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Li D, Lin L, Xu F, Feng T, Tao Y, Miao H, Yang F. Protein crotonylation: Basic research and clinical diseases. Biochem Biophys Rep 2024; 38:101694. [PMID: 38586826 PMCID: PMC10997999 DOI: 10.1016/j.bbrep.2024.101694] [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: 12/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
Crotonylation is an importantly conserved post-translational modification, which is completely different from acetylation. In recent years, it has been confirmed that crotonylation occurs on histone and non-histone. Crotonylated Histone primarily affects gene expression through transcriptional regulation, while non-histone Crotonylation mainly regulates protein functions including protein activity, localization, and stability, as well as protein-protein interactions. The change in protein expression and function will affect the physiological process of cells and even cause disease. Reviewing previous studies, this article summarizes the mechanisms of histone and non-histone crotonylation in regulating diseases and cellular physiological processes to explore the possibility of precise regulation of crotonylation sites as potential targets for disease treatment.
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Affiliation(s)
- Dongling Li
- School of Medicine, Chongqing University, Chongqing, 400044, China
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Ling Lin
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Fan Xu
- School of Medicine, Chongqing University, Chongqing, 400044, China
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Tianlin Feng
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Yang Tao
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- Department of Critical Care Medicine, Chongqing University Central Hospital, Chongqing, 400000, China
| | - Hongming Miao
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Fan Yang
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- Department of Biochemistry and Molecular Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
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2
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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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3
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Mills C, Sud A, Everall A, Chubb D, Lawrence SED, Kinnersley B, Cornish AJ, Bentham R, Houlston RS. Genetic landscape of interval and screen detected breast cancer. NPJ Precis Oncol 2024; 8:122. [PMID: 38806682 PMCID: PMC11133314 DOI: 10.1038/s41698-024-00618-6] [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: 02/14/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
Interval breast cancers (IBCs) are cancers diagnosed between screening episodes. Understanding the biological differences between IBCs and screen-detected breast-cancers (SDBCs) has the potential to improve mammographic screening and patient management. We analysed and compared the genomic landscape of 288 IBCs and 473 SDBCs by whole genome sequencing of paired tumour-normal patient samples collected as part of the UK 100,000 Genomes Project. Compared to SDBCs, IBCs were more likely to be lobular, higher grade, and triple negative. A more aggressive clinical phenotype was reflected in IBCs displaying features of genomic instability including a higher mutation rate and number of chromosomal structural abnormalities, defective homologous recombination and TP53 mutations. We did not however, find evidence to indicate that IBCs are associated with a significantly different immune response. While IBCs do not represent a unique molecular class of invasive breast cancer they exhibit a more aggressive phenotype, which is likely to be a consequence of the timing of tumour initiation. This information is relevant both with respect to treatment as well as informing the screening interval for mammography.
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Affiliation(s)
- Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre of Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew Everall
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Samuel E D Lawrence
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
- University College London Cancer Institute, University College London, London, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Robert Bentham
- University College London Cancer Institute, University College London, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK.
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4
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Liu G, Ma N, Cheng K, Feng Q, Ma X, Yue Y, Li Y, Zhang T, Gao X, Liang J, Zhang L, Wang X, Ren Z, Fu YX, Zhao X, Nie G. Bacteria-derived nanovesicles enhance tumour vaccination by trained immunity. NATURE NANOTECHNOLOGY 2024; 19:387-398. [PMID: 38052943 DOI: 10.1038/s41565-023-01553-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/18/2023] [Indexed: 12/07/2023]
Abstract
Trained immunity enhances the responsiveness of immune cells to subsequent infections or vaccinations. Here we demonstrate that pre-vaccination with bacteria-derived outer-membrane vesicles, which contain large amounts of pathogen-associated molecular patterns, can be used to potentiate, and enhance, tumour vaccination by trained immunity. Intraperitoneal administration of these outer-membrane vesicles to mice activates inflammasome signalling pathways and induces interleukin-1β secretion. The elevated interleukin-1β increases the generation of antigen-presenting cell progenitors. This results in increased immune response when tumour antigens are delivered, and increases tumour-antigen-specific T-cell activation. This trained immunity increased protection from tumour challenge in two distinct cancer models.
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Affiliation(s)
- Guangna Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Nana Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Keman Cheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Qingqing Feng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Xiaotu Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Yale Yue
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Yao Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Tianjiao Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Xiaoyu Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Lizhuo Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | - Xinwei Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China
| | | | - Yang-Xin Fu
- Changping Laboratory, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Xiao Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China.
- IGDB-NCNST Joint Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China.
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Cheng Y, Xu Y, Li H, Qiao Y, Wang Y, Su Y, Zhang J, Wang X, Song L, Ding J, Wang D, Zhu C, Xing Q. Genetic variants in the HLA region contribute to the risk of cerebral palsy. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167008. [PMID: 38163449 DOI: 10.1016/j.bbadis.2023.167008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Cerebral palsy (CP) is the most common physical disability in childhood, and genetic factors play an important role in its pathogenesis. However, the genetic contributions remain incompletely elucidated. Here, we conducted a two-stage association study between 1090 CP cases and 1100 healthy controls after whole exome sequencing. The human leukocyte antigen (HLA) allelic predispositions were further analyzed in overall CP and subgroups using multivariate logistic regression. We found a strong signal in the HLA region on chromosome 6, where rs3131787 harbored the most significant association with CP (P = 2.05 × 10-14, OR = 2.22). In comparison to controls, the carrier frequencies of HLA-B*13:02 were significantly higher in children with CP (9.82 % in control vs 19.27 % in CP, P = 1.03 × 10-4, OR = 2.17). Furthermore, the effect of HLA-B*13:02 on increasing the risk of CP mainly existed in cryptogenic CP without exposure to premature birth, low birth weight, birth asphyxia, or periventricular leukomalacia. This study indicated a strong association of HLA variants with CP, which implied that immune dysregulation resulting from immunogenetic variants might underlie the pathogenesis of CP. Our findings provide genetic evidence that an immunomodulator may serve as a promising therapeutic intervention for patients with CP by reinstating the neuroinflammation hemostasis.
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Affiliation(s)
- Ye Cheng
- Children's Hospital of Fudan University, and Institutes of Biomedical Sciences of Fudan University, Shanghai 201102, China; Shanghai Center for Women and Children's Health, Shanghai 200062, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou 450052, China
| | - Hongwei Li
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou 450052, China
| | - Yimeng Qiao
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou 450052, China
| | - Yangong Wang
- Children's Hospital of Fudan University, and Institutes of Biomedical Sciences of Fudan University, Shanghai 201102, China
| | - Yu Su
- Children's Hospital of Fudan University, and Institutes of Biomedical Sciences of Fudan University, Shanghai 201102, China
| | - Jin Zhang
- Children's Hospital of Fudan University, and Institutes of Biomedical Sciences of Fudan University, Shanghai 201102, China
| | - Xiaoyang Wang
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou 450052, China; Centre of Perinatal Medicine and Health, Institute of Clinical Science, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Lili Song
- Children's Hospital of Fudan University, and Institutes of Biomedical Sciences of Fudan University, Shanghai 201102, China
| | - Jian Ding
- Children's Hospital of Fudan University, and Institutes of Biomedical Sciences of Fudan University, Shanghai 201102, China
| | - Dan Wang
- Children's Hospital of Fudan University, and Institutes of Biomedical Sciences of Fudan University, Shanghai 201102, China
| | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, The Third Affiliated Hospital and Institute of Neuroscience of Zhengzhou University, Zhengzhou 450052, China; Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden; Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg 40530, Sweden.
| | - Qinghe Xing
- Children's Hospital of Fudan University, and Institutes of Biomedical Sciences of Fudan University, Shanghai 201102, China; Shanghai Center for Women and Children's Health, Shanghai 200062, China.
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Ding H, Hu B, Guo R. Comprehensive analysis of single cell and bulk data develops a promising prognostic signature for improving immunotherapy responses in ovarian cancer. PLoS One 2024; 19:e0298125. [PMID: 38346070 PMCID: PMC10861092 DOI: 10.1371/journal.pone.0298125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/19/2024] [Indexed: 02/15/2024] Open
Abstract
The tumor heterogeneity is an important cause of clinical therapy failure and yields distinct prognosis in ovarian cancer (OV). Using the advantages of integrated single cell RNA sequencing (scRNA-seq) and bulk data to decode tumor heterogeneity remains largely unexplored. Four public datasets were enrolled in this study, including E-MTAB-8107, TCGA-OV, GSE63885, and GSE26193 cohorts. Random forest algorithm was employed to construct a multi-gene prognostic panel and further evaluated by receiver operator characteristic (ROC), calibration curve, and Cox regression. Subsequently, molecular characteristics were deciphered, and treatments strategies were explored to deliver precise therapy. The landscape of cell subpopulations and functional characteristics, as well as the dynamic of macrophage cells were detailly depicted at single cell level, and then screened prognostic candidate genes. Based on the expression of candidate genes, a stable and robust cell characterized gene associated prognosis signature (CCIS) was developed, which harbored excellent performance at prognosis assessment and patient stratification. The ROC and calibration curves, and Cox regression analysis elucidated CCIS could serve as serve as an independent factor for predicting prognosis. Moreover, a promising clinical tool nomogram was also constructed according to stage and CCIS. Through comprehensive investigations, patients in low-risk group were charactered by favorable prognosis, elevated genomic variations, higher immune cell infiltrations, and superior antigen presentation. For individualized treatment, patients in low-risk group were inclined to better immunotherapy responses. This study dissected tumor heterogeneity and afforded a promising prognostic signature, which was conducive to facilitating clinical outcomes for patients with OV.
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Affiliation(s)
- Huanfei Ding
- Department of Ultrasound, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Medical Key Laboratory for Prevention and Treatment of Malignant Gynecological Tumor, Henan Province, China
| | - Bowen Hu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruixia Guo
- Medical Key Laboratory for Prevention and Treatment of Malignant Gynecological Tumor, Henan Province, China
- Department of Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Luo X, Qiu Y, Fitzsimonds ZR, Wang Q, Chen Q, Lei YL. Immune escape of head and neck cancer mediated by the impaired MHC-I antigen presentation pathway. Oncogene 2024; 43:388-394. [PMID: 38177410 DOI: 10.1038/s41388-023-02912-2] [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: 10/17/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Tumor immune evasion is a hallmark of Head and Neck Cancers. The advent of immune checkpoint inhibitors (ICIs) in the first-line setting has transformed the management of these tumors. Unfortunately, the response rate of Head and Neck Squamous Cell Carcinomas (HNSCC) to ICIs is below 15%, regardless of the human papillomavirus (HPV) status, which might be partially related with impaired antigen presentation machinery (APM). Mechanistically, HNSCC cells are usually defective in the expression of MHC-I associated APM, while this transcriptional pathway is critical for the activation of tumor-killing effector T-cells. To specifically illuminate the phenomenon and seek for therapeutic strategies, this review summarizes the most recently identified role of genetic and functional dysregulation of the MHC-I pathway, specifically through changes at the genetic, epigenetic, post-transcriptional, and post-translational levels, which substantially contributes to HNSCC immune escape and ICI resistance. Several treatment modalities can be potentially exploited to restore APM signaling in tumors, which improves anti-tumor immunity through the activation of interferons, vaccines or rimantadine against HPV and the inhibition of EGFR, SHP-2, PI3K and MEK. Additionally, the combinatorial use of radiotherapy or cytotoxic agents with ICIs can synergize to potentiate APM signaling. Future directions would include further dissection of MHC-I related APM signaling in HNSCC and whether reversing this inhibition in combination with ICIs would elicit a more robust immune response leading to improved response rates in HNSCC. Therapeutic approaches to restore the MHC-I antigen presentation machinery in Head and Neck Cancer. (Red color texts represent the according strategies and the outcomes).
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Affiliation(s)
- Xiaobo Luo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yan Qiu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zackary R Fitzsimonds
- Department of Periodontics and Oral Medicine, Department of Otolaryngology-Head and Neck Surgery, Rogel Cancer Center, the University of Michigan, Ann Arbor, MI, 48109, USA
| | - Qiuhao Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases & Research Unit of Oral Carcinogenesis and Management & Chinese Academy of Medical Sciences, Department of Oral Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Yu Leo Lei
- Department of Periodontics and Oral Medicine, Department of Otolaryngology-Head and Neck Surgery, Rogel Cancer Center, the University of Michigan, Ann Arbor, MI, 48109, USA.
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8
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Schurz H, Naranbhai V, Yates TA, Gilchrist JJ, Parks T, Dodd PJ, Möller M, Hoal EG, Morris AP, Hill AVS. Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture. eLife 2024; 13:e84394. [PMID: 38224499 PMCID: PMC10789494 DOI: 10.7554/elife.84394] [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: 10/23/2022] [Accepted: 11/23/2023] [Indexed: 01/17/2024] Open
Abstract
The heritability of susceptibility to tuberculosis (TB) disease has been well recognized. Over 100 genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicate. We established the International Tuberculosis Host Genetics Consortium to perform a multi-ancestry meta-analysis of GWAS, including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h2 = 26.3%, 95% CI 23.7-29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p<5 × 10-8) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value=5.2 × 10-9) but failed to replicate variants previously associated with TB susceptibility. These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressure.
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Affiliation(s)
- Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Massachusetts General HospitalBostonUnited States
- Dana-Farber Cancer InstituteBostonUnited States
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
- Harvard Medical SchoolBostonUnited States
| | - Tom A Yates
- Division of Infection and Immunity, Faculty of Medical Sciences, University College LondonLondonUnited Kingdom
| | - James J Gilchrist
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of OxfordOxfordUnited Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases Imperial College LondonLondonUnited Kingdom
| | - Peter J Dodd
- School of Health and Related Research, University of SheffieldSheffieldUnited Kingdom
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of ManchesterManchesterUnited Kingdom
| | - Adrian VS Hill
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Jenner Institute, University of OxfordOxfordUnited Kingdom
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Gipson DS, Wang CS, Salmon E, Gbadegesin R, Naik A, Sanna-Cherchi S, Fornoni A, Kretzler M, Merscher S, Hoover P, Kidwell K, Saleem M, Riella L, Holzman L, Jackson A, Olabisi O, Cravedi P, Freedman BS, Himmelfarb J, Vivarelli M, Harder J, Klein J, Burke G, Rheault M, Spino C, Desmond HE, Trachtman H. FSGS Recurrence Collaboration: Report of a Symposium. GLOMERULAR DISEASES 2024; 4:1-10. [PMID: 38348154 PMCID: PMC10859699 DOI: 10.1159/000535138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/30/2023] [Indexed: 02/15/2024]
Affiliation(s)
- Debbie S. Gipson
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Chia-Shi Wang
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Eloise Salmon
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Rasheed Gbadegesin
- Department of Medicine, Duke University, Durham, NC, USA
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Abhijit Naik
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Paul Hoover
- Department of Medicine, Harvard University, Cambridge, MA, USA
| | - Kelley Kidwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Moin Saleem
- Translational Health Sciences, University of Bristol, Bristol, UK
| | - Leonardo Riella
- Department of Medicine, Harvard University, Cambridge, MA, USA
| | - Lawrence Holzman
- Department of Internal Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Paolo Cravedi
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Marina Vivarelli
- Department of Pediatric Subspecialties, Bambino Gesù Children’s Hospital, Rome, Italy
| | - Jennifer Harder
- Department of Internal Medicine, University of Louisville, Louisville, KY, USA
| | - Jon Klein
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - George Burke
- Department of Surgery, University of Miami, Miami, FL, USA
| | - Michelle Rheault
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Cathie Spino
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Hailey E. Desmond
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Howard Trachtman
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
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10
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Houlston R, Culliford R, Lawrence S, Mills C, Tippu Z, Chubb D, Cornish A, Browining L, Kinnersley B, Bentham R, Sud A, Pallikonda H, Frangou A, Gruber A, Litchfield K, Wedge D, Larkin J, Turajlic S. Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma. RESEARCH SQUARE 2023:rs.3.rs-3675752. [PMID: 38106039 PMCID: PMC10723546 DOI: 10.21203/rs.3.rs-3675752/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a comprehensive description of its genomic landscape is lacking. We report the whole genome sequencing of 778 ccRCC patients enrolled in the 100,000 Genomes Project, providing the most detailed somatic mutational landscape to date. We identify new driver genes, which as well as emphasising the major role of epigenetic regulation in ccRCC highlight additional biological pathways extending opportunities for drug repurposing. Genomic characterisation identified patients with divergent clinical outcome; higher number of structural copy number alterations associated with poorer prognosis, whereas VHL mutations were independently associated with a better prognosis. The twin observations that higher T-cell infiltration is associated with better outcome and that genetically predicted immune evasion is not common supports the rationale for immunotherapy. These findings should inform personalised surveillance and treatment strategies for ccRCC patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Amit Sud
- The Institute of Cancer Research
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11
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Zhan Y, Tao Q, Lang Z, Lin L, Li X, Yu S, Yu Z, Zhou G, Wu K, Zhou Z, Yu Z, Zheng J. Serum ribonucleotide reductase M2 is a potential biomarker for diagnosing and monitoring liver fibrosis in chronic hepatitis B patients. J Med Virol 2023; 95:e29157. [PMID: 37814947 DOI: 10.1002/jmv.29157] [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: 06/11/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023]
Abstract
It is known that ribonucleotide reductase M2 (RRM2) could be induced by hepatitis B virus (HBV) via DNA damage response. However, whether RRM2 is a potential biomarker for diagnosing and monitoring liver fibrosis in chronic hepatitis B (CHB) patients is still unclear. In this study, CHB patients from GSE84044 (a transcriptome data from GEO data set) were downloaded and RRM2 was selected as a hub gene. Interestingly, a positive correlation was found between serum RRM2 and liver fibrosis stage. The similar results were found in CHB patients with normal alanine aminotransferase (ALT). Notably, RRM2 could effectively differentiate preliminary fibrosis from advanced fibrosis in CHB patients with/without normal ALT. In addition, RRM2 had a better performance in diagnosing liver fibrosis than two commonly used noninvasive methods (aspartate aminotransferase-to-platelet ratio index and fibrosis index based on the four factors), two classic fibrotic biomarkers (hyaluronic acid and type IV collagen) as well as Mac-2 binding protein glycosylation isomer, a known serum fibrosis marker. Moreover, CHB patients with high RRM2, who were associated with advanced fibrosis, had higher expressions of immune checkpoints. Overall, serum RRM2 may be a promising biomarker for diagnosing and monitoring liver fibrosis in CHB patients.
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Affiliation(s)
- Yating Zhan
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiqi Tao
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhichao Lang
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lifan Lin
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xinmiao Li
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Suhui Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhengping Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guangyao Zhou
- Department of Infectious Diseases, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kaifeng Wu
- Department of Laboratory Medicine, The First People's Hospital of Zunyi, Zunyi, China
| | - Zhenxu Zhou
- Department of Hernia and Abdominal Wall Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhixian Yu
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianjian Zheng
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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12
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Anzar I, Malone B, Samarakoon P, Vardaxis I, Simovski B, Fontenelle H, Meza-Zepeda LA, Stratford R, Keung EZ, Burgess M, Tawbi HA, Myklebost O, Clancy T. The interplay between neoantigens and immune cells in sarcomas treated with checkpoint inhibition. Front Immunol 2023; 14:1226445. [PMID: 37799721 PMCID: PMC10548483 DOI: 10.3389/fimmu.2023.1226445] [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: 05/21/2023] [Accepted: 07/10/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction Sarcomas are comprised of diverse bone and connective tissue tumors with few effective therapeutic options for locally advanced unresectable and/or metastatic disease. Recent advances in immunotherapy, in particular immune checkpoint inhibition (ICI), have shown promising outcomes in several cancer indications. Unfortunately, ICI therapy has provided only modest clinical responses and seems moderately effective in a subset of the diverse subtypes. Methods To explore the immune parameters governing ICI therapy resistance or immune escape, we performed whole exome sequencing (WES) on tumors and their matched normal blood, in addition to RNA-seq from tumors of 31 sarcoma patients treated with pembrolizumab. We used advanced computational methods to investigate key immune properties, such as neoantigens and immune cell composition in the tumor microenvironment (TME). Results A multifactorial analysis suggested that expression of high quality neoantigens in the context of specific immune cells in the TME are key prognostic markers of progression-free survival (PFS). The presence of several types of immune cells, including T cells, B cells and macrophages, in the TME were associated with improved PFS. Importantly, we also found the presence of both CD8+ T cells and neoantigens together was associated with improved survival compared to the presence of CD8+ T cells or neoantigens alone. Interestingly, this trend was not identified with the combined presence of CD8+ T cells and TMB; suggesting that a combined CD8+ T cell and neoantigen effect on PFS was important. Discussion The outcome of this study may inform future trials that may lead to improved outcomes for sarcoma patients treated with ICI.
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Affiliation(s)
- Irantzu Anzar
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | | | | | - Leonardo A. Meza-Zepeda
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Oslo University Hospital, Oslo, Norway
| | | | - Emily Z. Keung
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Melissa Burgess
- Department of Medical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ola Myklebost
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Trevor Clancy
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
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13
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Pasella M, Pisano F, Cannas B, Fanni A, Cocco E, Frau J, Lai F, Mocci S, Littera R, Giglio SR. Decision trees to evaluate the risk of developing multiple sclerosis. Front Neuroinform 2023; 17:1248632. [PMID: 37649987 PMCID: PMC10465164 DOI: 10.3389/fninf.2023.1248632] [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: 06/27/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction Multiple sclerosis (MS) is a persistent neurological condition impacting the central nervous system (CNS). The precise cause of multiple sclerosis is still uncertain; however, it is thought to arise from a blend of genetic and environmental factors. MS diagnosis includes assessing medical history, conducting neurological exams, performing magnetic resonance imaging (MRI) scans, and analyzing cerebrospinal fluid. While there is currently no cure for MS, numerous treatments exist to address symptoms, decelerate disease progression, and enhance the quality of life for individuals with MS. Methods This paper introduces a novel machine learning (ML) algorithm utilizing decision trees to address a key objective: creating a predictive tool for assessing the likelihood of MS development. It achieves this by combining prevalent demographic risk factors, specifically gender, with crucial immunogenetic risk markers, such as the alleles responsible for human leukocyte antigen (HLA) class I molecules and the killer immunoglobulin-like receptors (KIR) genes responsible for natural killer lymphocyte receptors. Results The study included 619 healthy controls and 299 patients affected by MS, all of whom originated from Sardinia. The gender feature has been disregarded due to its substantial bias in influencing the classification outcomes. By solely considering immunogenetic risk markers, the algorithm demonstrates an ability to accurately identify 73.24% of MS patients and 66.07% of individuals without the disease. Discussion Given its notable performance, this system has the potential to support clinicians in monitoring the relatives of MS patients and identifying individuals who are at an increased risk of developing the disease.
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Affiliation(s)
- Manuela Pasella
- Department of Electrical and Electronic Engineering, University of Cagliari, Cagliari, Italy
| | - Fabio Pisano
- Department of Electrical and Electronic Engineering, University of Cagliari, Cagliari, Italy
| | - Barbara Cannas
- Department of Electrical and Electronic Engineering, University of Cagliari, Cagliari, Italy
| | - Alessandra Fanni
- Department of Electrical and Electronic Engineering, University of Cagliari, Cagliari, Italy
| | - Eleonora Cocco
- Department of Medical Science and Public Health, Centro Sclerosi Multipla, University of Cagliari, Cagliari, Italy
| | - Jessica Frau
- Department of Medical Science and Public Health, Centro Sclerosi Multipla, University of Cagliari, Cagliari, Italy
| | - Francesco Lai
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Stefano Mocci
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Centre for Research University Services, University of Cagliari, Monserrato, Italy
| | - Roberto Littera
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Medical Genetics, R. Binaghi Hospital, ASSL Cagliari, ATS Sardegna, Cagliari, Italy
| | - Sabrina Rita Giglio
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Centre for Research University Services, University of Cagliari, Monserrato, Italy
- AART-ODV (Association for the Advancement of Research on Transplantation), Cagliari, Italy
- Medical Genetics, R. Binaghi Hospital, ASSL Cagliari, ATS Sardegna, Cagliari, Italy
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14
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Logunova N, Kapina M, Kondratieva E, Apt A. The H2-A Class II molecule α/β-chain cis-mismatch severely affects cell surface expression, selection of conventional CD4 + T cells and protection against TB infection. Front Immunol 2023; 14:1183614. [PMID: 37426653 PMCID: PMC10324577 DOI: 10.3389/fimmu.2023.1183614] [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: 03/10/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction To dissect the role of the part of the H2 complex comprised of the MHC-II genes in the control of tuberculosis (TB) infection, we previously established a panel of recombinant congenic mouse strains bearing different segments of the H2 j haplotype on the B6 (H2 b) genetic background. Fine genetic mapping, gene sequencing and assessment of TB phenotypes resulted in identification of the H2-Ab gene as a major factor of TB control. Methods We further narrowed the MHC-II H2 j interval by spotting a new recombination event, sequencing newly established DNA configuration and establishing a mouse strain B6.I-103 in which j/b recombination occurred within the coding sequence of the H2-Ab gene. Results Unexpectedly, a novel H2-Aα b/AβjE0 haplotype provided exclusively high susceptibility to TB challenge. Immunologic analysis revealed an altered CD4+ T-cell selection and maintenance in B6.I-103 mice, as well as seriously impaired expression of the H2-Aαb/Aβj molecule on the surface of antigen presenting cells. Unlike previously reported cases of Class II malfunctioning, the defective phenotype arose not from strong structural mutations, but from regular recombination events within the MHC-II recombination hot spot region. Discussion Our findings provide evidence that Class II α/β-chain cis-allelic mismatches created by regular genetic recombination may severely affect immune system functioning. This issue is discussed in the context of the MHC evolution.
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15
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Bayerl F, Meiser P, Donakonda S, Hirschberger A, Lacher SB, Pedde AM, Hermann CD, Elewaut A, Knolle M, Ramsauer L, Rudolph TJ, Grassmann S, Öllinger R, Kirchhammer N, Trefny M, Anton M, Wohlleber D, Höchst B, Zaremba A, Krüger A, Rad R, Obenauf AC, Schadendorf D, Zippelius A, Buchholz VR, Schraml BU, Böttcher JP. Tumor-derived prostaglandin E2 programs cDC1 dysfunction to impair intratumoral orchestration of anti-cancer T cell responses. Immunity 2023; 56:1341-1358.e11. [PMID: 37315536 DOI: 10.1016/j.immuni.2023.05.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/08/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
Type 1 conventional dendritic cells (cDC1s) are critical for anti-cancer immunity. Protective anti-cancer immunity is thought to require cDC1s to sustain T cell responses within tumors, but it is poorly understood how this function is regulated and whether its subversion contributes to immune evasion. Here, we show that tumor-derived prostaglandin E2 (PGE2) programmed a dysfunctional state in intratumoral cDC1s, disabling their ability to locally orchestrate anti-cancer CD8+ T cell responses. Mechanistically, cAMP signaling downstream of the PGE2-receptors EP2 and EP4 was responsible for the programming of cDC1 dysfunction, which depended on the loss of the transcription factor IRF8. Blockade of the PGE2-EP2/EP4-cDC1 axis prevented cDC1 dysfunction in tumors, locally reinvigorated anti-cancer CD8+ T cell responses, and achieved cancer immune control. In human cDC1s, PGE2-induced dysfunction is conserved and associated with poor cancer patient prognosis. Our findings reveal a cDC1-dependent intratumoral checkpoint for anti-cancer immunity that is targeted by PGE2 for immune evasion.
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Affiliation(s)
- Felix Bayerl
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Philippa Meiser
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sainitin Donakonda
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
| | - Anna Hirschberger
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian B Lacher
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Anna-Marie Pedde
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Chris D Hermann
- Institute of Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Anais Elewaut
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Moritz Knolle
- Institute for Artificial Intelligence in Medicine & Healthcare, School of Medicine, Technical University of Munich, Munich, Germany
| | - Lukas Ramsauer
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Thomas J Rudolph
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Simon Grassmann
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Nicole Kirchhammer
- Cancer Immunology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Marcel Trefny
- Cancer Immunology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Martina Anton
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Bastian Höchst
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Anne Zaremba
- Department for Dermatology, University Hospital Essen, Essen, Germany
| | - Achim Krüger
- Institute of Experimental Oncology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Anna C Obenauf
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dirk Schadendorf
- Department for Dermatology, University Hospital Essen, Essen, Germany
| | - Alfred Zippelius
- Cancer Immunology, Department of Biomedicine, University and University Hospital Basel, Basel, Switzerland
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Barbara U Schraml
- Walter-Brendel Center for Experimental Medicine, LMU Munich, Planegg-Martinsried, Germany; Biomedical Center, Institute for Cardiovascular Physiology and Pathophysiology, LMU Munich, Planegg-Martinsried, Germany
| | - Jan P Böttcher
- Institute of Molecular Immunology, School of Medicine, Technical University of Munich, Munich, Germany.
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16
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Palmer WH, Norman PJ. The impact of HLA polymorphism on herpesvirus infection and disease. Immunogenetics 2023; 75:231-247. [PMID: 36595060 PMCID: PMC10205880 DOI: 10.1007/s00251-022-01288-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/24/2022] [Indexed: 01/04/2023]
Abstract
Human Leukocyte Antigens (HLA) are cell surface molecules, central in coordinating innate and adaptive immune responses, that are targets of strong diversifying natural selection by pathogens. Of these pathogens, human herpesviruses have a uniquely ancient relationship with our species, where coevolution likely has reciprocating impact on HLA and viral genomic diversity. Consistent with this notion, genetic variation at multiple HLA loci is strongly associated with modulating immunity to herpesvirus infection. Here, we synthesize published genetic associations of HLA with herpesvirus infection and disease, both from case/control and genome-wide association studies. We analyze genetic associations across the eight human herpesviruses and identify HLA alleles that are associated with diverse herpesvirus-related phenotypes. We find that whereas most HLA genetic associations are virus- or disease-specific, HLA-A*01 and HLA-A*02 allotypes may be more generally associated with immune susceptibility and control, respectively, across multiple herpesviruses. Connecting genetic association data with functional corroboration, we discuss mechanisms by which diverse HLA and cognate receptor allotypes direct variable immune responses during herpesvirus infection and pathogenesis. Together, this review examines the complexity of HLA-herpesvirus interactions driven by differential T cell and Natural Killer cell immune responses.
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Affiliation(s)
- William H. Palmer
- Department of Biomedical Informatics, University of Colorado, Aurora, CO USA
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO USA
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado, Aurora, CO USA
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO USA
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17
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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18
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Wang H, Luo F, Shao X, Gao Y, Jiang N, Jia C, Li H, Chen R. Integrated Proteomics and Single-Cell Mass Cytometry Analysis Dissects the Immune Landscape of Ankylosing Spondylitis. Anal Chem 2023; 95:7702-7714. [PMID: 37126452 DOI: 10.1021/acs.analchem.3c00809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Mass cytometry is a powerful single-cell technology widely adopted to depict immune cell heterogeneity in different contexts. However, this method is only capable of examining several dozens of proteins simultaneously and requires a prior knowledge of the markers to be analyzed. Here we propose that the integration of mass cytometry with shot-gun proteomics may serve as a valuable tool to achieve an in-depth understanding of the immune system. By implementing such a strategy, we investigated the immune landscape of ankylosing spondylitis (AS), a chronic inflammatory arthritis with unclear etiology. The proteome alteration in peripheral blood mononuclear cells (PBMCs) was investigated by quantitative proteomics, and then mass cytometry analysis was conducted to decipher the immunome by considering the signaling molecules identified with differential expression by proteomics. As a result, we identified a wide spectrum of proteins dysregulated in AS, e.g., upregulation of glycolytic enzymes, downregulation of lipid transporters, and dysregulation of chemokine signaling molecules involved in proinflammatory cytokine production and leucocyte migration. Moreover, the single-cell analysis showed the upregulation of chemokine signaling regulators in subclusters of both innate and adaptive immune cells in AS. In addition, correlation analysis unveiled the interplay among Phenograph-identified subclusters of monocytes, CD4+ T cells, and CD8+ T cells. Taken together, our findings demonstrated that the integration of mass spectrometry-based proteomics and single-cell mass cytometry may serve as a useful tool to reveal clinically relevant information regarding useful targets and cellular phenotypes that could be further exploited to develop novel therapeutic strategies.
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Affiliation(s)
- Hao Wang
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou 450008, China
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Fengting Luo
- Department of Clinical Laboratory, Tianjin Hospital, Tianjin 300142, China
| | - Xianfeng Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Na Jiang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Chenxi Jia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing 102206, China
| | - Hongle Li
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou 450008, China
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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19
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The relevance of HLA class II genes in JAK2 V617F-positive myeloproliferative neoplasms. Hum Immunol 2023; 84:199-207. [PMID: 36707384 DOI: 10.1016/j.humimm.2023.01.006] [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: 05/13/2022] [Revised: 12/29/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
In the present study we analyzed the relevance of HLA class II in JAK2 V617F-positive (JAK2 V617F+) myeloproliferative neoplasms (MPNs) focusing on genotype diversity, associations with specific alleles and haplotypes and the level of gene expression. One hundred and thirty-nine JAK2 V617F+ MPN patients and 1083 healthy controls, typed by Next generation sequencing (NGS) were included in the study. Multivariate generalized linear models with age as a covariate were applied for analysis of HLA-II allele and haplotype associations. Publicly available gene expression datasets were used to analyze HLA-II pathway genes expression in CD34+ stem cells (SCs) from MPN patients and healthy controls. We did not observe differences in HLA evolutionary divergence (HED) between JAK2 V617F+ MPNs and healthy controls. Two alleles: HLA-DPB1*03:01, DQB1*04:02 and 4 haplotypes: DPB1*02:01-DQA1*05:05-DQB1*03:01-DRB1*11:01, DPB1*04:02-DQA1*05:05-DQB1*03:01-DRB1*11:03, DPB1*02:01-DQA1*01:04-DQB1*05:03-DRB1*14:04, and DPB1*04:01-DQA1*03:01-DQB1*03:02-DRB1*04:01 had significantly lower frequency in MPN patients compared to controls. Additionally, we observed HLA-II alleles and haplotypes with statistically higher frequencies in JAK2 V617F+ patients. Differential gene expression analysis showed down-regulation of HLA-DRB1, -DRA, -DMA, -DMB, -DOA,-DRB4, CIITA, and CD74 genes in JAK2 V617F+ MPN CD34+ SCs as compared to normal CD34 + SCs. In conclusion, this study provides evidence for the pleiotropic effects of HLA-II genes in JAK2 V617F-driven MPNs.
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Li YD, Si MR, Jiang SG, Yang QB, Jiang S, Yang LS, Huang JH, Chen X, Zhou FL, Li E. Transcriptome and molecular regulatory mechanisms analysis of gills in the black tiger shrimp Penaeus monodon under chronic low-salinity stress. Front Physiol 2023; 14:1118341. [PMID: 36935747 PMCID: PMC10014708 DOI: 10.3389/fphys.2023.1118341] [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: 12/07/2022] [Accepted: 02/14/2023] [Indexed: 03/05/2023] Open
Abstract
Background: Salinity is one of the main influencing factors in the culture environment and is extremely important for the survival, growth, development and reproduction of aquatic animals. Methods: In this study, a comparative transcriptome analysis (maintained for 45 days in three different salinities, 30 psu (HC group), 18 psu (MC group) and 3 psu (LC group)) was performed by high-throughput sequencing of economically cultured Penaeus monodon. P. monodon gill tissues from each treatment were collected for RNA-seq analysis to identify potential genes and pathways in response to low salinity stress. Results: A total of 64,475 unigenes were annotated in this study. There were 1,140 upregulated genes and 1,531 downregulated genes observed in the LC vs. HC group and 1,000 upregulated genes and 1,062 downregulated genes observed in the MC vs. HC group. In the LC vs. HC group, 583 DEGs significantly mapped to 37 signaling pathways, such as the NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, and PI3K-Akt signaling pathway; in the MC vs. HC group, 444 DEGs significantly mapped to 28 signaling pathways, such as the MAPK signaling pathway, Hippo signaling pathway and calcium signaling pathway. These pathways were significantly associated mainly with signal transduction, immunity and metabolism. Conclusions: These results suggest that low salinity stress may affect regulatory mechanisms such as metabolism, immunity, and signal transduction in addition to osmolarity in P. monodon. The greater the difference in salinity, the more significant the difference in genes. This study provides some guidance for understanding the low-salt domestication culture of P. monodon.
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Affiliation(s)
- Yun-Dong Li
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Meng-Ru Si
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qi-Bin Yang
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Song Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Li-Shi Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jian-Hua Huang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xu Chen
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Fa-Lin Zhou
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Fa-Lin Zhou, ; ErChao Li,
| | - ErChao Li
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Fa-Lin Zhou, ; ErChao Li,
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Korotaeva AA, Borunova AA, Kuzevanova AY, Zabotina TN, Alimov AA. [Molecular mechanisms of impaired antigenic presentation as a cause of tumor escape from immune surveillance]. Arkh Patol 2023; 85:76-83. [PMID: 38010642 DOI: 10.17116/patol20238506176] [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: 11/29/2023]
Abstract
The review summarizes data on the features of antigen presentation in tumor cells. The molecular mechanisms of the antitumor immune response are considered with an emphasis on the ability of tumor cells to avoid the action of immune surveillance. The features of expression of MHC molecules depending on treatment regimens are provided. Ways to improve existing and create new treatment regimens aimed at elimination of tumor cells because of antitumor immune response are discussed.
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Affiliation(s)
- A A Korotaeva
- Research Centre for Medical Genetics, Moscow, Russia
| | - A A Borunova
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | | | - T N Zabotina
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - A A Alimov
- Research Centre for Medical Genetics, Moscow, Russia
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Medeiros FS, da Silva MC, da Silva NCH, Gomes TT, Gomes RG, Paiva LA, dos Santos Gomes FO, Peixoto CA, Rygaard MCV, Welkovic S, Menezes MLB, Donadi EA, Lucena-Silva N. The antigen processing-associated transporter gene polymorphism: Role on gene and protein expression in HPV-infected pre-cancerous cervical lesion. Front Cell Infect Microbiol 2022; 12:979800. [PMID: 36619767 PMCID: PMC9811671 DOI: 10.3389/fcimb.2022.979800] [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: 06/28/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Human papillomavirus (HPV) is the major pathogen for cervical lesions. The evasion mechanism of the immune response and persistence of HPV infection can be influenced by polymorphisms (SNPs) in genes associated with transporter associated with antigen processing (TAP), which may change the peptide binding affinity or the TAP expression impacting the efficiency of peptide transport in the secretory pathway, and the presentation of peptides to cytotoxic T lymphocytes. This study aimed to evaluate the role of the TAP1 and TAP2 polymorphisms, TAP1, and TAP2 genes expressions, and protein levels in cervical cells presenting different degrees of pre-cancerous lesions in 296 immunocompetent women infected or not by HPV. TAP SNPs were genotyped by Sanger sequencing, and gene expression by real-time PCR. Aneuploidy was determined by DNA index using flow cytometry. TAP-1 and TAP-2 tissue expressions were evaluated by immunohistochemistry. The Asp697Gly SNP of TAP1 presented a risk for cellular aneuploidy (P=0.0244). HPV+ women had higher TAP-2 mRNA (P=0.0212) and protein (P<0.0001) levels. The TAP2D and TAP2E haplotypes were associated with the risk for aneuploidy and pre-cancerous lesions. In conclusion, nucleotide variability at the peptide binding region of peptide transporter genes, particularly of the TAP2 gene, may influence the HPV-peptide transportation from the cytosol to the endoplasmic reticulum, increasing the susceptibility to the development of high-grade cervical lesions.
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Affiliation(s)
- Fernanda Silva Medeiros
- Laboratory of Immunogenetics, Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | - Mauro César da Silva
- Laboratory of Immunogenetics, Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | | | - Thailany Thays Gomes
- Laboratory of Immunogenetics, Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | - Renan Garcia Gomes
- Laboratory of Molecular Biology, Institute of Integral Medicine Professor Fernando Figueira (IMIP) Hospital, Pediatric Oncology Service, Recife, Brazil
| | | | | | - Christina Alves Peixoto
- Laboratory of Ultrastructure, Department of Entomology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | - Maria Carolina Valença Rygaard
- Laboratory of Molecular Biology, Institute of Integral Medicine Professor Fernando Figueira (IMIP) Hospital, Pediatric Oncology Service, Recife, Brazil
| | - Stefan Welkovic
- Integrated Health Center Amaury de Medeiros (CISAM), University of Pernambuco, Recife, Brazil
| | | | - Eduardo Antônio Donadi
- Clinical Immunology Division, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Norma Lucena-Silva
- Laboratory of Immunogenetics, Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil,Laboratory of Molecular Biology, Institute of Integral Medicine Professor Fernando Figueira (IMIP) Hospital, Pediatric Oncology Service, Recife, Brazil,*Correspondence: Norma Lucena-Silva, ;
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23
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Single cell atlas identifies lipid-processing and immunomodulatory endothelial cells in healthy and malignant breast. Nat Commun 2022; 13:5511. [PMID: 36127427 PMCID: PMC9489707 DOI: 10.1038/s41467-022-33052-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/30/2022] [Indexed: 01/03/2023] Open
Abstract
Since a detailed inventory of endothelial cell (EC) heterogeneity in breast cancer (BC) is lacking, here we perform single cell RNA-sequencing of 26,515 cells (including 8433 ECs) from 9 BC patients and compare them to published EC taxonomies from lung tumors. Angiogenic ECs are phenotypically similar, while other EC subtypes are different. Predictive interactome analysis reveals known but also previously unreported receptor-ligand interactions between ECs and immune cells, suggesting an involvement of breast EC subtypes in immune responses. We also identify a capillary EC subtype (LIPEC (Lipid Processing EC)), which expresses genes involved in lipid processing that are regulated by PPAR-γ and is more abundant in peri-tumoral breast tissue. Retrospective analysis of 4648 BC patients reveals that treatment with metformin (an indirect PPAR-γ signaling activator) provides long-lasting clinical benefit and is positively associated with LIPEC abundance. Our findings warrant further exploration of this LIPEC/PPAR-γ link for BC treatment. Tumor blood vessels contribute to cancer growth, invasion and metastasis. Here, by using single cell transcriptomics, the authors report an inventory of endothelial cell heterogeneity in patients with breast cancer, including a subtype that expresses genes involved in lipid processing and is regulated by PPAR-γ.
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Tang F, Pan Z, Wang Y, Lan T, Wang M, Li F, Quan W, Liu Z, Wang Z, Li Z. Advances in the Immunotherapeutic Potential of Isocitrate Dehydrogenase Mutations in Glioma. Neurosci Bull 2022; 38:1069-1084. [PMID: 35670952 PMCID: PMC9468211 DOI: 10.1007/s12264-022-00866-1] [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: 11/22/2021] [Accepted: 02/16/2022] [Indexed: 11/26/2022] Open
Abstract
Isocitrate dehydrogenase (IDH) is an essential metabolic enzyme in the tricarboxylic acid cycle (TAC). The high mutation frequency of the IDH gene plays a complicated role in gliomas. In addition to affecting gliomas directly, mutations in IDH can also alter their immune microenvironment and can change immune-cell function in direct and indirect ways. IDH mutations mediate immune-cell infiltration and function by modulating immune-checkpoint gene expression and chemokine secretion. In addition, IDH mutation-derived D2-hydroxyglutarate can be absorbed by surrounding immune cells, also affecting their functioning. In this review, we summarize current knowledge about the effects of IDH mutations as well as other gene mutations on the immune microenvironment of gliomas. We also describe recent preclinical and clinical data related to IDH-mutant inhibitors for the treatment of gliomas. Finally, we discuss different types of immunotherapy and the immunotherapeutic potential of IDH mutations in gliomas.
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Affiliation(s)
- Feng Tang
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zhiyong Pan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Yi Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Tian Lan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Mengyue Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Fengping Li
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Wei Quan
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zhenyuan Liu
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China
| | - Zefen Wang
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China.
| | - Zhiqiang Li
- Brain Glioma Center and Department of Neurosurgery, Wuhan University Zhongnan Hospital, Wuhan, 430071, China.
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Ding J, Zheng Y, Wang G, Zheng J, Chai D. The performance and perspectives of dendritic cell vaccines modified by immune checkpoint inhibitors or stimulants. Biochim Biophys Acta Rev Cancer 2022; 1877:188763. [PMID: 35872287 DOI: 10.1016/j.bbcan.2022.188763] [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: 04/28/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022]
Abstract
Therapeutic dendritic cell (DC) vaccines stimulate the elimination of tumor cells by the immune system. However, while antigen-specific T cell responses induced by DC vaccines are commonly observed, the clinical response rate is relatively poor, necessitating vaccine optimization. There is evidence that the suppression of DC function by immune checkpoints hinders the anti-tumor immune responses mediated by DC vaccines, ultimately leading to the immune escape of the tumor cells. The use of immune checkpoint inhibitors (ICIs) and immune checkpoint activators (ICAs) has extended the immunotherapeutic range. It is known that both inhibitory and stimulatory checkpoint molecules are expressed by most DC subsets and can thus be used to manipulate the effectiveness of DC vaccines. Such manipulation has been investigated using strategies such as chemotherapy, agonistic or antagonistic antibodies, siRNA, shRNA, CRISPR-Cas9, soluble antibodies, lentiviruses, and adenoviruses to maximize the efficacy of DC vaccines. Thus, a deeper understanding of immune checkpoints may assist in the development of improved DC vaccines. Here, we review the actions of various ICIs or ICAs shown by preclinical studies, as well as their potential application in DC vaccines. New therapeutic interventional strategies for blocking and stimulating immune checkpoint molecules in DCs are also described in detail.
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Affiliation(s)
- Jiage Ding
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Yanyan Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China
| | - Gang Wang
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China.
| | - Junnian Zheng
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China.
| | - Dafei Chai
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China; Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China; Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, PR China.
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Zhu MM, Niu BW, Liu LL, Yang H, Qin BY, Peng XH, Chen LX, Liu Y, Wang C, Ren XN, Xu CH, Zhou XH, Li F. Development of a humanized HLA-A30 transgenic mouse model. Animal Model Exp Med 2022; 5:350-361. [PMID: 35791899 PMCID: PMC9434587 DOI: 10.1002/ame2.12225] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background There are remarkable genetic differences between animal major histocompatibility complex (MHC) systems and the human leukocyte antigen (HLA) system. HLA transgenic humanized mouse model systems offer a much better method to study the HLA‐A‐related principal mechanisms for vaccine development and HLA‐A‐restricted responses against infection in human. Methods A recombinant gene encoding the chimeric HLA‐A30 monochain was constructed. This HHD molecule contains the following: α1‐α2 domains of HLA‐A30, α3 and cytoplasmic domains of H‐2Db, linked at its N‐terminus to the C‐terminus of human β2m by a 15‐amino‐acid peptide linker. The recombinant gene encoding the chimeric HLA‐A30 monochain cassette was introduced into bacterial artificial chromosome (BAC) CH502‐67J3 containing the HLA‐A01 gene locus by Red‐mediated homologous recombination. Modified BAC CH502‐67J3 was microinjected into the pronuclei of wild‐type mouse oocytes. This humanized mouse model was further used to assess the immune responses against influenza A virus (H1N1) pdm09 clinically isolated from human patients. Immune cell population, cytokine production, and histopathology in the lung were analyzed. Results We describe a novel human β2m‐HLA‐A30 (α1α2)‐H‐2Db (α3 transmembrane cytoplasmic) (HHD) monochain transgenic mouse strain, which contains the intact HLA‐A01 gene locus including 49 kb 5′‐UTR and 74 kb 3′‐UTR of HLA‐A01*01. Five transgenic lines integrated into the large genomic region of HLA‐A gene locus were obtained, and the robust expression of exogenous transgene was detected in various tissues from A30‐18# and A30‐19# lines encompassing the intact flanking sequences. Flow cytometry revealed that the introduction of a large genomic region in HLA‐A gene locus can influence the immune cell constitution in humanized mice. Pdm09 infection caused a similar immune response among HLA‐A30 Tg humanized mice and wild‐type mice, and induced the rapid increase of cytokines, including IFN‐γ, TNF‐α, and IL‐6, in both HLA‐A30 humanized Tg mice and wild‐type mice. The expression of HLA‐A30 transgene was dramatically promoted in tissues from A30‐9# line at 3 days post‐infection (dpi). Conclusions We established a promising preclinical research animal model of HLA‐A30 Tg humanized mouse, which could accelerate the identification of novel HLA‐A30‐restricted epitopes and vaccine development, and support the study of HLA‐A‐restricted responses against infection in humans.
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Affiliation(s)
- Meng-Min Zhu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Bo-Wen Niu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Ling-Ling Liu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Hua Yang
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Bo-Yin Qin
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xiu-Hua Peng
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Li-Xiang Chen
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yang Liu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Chao Wang
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xiao-Nan Ren
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Chun-Hua Xu
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xiao-Hui Zhou
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
| | - Feng Li
- Department of Laboratory Animal Science, Shanghai Public Health Clinical Center, Shanghai, China
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Kuśnierczyk P. To Be or Not to Be: The Case of Endoplasmic Reticulum Aminopeptidase 2. Front Immunol 2022; 13:902567. [PMID: 35769458 PMCID: PMC9234130 DOI: 10.3389/fimmu.2022.902567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
To be, or not to be, that is the question. (William Shakespeare, Hamlet)
Endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2, respectively) play a role in trimming peptides that are too long to be bound and presented by class I HLA (HLA-I) molecules to CD8+ T cells. They may also affect the HLA-I-presented peptide repertoire by overtrimming potential epitopes. Both enzymes may also be released from the cell to cleave cytokine receptors and regulate blood pressure. Both enzymes are polymorphic, which affects their expression, specificity, and activity, resulting in their role in diseases associated with HLA-I. In this brief review, we concentrate on ERAP2, less investigated because of its lack in laboratory mice and 25% of humans, as well as a lower polymorphism. ERAP2 was found to be associated with several diseases and to influence ERAP1 effects. It was discovered recently that the defective ERAP2 gene, not encoding functional aminopeptidase, may nevertheless, during viral infections, produce a truncated protein isoform of unknown function, possibly interfering with ERAP1 and full-length ERAP2 by heterodimer formation. The disease associations of ERAP2, alone or in combination with ERAP1, are reviewed.
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Tuveri S, Debackere K, Marcelis L, Dierckxsens N, Demeulemeester J, Dimitriadou E, Dierickx D, Lefesvre P, Deraedt K, Graux C, Michaux L, Cools J, Tousseyn T, Vermeesch JR, Wlodarska I. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity. Genes Chromosomes Cancer 2022; 61:603-615. [PMID: 35611992 DOI: 10.1002/gcc.23069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/07/2022] Open
Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumour from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%) and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15) and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as 'second hit' in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukamia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma.
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Affiliation(s)
| | - Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | - Jonas Demeulemeester
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Daan Dierickx
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Lefesvre
- Department of Pathology, Free University Hospital, Brussels, Belgium
| | - Karen Deraedt
- Anatomo-Pathology, Hospital East Limburg, Genk, Belgium
| | - Carlos Graux
- Department of Hematology, Mont-Godinne University Hospital, Yvoir, Belgium
| | | | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Thomas Tousseyn
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
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Pishesha N, Harmand TJ, Ploegh HL. A guide to antigen processing and presentation. Nat Rev Immunol 2022; 22:751-764. [PMID: 35418563 DOI: 10.1038/s41577-022-00707-2] [Citation(s) in RCA: 193] [Impact Index Per Article: 96.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Antigen processing and presentation are the cornerstones of adaptive immunity. B cells cannot generate high-affinity antibodies without T cell help. CD4+ T cells, which provide such help, use antigen-specific receptors that recognize major histocompatibility complex (MHC) molecules in complex with peptide cargo. Similarly, eradication of virus-infected cells often depends on cytotoxic CD8+ T cells, which rely on the recognition of peptide-MHC complexes for their action. The two major classes of glycoproteins entrusted with antigen presentation are the MHC class I and class II molecules, which present antigenic peptides to CD8+ T cells and CD4+ T cells, respectively. This Review describes the essentials of antigen processing and presentation. These pathways are divided into six discrete steps that allow a comparison of the various means by which antigens destined for presentation are acquired and how the source proteins for these antigens are tagged for degradation, destroyed and ultimately displayed as peptides in complex with MHC molecules for T cell recognition.
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Affiliation(s)
- Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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30
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Wang H, Zúñiga-Pflücker JC. Thymic Microenvironment: Interactions Between Innate Immune Cells and Developing Thymocytes. Front Immunol 2022; 13:885280. [PMID: 35464404 PMCID: PMC9024034 DOI: 10.3389/fimmu.2022.885280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022] Open
Abstract
The thymus is a crucial organ for the development of T cells. T cell progenitors first migrate from the bone marrow into the thymus. During the journey to become a mature T cell, progenitors require interactions with many different cell types within the thymic microenvironment, such as stromal cells, which include epithelial, mesenchymal and other non-T-lineage immune cells. There are two crucial decision steps that are required for generating mature T cells: positive and negative selection. Each of these two processes needs to be performed efficiently to produce functional MHC-restricted T cells, while simultaneously restricting the production of auto-reactive T cells. In each step, there are various cell types that are required for the process to be carried out suitably, such as scavengers to clean up apoptotic thymocytes that fail positive or negative selection, and antigen presenting cells to display self-antigens during positive and negative selection. In this review, we will focus on thymic non-T-lineage immune cells, particularly dendritic cells and macrophages, and the role they play in positive and negative selection. We will also examine recent advances in the understanding of their participation in thymus homeostasis and T cell development. This review will provide a perspective on how the thymic microenvironment contributes to thymocyte differentiation and T cell maturation.
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Affiliation(s)
- Helen Wang
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Juan Carlos Zúñiga-Pflücker
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
- *Correspondence: Juan Carlos Zúñiga-Pflücker,
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31
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Jin Y, Li Y, Jiang L, Wang W, Zheng C, Chen M, Wu Y, Dai J, Chen J, Yu M, Zeng G, Hao M, Zeng B. The relationship between MHC−peptide interaction and resistance to virus in chickens. Immun Inflamm Dis 2022; 10:e596. [PMID: 35146947 PMCID: PMC8926493 DOI: 10.1002/iid3.596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction The MHC‐peptide interaction has a subtle influence on host resistance to virus. This paper aims to study the relationship between MHC‐peptide interaction and MHC‐related virus‐resistance. Methods By 3D homology modeling, the structure of chicken BF2 molecule BF2*0201 (PDB code: 4d0d) was studied and compared with the known structures of BF2 molecule BF2*0401 (PDB code: 4e0r) to elucidate the characteristics of BF2*0201‐binding antigenic peptides. Results The results show that due to the amino acid difference between the two binding groove of 4e0r and 4d0d, the size of the binding groove of the two are 1130 ų and1380 ų respectively, indicating the amino acid species that 4e0r binding peptide has lower selectivity than 4d0d; and because of large side chain conformation of Arg (especially Arg111) of 4e0r replaced by small side chain Tyr111 of 4d0d, the volume of central part of the binding groove of 4d0d is obviously larger than that of 4e0r, indicating that the restrictive of binding antigenic peptides for 4d0d is narrower than that of 4e0r; and on account of the chargeability of the binding groove of the two are different, namely the binding groove chargeability of 4e0r (strong positive polarity) and 4d0d (weak negative polarity). Conclusion There are generally more peptides presented by the BF2 of B2 haplotype than by that of B4 haplotype, leading to more resistance of B2 than that of B4 to virus.
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Affiliation(s)
- Yuan‐chang Jin
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Yu‐feng Li
- College of Agriculture and Food Engineering Baise University Baise People's Republic of China
| | - Li‐xia Jiang
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Wei Wang
- School of Life Science Hunan University of Science and Technology Xiangtan People's Republic of China
| | - Chuan‐dan Zheng
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Ming‐li Chen
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Yu‐jie Wu
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Juan Dai
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Jing‐fen Chen
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Min‐min Yu
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Gang Zeng
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Mei‐lin Hao
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
| | - Bo‐ping Zeng
- Characteristic Laboratory of Animal Resources Conservation and Utilization of Chishui River Basin, Department of Biology and Agriculture Zunyi Normal College Zunyi People's Republic of China
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32
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He J, Chen J, Han X, Gu Q, Liang J, Sun M, Liu S, Yao Y, Shi L. Association of HLA-DM and HLA class II Genes with Antibody Response Induced by Inactivated Japanese Encephalitis Vaccine. HLA 2022; 99:357-367. [PMID: 35118816 DOI: 10.1111/tan.14575] [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: 08/20/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
Abstract
HLA (HLA) class II molecules, HLA-DR, DP, and DQ, together with HLA II-like protein DM, play a dominant role in the processing and presentation of antigens, which may influence vaccine effectiveness. We previously demonstrated that variations in the HLA-DRB1, DPB1, and DQB1 genes may affect the neutralising antibody (NAb) response induced by the inactivated Japanese encephalitis vaccine (IJEV). In the present study, we genotyped HLA-DPA1, DQA1, DMA, and DMB genes and used previous HLA-DRB1, DPB1, and DQB1 data to evaluate the association of these genes with IJEV-induced NAbs, at both the seroconversion and geometric mean titres (GMTs). We confirmed the seropositive association of DQB1*02:01 and NAbs (0.156 vs. 0.075, Padj = 0.018; OR = 2.270; 95% CI = 1.285-3.999) and seronegative association of DQB1*02:02 (0.014 vs. 0.09, Padj = 0.0002; OR = 0.130; 95% CI = 0.047-0.400). Furthermore, the DMB*01:03-DMA*01:01-DPA1*01:03-DPB1*04:01 haplotype was associated with a negative response (0.020 vs. 0.074; Padj = 0.03; OR = 0.250; 95% CI = 0.097-0.649), whereas DRB1*15:02-DMB*01:01-DMA*01:01 was associated with a positive response (0.034 vs. 0; Padj = 0.044). In addition, DRB1*12:02, DRB1*13:02, DPB1*04:01, DPB1*05:01, DPB1*09:01, DQA1*06:01, and DQA1*01:02 were associated with a higher GMT of NAbs, whereas DRB1*11:01, DPB1*13:01, and DQA1*05:05 were associated with a lower GMT of NAbs. In conclusion, the present study suggests that variations in the HLA-DM and HLA class II genes, as well as their combined allotypes, may influence the IJEV NAbs at seroconversion and GMT levels. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jihong He
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Jun Chen
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Xue Han
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Qin Gu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Jiangli Liang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Mingbo Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Shuyuan Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Li Shi
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
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Turner TR, Hayward DR, Gymer AW, Barker DJ, Leen G, Cambridge CA, Macpherson HL, Georgiou X, Cooper MA, Lucas JAM, Nadeem D, Robinson J, Mayor NP, Marsh SGE. Widespread non‐coding polymorphism in
HLA
class
II
genes of International
HLA
and Immunogenetics Workshop cell lines. HLA 2022; 99:328-356. [DOI: 10.1111/tan.14571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Thomas R. Turner
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | - Arthur W. Gymer
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | - Gayle Leen
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | | | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | | | - Daud Nadeem
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
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34
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Pasharawipas T. Perspectives Concerning Various Symptoms of SARS-CoV-2 Detected Individuals. Open Microbiol J 2021. [DOI: 10.2174/1874285802115010152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
After exposure to SARS-CoV-2, varying symptoms of COVID-19 ranging from asymptomatic symptoms to morbidity and mortality have been exhibited in each individual. SARS-CoV-2 requires various cellular molecules for penetration into a target host cell. Angiotensin-converting enzyme2 (ACE2) acts as the viral receptor molecule. After attachment, SARS-CoV-2 also requires the transmembrane protease serine-2 (TMPRSS-2) and furin molecules, which serve as co-receptors for penetration into the target cell and for subsequent replication. In the meantime, a major histocompatibility complex (MHC) is required for the induction of adaptive immune cells, especially cytotoxic T cells and helper T cells, to clear the virally infected cells. This perspective review article proposes different aspects to explain the varying symptoms of the individuals who have been exposed to SARS-CoV-2, which relates to the polymorphisms of these involved molecules.
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35
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Li JX, Pang JS, Yin BT, Chen G, Chen JH, Luo JY, Yang X, Qin LT, Zeng JH, Chen P, Chen JB, Tang D. Down-Regulation of Activating Transcription Factor 3 (ATF3) in Hepatoblastoma and Its Relationship with Ferroptosis. Int J Gen Med 2021; 14:9401-9418. [PMID: 34908868 PMCID: PMC8664385 DOI: 10.2147/ijgm.s340939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose The molecular mechanisms and signal pathways of ferroptosis in hepatoblastoma (HB) have not yet been clarified. In previous studies, activating transcription factor 3 (ATF3) was reported to be correlated with several tumors, but the clinical significance of ATF3 has never been determined. Herein, we investigated the clinicopathological value and mechanisms of ATF3 in regulating ferroptosis in HB. Methods The mRNA microarray and RNA-sequencing data of 402 samples from our hospital and public databases were used to estimate ATF3 expression and assess its clinical role in HB. The standard mean difference (SMD) and summary receiver operating characteristic curves were utilized to judge the discrimination ability of ATF3 between HB and non-HB liver tissues. We examined the expression variation of ATF3 in HB cells after the treatment with erastin. We also predicted the target genes of ATF3 as a transcriptional factor from public Chromatin Immunoprecipitation-sequencing data and selected the ferroptosis-related genes for a signaling pathway analysis. Results In ten series, the pooled SMD for ATF3 was −0.91, demonstrating that ATF3 expression was predominantly lower in HB than in non-HB liver tissues. ATF3 down-regulation showed moderate potential to distinguish HB from non-HB liver tissues (area under curves = 0.83, 95% confidence interval = 0.79–0.86). Altogether, 4855 putative targets of ATF3 as a transcriptional factor were collected, among which, 60 genes were ferroptosis-related. Conclusion The down-regulated ATF3 expression may play a vital role in the occurrence of HB possible partially by regulating ferroptosis.
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Affiliation(s)
- Jing-Xiao Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jin-Shu Pang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Bin-Tong Yin
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jun-Hong Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jia-Yuan Luo
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xia Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Li-Ting Qin
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jiang-Hui Zeng
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People's Hospital, Nanning, Guangxi Zhuang Autonomous Region, 530031, People's Republic of China
| | - Peng Chen
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530031, People's Republic of China
| | - Jia-Bo Chen
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530031, People's Republic of China
| | - Deng Tang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
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36
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Ding Y, Cui M, Qian J, Wang C, Shen Q, Ren H, Li L, Zhang F, Zhang R. Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics. Front Genet 2021; 12:758041. [PMID: 34858474 PMCID: PMC8632457 DOI: 10.3389/fgene.2021.758041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Autoimmune diseases (ADs) are a broad range of diseases in which the immune response to self-antigens causes damage or disorder of tissues, and the genetic susceptibility is regarded as the key etiology of ADs. Accumulating evidence has suggested that there are certain commonalities among different ADs. However, the theoretical research about similarity between ADs is still limited. In this work, we first computed the genetic similarity between 26 ADs based on three measurements: network similarity (NetSim), functional similarity (FunSim), and semantic similarity (SemSim), and systematically identified three significant pairs of similar ADs: rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), myasthenia gravis (MG) and autoimmune thyroiditis (AIT), and autoimmune polyendocrinopathies (AP) and uveomeningoencephalitic syndrome (Vogt-Koyanagi-Harada syndrome, VKH). Then we investigated the gene ontology terms and pathways enriched by the three significant AD pairs through functional analysis. By the cluster analysis on the similarity matrix of 26 ADs, we embedded the three significant AD pairs in three different disease clusters respectively, and the ADs of each disease cluster might have high genetic similarity. We also detected the risk genes in common among the ADs which belonged to the same disease cluster. Overall, our findings will provide significant insight in the commonalities of different ADs in genetics, and contribute to the discovery of novel biomarkers and the development of new therapeutic methods for ADs.
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Affiliation(s)
- Yanjun Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin, China
| | - Mintian Cui
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jun Qian
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin, China
| | - Chao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qi Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongbiao Ren
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liangshuang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fengmin Zhang
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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37
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Pasharawipas T. Different Aspects Concerning Viral Infection and the Role of MHC Molecules in Viral Prevention. Open Microbiol J 2021. [DOI: 10.2174/1874285802115010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Major Histocompatibility Complex (MHC) molecules play a crucial role in inducing an adaptive immune response. T-cell epitopes require compatible MHC molecules to form MHC-peptide Complexes (pMHC) that activate the T-cell Receptors (TCR) of T-lymphocyte clones. MHCs are polymorphic molecules with wide varieties of gene alleles. There are two classes of MHC molecules, class I and II. Both classes have three classical loci HLA-A, -B, and –C are present in class I and HLA-DP, -DQ, and -DR in class II. To induce a compatible T-lymphocyte clone, the T-cell epitope requires the association of the compatible MHC molecule to form pMHC. Each MHC variant possesses a different groove that is capable of binding a different range of antigenic epitopes. Without the compatible MHC molecule, a T cell clone cannot be activated by a particular viral epitope. With the aim of preventing viral transmission, the efficiency of a viral vaccine is related to the existence of specific MHC alleles in the individual. This article proposes the roles of the MHC molecule to prevent viral infection. In addition, the association of the viral receptor molecule with the viral infection will also be discussed.
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38
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Wang J, Li F, Xu Y, Zheng X, Zhang C, Hu C, Xu Y, Mi W, Li X, Zhang Y. Dissecting immune cell stat regulation network reveals biomarkers to predict ICB therapy responders in melanoma. J Transl Med 2021; 19:296. [PMID: 34238310 PMCID: PMC8265039 DOI: 10.1186/s12967-021-02962-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/25/2021] [Indexed: 01/10/2023] Open
Abstract
Background Immunotherapy is a revolutionary strategy in cancer therapy, but the resistance of which is one of the important challenges. Detecting the regulation of immune cells and biomarkers concerning immune checkpoint blockade (ICB) therapy is of great significance. Methods Here, we firstly constructed regulation networks for 11 immune cell clusters by integrating biological pathway data and single cell sequencing data in metastatic melanoma with or without ICB therapy. We then dissected these regulation networks and identified differently expressed genes between responders and non-responders. Finally, we trained and validated a logistic regression model based on ligands and receptors in the regulation network to predict ICB therapy response. Results We discovered the regulation of genes across eleven immune cell stats. Functional analysis indicated that these stat-specific networks consensually enriched in immune response corrected pathways and highlighted antigen processing and presentation as a core pathway in immune cell regulation. Furthermore, some famous ligands like SIRPA, ITGAM, CD247and receptors like CD14, IL2 and HLA-G were differently expressed between cells of responders and non-responders. A predictive model of gene sets containing ligands and receptors performed accuracy prediction with AUCs above 0.7 in a validation dataset suggesting that they may be server as biomarkers for predicting immunotherapy response. Conclusions In summary, our study presented the gene–gene regulation landscape across 11 immune cell clusters and analysis of these networks revealed several important aspects and immunotherapy response biomarkers, which may provide novel insights into immune related mechanisms and immunotherapy response prediction. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02962-8.
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Affiliation(s)
- Jingwen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xuan Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Congxue Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Wanqi Mi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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39
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Li F, Zhu M, Niu B, Liu L, Peng X, Yang H, Qin B, Wang M, Ren X, Zhou X. Generation and expression analysis of BAC humanized mice carrying HLA-DP401 haplotype. Animal Model Exp Med 2021; 4:116-128. [PMID: 34179719 PMCID: PMC8212823 DOI: 10.1002/ame2.12158] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/17/2020] [Indexed: 11/13/2022] Open
Abstract
Background Human leukocyte antigen (HLA)-DP is much less studied than other HLA class II antigens, that is, HLA-DR and HLA-DQ, etc. However, the accumulating data have suggested the important roles of DP-restricted responses in the context of cancer, allergy, and infectious disease. Lack of animal models expressing these genes as authentic cis-haplotypes blocks our understanding for the role of HLA-DP haplotypes in immunity. Methods To explore the potential cis-acting control elements involved in the transcriptional regulation of the HLA-DPA1/DPB1 gene, we performed the expression analysis using bacterial artificial chromosome (BAC)-based transgenic humanized mice in the C57BL/6 background, which carried the entire HLA-DP401 gene locus. We further developed a mouse model of Staphylococcus aureus pneumonia in HLA-DP401 humanized transgenic mice, and performed the analysis on the expression pattern of HLA-DP401 and immunological responses in the model. Results In this study, we screened and identified a BAC clone spanning the entire HLA-DP gene locus. DNA from this clone was analyzed for integrity by pulsed-field gel electrophoresis and then microinjected into fertilized mouse oocytes to produce transgenic founder animals. Nine sets of PCR primers for regional markers with an average distance of 15 kb between each primer were used to confirm the integrity of the transgene in the five transgenic lines carrying the HLA-DPA1/DPB1 gene. Transgene copy numbers were determined by real-time PCR analysis. HLA-DP401 gene expression was analyzed at the mRNA and protein level. Although infection with S aureus Newman did not alter the percentage of immune cells in the spleen and thymus from the HLA-DP401-H2-Aβ1 humanized mice. Increased expression of HLA-DP401 was observed in the thymus of the humanized mice infected by S aureus. Conclusions We generated several BAC transgenic mice, and analyzed the expression of HLA-DPA1/DPB1 in those mice. A model of Saureus-induced pneumonia in the HLA-DP401-H2-Aβ1-/- humanized mice was further developed, and S aureus infection upregulated the HLA-DP401 expression in thymus of those humanized mice. These findings demonstrate the potential of those HLA-DPA1/DPB1 transgenic humanized mice for developing animal models of infectious diseases and MHC-associated immunological diseases.
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Affiliation(s)
- Feng Li
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Meng‐min Zhu
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Bo‐wen Niu
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Ling‐ling Liu
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Xiu‐hua Peng
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Hua Yang
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Bo‐yin Qin
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Meixiang Wang
- Department of Scientific ResearchShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Xiaonan Ren
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
| | - Xiaohui Zhou
- Department of Laboratory Animal ScienceShanghai Public Health Clinical CenterFudan UniveristyShanghaiChina
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40
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Wiśniewski A, Sobczyński M, Pawełczyk K, Porębska I, Jasek M, Wagner M, Niepiekło-Miniewska W, Kowal A, Dubis J, Jędruchniewicz N, Kuśnierczyk P. Polymorphisms of Antigen-Presenting Machinery Genes in Non-Small Cell Lung Cancer: Different Impact on Disease Risk and Clinical Parameters in Smokers and Never-Smokers. Front Immunol 2021; 12:664474. [PMID: 34149699 PMCID: PMC8212834 DOI: 10.3389/fimmu.2021.664474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/05/2021] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is strongly associated with cigarette smoking; nevertheless some never-smokers develop cancer. Immune eradication of cancer cells is dependent on polymorphisms of HLA class I molecules and antigen-processing machinery (APM) components. We have already published highly significant associations of single nucleotide polymorphisms (SNPs) of the ERAP1 gene with non-small cell lung cancer (NSCLC) in Chinese, but not in Polish populations. However, the smoking status of participants was not known in the previous study. Here, we compared the distribution of APM polymorphic variants in larger cohorts of Polish patients with NSCLC and controls, stratified according to their smoking status. We found significant but opposite associations in never-smokers and in smokers of all tested SNPs (rs26653, rs2287987, rs30187, and rs27044) but one (rs26618) in ERAP1. No significant associations were seen in other genes. Haplotype analysis indicated that the distribution of many ERAP1/2 haplotypes is opposite, depending on smoking status. Additionally, haplotypic combination of low activity ERAP1 and the lack of an active form of ERAP2 seems to favor the disease in never-smokers. We also revealed interesting associations of some APM polymorphisms with: age at diagnosis (ERAP1 rs26653), disease stage (ERAP1 rs27044, PSMB9 rs17587), overall survival (ERAP1 rs30187), and response to chemotherapy (ERAP1 rs27044). The results presented here may suggest the important role for ERAP1 in the anti-cancer response, which is different in smokers versus never-smokers, depending to some extent on the presence of ERAP2, and affecting NSCLC clinical course.
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Affiliation(s)
- Andrzej Wiśniewski
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Maciej Sobczyński
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Konrad Pawełczyk
- Department and Clinic of Thoracic Surgery, Wrocław Medical University, Wrocław, Poland
| | - Irena Porębska
- Department of Pulmonology and Lung Oncology, Wrocław Medical University, Wrocław, Poland
| | - Monika Jasek
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Marta Wagner
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Wanda Niepiekło-Miniewska
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Aneta Kowal
- Department of Pulmonology and Lung Oncology, Wrocław Medical University, Wrocław, Poland
| | - Joanna Dubis
- Research and Development Centre, Regional Specialist Hospital in Wrocław, Wrocław, Poland
| | - Natalia Jędruchniewicz
- Research and Development Centre, Regional Specialist Hospital in Wrocław, Wrocław, Poland
| | - Piotr Kuśnierczyk
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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41
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Aamdal E, Inderberg EM, Ellingsen EB, Rasch W, Brunsvig PF, Aamdal S, Heintz KM, Vodák D, Nakken S, Hovig E, Nyakas M, Guren TK, Gaudernack G. Combining a Universal Telomerase Based Cancer Vaccine With Ipilimumab in Patients With Metastatic Melanoma - Five-Year Follow Up of a Phase I/IIa Trial. Front Immunol 2021; 12:663865. [PMID: 34046035 PMCID: PMC8147687 DOI: 10.3389/fimmu.2021.663865] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/30/2021] [Indexed: 01/14/2023] Open
Abstract
Background Ipilimumab improves survival for patients with metastatic malignant melanoma. Combining a therapeutic cancer vaccine with ipilimumab may increase efficacy by providing enhanced anti-tumor immune responses. UV1 consists of three synthetic long peptides from human telomerase reverse transcriptase (hTERT). These peptides comprise epitopes recognized by T cells from cancer patients experiencing long-term survival following treatment with a first-generation hTERT vaccine, and generate long-lasting immune responses in cancer patients when used as monotherapy. The objective of this trial was to investigate the safety and efficacy of combining UV1 with ipilimumab in metastatic melanoma. Patients and Methods In this phase I/IIa, single center trial [NCT02275416], patients with metastatic melanoma received repeated UV1 vaccinations, with GM-CSF as an adjuvant, in combination with ipilimumab. Patients were evaluated for safety, efficacy and immune response. Immune responses against vaccine peptides were monitored in peripheral blood by measuring antigen-specific proliferation and IFN-γ production. Results Twelve patients were recruited. Adverse events were mainly diarrhea, injection site reaction, pruritus, rash, nausea and fatigue. Ten patients showed a Th1 immune response to UV1 peptides, occurring early and after few vaccinations. Three patients obtained a partial response and one patient a complete response. Overall survival was 50% at 5 years. Conclusion Treatment was well tolerated. The rapid expansion of UV1-specific Th1 cells in the majority of patients indicates synergy between UV1 vaccine and CTLA-4 blockade. This may have translated into clinical benefit, encouraging the combination of UV1 vaccination with standard of care treatment regimes containing ipilimumab/CTLA-4 blocking antibodies.
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Affiliation(s)
- Elin Aamdal
- Department of Oncology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Oncology, Akershus University Hospital, Lørenskog, Norway
| | | | - Espen Basmo Ellingsen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Ultimovacs Allmennaksjeselskap (ASA), Oslo, Norway
| | - Wenche Rasch
- Ultimovacs Allmennaksjeselskap (ASA), Oslo, Norway
| | | | - Steinar Aamdal
- Department of Oncology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Ultimovacs Allmennaksjeselskap (ASA), Oslo, Norway
| | - Karen-Marie Heintz
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Daniel Vodák
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Marta Nyakas
- Department of Oncology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Gustav Gaudernack
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Ultimovacs Allmennaksjeselskap (ASA), Oslo, Norway
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42
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Castro-Piedras I, Sharma M, Brelsfoard J, Vartak D, Martinez EG, Rivera C, Molehin D, Bright RK, Fokar M, Guindon J, Pruitt K. Nuclear Dishevelled targets gene regulatory regions and promotes tumor growth. EMBO Rep 2021; 22:e50600. [PMID: 33860601 DOI: 10.15252/embr.202050600] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 12/18/2022] Open
Abstract
Dishevelled (DVL) critically regulates Wnt signaling and contributes to a wide spectrum of diseases and is important in normal and pathophysiological settings. However, how it mediates diverse cellular functions remains poorly understood. Recent discoveries have revealed that constitutive Wnt pathway activation contributes to breast cancer malignancy, but the mechanisms by which this occurs are unknown and very few studies have examined the nuclear role of DVL. Here, we have performed DVL3 ChIP-seq analyses and identify novel target genes bound by DVL3. We show that DVL3 depletion alters KMT2D binding to novel targets and changes their epigenetic marks and mRNA levels. We further demonstrate that DVL3 inhibition leads to decreased tumor growth in two different breast cancer models in vivo. Our data uncover new DVL3 functions through its regulation of multiple genes involved in developmental biology, antigen presentation, metabolism, chromatin remodeling, and tumorigenesis. Overall, our study provides unique insight into the function of nuclear DVL, which helps to define its role in mediating aberrant Wnt signaling.
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Affiliation(s)
- Isabel Castro-Piedras
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Monica Sharma
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jennifer Brelsfoard
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - David Vartak
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Edgar G Martinez
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Cristian Rivera
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Deborah Molehin
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Robert K Bright
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
| | - Josee Guindon
- Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kevin Pruitt
- Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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43
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Contribution of Antigen-Processing Machinery Genetic Polymorphisms to Atopic Dermatitis. Life (Basel) 2021; 11:life11040333. [PMID: 33920176 PMCID: PMC8070454 DOI: 10.3390/life11040333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 01/12/2023] Open
Abstract
Atopic dermatitis (AD) is a chronic and recurrent inflammatory dermatosis. We recently described an association of the C allele of the single nucleotide polymorphism (SNP) rs26618 in the ERAP1 gene and a synergism of ERAP1 and ERAP2 effects on AD risk. Here, we examined whether polymorphisms of other antigen-presenting machinery genes encoding immunoproteasome components LMP2 and LMP7 and peptide transporter components TAP1 and TAP2 may also affect susceptibility to AD or its outcome. We found that the LMP7 rs2071543*T allele decreased disease risk by about 1.5-fold (odds ratio 0.66, 95% confidence interval 0.44–0.99). On the other hand, the LMP2 rs1351383*C allele reduced the mean age at diagnosis from 23 to 15 years (p < 0.001). Similarly, the TAP1 rs1135216*C allele decreased the mean age at diagnosis from almost 20 to 14 years (p = 0.033). The results are discussed in light of other reports on the role of these polymorphisms in human disease.
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44
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Dhatchinamoorthy K, Colbert JD, Rock KL. Cancer Immune Evasion Through Loss of MHC Class I Antigen Presentation. Front Immunol 2021; 12:636568. [PMID: 33767702 PMCID: PMC7986854 DOI: 10.3389/fimmu.2021.636568] [Citation(s) in RCA: 371] [Impact Index Per Article: 123.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 02/03/2023] Open
Abstract
Major histocompatibility class I (MHC I) molecules bind peptides derived from a cell's expressed genes and then transport and display this antigenic information on the cell surface. This allows CD8 T cells to identify pathological cells that are synthesizing abnormal proteins, such as cancers that are expressing mutated proteins. In order for many cancers to arise and progress, they need to evolve mechanisms to avoid elimination by CD8 T cells. MHC I molecules are not essential for cell survival and therefore one mechanism by which cancers can evade immune control is by losing MHC I antigen presentation machinery (APM). Not only will this impair the ability of natural immune responses to control cancers, but also frustrate immunotherapies that work by re-invigorating anti-tumor CD8 T cells, such as checkpoint blockade. Here we review the evidence that loss of MHC I antigen presentation is a frequent occurrence in many cancers. We discuss new insights into some common underlying mechanisms through which some cancers inactivate the MHC I pathway and consider some possible strategies to overcome this limitation in ways that could restore immune control of tumors and improve immunotherapy.
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45
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Abstract
Camels are domesticated animals that are highly adapted to the extreme desert ecosystem with relatively higher resistance to a wide range of pathogens compared to many other species from the same geographical region. Recently, there has been increased interest in the field of camel immunology. As the progress in the analysis of camel immunoglobulins has previously been covered in many recent reviews, this review intends to summarize published findings related to camel cellular immunology with a focus on the phenotype and functionality of camel leukocyte subpopulations. The review also describes the impact of different physiological (age and pregnancy) and pathological (e.g. infection) conditions on camel immune cells. Despite the progress achieved in the field of camel immunology, there are gaps in our complete understanding of the camel immune system. Questions remain regarding innate recognition mechanisms, the functional characterization of antigen-presenting cells, and the characterization of camel NK and cytotoxic T cells.
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Affiliation(s)
- Jamal Hussen
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Hans-Joachim Schuberth
- Institute of Immunology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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46
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Niepiekło-Miniewska W, Matusiak Ł, Narbutt J, Lesiak A, Kuna P, Wiśniewski A, Piekarska K, Nowak I, Kuśnierczyk P. Synergy of endoplasmic reticulum aminopeptidase 1 and 2 (ERAP1 and ERAP2) polymorphisms in atopic dermatitis: Effects on disease prevalence. Hum Immunol 2020; 82:121-123. [PMID: 33309189 DOI: 10.1016/j.humimm.2020.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 01/18/2023]
Abstract
Endoplasmic reticulum aminopeptidases ERAP1 and ERAP2 trim peptides to a length of 8-10 amino acids optimal for binding by HLA class I molecules. Although these two enzymes may work separately, but they may also form a heterodimer of enhanced trimming efficiency. We have earlier described a role for ERAP1 single nucleotide polymorphism rs26618 and HLA-C*05:01 as risk factors for atopic dermatitis (AD). Here, we examined whether ERAP2 single nucleotide polymorphism rs2248374, determining the presence or absence of the functional form of enzyme, would influence the rs26618 effect. Out of nine rs2248374 - rs26618 genotypic combinations, only one, rs2248374*A/A - rs26618*C/C, was associated with a risk of AD. Interestingly, the odds ratio increased from 1.10 (CI95%: 0.72; 1.69; p = 0.657) for ERAP2 rs2248374*A/A and 1.88 (CI95%: 1.07; 3.28; p = 0.025) for ERAP1 rs26618*C/C to 3.36 (CI95%: 1.41; 8.01; p = 0.004) for their combination, therefore revealing a synergistic effect.
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Affiliation(s)
- Wanda Niepiekło-Miniewska
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Łukasz Matusiak
- Department of Dermatology, Venereology and Allergology, Medical University of Wroclaw, Wrocław, Poland
| | - Joanna Narbutt
- 1st Department of Dermatology and Venereology, Medical University of Łódź, Łódź, Poland
| | - Aleksandra Lesiak
- 1st Department of Dermatology and Venereology, Medical University of Łódź, Łódź, Poland
| | - Piotr Kuna
- 2nd Chair of Internal Diseases, Medical University of Łódź, Poland; N. Barlicki Medical University Hospital, Łódź, Poland
| | - Andrzej Wiśniewski
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Karolina Piekarska
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Izabela Nowak
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Piotr Kuśnierczyk
- Laboratory of Immunogenetics and Tissue Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.
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47
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Polymorphisms in Processing and Antigen Presentation-Related Genes and Their Association with Host Susceptibility to Influenza A/H1N1 2009 Pandemic in a Mexican Mestizo Population. Viruses 2020; 12:v12111224. [PMID: 33138079 PMCID: PMC7692058 DOI: 10.3390/v12111224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
(1) Background: The influenza A/H1N1 pdm09 virus rapidly spread throughout the world. Despite the inflammatory and virus-degradation pathways described in the pathogenesis of influenza A virus (IAV) infection, little is known about the role of the single nucleotide polymorphisms (SNPs) in the genes involved in the processing and antigenic presentation-related mechanisms. (2) Methods: In this case-control study, we evaluated 17 SNPs in five genes (TAP1, TAP2, TAPBP, PSMB8, and PSMB9). One hundred and twenty-eight patients with influenza A/H1N1 infection (INF-P) and 111 healthy contacts (HC) were included; all of them are Mexican mestizo. (3) Results: In allele and genotype comparison, the rs241433/C allele (TAP2), as well as AG haplotype (rs3763365 and rs4148882), are associated with reduced risk for influenza A/H1N1 infection (p < 0.05). On the other hand, the rs2071888G allele (TAPBP) and GG haplotype (rs3763365 and rs9276810) are associated with a higher risk for influenza A/H1N1 infection. In addition, after adjustment for covariates, the association to a reduced risk for influenza A/H1N1 infection remains with rs241433/C allele (p < 0.0001, OR = 0.24, 95% CI = 0.13-0.43), and the association with TAPBP is also maintained with the G allele (p = 0.0095, OR = 1.89, 95% CI = 1.17-3.06) and GG genotype models (p < 0.05, OR = 2.18, 95% CI = 1.27-3.74). (4) Conclusion: The rs241433/C allele and AC genotype (TAP2) and the AG haplotype are associated with a reduced risk for influenza A/H1N1 infection. In addition, the rs2071888/G allele and GG genotype (TAPBP) and the GG haplotype are associated with a higher risk for developing influenza A/H1N1 infection in a Mexican mestizo population.
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48
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Ivanova M, Shivarov V. HLA genotyping meets response to immune checkpoint inhibitors prediction: A story just started. Int J Immunogenet 2020; 48:193-200. [PMID: 33112034 DOI: 10.1111/iji.12517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/27/2022]
Abstract
The implementation of the immune checkpoint blockade as a therapeutic option in contemporary oncology is one of the significant immunological achievements in the last century. Constantly accumulating evidence suggests that the response to immune checkpoint inhibitors (ICIs) is not universal. Therefore, it is critical to identify determinants for response, resistance and adverse effects of immune checkpoint therapy that could be developed as prognostic and predictive markers. Recent large scale analyses of cancer genome data revealed the key role of HLA class I and class II molecules in cancer immunoediting, and it appears that HLA diversity can predict response to ICIs. In the present review, we summarize the emerging data on the role of HLA germline variations as a marker for response to ICIs.
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Affiliation(s)
- Milena Ivanova
- Department of Clinical Immunology, University Hospital Alexandrovska, Medical University Sofia, Sofia, Bulgaria
| | - Velizar Shivarov
- Department of Genetics, St. Kliment Ohridski University, Sofia, Bulgaria
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49
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Engineering anti-cancer nanovaccine based on antigen cross-presentation. Biosci Rep 2020; 39:220729. [PMID: 31652460 PMCID: PMC6822533 DOI: 10.1042/bsr20193220] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 01/16/2023] Open
Abstract
Dendritic cells (DCs) present exogenous antigens on major histocompatibility complex (MHC) class I molecules, thereby activating CD8+ T cells, contributing to tumor elimination through a mechanism known as antigen cross-presentation. A variety of factors such as maturation state of DCs, co-stimulatory signals, T-cell microenvironment, antigen internalization routes and adjuvants regulate the process of DC-mediated antigen cross-presentation. Recently, the development of successful cancer immunotherapies may be attributed to the ability of DCs to cross-present tumor antigens. In this review article, we focus on the underlying mechanism of antigen cross-presentation and ways to improve antigen cross-presentation in different DC subsets. We have critically summarized the recent developments in the generation of novel nanovaccines for robust CD8+ T-cell response in cancer. In this context, we have reviewed nanocarriers that have been used for cancer immunotherapeutics based on antigen cross-presentation mechanism. Additionally, we have also expressed our views on the future applications of this mechanism in curing cancer.
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50
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Heijmans CMC, de Groot NG, Bontrop RE. Comparative genetics of the major histocompatibility complex in humans and nonhuman primates. Int J Immunogenet 2020; 47:243-260. [PMID: 32358905 DOI: 10.1111/iji.12490] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most gene-dense regions of the mammalian genome. Multiple genes within the human MHC (HLA) show extensive polymorphism, and currently, more than 26,000 alleles divided over 39 different genes are known. Nonhuman primate (NHP) species are grouped into great and lesser apes and Old and New World monkeys, and their MHC is studied mostly because of their important role as animal models in preclinical research or in connection with conservation biology purposes. The evolutionary equivalents of many of the HLA genes are present in NHP species, and these genes may also show abundant levels of polymorphism. This review is intended to provide a comprehensive comparison relating to the organization and polymorphism of human and NHP MHC regions.
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Affiliation(s)
- Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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