms to cause the differences remain unclear. Herein, we employed porcine enteroids that are a physiologically relevant model of the intestine to assess the host epithelial responses following infection with the three SECoVs (PEDV, TGEV, and PDCoV). Although SECoVs replicated similarly in jejunal enteroids, a parallel comparison of transcriptomics datasets uncovered that PEDV and TGEV infection induced similar transcriptional profiles and exhibited a more pronounced response with more differentially expressed genes (DEGs) in jejunal enteroids compared with PDCoV infection. Notably, TGEV and PDCoV induced high levels of type I and III IFNs and IFN-stimulated gene (ISG) responses, while PEDV displayed a delayed peak and elicited a much lesser extent of IFN responses. Furthermore, TGEV and PDCoV instead of PEDV elicited a substantial upregulation of antigen-presentation genes and T cell-recruiting chemokines in enteroids. Mechanistically, we demonstrated that IFNs treatment markedly elevated the expression of NOD-like receptor (NLR) family NLRC5 and major histocompatibility complex class I (MHC-I) molecules. Together, our results indicate unique and common viral strategies for manipulating the global IFN responses and antigen presentation utilized by SECoVs, which help us a better understanding of host-SECoVs interactions.
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48
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Perez MAS, Cuendet MA, Röhrig UF, Michielin O, Zoete V. Structural Prediction of Peptide-MHC Binding Modes. Methods Mol Biol 2022; 2405:245-282. [PMID: 35298818 DOI: 10.1007/978-1-0716-1855-4_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The immune system is constantly protecting its host from the invasion of pathogens and the development of cancer cells. The specific CD8+ T-cell immune response against virus-infected cells and tumor cells is based on the T-cell receptor recognition of antigenic peptides bound to class I major histocompatibility complexes (MHC) at the surface of antigen presenting cells. Consequently, the peptide binding specificities of the highly polymorphic MHC have important implications for the design of vaccines, for the treatment of autoimmune diseases, and for personalized cancer immunotherapy. Evidence-based machine-learning approaches have been successfully used for the prediction of peptide binders and are currently being developed for the prediction of peptide immunogenicity. However, understanding and modeling the structural details of peptide/MHC binding is crucial for a better understanding of the molecular mechanisms triggering the immunological processes, estimating peptide/MHC affinity using universal physics-based approaches, and driving the design of novel peptide ligands. Unfortunately, due to the large diversity of MHC allotypes and possible peptides, the growing number of 3D structures of peptide/MHC (pMHC) complexes in the Protein Data Bank only covers a small fraction of the possibilities. Consequently, there is a growing need for rapid and efficient approaches to predict 3D structures of pMHC complexes. Here, we review the key characteristics of the 3D structure of pMHC complexes before listing databases and other sources of information on pMHC structures and MHC specificities. Finally, we discuss some of the most prominent pMHC docking software.
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Affiliation(s)
- Marta A S Perez
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michel A Cuendet
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland.
| | - Vincent Zoete
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, Lausanne, Switzerland.
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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49
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Nuutila J, Hohenthal U, Oksi J, Jalava-Karvinen P. Rapid detection of bacterial infection using a novel single-tube, four-colour flow cytometric method: Comparison with PCT and CRP. EBioMedicine 2021; 74:103724. [PMID: 34844193 PMCID: PMC8633870 DOI: 10.1016/j.ebiom.2021.103724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/04/2021] [Accepted: 11/16/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND A key factor behind the unnecessary use of antibiotics is the lack of rapid and accurate diagnostic tests. In this study, we developed a novel and fast flow cytometric single-tube method to detect bacterial infections within 30 minutes. METHODS Quantitative flow cytometric four-colour analysis of host biomarkers CD35, CD64, CD329, and MHC class I expression on neutrophils and lymphocytes was performed on samples taken from 841 febrile patients with suspected infection. Obtained data was incorporated into the four-colour bacterial infection (FCBI)-index, using the developed bacterial infection algorithm. FINDINGS In distinguishing between microbiologically confirmed bacterial (n = 193) and viral (n = 291) infections, the FCBI-index method was superior to serum C-reactive protein (CRP) and procalcitonin (PCT). In 269 confirmed viral respiratory tract infections, 43% (95% CI: 37-49%) of the patients had an increased FCBI-index, suggesting probable bacterial coinfection. INTERPRETATION The proposed FCBI-index test might be a potent additional tool when assessing appropriateness of empiric antibiotic treatment. FUNDING This study has been financially supported by Turku University Hospital (Turku, Finland) and The Finnish Medical Foundation.
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Affiliation(s)
- Jari Nuutila
- Department of Life Technologies, University of Turku, Turku, Finland.
| | - Ulla Hohenthal
- Turku University Hospital, Department of Medicine, Turku, Finland; Faculty of Medicine, University of Turku, Turku, Finland
| | - Jarmo Oksi
- Turku University Hospital, Department of Medicine, Turku, Finland; Faculty of Medicine, University of Turku, Turku, Finland
| | - Päivi Jalava-Karvinen
- Turku University Hospital, Department of Medicine, Turku, Finland; Faculty of Medicine, University of Turku, Turku, Finland
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50
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Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis. Infect Immun 2021; 90:e0033421. [PMID: 34780277 PMCID: PMC9119117 DOI: 10.1128/iai.00334-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To identify sequences with a role in microbial pathogenesis, we assessed the adequacy of their annotation by existing controlled vocabularies and sequence databases. Our goal was to regularize descriptions of microbial pathogenesis for improved integration with bioinformatic applications. Here, we review the challenges of annotating sequences for pathogenic activity. We relate the categorization of more than 2,750 sequences of pathogenic microbes through a controlled vocabulary called Functions of Sequences of Concern (FunSoCs). These allow for an ease of description by both humans and machines. We provide a subset of 220 fully annotated sequences in the supplemental material as examples. The use of this compact (∼30 terms), controlled vocabulary has potential benefits for research in microbial genomics, public health, biosecurity, biosurveillance, and the characterization of new and emerging pathogens.
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