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Flender D, Vilenne F, Adams C, Boonen K, Valkenborg D, Baggerman G. Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39152539 DOI: 10.1002/mas.21905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/19/2024]
Abstract
Immunopeptidomics is becoming an increasingly important field of study. The capability to identify immunopeptides with pivotal roles in the human immune system is essential to shift the current curative medicine towards personalized medicine. Throughout the years, the field has matured, giving insight into the current pitfalls. Nowadays, it is commonly accepted that generalizing shotgun proteomics workflows is malpractice because immunopeptidomics faces numerous challenges. While many of these difficulties have been addressed, the road towards the ideal workflow remains complicated. Although the presence of Posttranslational modifications (PTMs) in the immunopeptidome has been demonstrated, their identification remains highly challenging despite their significance for immunotherapies. The large number of unpredictable modifications in the immunopeptidome plays a pivotal role in the functionality and these challenges. This review provides a comprehensive overview of the current advancements in immunopeptidomics. We delve into the challenges associated with identifying PTMs within the immunopeptidome, aiming to address the current state of the field.
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Affiliation(s)
- Daniel Flender
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- Health Unit, VITO, Mol, Belgium
| | - Frédérique Vilenne
- Health Unit, VITO, Mol, Belgium
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- ImmuneSpec, Niel, Belgium
| | - Dirk Valkenborg
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Geert Baggerman
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
- ImmuneSpec, Niel, Belgium
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Dong H, Wen C, He L, Zhang J, Xiang N, Liang L, Hu L, Li W, Liu J, Shi M, Hu Y, Chen S, Liu H, Yang X. Nilotinib boosts the efficacy of anti-PDL1 therapy in colorectal cancer by restoring the expression of MHC-I. J Transl Med 2024; 22:769. [PMID: 39143573 PMCID: PMC11325812 DOI: 10.1186/s12967-024-05572-2] [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: 05/20/2024] [Accepted: 08/04/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Although immune checkpoint inhibitors (ICIs) have revolutionized the landscape of cancer treatment, only a minority of colorectal cancer (CRC) patients respond to them. Enhancing tumor immunogenicity by increasing major histocompatibility complex I (MHC-I) surface expression is a promising strategy to boost the antitumor efficacy of ICIs. METHODS Dual luciferase reporter assays were performed to find drug candidates that can increase MHC-I expression. The effect of nilotinib on MHC-I expression was verified by dual luciferase reporter assays, qRT-PCR, flow cytometry and western blotting. The biological functions of nilotinib were evaluated through a series of in vitro and in vivo experiments. Using RNA-seq analysis, immunofluorescence assays, western blotting, flow cytometry, rescue experiments and microarray chip assays, the underlying molecular mechanisms were investigated. RESULTS Nilotinib induces MHC-I expression in CRC cells, enhances CD8+ T-cell cytotoxicity and subsequently enhances the antitumor effects of anti-PDL1 in both microsatellite instability and microsatellite stable models. Mechanistically, nilotinib promotes MHC-I mRNA expression via the cGAS-STING-NF-κB pathway and reduces MHC-I degradation by suppressing PCSK9 expression in CRC cells. PCSK9 may serve as a potential therapeutic target for CRC, with nilotinib potentially targeting PCSK9 to exert anti-CRC effects. CONCLUSION This study reveals a previously unknown role of nilotinib in antitumor immunity by inducing MHC-I expression in CRC cells. Our findings suggest that combining nilotinib with anti-PDL1 therapy may be an effective strategy for the treatment of CRC.
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Affiliation(s)
- Haiyan Dong
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Chuangyu Wen
- Department of Obstetrics and Gynecology, The Tenth Affiliated Hospital of Southern Medical University, Dongguan, 523059, Guangdong, China.
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, 60637, USA.
| | - Lu He
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of Neurology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Jingdan Zhang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Nanlin Xiang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Liumei Liang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Limei Hu
- Department of Clinical Laboratory Medicine, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, Guangxi, China
| | - Weiqian Li
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Jiaqi Liu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Mengchen Shi
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Yijia Hu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China
| | - Siyu Chen
- Guangdong Laboratory, GuangdongKey Laboratory Animal Lab, Animals Monitoring Institute, Guangzhou, 510633, Guangdong, China
| | - Huanliang Liu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
| | - Xiangling Yang
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, Guangdong, China.
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Naaz A, Turnquist HR, Gorantla VS, Little SR. Drug delivery strategies for local immunomodulation in transplantation: Bridging the translational gap. Adv Drug Deliv Rev 2024:115429. [PMID: 39142608 DOI: 10.1016/j.addr.2024.115429] [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: 02/15/2024] [Revised: 08/07/2024] [Accepted: 08/11/2024] [Indexed: 08/16/2024]
Abstract
Drug delivery strategies for local immunomodulation hold tremendous promise compared to current clinical gold-standard systemic immunosuppression as they could improve the benefit to risk ratio of life-saving or life-enhancing transplants. Such strategies have facilitated prolonged graft survival in animal models at lower drug doses while minimizing off-target effects. Despite the promising outcomes in preclinical animal studies, progression of these strategies to clinical trials has faced challenges. A comprehensive understanding of the translational barriers is a critical first step towards clinical validation of effective immunomodulatory drug delivery protocols proven for safety and tolerability in pre-clinical animal models. This review overviews the current state-of-the-art in local immunomodulatory strategies for transplantation and outlines the key challenges hindering their clinical translation.
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Affiliation(s)
- Afsana Naaz
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, PA 15261, United States; Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, 15213, United States.
| | - Heth R Turnquist
- Thomas E. Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA, 15213, United States; Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, United States; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, 15213, United States; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, United States.
| | - Vijay S Gorantla
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, United States; Departments of Surgery, Ophthalmology and Bioengineering, Wake Forest School of Medicine, Wake Forest Institute of Regenerative Medicine, Winston Salem, NC, 27101, United States.
| | - Steven R Little
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, PA 15261, United States; Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, United States; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, 15213, United States; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, United States; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, United States; Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, United States; Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, United States.
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Rogers J, Bajur AT, Salaita K, Spillane KM. Mechanical control of antigen detection and discrimination by T and B cell receptors. Biophys J 2024; 123:2234-2255. [PMID: 38794795 DOI: 10.1016/j.bpj.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024] Open
Abstract
The adaptive immune response is orchestrated by just two cell types, T cells and B cells. Both cells possess the remarkable ability to recognize virtually any antigen through their respective antigen receptors-the T cell receptor (TCR) and B cell receptor (BCR). Despite extensive investigations into the biochemical signaling events triggered by antigen recognition in these cells, our ability to predict or control the outcome of T and B cell activation remains elusive. This challenge is compounded by the sensitivity of T and B cells to the biophysical properties of antigens and the cells presenting them-a phenomenon we are just beginning to understand. Recent insights underscore the central role of mechanical forces in this process, governing the conformation, signaling activity, and spatial organization of TCRs and BCRs within the cell membrane, ultimately eliciting distinct cellular responses. Traditionally, T cells and B cells have been studied independently, with researchers working in parallel to decipher the mechanisms of activation. While these investigations have unveiled many overlaps in how these cell types sense and respond to antigens, notable differences exist. To fully grasp their biology and harness it for therapeutic purposes, these distinctions must be considered. This review compares and contrasts the TCR and BCR, placing emphasis on the role of mechanical force in regulating the activity of both receptors to shape cellular and humoral adaptive immune responses.
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Affiliation(s)
- Jhordan Rogers
- Department of Chemistry, Emory University, Atlanta, Georgia
| | - Anna T Bajur
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
| | - Katelyn M Spillane
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom; Department of Life Sciences, Imperial College London, London, United Kingdom.
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5
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Yan J, Song C, Liang J, La Y, Lai J, Pan R, Huang Z, Li B, Zhang P. Moderate Genetic Diversity of MHC Genes in an Isolated Small Population of Black-and-White Snub-Nosed Monkeys ( Rhinopithecus bieti). Animals (Basel) 2024; 14:2276. [PMID: 39123802 PMCID: PMC11310952 DOI: 10.3390/ani14152276] [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: 06/11/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species.
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Affiliation(s)
- Jibing Yan
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Chunmei Song
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Jiaqi Liang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Yanni La
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
| | - Jiandong Lai
- Baima Snow Mountain National Nature Reserve Administrative Bureau, Diqing 674500, China;
| | - Ruliang Pan
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
- International Center of Biodiversity and Primat Conservation, Dali University, Dali 671003, China
- School of Human Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Zhipang Huang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali 671003, China;
| | - Baoguo Li
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
- Shaanxi Institute of Zoology, Xi’an 710032, China
- College of Life Science, Yanan University, Yanan 710032, China
| | - Pei Zhang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi’an 710069, China; (J.Y.); (C.S.); (J.L.); (Y.L.); (R.P.)
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Huang H, Lu X, Guo J, Chen Y, Yi M, Jia K. Protective efficacy and immune responses of largemouth bass (Micropterus salmoides) immunized with an inactivated vaccine against the viral hemorrhagic septicemia virus genotype IVa. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109691. [PMID: 38871138 DOI: 10.1016/j.fsi.2024.109691] [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: 04/08/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Viral hemorrhagic septicemia virus (VHSV) poses a significant threat to the aquaculture industry, prompting the need for effective preventive measures. Here, we developed an inactivated VHSV and revealed the molecular mechanisms underlying the host's protective response against VHSV. The vaccine was created by treating VHSV with 0.05 % formalin at 16 °C for 48 h, which was determined to be the most effective inactivation method. Compared with nonvaccinated fish, vaccinated fish exhibited a remarkable increase in survival rate (99 %) and elevated levels of serum neutralizing antibodies, indicating strong immunization. To investigate the gene changes induced by vaccination, RNA sequencing was performed on spleen samples from control and vaccinated fish 14 days after vaccination. The analysis revealed 893 differentially expressed genes (DEGs), with notable up-regulation of immune-related genes such as annexin A1a, coxsackievirus and adenovirus receptor homolog, V-set domain-containing T-cell activation inhibitor 1-like, and heat shock protein 90 alpha class A member 1 tandem duplicate 2, indicating a vigorous innate immune response. Furthermore, KEGG enrichment analysis highlighted significant enrichment of DEGs in processes related to antigen processing and presentation, necroptosis, and viral carcinogenesis. GO enrichment analysis further revealed enrichment of DEGs related to the regulation of type I interferon (IFN) production, type I IFN production, and negative regulation of viral processes. Moreover, protein-protein interaction network analysis identified central hub genes, including IRF3 and HSP90AA1.2, suggesting their crucial roles in coordinating the immune response elicited by the vaccine. These findings not only confirm the effectiveness of our vaccine formulation but also offer valuable insights into the underlying immunological mechanisms, which can be valuable for future vaccine development and disease management in the aquaculture industry.
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Affiliation(s)
- Hao Huang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China.
| | - Xiaobing Lu
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China.
| | - Jiasen Guo
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China.
| | - Yihong Chen
- Institute of Modern Aquaculture Science and Engineering (IMASE)/Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou, 510631, China.
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China.
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China.
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Aleman M. Inflammatory and Immune-Mediated Myopathies, What Do We Know? Vet Clin North Am Equine Pract 2024; 40:207-218. [PMID: 38852014 DOI: 10.1016/j.cveq.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024] Open
Abstract
Inflammatory myopathies or myositis encompass diseases characterized by the presence of inflammatory cellular infiltrates, mainly polymorphonuclear cells and/or lymphocytes, in muscle. This is in contrast to most forms of muscle disease characterized by myodegeneration that results in macrophage infiltration. Inflammatory myopathies could have infectious or noninfectious causes. Noninfectious causes consist of primary (genetic, autoimmune) or acquired immune-mediated disease. Focal, multifocal or diffuse, acute or recurrent forms of disease can occur. This article will mainly review immune-mediated myopathies in horses. Myositis directly caused by infection such as Clostridium spp and others will not be discussed here.
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Affiliation(s)
- Monica Aleman
- SVM: Department of Medicine and Epidemiology, University of California, Davis, Tupper Hall 2108, One Shields Avenue, Davis, CA 95616, USA.
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8
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Zhong Y, Zhang H, Wang P, Zhao J, Ge Y, Sun Z, Wang Z, Li J, Hu S. Auger emitter in combination with Olaparib suppresses tumor growth via promoting antitumor immune responses in pancreatic cancer. Invest New Drugs 2024; 42:442-453. [PMID: 38941055 DOI: 10.1007/s10637-024-01454-y] [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: 04/22/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
The present study aimed to clarify the hypothesis that auger emitter 125I particles in combination with PARP inhibitor Olaparib could inhibit pancreatic cancer progression by promoting antitumor immune response. Pancreatic cancer cell line (Panc02) and mice subcutaneously inoculated with Panc02 cells were employed for the in vitro and in vivo experiments, respectively, followed by 125I and Olaparib administrations. The apoptosis and CRT exposure of Panc02 cells were detected using flow cytometry assay. QRT-PCR, immunofluorescence, immunohistochemical analysis, and western blot were employed to examine mRNA and protein expression. Experimental results showed that 125I combined with Olaparib induced immunogenic cell death and affected antigen presentation in pancreatic cancer. 125I in combination with Olaparib influenced T cells and dendritic cells by up-regulating CD4, CD8, CD69, Caspase3, CD86, granzyme B, CD80, and type I interferon (IFN)-γ and down-regulating Ki67 in vivo. The combination also activated the cyclic GMP-AMP synthase stimulator of IFN genes (Sting) pathway in Panc02 cells. Moreover, Sting knockdown alleviated the effect of the combination of 125I and Olaparib on pancreatic cancer progression. In summary, 125I in combination with Olaparib inhibited pancreatic cancer progression through promoting antitumor immune responses, which may provide a potential treatment for pancreatic cancer.
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Affiliation(s)
- Yanqi Zhong
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China
| | - Heng Zhang
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China
| | - Peng Wang
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China
| | - Jing Zhao
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China
| | - Yuxi Ge
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China
| | - Zongqiong Sun
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China
| | - Zi Wang
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China
| | - Jie Li
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China.
| | - Shudong Hu
- Department of Radiology, Affiliated Hospital of Jiangnan University, No. 1000, Hefeng Road, Wuxi, Jiangsu, 214000, China.
- Institute of Translational Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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Miyahira AK, Kamran SC, Jamaspishvili T, Marshall CH, Maxwell KN, Parolia A, Zorko NA, Pienta KJ, Soule HR. Disrupting prostate cancer research: Challenge accepted; report from the 2023 Coffey-Holden Prostate Cancer Academy Meeting. Prostate 2024; 84:993-1015. [PMID: 38682886 DOI: 10.1002/pros.24721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024]
Abstract
INTRODUCTION The 2023 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, themed "Disrupting Prostate Cancer Research: Challenge Accepted," was convened at the University of California, Los Angeles, Luskin Conference Center, in Los Angeles, CA, from June 22 to 25, 2023. METHODS The 2023 marked the 10th Annual CHPCA Meeting, a discussion-oriented scientific think-tank conference convened annually by the Prostate Cancer Foundation, which centers on innovative and emerging research topics deemed pivotal for advancing critical unmet needs in prostate cancer research and clinical care. The 2023 CHPCA Meeting was attended by 81 academic investigators and included 40 talks across 8 sessions. RESULTS The central topic areas covered at the meeting included: targeting transcription factor neo-enhancesomes in cancer, AR as a pro-differentiation and oncogenic transcription factor, why few are cured with androgen deprivation therapy and how to change dogma to cure metastatic prostate cancer without castration, reducing prostate cancer morbidity and mortality with genetics, opportunities for radiation to enhance therapeutic benefit in oligometastatic prostate cancer, novel immunotherapeutic approaches, and the new era of artificial intelligence-driven precision medicine. DISCUSSION This article provides an overview of the scientific presentations delivered at the 2023 CHPCA Meeting, such that this knowledge can help in facilitating the advancement of prostate cancer research worldwide.
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Affiliation(s)
- Andrea K Miyahira
- Science Department, Prostate Cancer Foundation, Santa Monica, California, USA
| | - Sophia C Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tamara Jamaspishvili
- Department of Pathology and Laboratory Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Catherine H Marshall
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kara N Maxwell
- Department of Medicine-Hematology/Oncology and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medicine Service, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
| | - Abhijit Parolia
- Department of Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicholas A Zorko
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
- University of Minnesota Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Howard R Soule
- Science Department, Prostate Cancer Foundation, Santa Monica, California, USA
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10
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Zhanzak Z, Cina D, Johnson AC, Larsen CP. Implications of MHC-restricted immunopeptidome in transplantation. Front Immunol 2024; 15:1436233. [PMID: 39035001 PMCID: PMC11257886 DOI: 10.3389/fimmu.2024.1436233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024] Open
Abstract
The peptide presentation by donor and recipient major histocompatibility complex (MHC) molecules is the major driver of T-cell responses in transplantation. In this review, we address an emerging area of interest, the application of immunopeptidome in transplantation, and describe the potential opportunities that exist to use peptides for targeting alloreactive T cells. The immunopeptidome, the set of peptides presented on an individual's MHC, plays a key role in immune surveillance. In transplantation, the immunopeptidome is heavily influenced by MHC-derived peptides, delineating a key subset of the diverse peptide repertoire implicated in alloreactivity. A better understanding of the immunopeptidome in transplantation has the potential to open up new approaches to identify, characterize, longitudinally quantify, and therapeutically target donor-specific T cells and ultimately support more personalized immunotherapies to prevent rejection and promote allograft tolerance.
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Affiliation(s)
- Zhuldyz Zhanzak
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
- Emory Transplant Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Davide Cina
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
- Emory Transplant Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Aileen C. Johnson
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
- Emory Transplant Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Christian P. Larsen
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
- Emory Transplant Center, Emory University School of Medicine, Atlanta, GA, United States
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Machaca V, Goyzueta V, Cruz MG, Sejje E, Pilco LM, López J, Túpac Y. Transformers meets neoantigen detection: a systematic literature review. J Integr Bioinform 2024; 0:jib-2023-0043. [PMID: 38960869 DOI: 10.1515/jib-2023-0043] [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: 10/24/2023] [Accepted: 03/20/2024] [Indexed: 07/05/2024] Open
Abstract
Cancer immunology offers a new alternative to traditional cancer treatments, such as radiotherapy and chemotherapy. One notable alternative is the development of personalized vaccines based on cancer neoantigens. Moreover, Transformers are considered a revolutionary development in artificial intelligence with a significant impact on natural language processing (NLP) tasks and have been utilized in proteomics studies in recent years. In this context, we conducted a systematic literature review to investigate how Transformers are applied in each stage of the neoantigen detection process. Additionally, we mapped current pipelines and examined the results of clinical trials involving cancer vaccines.
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Affiliation(s)
| | | | | | - Erika Sejje
- Universidad Nacional de San Agustín, Arequipa, Perú
| | | | | | - Yván Túpac
- 187038 Universidad Católica San Pablo , Arequipa, Perú
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12
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Krenz B, Lee J, Kannan T, Eilers M. Immune evasion: An imperative and consequence of MYC deregulation. Mol Oncol 2024. [PMID: 38957016 DOI: 10.1002/1878-0261.13695] [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: 02/07/2024] [Revised: 05/08/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
MYC has been implicated in the pathogenesis of a wide range of human tumors and has been described for many years as a transcription factor that regulates genes with pleiotropic functions to promote tumorigenic growth. However, despite extensive efforts to identify specific target genes of MYC that alone could be responsible for promoting tumorigenesis, the field is yet to reach a consensus whether this is the crucial function of MYC. Recent work shifts the view on MYC's function from being a gene-specific transcription factor to an essential stress resilience factor. In highly proliferating cells, MYC preserves cell integrity by promoting DNA repair at core promoters, protecting stalled replication forks, and/or preventing transcription-replication conflicts. Furthermore, an increasing body of evidence demonstrates that MYC not only promotes tumorigenesis by driving cell-autonomous growth, but also enables tumors to evade the host's immune system. In this review, we summarize our current understanding of how MYC impairs antitumor immunity and why this function is evolutionarily hard-wired to the biology of the MYC protein family. We show why the cell-autonomous and immune evasive functions of MYC are mutually dependent and discuss ways to target MYC proteins in cancer therapy.
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Affiliation(s)
- Bastian Krenz
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, Würzburg, Germany
| | - Jongkuen Lee
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Toshitha Kannan
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
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Yuan S, Sun M, Ma D, Guo X, Wang Z, Niu J, Jiang W, He Y, Wei M, Qi J. Exploring the underlying mechanisms of enteritis impact on golden pompano (Trachinotus ovatus) through multi-omics analysis. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109616. [PMID: 38734118 DOI: 10.1016/j.fsi.2024.109616] [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: 02/11/2024] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Enteritis posed a significant health challenge to golden pompano (Trachinotus ovatus) populations. In this research, a comprehensive multi-omics strategy was implemented to elucidate the pathogenesis of enteritis by comparing both healthy and affected golden pompano. Histologically, enteritis was characterized by villi adhesion and increased clustering after inflammation. Analysis of the intestinal microbiota revealed a significant increase (P < 0.05) in the abundance of specific bacterial strains, including Photobacterium and Salinivibrio, in diseased fish compared to the healthy group. Metabolomic analysis identified 5479 altered metabolites, with significant impacts on terpenoid and polyketide metabolism, as well as lipid metabolism (P < 0.05). Additionally, the concentrations of several compounds such as calcitetrol, vitamin D2, arachidonic acid, and linoleic acid were significantly reduced in the intestines of diseased fish post-enteritis (P < 0.05), with the detection of harmful substances such as Efonidipine. In transcriptomic profiling, enteritis induced 68 upregulated and 73 downregulated genes, predominantly affecting steroid hormone receptor activity (P < 0.05). KEGG pathway enrichment analysis highlighted upregulation of SQLE and CYP51 in steroidogenesis, while the HSV-1 associated MHC1 gene exhibited significant downregulation. Integration of multi-omics results suggested a potential pathogenic mechanism: enteritis may have resulted from concurrent infection of harmful bacteria, specifically Photobacterium and Salinivibrio, along with HSV-1. Efonidipine production within the intestinal tract may have blocked certain calcium ion channels, leading to downregulation of MHC1 gene expression and reduced extracellular immune recognition. Upregulation of SQLE and CYP51 genes stimulated steroid hormone synthesis within cells, which, upon binding to G protein-coupled receptors, influenced calcium ion transport, inhibited immune activation reactions, and further reduced intracellular synthesis of anti-inflammatory substances like arachidonic acid. Ultimately, this cascade led to inflammation progression, weakened intestinal peristalsis, and villi adhesion. This study utilized multi-level omics detection to investigate the pathological symptoms of enteritis and proposed a plausible pathogenic mechanism, providing innovative insights into enteritis verification and treatment in offshore cage culture of golden pompano.
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Affiliation(s)
- Shipeng Yuan
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266003, China
| | - Minmin Sun
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Di Ma
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaodan Guo
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zhuoyu Wang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jingjing Niu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Weiming Jiang
- Guangxi Academy of Fishery Sciences, No.8,Qingshan Load, Nanning, Guangxi, 530021, China
| | - Yan He
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Mingli Wei
- Guangxi Academy of Fishery Sciences, No.8,Qingshan Load, Nanning, Guangxi, 530021, China.
| | - Jie Qi
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute / MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
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14
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Henningsen K, Martinez I, Costa RJS. Exertional Stress-induced Pathogenic Luminal Content Translocation - Friend or Foe? Int J Sports Med 2024; 45:559-571. [PMID: 38286406 DOI: 10.1055/a-2235-1629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The incidence of perturbed gastrointestinal integrity, as well as resulting systemic immune responses and gastrointestinal symptoms, otherwise known as exercised-induced gastrointestinal syndrome (EIGS), is common among individuals who partake in prolonged exercise. EIGS may cause the translocation of pathogenic material, including whole bacteria and bacterial endotoxins, from the lumen into circulation, which may progress into clinical consequences such as sepsis, and potentially subsequent fatality. However, further investigation is warranted to assess the possibility of food allergen and/or digestive enzyme luminal to circulatory translocation in response to exercise, and the clinical consequences. Findings from this narrative literature review demonstrate evidence that whole bacteria and bacterial endotoxins translocation from the gastrointestinal lumen to systemic circulation occurs in response to exercise stress, with a greater propensity of translocation occurring with accompanying heat exposure. It has also been demonstrated that food allergens can translocate from the lumen to systemic circulation in response to exercise stress and initiate anaphylaxis. To date, no research investigating the effect of exercise on the translocation of digestive enzymes from the lumen into systemic circulation exists. It is evident that EIGS and consequential pathogenic translocation presents life-threatening clinical implications, warranting the development and implementation of effective management strategies in at-risk populations.
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Affiliation(s)
- Kayla Henningsen
- Nutrition Dietetics & Food, Monash University Faculty of Medicine Nursing and Health Sciences, Notting Hill, Australia
| | - Isabel Martinez
- Nutrition Dietetics & Food, Monash University Faculty of Medicine Nursing and Health Sciences, Notting Hill, Australia
| | - Ricardo J S Costa
- Nutrition Dietetics & Food, Monash University Faculty of Medicine Nursing and Health Sciences, Notting Hill, Australia
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15
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Liu Q, Ma F, Zhang G. Molecular subtyping of skin cutaneous melanoma based on inflammatory response. Heliyon 2024; 10:e33088. [PMID: 39005905 PMCID: PMC11239590 DOI: 10.1016/j.heliyon.2024.e33088] [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: 12/21/2023] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
The inflammatory response plays a crucial role in determining the prognosis and therapeutic response of skin cutaneous melanoma (SKCM). However, the molecular subtypes based on the inflammatory response and their clinical significance in SKCM have not been extensively studied. Clustering analyses to identify inflammation subtypes of SKCM based on the expression levels of inflammation response gene. We identified three subtypes: Inflammation_H, Inflammation_M, and Inflammation_L, which offer a more nuanced understanding of the complex relationship between inflammation and SKCM. The Inflammation_H subtype is associated with the most favourable prognosis, and is characterised by high levels of immune infiltrates and PD-L1 expression, low levels of stemness, high differentiation, and high genomic stability. In contrast, the Inflammation_L subtype has the least favourable prognosis, with the lowest levels of immune infiltrates and PD-L1 expression, high levels of stemness, low differentiation, and low genomic stability. In addition, the Inf-score, which is a linear risk scoring model based on the expression levels of inflammatory response genes, can be a useful tool for clinicians to assess SKCM prognosis and guide therapeutic decisions. This scoring model shows promise for clinical use in predicting patient outcomes and helps clinicians tailor treatments for individual patients. In conclusion, these findings represent a significant contribution to our understanding of the molecular subtypes of SKCM based on the levels of inflammatory response genes and their potential clinical significance. However, further studies are necessary to validate these findings and explore the underlying mechanisms of different subtypes.
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Affiliation(s)
- Qian Liu
- Big Data Institute, Central South University, Changsha, Hunan, China
| | - Fangyu Ma
- Health Management center Xiangya Hospital, Central South University, China
| | - Guanxiong Zhang
- The Department of Dermatology, Xiangya Hospital, Central South University, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, China
- Furong Laboratory, Changsha, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, China
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16
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Zhang Q, Wang C, Qin M, Ye Y, Mo Y, Meng Q, Yang G, Feng G, Lin R, Xian S, Wei J, Chen S, Wang S, Mo Z. Investigating cellular similarities and differences between upper tract urothelial carcinoma and bladder urothelial carcinoma using single-cell sequencing. Front Immunol 2024; 15:1298087. [PMID: 38903524 PMCID: PMC11187293 DOI: 10.3389/fimmu.2024.1298087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
Background Upper tract urothelial carcinoma (UTUC) and bladder urothelial carcinoma (BLCA) both originate from uroepithelial tissue, sharing remarkably similar clinical manifestations and therapeutic modalities. However, emerging evidence suggests that identical treatment regimens may lead to less favorable outcomes in UTUC compared to BLCA. Therefore, it is imperative to explore molecular processes of UTUC and identify biological differences between UTUC and BLCA. Methods In this study, we performed a comprehensive analysis using single-cell RNA sequencing (scRNA-seq) on three UTUC cases and four normal ureteral tissues. These data were combined with publicly available datasets from previous BLCA studies and RNA sequencing (RNA-seq) data for both cancer types. This pooled analysis allowed us to delineate the transcriptional differences among distinct cell subsets within the microenvironment, thus identifying critical factors contributing to UTUC progression and phenotypic differences between UTUC and BLCA. Results scRNA-seq analysis revealed seemingly similar but transcriptionally distinct cellular identities within the UTUC and BLCA ecosystems. Notably, we observed striking differences in acquired immunological landscapes and varied cellular functional phenotypes between these two cancers. In addition, we uncovered the immunomodulatory functions of vein endothelial cells (ECs) in UTUC, and intercellular network analysis demonstrated that fibroblasts play important roles in the microenvironment. Further intersection analysis showed that MARCKS promote UTUC progression, and immunohistochemistry (IHC) staining revealed that the diverse expression patterns of MARCKS in UTUC, BLCA and normal ureter tissues. Conclusion This study expands our multidimensional understanding of the similarities and distinctions between UTUC and BLCA. Our findings lay the foundation for further investigations to develop diagnostic and therapeutic targets for UTUC.
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Affiliation(s)
- Qingyun Zhang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Chengbang Wang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Min Qin
- Human Sperm Bank, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yu Ye
- Department of Emergency, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yingxi Mo
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Qinggui Meng
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Guanglin Yang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Guanzheng Feng
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Rui Lin
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Shinan Xian
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Jueling Wei
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Shan Wang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Zengnan Mo
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
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Jia Y, Wu Q, Li Y, Ma M, Song W, Chen R, Yao Y, Nair V, Zhang N, Liao M, Dai M. Revealing novel and conservative T-cell epitopes with MHC B2 restriction on H9N2 avian influenza virus (AIV). J Biol Chem 2024; 300:107395. [PMID: 38768812 PMCID: PMC11223079 DOI: 10.1016/j.jbc.2024.107395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
B2 haplotype major histocompatibility complex (MHC) has been extensively reported to confer resistance to various avian diseases. But its peptide-binding motif is unknown, and the presenting peptide is rarely identified. Here, we identified its peptide-binding motif (X-A/V/I/L/P/S/G-X-X-X-X-X-X-V/I/L) in vitro using Random Peptide Library-based MHC I LC-MS/MS analysis. To further clarify the structure basis of motif, we determined the crystal structure of the BF2∗02:01-PB2552-560 complex at 1.9 Å resolution. We found that BF2∗02:01 had a relatively wide antigen-binding groove, and the structural characterization of pockets was consistent with the characterization of peptide-binding motif. The wider features of the peptide-binding motif and increased number of peptides bound by BF2∗02:01 than BF2∗04:01 might resolve the puzzles for the presence of potential H9N2 resistance in B2 chickens. Afterward, we explored the H9N2 avian influenza virus (AIV)-induced cellular immune response in B2 haplotype chickens in vivo. We found that ratio of CD8+ T cell and kinetic expression of cytotoxicity genes including Granzyme K, interferon-γ, NK lysin, and poly-(ADP-ribose) polymerase in peripheral blood mononuclear cells were significantly increased in defending against H9N2 AIV infection. Especially, we selected 425 epitopes as candidate epitopes based on the peptide-binding motif and further identified four CD8+ T-cell epitopes on H9N2 AIV including NS198-106, PB2552-560, NP182-190, and NP455-463 via ELI-spot interferon-γ detections after stimulating memory lymphocytes with peptides. More importantly, these epitopes were found to be conserved in H7N9 AIV and H9N2 AIV. These findings provide direction for developing effective T cell epitope vaccines using well-conserved internal viral antigens in chickens.
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Affiliation(s)
- Yusheng Jia
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China
| | - Qingxin Wu
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China
| | - Yilin Li
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China
| | - Mulin Ma
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China
| | - Wei Song
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China
| | - Rongmao Chen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China
| | - Yongxiu Yao
- Viral Oncogenesis Group, The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Surrey, United Kingdom
| | - Venugopal Nair
- Viral Oncogenesis Group, The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Surrey, United Kingdom; Department of Zoology, Oxford University, Oxford, United Kingdom
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.
| | - Manman Dai
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.
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Dong W, Tomita K, Sawada A, Hasebe M, Inoue M, Momose K, Nakamura T, Teraoka H. Possible Shifts in the Genetic Diversity of Red-crowned Cranes ( Grus japonensis) in Hokkaido, Japan: Indications of Continental Gene Flow. Animals (Basel) 2024; 14:1633. [PMID: 38891680 PMCID: PMC11171382 DOI: 10.3390/ani14111633] [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: 05/09/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Red-crowned cranes (Grus japonensis) consist of two distinct groups: the continental population and the island population. The island population, localized in Hokkaido, Japan, exhibits very low genetic diversity due to its rapid recovery from the brink of extinction. Our previous research in 2018 highlighted a possible mating between a male from the continental population, with the Gj5 haplotype, and a female from the island population, with the Gj2 haplotype, at Hitominuma Sawmp shore in northern Hokkaido. The present study attempted to unravel the distribution of their offspring by examining the major histocompatibility complex (MHC) of this mixed breeding pair compared with samples collected from cranes in northern and southeastern Hokkaido between 2008 and 2022. The analysis identified 55 MHC types, including 10 known types in a dataset of 89 crane samples, based on amino acid sequences. A total of 58 MHC types were recognized, based on nucleotide sequences, as there were many cases in which the same amino acid sequence had different nucleotide sequences. The five DNA types of MHC in the Hitominuma Swamp male were predominantly identified in eight cranes from northern Hokkaido and one chick from southeastern Hokkaido. In addition, population genetic analysis, based on insertion/deletion (InDel) polymorphisms, indicates distinct population differentiation between the northern and southeastern regions of Hokkaido. These results suggest that genetic contributions from the continental red-crowned crane population have already been integrated into the Hokkaido populations, with a more pronounced influence in northern Hokkaido.
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Affiliation(s)
- Wenjing Dong
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (W.D.); (K.T.); (T.N.)
| | - Kai Tomita
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (W.D.); (K.T.); (T.N.)
| | - Akira Sawada
- Faculty of Human Sciences, Waseda University, Tokorozawa 359-1192, Japan;
| | - Makoto Hasebe
- NPO Sarobetsu Eco Network, Toyotomi 098-4100, Japan;
| | - Masako Inoue
- NPO Red-crowned Crane Conservancy, Kushiro 085-0036, Japan; (M.I.); (K.M.)
| | - Kunikazu Momose
- NPO Red-crowned Crane Conservancy, Kushiro 085-0036, Japan; (M.I.); (K.M.)
| | - Tatsuro Nakamura
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (W.D.); (K.T.); (T.N.)
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; (W.D.); (K.T.); (T.N.)
- NPO Red-crowned Crane Conservancy, Kushiro 085-0036, Japan; (M.I.); (K.M.)
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19
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Wang S, Zheng L, Wei X, Qu Z, Du L, Wang S, Zhang N. Amino acid insertion in Bat MHC-I enhances complex stability and augments peptide presentation. Commun Biol 2024; 7:586. [PMID: 38755285 PMCID: PMC11099071 DOI: 10.1038/s42003-024-06292-5] [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: 08/04/2023] [Accepted: 05/05/2024] [Indexed: 05/18/2024] Open
Abstract
Bats serve as reservoirs for numerous zoonotic viruses, yet they typically remain asymptomatic owing to their unique immune system. Of particular significance is the MHC-I in bats, which plays crucial role in anti-viral response and exhibits polymorphic amino acid (AA) insertions. This study demonstrated that both 5AA and 3AA insertions enhance the thermal stability of the bat MHC-I complex and enrich the diversity of bound peptides in terms of quantity and length distribution, by stabilizing the 310 helix, a region prone to conformational changes during peptide loading. However, the mismatched insertion could diminish the stability of bat pMHC-I. We proposed that a suitable insertion may help bat MHC-I adapt to high body temperatures during flight while enhancing antiviral responses. Moreover, this site-specific insertions may represent a strategy of evolutionary adaptation of MHC-I molecules to fluctuations in body temperature, as similar insertions have been found in other lower vertebrates.
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Affiliation(s)
- Suqiu Wang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, PR China
| | - Liangzhen Zheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, PR China
- Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, PR China
| | - Xiaohui Wei
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, PR China
| | - Zehui Qu
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, PR China
| | - Liubao Du
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, PR China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai, 200030, PR China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Nianzhi Zhang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, PR China.
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20
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Leong SL, Murdolo L, Maddumage JC, Koutsakos M, Kedzierska K, Purcell AW, Gras S, Grant EJ. Characterisation of novel influenza-derived HLA-B*18:01-restricted epitopes. Clin Transl Immunology 2024; 13:e1509. [PMID: 38737448 PMCID: PMC11087170 DOI: 10.1002/cti2.1509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Objectives Seasonal influenza viruses cause roughly 650 000 deaths annually despite available vaccines. CD8+ T cells typically recognise influenza-derived peptides from internal structural and non-structural influenza proteins and are an attractive avenue for future vaccine design as they could reduce the severity of disease following infection with diverse influenza strains. CD8+ T cells recognise peptides presented by the highly polymorphic Human Leukocyte Antigens class I molecules (HLA-I). Each HLA-I variant has distinct peptide binding preferences, representing a significant obstacle for designing vaccines that elicit CD8+ T cell responses across broad populations. Consequently, the rational design of a CD8+ T cell-mediated vaccine would require the identification of highly immunogenic peptides restricted to a range of different HLA molecules. Methods Here, we assessed the immunogenicity of six recently published novel influenza-derived peptides identified by mass-spectrometry and predicted to bind to the prevalent HLA-B*18:01 molecule. Results Using CD8+ T cell activation assays and protein biochemistry, we showed that 3/6 of the novel peptides were immunogenic in several HLA-B*18:01+ individuals and confirmed their HLA-B*18:01 restriction. We subsequently compared CD8+ T cell responses towards the previously identified highly immunogenic HLA-B*18:01-restricted NP219 peptide. Using X-ray crystallography, we solved the first crystal structures of HLA-B*18:01 presenting immunogenic influenza-derived peptides. Finally, we dissected the first TCR repertoires specific for HLA-B*18:01 restricted pathogen-derived peptides, identifying private and restricted repertoires against each of the four peptides. Conclusion Overall the characterisation of these novel immunogenic peptides provides additional HLA-B*18:01-restricted vaccine targets derived from the Matrix protein 1 and potentially the non-structural protein and the RNA polymerase catalytic subunit of influenza viruses.
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Affiliation(s)
- Samuel Liwei Leong
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Lawton Murdolo
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Janesha C Maddumage
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVICAustralia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and ImmunityUniversity of MelbourneMelbourneVICAustralia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Stephanie Gras
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
| | - Emma J Grant
- Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment (SABE)La Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
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21
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Zhao Z, Bashiri S, Ziora ZM, Toth I, Skwarczynski M. COVID-19 Variants and Vaccine Development. Viruses 2024; 16:757. [PMID: 38793638 PMCID: PMC11125726 DOI: 10.3390/v16050757] [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: 04/22/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), the global pandemic caused by severe acute respiratory syndrome 2 virus (SARS-CoV-2) infection, has caused millions of infections and fatalities worldwide. Extensive SARS-CoV-2 research has been conducted to develop therapeutic drugs and prophylactic vaccines, and even though some drugs have been approved to treat SARS-CoV-2 infection, treatment efficacy remains limited. Therefore, preventive vaccination has been implemented on a global scale and represents the primary approach to combat the COVID-19 pandemic. Approved vaccines vary in composition, although vaccine design has been based on either the key viral structural (spike) protein or viral components carrying this protein. Therefore, mutations of the virus, particularly mutations in the S protein, severely compromise the effectiveness of current vaccines and the ability to control COVID-19 infection. This review begins by describing the SARS-CoV-2 viral composition, the mechanism of infection, the role of angiotensin-converting enzyme 2, the host defence responses against infection and the most common vaccine designs. Next, this review summarizes the common mutations of SARS-CoV-2 and how these mutations change viral properties, confer immune escape and influence vaccine efficacy. Finally, this review discusses global strategies that have been employed to mitigate the decreases in vaccine efficacy encountered against new variants.
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Affiliation(s)
- Ziyao Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Sahra Bashiri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
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22
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Grauwet K, Berger T, Kann MC, Silva H, Larson R, Leick MB, Bailey SR, Bouffard AA, Millar D, Gallagher K, Turtle CJ, Frigault MJ, Maus MV. Stealth transgenes enable CAR-T cells to evade host immune responses. J Immunother Cancer 2024; 12:e008417. [PMID: 38724463 PMCID: PMC11086422 DOI: 10.1136/jitc-2023-008417] [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] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Adoptive cell therapy, such as chimeric antigen receptor (CAR)-T cell therapy, has improved patient outcomes for hematological malignancies. Currently, four of the six FDA-approved CAR-T cell products use the FMC63-based αCD19 single-chain variable fragment, derived from a murine monoclonal antibody, as the extracellular binding domain. Clinical studies demonstrate that patients develop humoral and cellular immune responses to the non-self CAR components of autologous CAR-T cells or donor-specific antigens of allogeneic CAR-T cells, which is thought to potentially limit CAR-T cell persistence and the success of repeated dosing. METHODS In this study, we implemented a one-shot approach to prevent rejection of engineered T cells by simultaneously reducing antigen presentation and the surface expression of both Classes of the major histocompatibility complex (MHC) via expression of the viral inhibitors of transporter associated with antigen processing (TAPi) in combination with a transgene coding for shRNA targeting class II MHC transactivator (CIITA). The optimal combination was screened in vitro by flow cytometric analysis and mixed lymphocyte reaction assays and was validated in vivo in mouse models of leukemia and lymphoma. Functionality was assessed in an autologous setting using patient samples and in an allogeneic setting using an allogeneic mouse model. RESULTS The combination of the Epstein-Barr virus TAPi and an shRNA targeting CIITA was efficient and effective at reducing cell surface MHC classes I and II in αCD19 'stealth' CAR-T cells while retaining in vitro and in vivo antitumor functionality. Mixed lymphocyte reaction assays and IFNγ ELISpot assays performed with T cells from patients previously treated with autologous αCD19 CAR-T cells confirm that CAR T cells expressing the stealth transgenes evade allogeneic and autologous anti-CAR responses, which was further validated in vivo. Importantly, we noted anti-CAR-T cell responses in patients who had received multiple CAR-T cell infusions, and this response was reduced on in vitro restimulation with autologous CARs containing the stealth transgenes. CONCLUSIONS Together, these data suggest that the proposed stealth transgenes may reduce the immunogenicity of autologous and allogeneic cellular therapeutics. Moreover, patient data indicate that repeated doses of autologous FMC63-based αCD19 CAR-T cells significantly increased the anti-CAR T cell responses in these patients.
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Affiliation(s)
- Korneel Grauwet
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Trisha Berger
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
| | - Michael C Kann
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
| | - Harrison Silva
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
| | - Rebecca Larson
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Mark B Leick
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stefanie R Bailey
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Amanda A Bouffard
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
| | - David Millar
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kathleen Gallagher
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Cameron J Turtle
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Matthew J Frigault
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marcela V Maus
- Cellular Immunotherapy Program, Krantz Family Center for Cancer Research, Massachusetts General Hosptial, Charlestown, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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23
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Kim GJ, Elnaggar JH, Varnado M, Feehan AK, Tauzier D, Rose R, Lamers SL, Sevalia M, Nicholas N, Gravois E, Fort D, Crabtree JS, Miele L. A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population. Front Immunol 2024; 15:1357731. [PMID: 38784379 PMCID: PMC11112498 DOI: 10.3389/fimmu.2024.1357731] [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: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
Long-term immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the identification of T-cell epitopes affecting host immunogenicity. In this computational study, we explored the CD8+ epitope diversity estimated in 27 of the most common HLA-A and HLA-B alleles, representing most of the United States population. Analysis of 16 SARS-CoV-2 variants [B.1, Alpha (B.1.1.7), five Delta (AY.100, AY.25, AY.3, AY.3.1, AY.44), and nine Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, XBB.1.5)] in analyzed MHC class I alleles revealed that SARS-CoV-2 CD8+ epitope conservation was estimated at 87.6%-96.5% in spike (S), 92.5%-99.6% in membrane (M), and 94.6%-99% in nucleocapsid (N). As the virus mutated, an increasing proportion of S epitopes experienced reduced predicted binding affinity: 70% of Omicron BQ.1-XBB.1.5 S epitopes experienced decreased predicted binding, as compared with ~3% and ~15% in the earlier strains Delta AY.100-AY.44 and Omicron BA.1-BA.5, respectively. Additionally, we identified several novel candidate HLA alleles that may be more susceptible to severe disease, notably HLA-A*32:01, HLA-A*26:01, and HLA-B*53:01, and relatively protected from disease, such as HLA-A*31:01, HLA-B*40:01, HLA-B*44:03, and HLA-B*57:01. Our findings support the hypothesis that viral genetic variation affecting CD8 T-cell epitope immunogenicity contributes to determining the clinical severity of acute COVID-19. Achieving long-term COVID-19 immunity will require an understanding of the relationship between T cells, SARS-CoV-2 variants, and host MHC class I genetics. This project is one of the first to explore the SARS-CoV-2 CD8+ epitope diversity that putatively impacts much of the United States population.
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Affiliation(s)
- Grace J. Kim
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jacob H. Elnaggar
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- Department of Microbiology, Immunology, and Parasitology, Lousiana State University Health Sciences Center (LSUHSC), New Orleans, LA, United States
| | - Mallory Varnado
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Amy K. Feehan
- Research and Development, Oschner Medical Center, New Orleans, LA, United States
| | - Darlene Tauzier
- Department of Pathology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Rebecca Rose
- Research and Development, BioInfoExperts, LLC, Thibodaux, LA, United States
| | - Susanna L. Lamers
- Research and Development, BioInfoExperts, LLC, Thibodaux, LA, United States
| | - Maya Sevalia
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Najah Nicholas
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Elizabeth Gravois
- Department of Pathology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Daniel Fort
- Research and Development, Oschner Medical Center, New Orleans, LA, United States
| | - Judy S. Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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24
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Lischer C, Eberhardt M, Flamann C, Berges J, Güse E, Wessely A, Weich A, Retzlaff J, Dörrie J, Schaft N, Wiesinger M, März J, Schuler-Thurner B, Knorr H, Gupta S, Singh KP, Schuler G, Heppt MV, Koch EAT, van Kleef ND, Freen-van Heeren JJ, Turksma AW, Wolkenhauer O, Hohberger B, Berking C, Bruns H, Vera J. Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy. J Immunother Cancer 2024; 12:e008104. [PMID: 38724462 PMCID: PMC11086525 DOI: 10.1136/jitc-2023-008104] [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] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Tumor-associated antigens and their derived peptides constitute an opportunity to design off-the-shelf mainline or adjuvant anti-cancer immunotherapies for a broad array of patients. A performant and rational antigen selection pipeline would lay the foundation for immunotherapy trials with the potential to enhance treatment, tremendously benefiting patients suffering from rare, understudied cancers. METHODS We present an experimentally validated, data-driven computational pipeline that selects and ranks antigens in a multipronged approach. In addition to minimizing the risk of immune-related adverse events by selecting antigens based on their expression profile in tumor biopsies and healthy tissues, we incorporated a network analysis-derived antigen indispensability index based on computational modeling results, and candidate immunogenicity predictions from a machine learning ensemble model relying on peptide physicochemical characteristics. RESULTS In a model study of uveal melanoma, Human Leukocyte Antigen (HLA) docking simulations and experimental quantification of the peptide-major histocompatibility complex binding affinities confirmed that our approach discriminates between high-binding and low-binding affinity peptides with a performance similar to that of established methodologies. Blinded validation experiments with autologous T-cells yielded peptide stimulation-induced interferon-γ secretion and cytotoxic activity despite high interdonor variability. Dissecting the score contribution of the tested antigens revealed that peptides with the potential to induce cytotoxicity but unsuitable due to potential tissue damage or instability of expression were properly discarded by the computational pipeline. CONCLUSIONS In this study, we demonstrate the feasibility of the de novo computational selection of antigens with the capacity to induce an anti-tumor immune response and a predicted low risk of tissue damage. On translation to the clinic, our pipeline supports fast turn-around validation, for example, for adoptive T-cell transfer preparations, in both generalized and personalized antigen-directed immunotherapy settings.
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Affiliation(s)
- Christopher Lischer
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Martin Eberhardt
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Cindy Flamann
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Berges
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Esther Güse
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Anja Wessely
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Adrian Weich
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Jimmy Retzlaff
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Jan Dörrie
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Niels Schaft
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Manuel Wiesinger
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Johannes März
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Beatrice Schuler-Thurner
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Harald Knorr
- Department of Ophthalmology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
- CCC Erlangen-EMN, Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Krishna Pal Singh
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Gerold Schuler
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Markus Vincent Heppt
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Elias Andreas Thomas Koch
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | | | | | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Bettina Hohberger
- Department of Ophthalmology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
- CCC Erlangen-EMN, Erlangen, Germany
| | - Carola Berking
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Department of Dermatology, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Heiko Bruns
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Julio Vera
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Department of Dermatology, FAU Erlangen-Nürnberg, Erlangen, Germany
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25
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Weisbrod L, Capriotti L, Hofmann M, Spieler V, Dersch H, Voedisch B, Schmidt P, Knake S. FASTMAP-a flexible and scalable immunopeptidomics pipeline for HLA- and antigen-specific T-cell epitope mapping based on artificial antigen-presenting cells. Front Immunol 2024; 15:1386160. [PMID: 38779658 PMCID: PMC11109385 DOI: 10.3389/fimmu.2024.1386160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
The study of peptide repertoires presented by major histocompatibility complex (MHC) molecules and the identification of potential T-cell epitopes contribute to a multitude of immunopeptidome-based treatment approaches. Epitope mapping is essential for the development of promising epitope-based approaches in vaccination as well as for innovative therapeutics for autoimmune diseases, infectious diseases, and cancer. It also plays a critical role in the immunogenicity assessment of protein therapeutics with regard to safety and efficacy concerns. The main challenge emerges from the highly polymorphic nature of the human leukocyte antigen (HLA) molecules leading to the requirement of a peptide mapping strategy for a single HLA allele. As many autoimmune diseases are linked to at least one specific antigen, we established FASTMAP, an innovative strategy to transiently co-transfect a single HLA allele combined with a disease-specific antigen into a human cell line. This approach allows the specific identification of HLA-bound peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using FASTMAP, we found a comparable spectrum of endogenous peptides presented by the most frequently expressed HLA alleles in the world's population compared to what has been described in literature. To ensure a reliable peptide mapping workflow, we combined the HLA alleles with well-known human model antigens like coagulation factor VIII, acetylcholine receptor subunit alpha, protein structures of the SARS-CoV-2 virus, and myelin basic protein. Using these model antigens, we have been able to identify a broad range of peptides that are in line with already published and in silico predicted T-cell epitopes of the specific HLA/model antigen combination. The transient co-expression of a single affinity-tagged MHC molecule combined with a disease-specific antigen in a human cell line in our FASTMAP pipeline provides the opportunity to identify potential T-cell epitopes/endogenously processed MHC-bound peptides in a very cost-effective, fast, and customizable system with high-throughput potential.
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Affiliation(s)
- Luisa Weisbrod
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Luigi Capriotti
- Analytical Biochemistry, Research and Development, CSL Behring AG, Bern, Switzerland
| | - Marco Hofmann
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Valerie Spieler
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Herbert Dersch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Bernd Voedisch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Peter Schmidt
- Protein Biochemistry, Bio21 Institute, CSL Limited, Parkville, VIC, Australia
| | - Susanne Knake
- Department of Neurology, Epilepsy Center Hessen, Philipps University Marburg, Marburg, Germany
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Wang N, Waghray D, Caveney NA, Jude KM, Garcia KC. Structural insights into human MHC-II association with invariant chain. Proc Natl Acad Sci U S A 2024; 121:e2403031121. [PMID: 38687785 PMCID: PMC11087810 DOI: 10.1073/pnas.2403031121] [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: 02/13/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
The loading of processed peptides on to major histocompatibility complex II (MHC-II) molecules for recognition by T cells is vital to cell-mediated adaptive immunity. As part of this process, MHC-II associates with the invariant chain (Ii) during biosynthesis in the endoplasmic reticulum to prevent premature peptide loading and to serve as a scaffold for subsequent proteolytic processing into MHC-II-CLIP. Cryo-electron microscopy structures of full-length Human Leukocyte Antigen-DR (HLA-DR) and HLA-DQ complexes associated with Ii, resolved at 3.0 to 3.1 Å, elucidate the trimeric assembly of the HLA/Ii complex and define atomic-level interactions between HLA, Ii transmembrane domains, loop domains, and class II-associated invariant chain peptides (CLIP). Together with previous structures of MHC-II peptide loading intermediates DO and DM, our findings complete the structural path governing class II antigen presentation.
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Affiliation(s)
- Nan Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
| | - Nathanael A. Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
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Hai NTT, Nhung VP, Tam NTT, Ngoc TTB, Thuong MTH, Dai HV, Duong NT, Hai NV, Ton ND, Thach PN, Ha NH. HLA alleles associated with susceptibility and severity of the COVID-19 in Vietnamese. Hum Immunol 2024; 85:110796. [PMID: 38580537 DOI: 10.1016/j.humimm.2024.110796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
The diversity of clinical manifestations in COVID-19 has been observed not only among individuals but also among various populations in globally. HLA molecules play a central role in physiology, protective immunity, and deleterious, disease-related autoimmune reactivity or overreaction. This study exploited the association between HLA frequencies and SARS-CoV-2 susceptibility and disease severity among the Vietnamese cohort (159 patients and 52 controls). A significant difference in frequency of both HLA class I and II in mild, moderate, and severe/fatal COVID-19 patients and negative exposure individuals - the controls were observed. Regarding SARS-CoV-2 sensitivity, HLA-A*03:01, 30:01, HLA-DQA1*01:02, DRB1*15:01, and DRB5*02:02 presented higher frequency in the control group compared with infected patients but DRB1 09:01 frequency was higher in infected patients. Regarding COVID-19 severity, HLA-F*01:01, 01:03 and DPA1*01:03 and 02:01, DPB1*04:01, DQA1*01:02, and DQB1*05:02 alleles were detected with higher frequency in severe patients but DOB*01:01, DRB1*05:01 and 09:01 had a significantly higher frequency in the mild group than remaining groups. Surprisingly, HLA-DQA1*01:02 and DRB1*09:01 alleles were identified with both inversely potential roles in protective function and severe risk. The obtained data herein will contribute to explore on the role of host genetic background in the pathology of COVID-19 disease.
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Affiliation(s)
- Nguyen Thi Thanh Hai
- National Hospital for Tropical Diseases, Kim Chung, Dong Anh, Hanoi 10000, Viet Nam; Department of Biochemistry, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 10000, Viet Nam
| | - Vu Phuong Nhung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam
| | - Nguyen Thi Thanh Tam
- Department of Biochemistry, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 10000, Viet Nam
| | - Tran Thi Bich Ngoc
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam
| | - Ma Thi Huyen Thuong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam
| | - Ha Van Dai
- National Hospital for Tropical Diseases, Kim Chung, Dong Anh, Hanoi 10000, Viet Nam
| | - Nguyen Thuy Duong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Viet Nam
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Viet Nam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Viet Nam
| | - Pham Ngoc Thach
- National Hospital for Tropical Diseases, Kim Chung, Dong Anh, Hanoi 10000, Viet Nam
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Viet Nam.
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Sira EMJS, Banico EC, Odchimar NMO, Fajardo LE, Fremista FF, Refuerzo HAB, Dictado APA, Orosco FL. Immunoinformatics approach for designing a multiepitope subunit vaccine against porcine epidemic diarrhea virus genotype IIA spike protein. Open Vet J 2024; 14:1224-1242. [PMID: 38938443 PMCID: PMC11199741 DOI: 10.5455/ovj.2024.v14.i5.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 06/29/2024] Open
Abstract
Background Porcine epidemic diarrhea (PED), caused by the porcine epidemic diarrhea virus (PEDV), is associated with high mortality and morbidity rates, especially in neonatal pigs. This has resulted in significant economic losses for the pig industry. PEDV genotype II-based vaccines were found to confer better immunity against both heterologous and homologous challenges; specifically, spike (S) proteins, which are known to play a significant role during infection, are ideal for vaccine development. Aim This study aims to design a multi-epitope subunit vaccine targeting the S protein of the PEDV GIIa strain using an immunoinformatics approach. Methods Various bioinformatics tools were used to predict HTL, CTL, and B-cell epitopes. The epitopes were connected using appropriate linkers and conjugated with the CTB adjuvant and M-ligand. The final multiepitope vaccine construct (fMEVc) was then docked to toll-like receptor 4 (TLR4). The stability of the fMEVc-TLR4 complex was then simulated using GROMACS. C-immsim was then used to predict the in vitro immune response of the fMEVc. Results Six epitopes were predicted to induce antibody production, ten epitopes were predicted to induce CTL responses, and four epitopes were predicted to induce HTL responses. The assembled epitopes conjugated with the CTB adjuvant and M-ligand, fMEVc, is antigenic, non-allergenic, stable, and soluble. The construct showed a favorable binding affinity for TLR4, and the protein complex was shown to be stable through molecular dynamics simulations. A robust immune response was induced after immunization, as demonstrated through immune stimulation. Conclusion In conclusion, the multi-epitope subunit vaccine construct for PEDV designed in this study exhibits promising antigenicity, stability, and immunogenicity, eliciting robust immune responses and suggesting its potential as a candidate for further vaccine development.
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Affiliation(s)
- Ella Mae Joy S. Sira
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
| | - Edward C. Banico
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
| | - Nyzar Mabeth O. Odchimar
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
| | - Lauren Emily Fajardo
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
| | - Ferdinand F. Fremista
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Philippines
| | | | - Ana Patrisha A. Dictado
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Philippines
| | - Fredmoore L. Orosco
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Philippines
- S&T Fellows Program, Department of Science and Technology, Taguig City, Philippines
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Desai N, Chavda V, Singh TRR, Thorat ND, Vora LK. Cancer Nanovaccines: Nanomaterials and Clinical Perspectives. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401631. [PMID: 38693099 DOI: 10.1002/smll.202401631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/30/2024] [Indexed: 05/03/2024]
Abstract
Cancer nanovaccines represent a promising frontier in cancer immunotherapy, utilizing nanotechnology to augment traditional vaccine efficacy. This review comprehensively examines the current state-of-the-art in cancer nanovaccine development, elucidating innovative strategies and technologies employed in their design. It explores both preclinical and clinical advancements, emphasizing key studies demonstrating their potential to elicit robust anti-tumor immune responses. The study encompasses various facets, including integrating biomaterial-based nanocarriers for antigen delivery, adjuvant selection, and the impact of nanoscale properties on vaccine performance. Detailed insights into the complex interplay between the tumor microenvironment and nanovaccine responses are provided, highlighting challenges and opportunities in optimizing therapeutic outcomes. Additionally, the study presents a thorough analysis of ongoing clinical trials, presenting a snapshot of the current clinical landscape. By curating the latest scientific findings and clinical developments, this study aims to serve as a comprehensive resource for researchers and clinicians engaged in advancing cancer immunotherapy. Integrating nanotechnology into vaccine design holds immense promise for revolutionizing cancer treatment paradigms, and this review provides a timely update on the evolving landscape of cancer nanovaccines.
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Affiliation(s)
- Nimeet Desai
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502285, India
| | - Vivek Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad, 380009, India
| | | | - Nanasaheb D Thorat
- Limerick Digital Cancer Research Centre (LDCRC), University of Limerick, Castletroy, Limerick, V94T9PX, Ireland
- Department of Physics, Bernal Institute, Castletroy, Limerick, V94T9PX, Ireland
- Nuffield Department of Women's & Reproductive Health, Medical Science Division, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
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Gu R, Pan J, Awan MUN, Sun X, Yan F, Bai L, Bai J. The major histocompatibility complex participates in Parkinson's disease. Pharmacol Res 2024; 203:107168. [PMID: 38583689 DOI: 10.1016/j.phrs.2024.107168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease characterized by progressive loss of dopaminergic neurons in the substantia nigra and the aggregation of alpha-synuclein (α-syn). The central nervous system (CNS) has previously been considered as an immune-privileged area. However, studies have shown that the immune responses are involved in PD. The major histocompatibility complex (MHC) presents antigens from antigen-presenting cells (APCs) to T lymphocytes, immune responses will be induced. MHCs are expressed in microglia, astrocytes, and dopaminergic neurons. Single nucleotide polymorphisms in MHC are related to the risk of PD. The aggregated α-syn triggers the expression of MHCs by activating glia cells. CD4+ and CD8+ T lymphocytes responses and microglia activation are detected in brains of PD patients. In addiction immune responses further increase blood-brain barrier (BBB) permeability and T cell infiltration in PD. Thus, MHCs are involved in PD through participating in immune and inflammatory responses.
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Affiliation(s)
- Rou Gu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Jianyu Pan
- Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Maher Un Nisa Awan
- Medical School, Kunming University of Science and Technology, Kunming 650500, China; Department of Neurology, The Affiliated Hospital of Yunnan University, Kunming 650500, China
| | - Xiaowei Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Fang Yan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Liping Bai
- Medical School, Kunming University of Science and Technology, Kunming 650500, China
| | - Jie Bai
- Medical School, Kunming University of Science and Technology, Kunming 650500, China.
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Tang Z, Wang S, Du L, Hu D, Chen X, Zheng H, Ding H, Chen S, Zhang L, Zhang N. The impact of micropolymorphism in Anpl-UAA on structural stability and peptide presentation. Int J Biol Macromol 2024; 267:131665. [PMID: 38636758 DOI: 10.1016/j.ijbiomac.2024.131665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Micropolymorphism significantly shapes the peptide-binding characteristics of major histocompatibility complex class I (MHC-I) molecules, affecting the host's resistance to pathogens, which is particularly pronounced in avian species displaying the "minimal essential MHC" expression pattern. In this study, we compared two duck MHC-I alleles, Anpl-UAA*77 and Anpl-UAA*78, that exhibit markedly different peptide binding properties despite their high sequence homology. Through mutagenesis experiments and crystallographic analysis of complexes with the influenza virus-derived peptide AEAIIVAMV (AEV9), we identified a critical role for the residue at position 62 in regulating hydrogen-bonding interactions between the peptide backbone and the peptide-binding groove. This modulation affects the characteristics of the B pocket and the stability of the loop region between the 310 helix and the α1 helix, leading to significant changes in the structure and stability of the peptide-MHC-I complex (pMHC-I). Moreover, the proportion of different residues at position 62 among Anpl-UAAs may reflect the correlation between pAnpl-UAA stability and duck body temperature. This research not only advances our understanding of the Anpl-UAA structure but also deepens our insight into the impact of MHC-I micropolymorphism on peptide binding.
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Affiliation(s)
- Ziche Tang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Suqiu Wang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Liubao Du
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Dongmei Hu
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaoming Chen
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hanyin Zheng
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Han Ding
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shiwen Chen
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lin Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan 250100, Shandong, China.
| | - Nianzhi Zhang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China..
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Nong T, Shih NR, Bray RA, Lopez-Cepero M, Murphey C, Nickerson PW, Lee JH. Identification of Antibodies to DQβ:DRα Interisotypic Heterodimers in Human Sera. Transplantation 2024; 108:1142-1148. [PMID: 38303109 DOI: 10.1097/tp.0000000000004914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
BACKGROUND HLA class II antigens, DR, DQ, and DP, comprised an α and β chains, which typically combine, within the same isotype, to form the major histocompatibility complex:peptide complex. Interisotypic pairing is not commonly observed. Although reports of DQβ:DRα heterodimers exist, the pairing was reported to be unstable and, therefore, not studied to any extent. METHODS DQβ:DRα single antigens were produced through transfectant cell lines and used to identify and characterize positive reactive human sera by a multiplex bead-based assay. RESULTS Stable DQβ:DRα transfectants were constructed. Cell surface staining with class II-specific monoclonal antibodies revealed that some DQB1 alleles appear to be more efficient in expressing DQβ:DRα heterodimers. Interestingly, alleles within the same serological group varied in their efficiency of forming dimers on the cell surface. For example, DQβ0601:DRα had the highest transfection and cell membrane expression efficiency among 16 common DQB1 alleles tested. In contrast, DQβ0603:DRα-positive transfectants demonstrated minimal surface expression. Assembly of DQβ0601:DRα was not affected by the presence of a DQα chain. DQβ0601:DRα and DQβ0603:DRα single-antigen beads were used to screen human sera. Positive sera were identified that reacted to the unique epitopes of DQβ0601:DRα protein on the cell surface of the transfectants. CONCLUSIONS Our studies have demonstrated that unique DQβ:DRα heterodimers can be formed and are stably expressed on the cell surface. Such antigenic combinations, presented on single-antigen beads, demonstrated that patient sera can react with such heterodimers. Investigations on the potential clinical roles of antibodies against such interisotypic heterodimers are now possible.
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Affiliation(s)
- Thoa Nong
- Terasaki Innovation Center, Los Angeles, CA
| | | | - Robert A Bray
- Department of Pathology, Emory University, Atlanta, GA
| | | | | | - Peter W Nickerson
- Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
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Kohansal Vajari M, Ehsan M, Ghiasi S, Fooladi S, Karami N, Hassanshahi G, Fatemi A. Human Leukocyte Antigen Alleles (HLA-A, HLA-B, and HLA-DRB1) are associated with Acute Lymphoblastic Leukemia (ALL) : A Case-Control Study in a Sample of Iranian Population. Asian Pac J Cancer Prev 2024; 25:1507-1513. [PMID: 38809622 PMCID: PMC11318837 DOI: 10.31557/apjcp.2024.25.5.1507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 02/22/2024] [Indexed: 05/31/2024] Open
Abstract
OBJECTIVE This study seeks to elucidate the association between HLA-A, HLA-B, and HLA-DRB1 alleles and their relative risk contributions to ALL within an Iranian cohort. METHODS Utilizing a robust case-control design, this research involved 71 ALL patients and 71 age and sex-matched healthy individuals. Genotyping of specified HLA alleles was performed using the advanced PCR-SSP technique. RESULTS Our findings reveal a marked increase in the prevalence of the HLA-DRB1*04 allele among patients diagnosed with ALL compared to the control group (P<0.027). Conversely, the alleles HLA-A*26 (P=0.025), HLA-A*33 (P=0.020), and HLA-DRB1*03 (P=0.035) were observed at significantly reduced frequencies within the patient population. CONCLUSION Our findings highlight HLA-DRB1*04 as a potential genetic marker for increased susceptibility to ALL, while HLA-A*26, HLA-A*33, and HLA-DRB1*03 emerge as protective factors.
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Affiliation(s)
- Mahdi Kohansal Vajari
- Student of Research Committee, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Mohsen Ehsan
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Science, Tehran, Iran.
| | - Saeedeh Ghiasi
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Saba Fooladi
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
- Student Research Committee, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Najibe Karami
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Gholamhossein Hassanshahi
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Ahmad Fatemi
- Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran.
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Cardeira-da-Silva J, Wang Q, Sagvekar P, Mintcheva J, Latting S, Günther S, Ramadass R, Yekelchyk M, Preussner J, Looso M, Junker JP, Stainier DYR. Antigen presentation plays positive roles in the regenerative response to cardiac injury in zebrafish. Nat Commun 2024; 15:3637. [PMID: 38684665 PMCID: PMC11058276 DOI: 10.1038/s41467-024-47430-1] [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: 04/25/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
In contrast to adult mammals, adult zebrafish can fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which components of the immune response are required during regeneration is unclear. Here, we report positive roles for the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. We find that following the initial innate immune response, activated endocardial cells (EdCs), as well as immune cells, start expressing antigen presentation genes. We also observe that T helper cells, a.k.a. Cd4+ T cells, lie in close physical proximity to these antigen-presenting EdCs. We targeted Major Histocompatibility Complex (MHC) class II antigen presentation by generating cd74a; cd74b mutants, which display a defective immune response. In these mutants, Cd4+ T cells and activated EdCs fail to efficiently populate the injured tissue and EdC proliferation is significantly decreased. cd74a; cd74b mutants exhibit additional defects in cardiac regeneration including reduced cardiomyocyte dedifferentiation and proliferation. Notably, Cd74 also becomes activated in neonatal mouse EdCs following cardiac injury. Altogether, these findings point to positive roles for antigen presentation during cardiac regeneration, potentially involving interactions between activated EdCs, classical antigen-presenting cells, and Cd4+ T cells.
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Affiliation(s)
- João Cardeira-da-Silva
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
| | - Qianchen Wang
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Pooja Sagvekar
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Janita Mintcheva
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Humboldt University of Berlin, Berlin, Germany
| | - Stephan Latting
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Radhan Ramadass
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michail Yekelchyk
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jens Preussner
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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Schafer S, Chen K, Ma L. Crosstalking with Dendritic Cells: A Path to Engineer Advanced T Cell Immunotherapy. FRONTIERS IN SYSTEMS BIOLOGY 2024; 4:1372995. [PMID: 38911455 PMCID: PMC11192543 DOI: 10.3389/fsysb.2024.1372995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Crosstalk between dendritic cells (DCs) and T cells plays a crucial role in modulating immune responses in natural and pathological conditions. DC-T cell crosstalk is achieved through contact-dependent (i.e., immunological synapse) and contact-independent mechanisms (i.e., cytokines). Activated DCs upregulate co-stimulatory signals and secrete proinflammatory cytokines to orchestrate T cell activation and differentiation. Conversely, activated T helper cells "license" DCs towards maturation, while regulatory T cells (Tregs) silence DCs to elicit tolerogenic immunity. Strategies to efficiently modulate the DC-T cell crosstalk can be harnessed to promote immune activation for cancer immunotherapy or immune tolerance for the treatment of autoimmune diseases. Here, we review the natural crosstalk mechanisms between DC and T cells. We highlight bioengineering approaches to modulate DC-T cell crosstalk, including conventional vaccines, synthetic vaccines, and DC-mimics, and key seminal studies leveraging these approaches to steer immune response for the treatment of cancer and autoimmune diseases.
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Affiliation(s)
- Sogand Schafer
- Center for Craniofacial Innovation, Children’s Hospital of Philadelphia Research Institute, Children’s Hospital of Philadelphia, PA 19104, USA
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Children’s Hospital of Philadelphia, PA 19104, USA
| | - Kaige Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leyuan Ma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, US
- The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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36
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Chauhan S, Jaiswal S, Jakhmola V, Singh B, Bhattacharya S, Garg M, Sengupta S. Potential role of p53 deregulation in modulating immune responses in human malignancies: A paradigm to develop immunotherapy. Cancer Lett 2024; 588:216766. [PMID: 38408603 PMCID: PMC7615729 DOI: 10.1016/j.canlet.2024.216766] [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: 01/19/2024] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
The crucial role played by the oncogenic expression of TP53, stemming from mutation or amyloid formation, in various human malignancies has been extensively studied over the past two decades. Interestingly, the potential role of TP53 as a crucial player in modulating immune responses has provided new insight into the field of cancer biology. The loss of p53's transcriptional functions and/or the acquisition of tumorigenic properties can efficiently modulate the recruitment and functions of myeloid and lymphoid cells, ultimately leading to the evasion of immune responses in human tumors. Consequently, the oncogenic nature of the tumor suppressor p53 can dynamically alter the function of immune cells, providing support for tumor progression and metastasis. This review comprehensively explores the dual role of p53 as both the guardian of the genome and an oncogenic driver, especially in the context of regulation of autophagy, apoptosis, the tumor microenvironment, immune cells, innate immunity, and adaptive immune responses. Additionally, the focus of this review centers on how p53 status in the immune response can be harnessed for the development of tailored therapeutic strategies and their potential application in immunotherapy against human malignancies.
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Affiliation(s)
- Shivi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Shivani Jaiswal
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Vibhuti Jakhmola
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Bhavana Singh
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Sujata Bhattacharya
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India.
| | - Shinjinee Sengupta
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Sector-125, Noda, 201313, India.
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Sheikhlary S, Lopez DH, Moghimi S, Sun B. Recent Findings on Therapeutic Cancer Vaccines: An Updated Review. Biomolecules 2024; 14:503. [PMID: 38672519 PMCID: PMC11048403 DOI: 10.3390/biom14040503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer remains one of the global leading causes of death and various vaccines have been developed over the years against it, including cell-based, nucleic acid-based, and viral-based cancer vaccines. Although many vaccines have been effective in in vivo and clinical studies and some have been FDA-approved, there are major limitations to overcome: (1) developing one universal vaccine for a specific cancer is difficult, as tumors with different antigens are different for different individuals, (2) the tumor antigens may be similar to the body's own antigens, and (3) there is the possibility of cancer recurrence. Therefore, developing personalized cancer vaccines with the ability to distinguish between the tumor and the body's antigens is indispensable. This paper provides a comprehensive review of different types of cancer vaccines and highlights important factors necessary for developing efficient cancer vaccines. Moreover, the application of other technologies in cancer therapy is discussed. Finally, several insights and conclusions are presented, such as the possibility of using cold plasma and cancer stem cells in developing future cancer vaccines, to tackle the major limitations in the cancer vaccine developmental process.
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Affiliation(s)
- Sara Sheikhlary
- Department of Biomedical Engineering, College of Engineering, The University of Arizona, Tucson, AZ 85721, USA
| | - David Humberto Lopez
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
| | - Sophia Moghimi
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
| | - Bo Sun
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (D.H.L.); (S.M.)
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38
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Alganmi N, Bashanfar A, Alotaibi R, Banjar H, Karim S, Mirza Z, Abusamra H, Al-Attas M, Turkistany S, Abuzenadah A. Uncovering hidden genetic risk factors for breast and ovarian cancers in BRCA-negative women: a machine learning approach in the Saudi population. PeerJ Comput Sci 2024; 10:e1942. [PMID: 38660159 PMCID: PMC11042021 DOI: 10.7717/peerj-cs.1942] [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: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 04/26/2024]
Abstract
Breast and ovarian cancers are prevalent worldwide, with genetic factors such as BRCA1 and BRCA2 mutations playing a significant role. However, not all patients carry these mutations, making it challenging to identify risk factors. Researchers have turned to whole exome sequencing (WES) as a tool to identify genetic risk factors in BRCA-negative women. WES allows the sequencing of all protein-coding regions of an individual's genome, providing a comprehensive analysis that surpasses traditional gene-by-gene sequencing methods. This technology offers efficiency, cost-effectiveness and the potential to identify new genetic variants contributing to the susceptibility to the diseases. Interpreting WES data for disease-causing variants is challenging due to its complex nature. Machine learning techniques can uncover hidden genetic-variant patterns associated with cancer susceptibility. In this study, we used the extreme gradient boosting (XGBoost) and random forest (RF) algorithms to identify BRCA-related cancer high-risk genes specifically in the Saudi population. The experimental results exposed that the RF method scored superior performance with an accuracy of 88.16% and an area under the receiver-operator characteristic curve of 0.95. Using bioinformatics analysis tools, we explored the top features of the high-accuracy machine learning model that we built to enhance our knowledge of genetic interactions and find complex genetic patterns connected to the development of BRCA-related cancers. We were able to identify the significance of HLA gene variations in these WES datasets for BRCA-related patients. We find that immune response mechanisms play a major role in the development of BRCA-related cancer. It specifically highlights genes associated with antigen processing and presentation, such as HLA-B, HLA-A and HLA-DRB1 and their possible effects on tumour progression and immune evasion. In summary, by utilizing machine learning approaches, we have the potential to aid in the development of precision medicine approaches for early detection and personalized treatment strategies.
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Affiliation(s)
- Nofe Alganmi
- Computer Science, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arwa Bashanfar
- Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Alotaibi
- Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haneen Banjar
- Computer Science, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heba Abusamra
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Manal Al-Attas
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shereen Turkistany
- Center of Innovation Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adel Abuzenadah
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Ghaffar SA, Tahir H, Muhammad S, Shahid M, Naqqash T, Faisal M, Albekairi TH, Alshammari A, Albekairi NA, Manzoor I. Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches. Front Immunol 2024; 15:1380732. [PMID: 38690283 PMCID: PMC11058264 DOI: 10.3389/fimmu.2024.1380732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Haemophilus parainfluenzae is a Gram-negative opportunist pathogen within the mucus of the nose and mouth without significant symptoms and has an ability to cause various infections ranging from ear, eye, and sinus to pneumonia. A concerning development is the increasing resistance of H. parainfluenzae to beta-lactam antibiotics, with the potential to cause dental infections or abscesses. The principal objective of this investigation is to utilize bioinformatics and immuno-informatic methodologies in the development of a candidate multi-epitope Vaccine. The investigation focuses on identifying potential epitopes for both B cells (B lymphocytes) and T cells (helper T lymphocytes and cytotoxic T lymphocytes) based on high non-toxic and non-allergenic characteristics. The selection process involves identifying human leukocyte antigen alleles demonstrating strong associations with recognized antigenic and overlapping epitopes. Notably, the chosen alleles aim to provide coverage for 90% of the global population. Multi-epitope constructs were designed by using suitable linker sequences. To enhance the immunological potential, an adjuvant sequence was incorporated using the EAAAK linker. The final vaccine construct, comprising 344 amino acids, was achieved after the addition of adjuvants and linkers. This multi-epitope Vaccine demonstrates notable antigenicity and possesses favorable physiochemical characteristics. The three-dimensional conformation underwent modeling and refinement, validated through in-silico methods. Additionally, a protein-protein molecular docking analysis was conducted to predict effective binding poses between the multi-epitope Vaccine and the Toll-like receptor 4 protein. The Molecular Dynamics (MD) investigation of the docked TLR4-vaccine complex demonstrated consistent stability over the simulation period, primarily attributed to electrostatic energy. The docked complex displayed minimal deformation and enhanced rigidity in the motion of residues during the dynamic simulation. Furthermore, codon translational optimization and computational cloning was performed to ensure the reliability and proper expression of the multi-Epitope Vaccine. It is crucial to emphasize that despite these computational validations, experimental research in the laboratory is imperative to demonstrate the immunogenicity and protective efficacy of the developed vaccine. This would involve practical assessments to ascertain the real-world effectiveness of the multi-epitope Vaccine.
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Affiliation(s)
- Sana Abdul Ghaffar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Haneen Tahir
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sher Muhammad
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Thamer H. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Irfan Manzoor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- Department of Biology, Indiana University, Bloomington, IN, United States
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40
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Engler-Chiurazzi E. B cells and the stressed brain: emerging evidence of neuroimmune interactions in the context of psychosocial stress and major depression. Front Cell Neurosci 2024; 18:1360242. [PMID: 38650657 PMCID: PMC11033448 DOI: 10.3389/fncel.2024.1360242] [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: 12/22/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
The immune system has emerged as a key regulator of central nervous system (CNS) function in health and in disease. Importantly, improved understanding of immune contributions to mood disorders has provided novel opportunities for the treatment of debilitating stress-related mental health conditions such as major depressive disorder (MDD). Yet, the impact to, and involvement of, B lymphocytes in the response to stress is not well-understood, leaving a fundamental gap in our knowledge underlying the immune theory of depression. Several emerging clinical and preclinical findings highlight pronounced consequences for B cells in stress and MDD and may indicate key roles for B cells in modulating mood. This review will describe the clinical and foundational observations implicating B cell-psychological stress interactions, discuss potential mechanisms by which B cells may impact brain function in the context of stress and mood disorders, describe research tools that support the investigation of their neurobiological impacts, and highlight remaining research questions. The goal here is for this discussion to illuminate both the scope and limitations of our current understanding regarding the role of B cells, stress, mood, and depression.
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Affiliation(s)
- Elizabeth Engler-Chiurazzi
- Department of Neurosurgery and Neurology, Clinical Neuroscience Research Center, Tulane Brain Institute, Tulane University School of Medicine, New Orleans, LA, United States
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41
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Wickenberg M, Mercier R, Yap M, Walker J, Baker K, LaPointe P. Hsp90 inhibition leads to an increase in surface expression of multiple immunological receptors in cancer cells. Front Mol Biosci 2024; 11:1334876. [PMID: 38645275 PMCID: PMC11027010 DOI: 10.3389/fmolb.2024.1334876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone important for maintaining protein homeostasis (proteostasis) in the cell. Hsp90 inhibitors are being explored as cancer therapeutics because of their ability to disrupt proteostasis. Inhibiting Hsp90 increases surface density of the immunological receptor Major Histocompatibility Complex 1 (MHC1). Here we show that this increase occurs across multiple cancer cell lines and with both cytosol-specific and pan-Hsp90 inhibitors. We demonstrate that Hsp90 inhibition also alters surface expression of both IFNGR and PD-L1, two additional immunological receptors that play a significant role in anti-tumour or anti-immune activity in the tumour microenvironment. Hsp90 also negatively regulates IFN-γ activity in cancer cells, suggesting it has a unique role in mediating the immune system's response to cancer. Our data suggests a strong link between Hsp90 activity and the pathways that govern anti-tumour immunity. This highlights the potential for the use of an Hsp90 inhibitor in combination with another currently available cancer treatment, immune checkpoint blockade therapy, which works to prevent immune evasion of cancer cells. Combination checkpoint inhibitor therapy and the use of an Hsp90 inhibitor may potentiate the therapeutic benefits of both treatments and improve prognosis for cancer patients.
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Affiliation(s)
- Madison Wickenberg
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Rebecca Mercier
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Megan Yap
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - John Walker
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kristi Baker
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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42
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Zhang L, Song W, Zhu T, Liu Y, Chen W, Cao Y. ConvNeXt-MHC: improving MHC-peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model. Brief Bioinform 2024; 25:bbae133. [PMID: 38561979 PMCID: PMC10985285 DOI: 10.1093/bib/bbae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/11/2024] [Accepted: 03/02/2024] [Indexed: 04/04/2024] Open
Abstract
Peptide binding to major histocompatibility complex (MHC) proteins plays a critical role in T-cell recognition and the specificity of the immune response. Experimental validation such peptides is extremely resource-intensive. As a result, accurate computational prediction of binding peptides is highly important, particularly in the context of cancer immunotherapy applications, such as the identification of neoantigens. In recent years, there is a significant need to continually improve the existing prediction methods to meet the demands of this field. We developed ConvNeXt-MHC, a method for predicting MHC-I-peptide binding affinity. It introduces a degenerate encoding approach to enhance well-established panspecific methods and integrates transfer learning and semi-supervised learning methods into the cutting-edge deep learning framework ConvNeXt. Comprehensive benchmark results demonstrate that ConvNeXt-MHC outperforms state-of-the-art methods in terms of accuracy. We expect that ConvNeXt-MHC will help us foster new discoveries in the field of immunoinformatics in the distant future. We constructed a user-friendly website at http://www.combio-lezhang.online/predict/, where users can access our data and application.
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Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Wenkai Song
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Tinghao Zhu
- College of Computer Science, Sichuan University, Chengdu 610065, China
- Nuclear Power Institute of China, Chengdu 610213, China
| | - Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 29 Wangjiang Road, Chengdu 610065, China
| | - Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 29 Wangjiang Road, Chengdu 610065, China
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Fasoulis R, Rigo MM, Lizée G, Antunes DA, Kavraki LE. APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. J Chem Inf Model 2024; 64:1730-1750. [PMID: 38415656 PMCID: PMC10936522 DOI: 10.1021/acs.jcim.3c01667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
The recognition of peptides bound to class I major histocompatibility complex (MHC-I) receptors by T-cell receptors (TCRs) is a determinant of triggering the adaptive immune response. While the exact molecular features that drive the TCR recognition are still unknown, studies have suggested that the geometry of the joint peptide-MHC (pMHC) structure plays an important role. As such, there is a definite need for methods and tools that accurately predict the structure of the peptide bound to the MHC-I receptor. In the past few years, many pMHC structural modeling tools have emerged that provide high-quality modeled structures in the general case. However, there are numerous instances of non-canonical cases in the immunopeptidome that the majority of pMHC modeling tools do not attend to, most notably, peptides that exhibit non-standard amino acids and post-translational modifications (PTMs) or peptides that assume non-canonical geometries in the MHC binding cleft. Such chemical and structural properties have been shown to be present in neoantigens; therefore, accurate structural modeling of these instances can be vital for cancer immunotherapy. To this end, we have developed APE-Gen2.0, a tool that improves upon its predecessor and other pMHC modeling tools, both in terms of modeling accuracy and the available modeling range of non-canonical peptide cases. Some of the improvements include (i) the ability to model peptides that have different types of PTMs such as phosphorylation, nitration, and citrullination; (ii) a new and improved anchor identification routine in order to identify and model peptides that exhibit a non-canonical anchor conformation; and (iii) a web server that provides a platform for easy and accessible pMHC modeling. We further show that structures predicted by APE-Gen2.0 can be used to assess the effects that PTMs have in binding affinity in a more accurate manner than just using solely the sequence of the peptide. APE-Gen2.0 is freely available at https://apegen.kavrakilab.org.
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Affiliation(s)
- Romanos Fasoulis
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Mauricio M. Rigo
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Gregory Lizée
- Department
of Melanoma Medical Oncology—Research, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Dinler A. Antunes
- Department
of Biology and Biochemistry, University
of Houston, Houston, Texas 77004, United States
| | - Lydia E. Kavraki
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
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44
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Larson AC, Knoche SM, Brumfield GL, Doty KR, Gephart BD, Moore-Saufley PR, Solheim JC. Gemcitabine Modulates HLA-I Regulation to Improve Tumor Antigen Presentation by Pancreatic Cancer Cells. Int J Mol Sci 2024; 25:3211. [PMID: 38542184 PMCID: PMC10970070 DOI: 10.3390/ijms25063211] [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: 01/30/2024] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 04/26/2024] Open
Abstract
Pancreatic cancer is a lethal disease, harboring a five-year overall survival rate of only 13%. Current treatment approaches thus require modulation, with attention shifting towards liberating the stalled efficacy of immunotherapies. Select chemotherapy drugs which possess inherent immune-modifying behaviors could revitalize immune activity against pancreatic tumors and potentiate immunotherapeutic success. In this study, we characterized the influence of gemcitabine, a chemotherapy drug approved for the treatment of pancreatic cancer, on tumor antigen presentation by human leukocyte antigen class I (HLA-I). Gemcitabine increased pancreatic cancer cells' HLA-I mRNA transcripts, total protein, surface expression, and surface stability. Temperature-dependent assay results indicated that the increased HLA-I stability may be due to reduced binding of low affinity peptides. Mass spectrometry analysis confirmed changes in the HLA-I-presented peptide pool post-treatment, and computational predictions suggested improved affinity and immunogenicity of peptides displayed solely by gemcitabine-treated cells. Most of the gemcitabine-exclusive peptides were derived from unique source proteins, with a notable overrepresentation of translation-related proteins. Gemcitabine also increased expression of select immunoproteasome subunits, providing a plausible mechanism for its modulation of the HLA-I-bound peptidome. Our work supports continued investigation of immunotherapies, including peptide-based vaccines, to be used with gemcitabine as new combination treatment modalities for pancreatic cancer.
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Affiliation(s)
- Alaina C. Larson
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shelby M. Knoche
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Gabrielle L. Brumfield
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kenadie R. Doty
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Benjamin D. Gephart
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Joyce C. Solheim
- Eppley Institute for Research in Cancer & Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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45
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Liu Y, Huang Y, Cui HW, Wang Y, Ma Z, Xiang Y, Xin HY, Liang JQ, Xin HW. Perspective view of allogeneic IgG tumor immunotherapy. Cancer Cell Int 2024; 24:100. [PMID: 38461238 PMCID: PMC10924995 DOI: 10.1186/s12935-024-03290-9] [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: 11/29/2023] [Accepted: 03/01/2024] [Indexed: 03/11/2024] Open
Abstract
Allogeneic tumors are eradicated by host immunity; however, it is unknown how it is initiated until the report in Nature by Yaron Carmi et al. in 2015. Currently, we know that allogeneic tumors are eradicated by allogeneic IgG via dendritic cells. AlloIgG combined with the dendritic cell stimuli tumor necrosis factor alpha and CD40L induced tumor eradication via the reported and our proposed potential signaling pathways. AlloIgG triggers systematic immune responses targeting multiple antigens, which is proposed to overcome current immunotherapy limitations. The promising perspectives of alloIgG immunotherapy would have advanced from mouse models to clinical trials; however, there are only 6 published articles thus far. Therefore, we hope this perspective view will provide an initiative to promote future discussion.
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Affiliation(s)
- Ying Liu
- Department of Radiology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, 434000, Hubei, China
- Laboratory of Oncology, School of Basic Medicine, Center for Molecular Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, Hubei, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Yuanyi Huang
- Department of Radiology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, 434000, Hubei, China
| | - Hong-Wei Cui
- Center for Breast Cancer, Peking University Cancer Hospital at Inner Mongolia Campus and Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, 010021, Inner Mongolia, China
| | - YingYing Wang
- Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - ZhaoWu Ma
- Laboratory of Oncology, School of Basic Medicine, Center for Molecular Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, Hubei, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Ying Xiang
- Laboratory of Oncology, School of Basic Medicine, Center for Molecular Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, Hubei, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Hong-Yi Xin
- The Doctoral Scientific Research Center, People's Hospital of Lianjiang, Guangdong, 524400, China.
- The Doctoral Scientific Research Center, People's Hospital of Lianjiang, Guangdong Medical University, Guangdong, 524400, China.
| | - Jun-Qing Liang
- Center for Breast Cancer, Peking University Cancer Hospital at Inner Mongolia Campus and Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, 010021, Inner Mongolia, China.
| | - Hong-Wu Xin
- Laboratory of Oncology, School of Basic Medicine, Center for Molecular Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, Hubei, China.
- Key Laboratory of Human Genetic Diseases Research of Inner Mongolia, Research Centre of Molecular Medicine, Medical College of Chifeng University, Chifeng, 024000, Inner Mongolian Autonomous Region, China.
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46
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Zolg S, Donzelli L, Geiss-Friedlander R. N-terminal processing by dipeptidyl peptidase 9: Cut and Go! Biochimie 2024:S0300-9084(24)00052-X. [PMID: 38461970 DOI: 10.1016/j.biochi.2024.03.002] [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: 01/16/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Dipeptidyl peptidase 9 (DPP9) is an intracellular amino-dipeptidase with physiological roles in the immune system, DNA repair and mitochondria homeostasis, while its deregulation is linked to cancer progression and immune-associated defects. Through its rare ability to cleave a peptide bond following the imino-acid proline, DPP9 acts as a molecular switch that regulates key proteins, such as the tumor-suppressor BRCA2. In this review we will discuss key concepts underlying the outcomes of protein processing by DPP9, including substrate turn-over by the N-degron pathway. Additionally, we will review non-enzymatic roles and the regulation of DPP9 by discussing the interactome of this protease, which includes SUMO1, Filamin A, NLRP1 and CARD8.
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Affiliation(s)
- Samuel Zolg
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Laura Donzelli
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - Ruth Geiss-Friedlander
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany.
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47
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Maguire C, Wang C, Ramasamy A, Fonken C, Morse B, Lopez N, Wylie D, Melamed E. Molecular Mimicry as a Mechanism of Viral Immune Evasion and Autoimmunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583134. [PMID: 38496443 PMCID: PMC10942439 DOI: 10.1101/2024.03.08.583134] [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
Mimicry of host protein structures ("molecular mimicry") is a common mechanism employed by viruses to evade the host's immune system. To date, studies have primarily evaluated molecular mimicry in the context of full protein structural mimics. However, recent work has demonstrated that short linear amino acid (AA) molecular mimics can elicit cross-reactive antibodies and T-cells from the host, which may contribute to development and progression of autoimmunity. Despite this, the prevalence of molecular mimics throughout the human virome has not been fully explored. In this study, we evaluate 134 human infecting viruses and find significant usage of linear mimicry across the virome, particularly those in the herpesviridae and poxviridae families. Furthermore, we identify that proteins involved in cellular replication and inflammation, those expressed from autosomes, the X chromosome, and in thymic cells are over-enriched in viral mimicry. Finally, we demonstrate that short linear mimicry from Epstein-Barr virus (EBV) is significantly higher in auto-antibodies found in multiple sclerosis patients to a greater degree than previously appreciated. Our results demonstrate that human-infecting viruses frequently leverage mimicry in the course of their infection, point to substantial evolutionary pressure for mimicry, and highlight mimicry's important role in human autoimmunity. Clinically, our findings could translate to development of novel therapeutic strategies that target viral infections linked to autoimmunity, with the goal of eliminating disease-associated latent viruses and preventing their reactivation.
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Affiliation(s)
- Cole Maguire
- The University of Texas at Austin, Department of Neurology
| | - Chumeng Wang
- The University of Texas at Austin, Department of Neurology
| | | | - Cara Fonken
- The University of Texas at Austin, Department of Neurology
| | - Brinkley Morse
- The University of Texas at Austin, Department of Neurology
| | - Nathan Lopez
- The University of Texas at Austin, Department of Neurology
| | - Dennis Wylie
- The University of Texas at Austin, Center for Biomedical Research Support
| | - Esther Melamed
- The University of Texas at Austin, Department of Neurology
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48
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Murphy DA, Osteicochea D, Atkins A, Sannes C, McClarnon Z, Adjei IM. Optimizing Oxygen-Production Kinetics of Manganese Dioxide Nanoparticles Improves Hypoxia Reversal and Survival in Mice with Bone Metastases. Mol Pharm 2024; 21:1125-1136. [PMID: 38365202 PMCID: PMC10979454 DOI: 10.1021/acs.molpharmaceut.3c00671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Persistent hypoxia in bone metastases induces an immunosuppressive environment, limiting the effectiveness of immunotherapies. To address chronic hypoxia, we have developed manganese dioxide (MnO2) nanoparticles with tunable oxygen production kinetics for sustained oxygenation in bone metastases lesions. Using polyethylene glycol (PEG)-stabilized MnO2 or poly(lactic[50]-co-glycolic[50] acid) (50:50 PLGA), poly(lactic[75]-co-glycolic[25] acid) (75:25 PLGA), and polylactic acid (PLA)-encapsulated MnO2 NPs, we demonstrate that polymer hydrophobicity attenuates burst oxygen production and enables tunable oxygen production kinetics. The PEG-MnO2 NPs resulted in rapid hypoxia reduction in spheroids, which was rapidly attenuated, while the PLA-MnO2 NPs exhibited delayed hypoxia control in cancer spheroids. The 50:50 PLGA-MnO2 NPs exhibited the best short- and long-term control of hypoxia in cancer spheroids, resulting in sustained regulation of the expression of HIF-1α and immunosuppressive genes. The sustained control of hypoxia by the 50:50 PLGA-MnO2 NPs enhanced the cytotoxicity of natural killer cells against cancer spheroids. In vivo, 50:50 PLGA-MnO2 showed greater accumulation in the long bones and pelvis, common sites for bone metastases. The NPs decreased hypoxia in bone metastases and decreased regulatory T cell levels, resulting in enhanced survival of mice with established bone metastases.
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Affiliation(s)
- David A Murphy
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Daniela Osteicochea
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Aidan Atkins
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Caitlin Sannes
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Zachary McClarnon
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Isaac M Adjei
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
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49
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Fasoulis R, Rigo MM, Antunes DA, Paliouras G, Kavraki LE. Transfer learning improves pMHC kinetic stability and immunogenicity predictions. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2024; 13:100030. [PMID: 38577265 PMCID: PMC10994007 DOI: 10.1016/j.immuno.2023.100030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
The cellular immune response comprises several processes, with the most notable ones being the binding of the peptide to the Major Histocompability Complex (MHC), the peptide-MHC (pMHC) presentation to the surface of the cell, and the recognition of the pMHC by the T-Cell Receptor. Identifying the most potent peptide targets for MHC binding, presentation and T-cell recognition is vital for developing peptide-based vaccines and T-cell-based immunotherapies. Data-driven tools that predict each of these steps have been developed, and the availability of mass spectrometry (MS) datasets has facilitated the development of accurate Machine Learning (ML) methods for class-I pMHC binding prediction. However, the accuracy of ML-based tools for pMHC kinetic stability prediction and peptide immunogenicity prediction is uncertain, as stability and immunogenicity datasets are not abundant. Here, we use transfer learning techniques to improve stability and immunogenicity predictions, by taking advantage of a large number of binding affinity and MS datasets. The resulting models, TLStab and TLImm, exhibit comparable or better performance than state-of-the-art approaches on different stability and immunogenicity test sets respectively. Our approach demonstrates the promise of learning from the task of peptide binding to improve predictions on downstream tasks. The source code of TLStab and TLImm is publicly available at https://github.com/KavrakiLab/TL-MHC.
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Affiliation(s)
- Romanos Fasoulis
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
| | - Mauricio Menegatti Rigo
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
| | - Dinler Amaral Antunes
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd, Houston, 77004, TX, United States
| | - Georgios Paliouras
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E and 27 Neapoleos St, Athens, 15341, Greece
| | - Lydia E. Kavraki
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
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50
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Poddar A, Ahmady F, Rao SR, Sharma R, Kannourakis G, Prithviraj P, Jayachandran A. The role of pregnancy associated plasma protein-A in triple negative breast cancer: a promising target for achieving clinical benefits. J Biomed Sci 2024; 31:23. [PMID: 38395880 PMCID: PMC10885503 DOI: 10.1186/s12929-024-01012-x] [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: 07/20/2023] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Pregnancy associated plasma protein-A (PAPP-A) plays an integral role in breast cancer (BC), especially triple negative breast cancer (TNBC). This subtype accounts for the most aggressive BC, possesses high tumor heterogeneity, is least responsive to standard treatments and has the poorest clinical outcomes. There is a critical need to address the lack of effective targeted therapeutic options available. PAPP-A is a protein that is highly elevated during pregnancy. Frequently, higher PAPP-A expression is detected in tumors than in healthy tissues. The increase in expression coincides with increased rates of aggressive cancers. In BC, PAPP-A has been demonstrated to play a role in tumor initiation, progression, metastasis including epithelial-mesenchymal transition (EMT), as well as acting as a biomarker for predicting patient outcomes. In this review, we present the role of PAPP-A, with specific focus on TNBC. The structure and function of PAPP-A, belonging to the pappalysin subfamily, and its proteolytic activity are assessed. We highlight the link of BC and PAPP-A with respect to the IGFBP/IGF axis, EMT, the window of susceptibility and the impact of pregnancy. Importantly, the relevance of PAPP-A as a TNBC clinical marker is reviewed and its influence on immune-related pathways are explored. The relationship and mechanisms involving PAPP-A reveal the potential for more treatment options that can lead to successful immunotherapeutic targets and the ability to assist with better predicting clinical outcomes in TNBC.
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Affiliation(s)
- Arpita Poddar
- Fiona Elsey Cancer Research Institute, Victoria, Australia
- Federation University, Victoria, Australia
- RMIT University, Victoria, Australia
| | - Farah Ahmady
- Fiona Elsey Cancer Research Institute, Victoria, Australia
- Federation University, Victoria, Australia
| | - Sushma R Rao
- Fiona Elsey Cancer Research Institute, Victoria, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Revati Sharma
- Fiona Elsey Cancer Research Institute, Victoria, Australia
- Federation University, Victoria, Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Victoria, Australia
- Federation University, Victoria, Australia
| | - Prashanth Prithviraj
- Fiona Elsey Cancer Research Institute, Victoria, Australia
- Federation University, Victoria, Australia
| | - Aparna Jayachandran
- Fiona Elsey Cancer Research Institute, Victoria, Australia.
- Federation University, Victoria, Australia.
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