1
|
Zhu X, Ma E, Ning K, Feng X, Quan W, Wang F, Zhu C, Ma Y, Dong Y, Jiang Q. A comparative analysis of TCR immune repertoire in COVID-19 patients. Hum Immunol 2024; 85:110795. [PMID: 38582657 DOI: 10.1016/j.humimm.2024.110795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
The coronavirus disease 2019 (COVID-19) has merged as a global health threat since its outbreak in December 2019. Despite widespread recognition, there has been a paucity of studies focusing on the T cell receptor (TCR) bias in adaptive immunity induced by SARS-CoV-2. This research conducted a comparative analysis of the TCR immune repertoire to identify notable αβ TCR bias sequences associated with the SARS-CoV-2 virus antigen. The present study encompassed 73 symptomatic COVID-19 patients, categorized as moderate/mild or severe/critical, along with 9 healthy controls. Our findings revealed specific TCR chains prominently utilized by moderate and severe patients, identified as TRAV30-J34-TRBV3-1-J2-7 and TRAV12-3-J6-TRBV28-J1-1, respectively. Additionally, our research explored critical TCR preferences in the bronchoalveolar lavage fluid (BALF) of COVID-19 patients at various disease stages. Indeed, monitoring the dynamics of immune repertoire changes in COVID-19 patients could serve as a crucial biomarker for predicting disease progression and recovery. Furthermore, the study explored TCR bias in both peripheral blood mononuclear cells (PBMCs) and BALF. The most common αβ VJ pair observed in BALF was TRAV12-3-J18-TRBV7-6-J2-7. In addition, a comparative analysis with the VDJdb database indicated that the HLA-A*02:01 allele exhibited the widest distribution and highest frequency in COVID-19 patients across different periods. This comprehensive examination provided a global characterization of the TCR immune repertoire in COVID-19 patients, contributing significantly to our understanding of TCR bias induced by SARS-CoV-2.
Collapse
MESH Headings
- Humans
- COVID-19/immunology
- SARS-CoV-2/immunology
- Male
- Female
- Middle Aged
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Adult
- Bronchoalveolar Lavage Fluid/immunology
- Aged
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Adaptive Immunity/immunology
- Severity of Illness Index
Collapse
Affiliation(s)
- Xiao Zhu
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China; Lead Contact.
| | - Enze Ma
- School of Computer Science and Information Engineering, Harbin Normal University, Harbin, Heilongjiang, China
| | - Ke Ning
- School of Computer Science and Information Engineering, Harbin Normal University, Harbin, Heilongjiang, China
| | - Xiangyan Feng
- Department of Hematology, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China.
| | - Wei Quan
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China
| | - Fei Wang
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China
| | - Chaoqun Zhu
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China
| | - Yuanjun Ma
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China
| | - Yucui Dong
- Department of Immunology, Binzhou Medical University, Yantai, Shandong, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
| |
Collapse
|
2
|
Koo D, Mao Z, Dimatteo R, Noguchi M, Tsubamoto N, McLaughlin J, Tran W, Lee S, Cheng D, de Rutte J, Burton Sojo G, Witte ON, Di Carlo D. Defining T cell receptor repertoires using nanovial-based binding and functional screening. Proc Natl Acad Sci U S A 2024; 121:e2320442121. [PMID: 38536748 PMCID: PMC10998554 DOI: 10.1073/pnas.2320442121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/27/2024] [Indexed: 04/08/2024] Open
Abstract
The ability to selectively bind to antigenic peptides and secrete effector molecules can define rare and low-affinity populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs inducing the secretion of effector molecules including IFN-γ and granzyme B that are accumulated on nanovials, allowing sorting based on both binding and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes and secretions with oligo-barcoded detection antibodies, we could accurately link TCR sequences to specific targets and rank each TCR based on the corresponding cell's secretion level. Using the technique, we identified an expanded repertoire of functional TCRs targeting viral antigens with high specificity and found rare TCRs with activity against cancer-specific splicing-enhanced epitopes.
Collapse
Affiliation(s)
- Doyeon Koo
- Department of Bioengineering, University of California, Los Angeles, CA90095
| | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA90095
| | - Miyako Noguchi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Natalie Tsubamoto
- Department of Bioengineering, University of California, Los Angeles, CA90095
| | - Jami McLaughlin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Wendy Tran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Sohyung Lee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA90095
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
| | - Joseph de Rutte
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Partillion Bioscience, Pasadena, CA91107
| | - Giselle Burton Sojo
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Owen N. Witte
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Partillion Bioscience, Pasadena, CA91107
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA90095
- California NanoSystems Institute, Los Angeles, CA90095
| |
Collapse
|
3
|
Zong K, Yuan P, Wang R, Luo Q, Yang Y, Zhang X, Song Q, Du H, Gao C, Song J, Zhan W, Zhang M, Wang Y, Lin Q, Yao H, Xie B, Han J. Characteristics of innate, humoral and cellular immunity in children with non-severe SARS-CoV-2 infection. J Infect 2024; 88:158-166. [PMID: 38101522 DOI: 10.1016/j.jinf.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/25/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The symptoms of children infected with SARS-CoV-2 are mainly asymptomatic, mild, moderate, and a few severe cases. To understand the immune response characteristics of children infected with SARS-COV-2 who do not develop severe cases, 82 children infected with the SARS-CoV-2 delta strain were recruited in this study. Our results showed that high levels of IgG, IgM, and neutralization antibodies appeared in children infected with SARS-CoV-2. SARS-CoV-2 induced upregulation of both pro-inflammatory factors including TNF-α and anti-inflammatory factors including IL-4 and IL-13 in the children, even IL-10. The expression of INF-α in infected children also showed a significant increase compared to healthy children. However, IL-6, one of the important inflammatory factors, did not show an increase in infected children. It is worth noting that a large number of chemokines reduced in the SARS-CoV-2-infected children. Subsequently, TCR Repertoire, TCRβ bias, and preferential usage were analyzed on data of TCR next-generation sequencing from 8 SARS-CoV-2-infected children and 8 healthy controls. We found a significant decrease in TCR clonal diversity and a significant increase in TCR clonal expansion in SARS-CoV-2-infected children compared to healthy children. The most frequent V and J genes in SARS-CoV-2 children were TRBV28 and TRBJ2-1. The most frequently VβJ gene pairing in SARS-CoV-2 infected children was TRBV20-1-TRBJ2-1. The strong antiviral antibody levels, low expression of key pro-inflammatory factors, significant elevation of anti-inflammatory factors, and downregulation of many chemokines jointly determine that SARS-CoV-2-infected children rarely develop severe cases. Overall, our findings shed a light on the immune response of non-severe children infected with SARS-CoV-2.
Collapse
Affiliation(s)
- Kexin Zong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Ping Yuan
- Fujian Provincial Key Laboratory of Zoonosis Research (Fujian Center for Disease Control and Prevention); The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou, Fujian 350011, China
| | - Ruifang Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Qin Luo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Yanqing Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Xiaohong Zhang
- Fujian Provincial Key Laboratory of Zoonosis Research (Fujian Center for Disease Control and Prevention); The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou, Fujian 350011, China
| | - Qinqin Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Haijun Du
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Chen Gao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Juan Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Weihua Zhan
- Putian Center for Disease Control and Prevention, Putian, Fujian 351106, China
| | - Mengjie Zhang
- Putian Center for Disease Control and Prevention, Putian, Fujian 351106, China
| | - Yanhai Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China
| | - Qunying Lin
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Putian University, Putian, Fujian 351100, China
| | - Hailan Yao
- Department of Biochemistry & Immunology, Capital Institute of Pediatrics, YaBao Rd, Beijing 100020, China.
| | - Baosong Xie
- Department of Pulmonary and Critical Care Medicine, Fujian Provincial Hospital; Fujian Shengli Medical College, Fujian Medical University, Fuzhou, Fujian 350001, China.
| | - Jun Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing 102206, China.
| |
Collapse
|
4
|
Quan Z, Qi A, Ma S, Li Y, Chen H, Yu X, Dong T, Li K, Qiu Y. Altered T-cell receptor β repertoire in adults with SARS CoV-2 inactivated vaccine of BBIBP-CorV. Mol Immunol 2023; 162:54-63. [PMID: 37647774 DOI: 10.1016/j.molimm.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Abstract
OBJECTIVE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the prolonged and widespread epidemic of coronavirus disease 2019 (COVID-19). The inactivated BBIBP-CorV vaccine has shown safety, efficacy and immunogenicity against COVID-19 in in-vitro studies and clinical trials. However, the characteristics changes of the TCRβ repertoire in patients receiving BBIBP-CorV remain unclear. METHODS TCRβ repertoire difference were analyzed between 54 uninfected subjects who received a third dose of the enhanced BBIBP-CorV vaccine and the 16 healthy donors who did not receive the vaccine and 44 COVID-19 patients with different courses of disease (asymptomatic, symptomatic and convalescent). Furthermore, antibody response, anti-inflammatory and pro-inflammatory cytokines also were examined. RESULTS We found that the third dose inactivated coronavirus vaccine induced widespread changes including the increased TCRβ repertoire diversity, a much shorter CDR3 length and high usage of V-J genes segments. Meanwhile, the vaccine-responding clones were also predicted. The results of the antibody response showed that 90.7 % of the vaccinated individuals were positive for NAb seroconversion and 88.9 % for IgG antibody about 60 days after the third dose. The concentration of IL-2 increased significantly compared to baseline inoculation. CONCLUSION Altered TCRβ repertoire in adults with SARS CoV-2 inactivated vaccine of BBIBP-CorV clarified the specific immunity induced by inactivated vaccines. Our research provides insights into the adaptive immune response induced by the new inactivated SARS-CoV-2 vaccine and strengthens the development of immunotherapy.
Collapse
Affiliation(s)
- Zhihui Quan
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Translational Medicine Institute of Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Aihong Qi
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China
| | - Shuwen Ma
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China
| | - Yanling Li
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Hui Chen
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Xue Yu
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Translational Medicine Institute of Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Tingyan Dong
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China.
| | - Kui Li
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Translational Medicine Institute of Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China.
| | - Yurong Qiu
- Guangzhou Huayin Medical Laboratory Center Co., Ltd, Guangzhou, China; Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China.
| |
Collapse
|
5
|
Meza L, Zengin Z, Salgia S, Malhotra J, Karczewska E, Dorff T, Tripathi A, Ely J, Kelley E, Mead H, Hsu J, Dizman N, Salgia N, Chawla N, Chehrazi-Raffle A, Muddasani R, Govindarajan A, Rock A, Liu S, Salgia R, Trent J, Altin J, Pal SK. Twelve-Month Follow-up of the Immune Response After COVID-19 Vaccination in Patients with Genitourinary Cancers: A Prospective Cohort Analysis. Oncologist 2023; 28:e748-e755. [PMID: 36971500 PMCID: PMC10485287 DOI: 10.1093/oncolo/oyad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/10/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Vaccinations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have had a transformative impact on morbidity and mortality. However, the long-term impact of vaccination on patients with genitourinary cancers is currently unknown. MATERIALS AND METHODS This study aimed to assess seroconversion rates in patients with genitourinary cancers receiving COVID-19 vaccination. Patients with prostate cancer, renal cell carcinoma, or urothelial cancer who had not been vaccinated for COVID-19 were included. Blood samples were obtained at baseline and after 2, 6, and 12 months of one dose of an FDA-approved COVID-19 vaccine. Antibody titer analysis was performed using the SCoV-2 Detect IgG ELISA assay, and the results were reported as immune status ratio (ISR). A paired t-test was used for comparison of ISR values between timepoints. In addition, T-cell receptor (TCR) sequencing was performed to assess for differences in TCR repertoire 2 months after vaccination. RESULTS Out of 133 patients enrolled, 98 baseline blood samples were collected. At 2-, 6-, and 12-month time points 98, 70, and 50 samples were collected, respectively. Median age was 67 (IQR, 62-75), with the majority of patients diagnosed with prostate (55.1%) or renal cell carcinoma (41.8%). Compared to baseline (0.24 [95% CI, 0.19-0.31]) a significant increase in the geometric mean ISR values was observed at the 2-month timepoint (5.59 [4.76-6.55]) (P < .001). However, at the 6-month timepoint, a significant decrease in the ISR values was observed (4.66 [95% CI, 4.04-5.38]; P < .0001). Notably, at the 12-month timepoint, the addition of a booster dose resulted in an absolute increase in the ISR values compared to those who did not receive a booster dose (P = .04). CONCLUSIONS Only a minority of patients with genitourinary cancers did not ultimately achieve satisfactory seroconversion after receiving commercial COVID-19 vaccination. Cancer type or treatment rendered did not appear to affect the immune response mounted after vaccination.
Collapse
Affiliation(s)
- Luis Meza
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Zeynep Zengin
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sabrina Salgia
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jasnoor Malhotra
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ewa Karczewska
- Department of Immuno-Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Tanya Dorff
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Abhishek Tripathi
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jennifer Ely
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, AZ, USA
| | - Erin Kelley
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, AZ, USA
| | - Heather Mead
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, AZ, USA
| | - JoAnn Hsu
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Nazli Dizman
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Nicholas Salgia
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Neal Chawla
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Alex Chehrazi-Raffle
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ramya Muddasani
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ameish Govindarajan
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Adam Rock
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sandy Liu
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ravi Salgia
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jeffrey Trent
- Integrated Cancer Genomics Division, Translational Genomics Institute, Phoenix, AZ, USA
| | - John Altin
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, AZ, USA
| | - Sumanta K Pal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| |
Collapse
|
6
|
Miao Y, Shi Z, Zhang W, Zhu L, Tang S, Chen H, Wang X, Du Q, Li S, Zhang Y, Luo W, Jin X, Fang M, Zhou H. Immune Repertoire Profiling Reveals Its Clinical Application Potential and Triggers for Neuromyelitis Optica Spectrum Disorders. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2023; 10:e200134. [PMID: 37414573 DOI: 10.1212/nxi.0000000000200134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/27/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND AND OBJECTIVES Neuromyelitis optica spectrum disorders (NMOSD) is widely recognized as a CNS demyelinating disease associated with AQP4-IgG (T cell-dependent antibody), and its trigger is still unclear. In addition, although the treatment of NMOSD currently can rely on traditional immunosuppressive and modulating agents, effective methods to predict the efficacy of these therapeutics are lacking. METHODS In this study, high-throughput T-cell receptor (TCR) sequencing was performed on peripheral blood from 151 pretreatment patients with AQP4-IgG+ NMOSD and 151 healthy individuals. We compared the TCR repertoire of those with NMOSD with that of healthy individuals and identified TCR clones that were significantly enriched in NMOSD. In addition, we treated 28 patients with AQP4-IgG+ NMOSD with immunosuppressants and followed up for 6 months to compare changes in NMOSD-specific TCRs (NMOSD-TCRs) before and after treatment. Moreover, we analyzed transcriptome and single-cell B-cell receptor (BCR) data from public databases and performed T-cell activation experiments using antigenic epitopes of cytomegalovirus (CMV) to further explore the triggers of AQP4-IgG+ NMOSD. RESULTS Compared with healthy controls, patients with AQP4-IgG+ NMOSD had significantly reduced diversity and shorter CDR3 length of TCRβ repertoire. Furthermore, we identified 597 NMOSD-TCRs with a high sequence similarity that have the potential to be used in the diagnosis and prognosis of NMOSD. The characterization of NMOSD-TCRs and pathology-associated clonotype annotation indicated that the occurrence of AQP4-IgG+ NMOSD may be associated with CMV infection, which was further corroborated by transcriptome and single-cell BCR analysis results from public databases and T-cell activation experiments. DISCUSSION Our findings suggest that the occurrence of AQP4-IgG+ NMOSD may be associated with CMV infection. In conclusion, our study provides new clues to uncover the causative factors of AQP4-IgG+ NMOSD and provides a theoretical foundation for treating and monitoring the disease.
Collapse
Affiliation(s)
- Yu Miao
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Ziyan Shi
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Wei Zhang
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Lin Zhu
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Shanshan Tang
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Hongxi Chen
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Xiaofei Wang
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Qin Du
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China.
| | - Shuaicheng Li
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China.
| | - Ying Zhang
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Wenqin Luo
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China
| | - Xin Jin
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China.
| | - Mingyan Fang
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China.
| | - Hongyu Zhou
- From the College of Life Sciences (M., X.J.), University of Chinese Academy of Sciences, Beijing; Department of Neurology (Z.S., L.Z., S.T., H.C., X.W., Q.D., Y.Z., W.L., M.F., H.Z.), West China Hospital, Sichuan University, Chengdu; and City University of Hong Kong (W.Z., S.L.), Shenzhen Research Institute, China.
| |
Collapse
|
7
|
Xu J, Li XX, Yuan N, Li C, Yang JG, Cheng LM, Lu ZX, Hou HY, Zhang B, Hu H, Qian Y, Liu XX, Li GC, Wang YD, Chu M, Dong CR, Liu F, Ge QG, Yang YJ. T cell receptor β repertoires in patients with COVID-19 reveal disease severity signatures. Front Immunol 2023; 14:1190844. [PMID: 37475855 PMCID: PMC10355153 DOI: 10.3389/fimmu.2023.1190844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/06/2023] [Indexed: 07/22/2023] Open
Abstract
Background The immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are crucial in maintaining a delicate balance between protective effects and harmful pathological reactions that drive the progression of coronavirus disease 2019 (COVID-19). T cells play a significant role in adaptive antiviral immune responses, making it valuable to investigate the heterogeneity and diversity of SARS-CoV-2-specific T cell responses in COVID-19 patients with varying disease severity. Methods In this study, we employed high-throughput T cell receptor (TCR) β repertoire sequencing to analyze TCR profiles in the peripheral blood of 192 patients with COVID-19, including those with moderate, severe, or critical symptoms, and compared them with 81 healthy controls. We specifically focused on SARS-CoV-2-associated TCR clonotypes. Results We observed a decrease in the diversity of TCR clonotypes in COVID-19 patients compared to healthy controls. However, the overall abundance of dominant clones increased with disease severity. Additionally, we identified significant differences in the genomic rearrangement of variable (V), joining (J), and VJ pairings between the patient groups. Furthermore, the SARS-CoV-2-associated TCRs we identified enabled accurate differentiation between COVID-19 patients and healthy controls (AUC > 0.98) and distinguished those with moderate symptoms from those with more severe forms of the disease (AUC > 0.8). These findings suggest that TCR repertoires can serve as informative biomarkers for monitoring COVID-19 progression. Conclusions Our study provides valuable insights into TCR repertoire signatures that can be utilized to assess host immunity to COVID-19. These findings have important implications for the use of TCR β repertoires in monitoring disease development and indicating disease severity.
Collapse
Affiliation(s)
- Jing Xu
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital & National Center for Cardiovascular Diseases, Beijing, China
- Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiao-xiao Li
- Department of Pharmacy and Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Li
- Department of Pharmacy and Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Jin-gang Yang
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital & National Center for Cardiovascular Diseases, Beijing, China
- Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li-ming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhong-xin Lu
- Department of Medical Laboratory, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong-yan Hou
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Zhang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Hu
- Department of Medical Laboratory, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Qian
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-xuan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guo-chao Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Yue-dan Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China
| | - Ming Chu
- Department of Immunology, School of Basic Medical Sciences, Peking University, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China
| | - Chao-ran Dong
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Saudi Arabia
| | - Qing-gang Ge
- Department of Pharmacy and Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Yue-jin Yang
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital & National Center for Cardiovascular Diseases, Beijing, China
- Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| |
Collapse
|
8
|
Liu Y, Chen S, Liu S, Wallace KL, Zille M, Zhang J, Wang J, Jiang C. T-cell receptor signaling modulated by the co-receptors: Potential targets for stroke treatment. Pharmacol Res 2023; 192:106797. [PMID: 37211238 DOI: 10.1016/j.phrs.2023.106797] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/02/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
Stroke is a severe and life-threatening disease, necessitating more research on new treatment strategies. Infiltrated T lymphocytes, an essential adaptive immune cell with extensive effector function, are crucially involved in post-stroke inflammation. Immediately after the initiation of the innate immune response triggered by microglia/macrophages, the adaptive immune response associated with T lymphocytes also participates in the complex pathophysiology of stroke and partially informs the outcome of stroke. Preclinical and clinical studies have revealed the conflicting roles of T cells in post-stroke inflammation and as potential therapeutic targets. Therefore, exploring the mechanisms that underlie the adaptive immune response associated with T lymphocytes in stroke is essential. The T-cell receptor (TCR) and its downstream signaling regulate T lymphocyte differentiation and activation. This review comprehensively summarizes the various molecules that regulate TCR signaling and the T-cell response. It covers both the co-stimulatory and co-inhibitory molecules and their roles in stroke. Because immunoregulatory therapies targeting TCR and its mediators have achieved great success in some proliferative diseases, this article also summarizes the advances in therapeutic strategies related to TCR signaling in lymphocytes after stroke, which can facilitate translation. DATA AVAILABILITY: No data was used for the research described in the article.
Collapse
Affiliation(s)
- Yuanyuan Liu
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, P. R. China
| | - Shuai Chen
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, P. R. China
| | - Simon Liu
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD, 20814, USA
| | - Kevin L Wallace
- College of Mathematical and Natural Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Marietta Zille
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, A-1090 Vienna, Austria
| | - Jiewen Zhang
- Department of Neurology, People's Hospital of Zhengzhou University, 450000, Zhengzhou, P. R. China.
| | - Jian Wang
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, P. R. China; Department of Anatomy, School of Basic Medical Sciences, Zhengzhou University, 450001, Zhengzhou, P. R. China.
| | - Chao Jiang
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, P. R. China.
| |
Collapse
|
9
|
Peng X, Lei Y, Feng P, Jia L, Ma J, Zhao D, Zeng J. Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00634-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
10
|
Zornikova KV, Sheetikov SA, Rusinov AY, Iskhakov RN, Bogolyubova AV. Architecture of the SARS-CoV-2-specific T cell repertoire. Front Immunol 2023; 14:1070077. [PMID: 37020560 PMCID: PMC10067759 DOI: 10.3389/fimmu.2023.1070077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
The T cell response plays an indispensable role in the early control and successful clearance of SARS-CoV-2 infection. However, several important questions remain about the role of cellular immunity in COVID-19, including the shape and composition of disease-specific T cell repertoires across convalescent patients and vaccinated individuals, and how pre-existing T cell responses to other pathogens—in particular, common cold coronaviruses—impact susceptibility to SARS-CoV-2 infection and the subsequent course of disease. This review focuses on how the repertoire of T cell receptors (TCR) is shaped by natural infection and vaccination over time. We also summarize current knowledge regarding cross-reactive T cell responses and their protective role, and examine the implications of TCR repertoire diversity and cross-reactivity with regard to the design of vaccines that confer broader protection against SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Yu Rusinov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam N. Iskhakov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Apollinariya V. Bogolyubova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- *Correspondence: Apollinariya V. Bogolyubova,
| |
Collapse
|
11
|
Lin F, Lin X, Fu B, Xiong Y, Zaky MY, Wu H. Functional studies of HLA and its role in SARS-CoV-2: Stimulating T cell response and vaccine development. Life Sci 2023; 315:121374. [PMID: 36621539 PMCID: PMC9815883 DOI: 10.1016/j.lfs.2023.121374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
In the biological immune process, the major histocompatibility complex (MHC) plays an indispensable role in the expression of HLA molecules in the human body when viral infection activates the T-cell response to remove the virus. Since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2019, how to address and prevent SARS-CoV-2 has become a common problem facing all mankind. The T-cell immune response activated by MHC peptides is a way to construct a defense line and reduce the transmission and harm of the virus. Presentation of SARS-CoV-2 antigen is associated with different types of HLA phenotypes, and different HLA phenotypes induce different immune responses. The prediction of SARS-CoV-2 mutation information and the design of vaccines based on HLAs can effectively activate autoimmunity and cope with virus mutations, which can provide some references for the prevention and treatment of SARS-CoV-2.
Collapse
Affiliation(s)
- Feng Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Xiaoyuan Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Mohamed Y Zaky
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, P.O. Box 62521, Beni-Suef, Egypt; Department of Oncology and Department of Biomedical and Clinical Science, Faculty of Medicine, Linköping University, Sweden
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
| |
Collapse
|
12
|
Wang L, Peng HY, Pham A, Villazana E, Ballard DJ, Das JK, Kumar A, Xiong X, Song J. T Cell Response to SARS-CoV-2 Coinfection and Comorbidities. Pathogens 2023; 12:321. [PMID: 36839596 PMCID: PMC9965203 DOI: 10.3390/pathogens12020321] [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: 12/16/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
For the past three years, COVID-19 has become an increasing global health issue. Adaptive immune cells, especially T cells, have been extensively investigated in regard to SARS-CoV-2 infection. However, human health and T cell responses are also impacted by many other pathogens and chronic diseases. We have summarized T cell performance during SARS-CoV-2 coinfection with other viruses, bacteria, and parasites. Furthermore, we distinguished if those altered T cell statuses under coinfection would affect their clinical outcomes, such as symptom severity and hospitalization demand. T cell alteration in diabetes, asthma, and hypertension patients with SARS-CoV-2 infection was also investigated in our study. We have summarized whether changes in T cell response influence the clinical outcome during comorbidities.
Collapse
Affiliation(s)
- Liqing Wang
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Hao-Yun Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Aspen Pham
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Eber Villazana
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Darby J. Ballard
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Jugal Kishore Das
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Anil Kumar
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Xiaofang Xiong
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Jianxun Song
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| |
Collapse
|
13
|
Kashima Y, Mizutani T, Nakayama-Hosoya K, Moriyama S, Matsumura T, Yoshimura Y, Sasaki H, Horiuchi H, Miyata N, Miyazaki K, Tachikawa N, Takahashi Y, Suzuki T, Sugano S, Matano T, Kawana-Tachikawa A, Suzuki Y. Multimodal single-cell analyses of peripheral blood mononuclear cells of COVID-19 patients in Japan. Sci Rep 2023; 13:1935. [PMID: 36732528 PMCID: PMC9893982 DOI: 10.1038/s41598-023-28696-9] [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: 09/06/2022] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
SARS-CoV-2 continues to spread worldwide. Patients with COVID-19 show distinct clinical symptoms. Although many studies have reported various causes for the diversity of symptoms, the underlying mechanisms are not fully understood. Peripheral blood mononuclear cells from COVID-19 patients were collected longitudinally, and single-cell transcriptome and T cell receptor repertoire analysis was performed. Comparison of molecular features and patients' clinical information revealed that the proportions of cells present, and gene expression profiles differed significantly between mild and severe cases; although even among severe cases, substantial differences were observed among the patients. In one severely-infected elderly patient, an effective antibody response seemed to have failed, which may have caused prolonged viral clearance. Naïve T cell depletion, low T cell receptor repertoire diversity, and aberrant hyperactivation of most immune cell subsets were observed during the acute phase in this patient. Through this study, we provided a better understanding of the diversity of immune landscapes and responses. The information obtained from this study can help medical professionals develop personalized optimal clinical treatment strategies for COVID-19.
Collapse
Affiliation(s)
- Yukie Kashima
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Taketoshi Mizutani
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | | | - Saya Moriyama
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takayuki Matsumura
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiro Yoshimura
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Hiroaki Sasaki
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Hiroshi Horiuchi
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Nobuyuki Miyata
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Kazuhito Miyazaki
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Natsuo Tachikawa
- Department of Infectious Diseases, Yokohama Municipal Citizens' Hospital, Kanagawa, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sumio Sugano
- Institute of Kashiwa-No-Ha Omics Gate, Kashiwa, Chiba, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,Department of AIDS Vaccine Development, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Laboratory of Functional Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| |
Collapse
|
14
|
Nurzat Y, Zhu Z, Zhang Y, Xu H. Invariant chain of the MAIT-TCR vα7.2-Jα33 as a novel diagnostic biomarker for keloids. Exp Dermatol 2023; 32:186-197. [PMID: 36309840 DOI: 10.1111/exd.14700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 10/06/2022] [Accepted: 10/27/2022] [Indexed: 11/28/2022]
Abstract
Keloids are pathological scars that invade normal surrounding tissue without self-limitation, causing pain, itching, cosmetic disfigurement, etc. Knowledge of the molecular mechanisms underlying keloids remains unclear; thus, there are no available biomarkers for its diagnosis, resulting in a diagnostic accuracy of only 81%, which may be resolved by seeking an effective biomarker. Given that keloids possess pathogenic features similar to those of autoimmune skin disease, this study aimed to utilise the single-cell V(D)J sequencing method to identify a potential biomarker and clarify the underlying biological mechanisms. Single-cell V(D)J sequencing was used to detect T cell receptor (TCR) diversity between keloid patients and healthy donors using peripheral blood samples, the results of which were further validated using reverse transcription-polymerase chain reaction (RT-PCR). Flow cytometry was used to analyse the mucosal-associated invariant T (MAIT) cell percentage, cytokine production, and activation marker expression levels in peripheral blood samples of keloid patients and normal donors. An immunofluorescence test was used to quantitatively analyse the distribution of MAIT cells in scar and healthy donor skin tissues. Single-cell V(D)J sequencing analysis showed that the usage frequency of the TRAJ33-one invariant chain of the TCR of MAIT cells was decreased in keloid patients. This result was validated by RT-PCR, which showed that significantly lower TCR Vα7.2-Jα33 was expressed in keloid patients compared with that in healthy donors and hypertrophic scar patients (p < 0.05). Flow cytometry and immunofluorescence tests further verified that MAIT cells decreased significantly both in the peripheral blood sample and lesions of keloid patients compared with those of healthy controls (p < 0.05). MAIT cells from keloid patients secreted less interferon (IFN)-γ than those from the healthy controls and hypertrophic scar group (p < 0.001). The percentage of PLZF+ MAIT cells was lowest in the peripheral blood samples of keloid patients (p < 0.05). The percentage of IL-18+ MAIT cells was lower in the peripheral blood samples of keloid patients compared with that in healthy donors (p < 0.05). These findings indicate that MAIT cells could be associated with keloids and may serve as potential biomarkers or therapeutic targets in the diagnosis of keloids.
Collapse
Affiliation(s)
- Yeltai Nurzat
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Zhu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yixin Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Heng Xu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
15
|
Koo D, Mao Z, Dimatteo R, Tsubamoto N, Noguchi M, McLaughlin J, Tran W, Lee S, Cheng D, de Rutte J, Sojo GB, Witte ON, Di Carlo D. Defining T cell receptor repertoires using nanovial-based affinity and functional screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524440. [PMID: 36711524 PMCID: PMC9882161 DOI: 10.1101/2023.01.17.524440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ability to selectively bind to antigenic peptides and secrete cytokines can define populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with millions of peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs and secrete cytokines on nanovials, allowing sorting based on both affinity and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes we could link TCR sequence to targets with 100% accuracy. We identified with high specificity an expanded repertoire of functional TCRs targeting viral antigens compared to standard techniques.
Collapse
Affiliation(s)
- Doyeon Koo
- Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Natalie Tsubamoto
- Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Miyako Noguchi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Jami McLaughlin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Wendy Tran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Sohyung Lee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Joseph de Rutte
- Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Partillion Bioscience; Los Angeles, CA 90095, USA
| | - Giselle Burton Sojo
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Owen N. Witte
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
- Partillion Bioscience; Los Angeles, CA 90095, USA
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles; Los Angeles, CA 90095, USA
- California NanoSystems Institute; Los Angeles, CA 90095, USA
| |
Collapse
|
16
|
Ziemssen T, Groth M, Ettle B, Bopp T. Immune Response to SARS-CoV-2 mRNA Vaccines in an Open-Label Multicenter Study in Participants with Relapsing Multiple Sclerosis Treated with Ofatumumab. Vaccines (Basel) 2022; 10:vaccines10122167. [PMID: 36560576 PMCID: PMC9782480 DOI: 10.3390/vaccines10122167] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND It is unclear whether multiple sclerosis (MS) patients receiving ofatumumab mount an immune response after SARS-CoV-2 mRNA vaccination. METHODS KYRIOS is an ongoing, multicenter, open-label, prospective clinical study on immune responses in MS patients after initial or booster SARS-CoV-2 mRNA vaccination prior to (cohort 1) or during (cohort 2) ofatumumab treatment. We report one-week and one-month results of the initial vaccination. A comparison with patients vaccinated while receiving beta-interferon, glatiramer acetate, dimethyl fumarate, teriflunomide or no treatment was included (cohort 3). RESULTS In total, 11 patients received their initial vaccination during the study. The primary endpoint of SARS-CoV-2-specific T-cells at month 1 was reached by 80.0% of patients in cohort 1 (N = 6) and 100.0% in cohort 2 (N = 5). T-cell reactivity peaked at week 1. All cohort 1 patients reached seroconversion for SARS-CoV-2 neutralizing antibodies at week 1 and month 1. In cohort 2, neutralizing antibodies increased in all patients and exceeded the cut-off for seropositivity in 40.0% of patients at week 1 and 25.0% at month 1. Immune responses in cohort 3 were comparable to cohort 1. CONCLUSION Presence of T-cell response and increase in levels of neutralizing antibodies, although less pronounced compared to controls, suggest that MS patients receiving ofatumumab are able to mount an immune response to SARS-CoV-2 mRNA vaccination.
Collapse
Affiliation(s)
- Tjalf Ziemssen
- Department of Neurology, Center of Clinical Neuroscience, University Hospital Carl Gustav Carus at the TU Dresden, 01307 Dresden, Germany
- Correspondence:
| | - Marie Groth
- Novartis Pharma GmbH, 90429 Nuremberg, Germany
| | | | - Tobias Bopp
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| |
Collapse
|
17
|
Zhang W, Zhang Q, Zhu C, Shi Z, Shao C, Chen Y, Wang N, Jiang Y, Liang Q, Wang K. The intrarenal landscape of T cell receptor repertoire in clear cell renal cell cancer. J Transl Med 2022; 20:558. [PMID: 36463235 PMCID: PMC9719196 DOI: 10.1186/s12967-022-03771-3] [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: 06/25/2022] [Accepted: 11/13/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Clear cell renal cell cancer (ccRCC) is accompanied by T-cell infiltration. In this study, we sought to determine the difference in T-cell infiltration and the T-cell receptor (TCR) immune repertoire between ccRCC and peritumour tissue. METHODS T-cell infiltration was examined using immunohistochemistry (IHC) and haematoxylin and eosin (HE) staining. The chi-squared test and Pearson correlation analysis were applied to evaluate the relationship between clinical traits and CD3, CD4, and CD8 expression. Immune repertoire sequencing (IR-Seq) was used to describe the profile of the TCR repertoire. RESULTS The adjacent tissue showed increased expression of CD3, CD4 and CD8 compared with ccRCC tissue (PCD3 = 0.033; PCD4 = 0.014; PCD8 = 0.004). Indicated CD3+ T-cell density in ccRCC tissue was positively correlated with that in peritumour tissue (P = 0.010, r = 0.514), which implied the T cells in peritumour tissue directly infect the number of cells infiltrating in ccRCC tissue. Moreover, there was a positive correlation between Vimentin expression and indicated positive T-cell marker in ccRCC tissue (PCD3 = 0.035; PCD4 = 0.020; PCD8 = 0.027). Advanced stage revealed less CD4+ T-cell infiltration in ccRCC tissue (PCD4 = 0.023). The results from IR-Seq revealed an obvious increase in VJ and VDJ segment usage, as well as higher complementarity-determining region 3 (CDR3) amino acid (aa) clonotypes in ccRCC. The matched antigen recognized by the TCR of ccRCC may be potential targets. CONCLUSIONS The current study collectively demonstrates diminished T-cell infiltration and increased CDR3 aa diversity in ccRCC, which may be associated with immunotherapeutic targets for ccRCC patients.
Collapse
Affiliation(s)
- Wei Zhang
- Department of Pathology, The 971 Hospital of People’s Liberation Army Navy, Qingdao, China
| | - Qian Zhang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chao Zhu
- grid.411525.60000 0004 0369 1599Department of Nephrology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhiyuan Shi
- grid.12955.3a0000 0001 2264 7233Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chen Shao
- grid.12955.3a0000 0001 2264 7233Department of Urology, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yujie Chen
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Nan Wang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yanxia Jiang
- grid.412521.10000 0004 1769 1119Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qing Liang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Kejia Wang
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, Xiamen Key Laboratory of Regeneration Medicine, Organ Transplantation Institute of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| |
Collapse
|
18
|
Bao L, Geng Z, Wang J, He L, Kang A, Song J, Huang X, Zhang Y, Liu Q, Jiang T, Pang Y, Niu Y, Zhang R. Attenuated T cell activation and rearrangement of T cell receptor β repertoire in silica nanoparticle-induced pulmonary fibrosis of mice. ENVIRONMENTAL RESEARCH 2022; 213:113678. [PMID: 35710025 DOI: 10.1016/j.envres.2022.113678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Silica nanoparticles (SiNPs) cause pulmonary fibrosis through a complex immune response, but the underlying mechanisms by which SiNPs interact with T cells and affect their functions remain unclear. The T cell receptor (TCR) repertoire is closely related to T cell activation and proliferation and mediates innate and adaptive immunity. High-throughput sequencing of the TCR enables comprehensive monitoring of the immune microenvironment. Here, the role of the TCRβ repertoire was explored using a mouse model of SiNP-induced pulmonary fibrosis and a co-culture of RAW264.7 and CD4+ T cells. Our results demonstrated increased TCRβ expression and decreased CD25 and CD69 expression in CD4+ T cells from peripheral blood and lung collected 14 days after the induction of pulmonary fibrosis by SiNPs. Simultaneously, SiNPs significantly decreased CD25 and CD69 expression in CD4+ T cells in vitro via RAW264.7 cell presentation. Mechanistically, pLCK and pZap70 expression, involved in mediating T cell activation, were also decreased in the lung of mice with SiNP-induced pulmonary fibrosis. Furthermore, the profile of the TCRβ repertoire in mice with SiNP-induced pulmonary fibrosis showed that SiNPs markedly altered the usage of V genes, VJ gene combinations, and CDR3 amino acids in lung tissue. Collectively, our data suggested that SiNPs could interfere with T cell activation by macrophage presentation via the LCK/Zap70 pathway and rearrange the TCRβ repertoire for adaptive immunity and the pulmonary microenvironment.
Collapse
Affiliation(s)
- Lei Bao
- Department of Occupational Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
| | - Zihan Geng
- Department of Occupational Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Juan Wang
- Department of Statistics, Hebei General Hospital, Shijiazhuang, Hebei, 050000, China
| | - Liyi He
- Department of Occupational Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Aijuan Kang
- Department of Occupational Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Jianshi Song
- School of Basic Medical, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Xiaoyan Huang
- Department of Occupational Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Yaling Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Qingping Liu
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Tao Jiang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Yaxian Pang
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China; Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Yujie Niu
- Department of Occupational Health and Environmental Health, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China; Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
| | - Rong Zhang
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China; Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, Hebei, 050017, China.
| |
Collapse
|
19
|
Räuber S, Korsen M, Huntemann N, Rolfes L, Müntefering T, Dobelmann V, Hermann AM, Kölsche T, von Wnuck Lipinski K, Schroeter CB, Nelke C, Regner-Nelke L, Ingwersen J, Pawlitzki M, Teegen B, Barnett MH, Hartung HP, Aktas O, Albrecht P, Levkau B, Melzer N, Ruck T, Meuth SG, Kremer D. Immune response to SARS-CoV-2 vaccination in relation to peripheral immune cell profiles among patients with multiple sclerosis receiving ocrelizumab. J Neurol Neurosurg Psychiatry 2022; 93:978-985. [PMID: 35193952 PMCID: PMC8889453 DOI: 10.1136/jnnp-2021-328197] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Vaccination has proven to be effective in preventing SARS-CoV-2 transmission and severe disease courses. However, immunocompromised patients have not been included in clinical trials and real-world clinical data point to an attenuated immune response to SARS-CoV-2 vaccines among patients with multiple sclerosis (MS) receiving immunomodulatory therapies. METHODS We performed a retrospective study including 59 ocrelizumab (OCR)-treated patients with MS who received SARS-CoV-2 vaccination. Anti-SARS-CoV-2-antibody titres, routine blood parameters and peripheral immune cell profiles were measured prior to the first (baseline) and at a median of 4 weeks after the second vaccine dose (follow-up). Moreover, the SARS-CoV-2-specific T cell response and peripheral B cell subsets were analysed at follow-up. Finally, vaccination-related adverse events were assessed. RESULTS After vaccination, we found anti-SARS-CoV-2(S) antibodies in 27.1% and a SARS-CoV-2-specific T cell response in 92.7% of MS cases. T cell-mediated interferon (IFN)-γ release was more pronounced in patients without anti-SARS-CoV-2(S) antibodies. Antibody titres positively correlated with peripheral B cell counts, time since last infusion and total IgM levels. They negatively correlated with the number of previous infusion cycles. Peripheral plasma cells were increased in antibody-positive patients. A positive correlation between T cell response and peripheral lymphocyte counts was observed. Moreover, IFN-γ release was negatively correlated with the time since the last infusion. CONCLUSION In OCR-treated patients with MS, the humoral immune response to SARS-CoV-2 vaccination is attenuated while the T cell response is preserved. However, it is still unclear whether T or B cell-mediated immunity is required for effective clinical protection. Nonetheless, given the long-lasting clinical effects of OCR, monitoring of peripheral B cell counts could facilitate individualised treatment regimens and might be used to identify the optimal time to vaccinate.
Collapse
Affiliation(s)
- Saskia Räuber
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Melanie Korsen
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Niklas Huntemann
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Leoni Rolfes
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Thomas Müntefering
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vera Dobelmann
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander M Hermann
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tristan Kölsche
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karin von Wnuck Lipinski
- Institute of Molecular Medicine III, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christina B Schroeter
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Nelke
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Liesa Regner-Nelke
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jens Ingwersen
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marc Pawlitzki
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Bianca Teegen
- Clinical Immunological Laboratory Prof. Dr. med. Winfried Stöcker, Lübeck, Germany
| | - Michael Harry Barnett
- Brain and Mind Centre, The University of Sydney, Camperdown, New South Wales, Australia.,Sydney Neuroimaging Analysis Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Hans-Peter Hartung
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Brain and Mind Centre, The University of Sydney, Camperdown, New South Wales, Australia.,Department of Neurology, Medical University of Vienna, Vienna, Austria.,Department of Neurology, Palacky University, Olomouc, Czech Republic
| | - Orhan Aktas
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Philipp Albrecht
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Bodo Levkau
- Institute of Molecular Medicine III, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nico Melzer
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sven G Meuth
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - David Kremer
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
20
|
T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer. Int J Mol Sci 2022; 23:ijms23158590. [PMID: 35955721 PMCID: PMC9369427 DOI: 10.3390/ijms23158590] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
The immune system is a dynamic feature of each individual and a footprint of our unique internal and external exposures. Indeed, the type and level of exposure to physical and biological agents shape the development and behavior of this complex and diffuse system. Many pathological conditions depend on how our immune system responds or does not respond to a pathogen or a disease or on how the regulation of immunity is altered by the disease itself. T-cells are important players in adaptive immunity and, together with B-cells, define specificity and monitor the internal and external signals that our organism perceives through its specific receptors, TCRs and BCRs, respectively. Today, high-throughput sequencing (HTS) applied to the TCR repertoire has opened a window of opportunity to disclose T-cell repertoire development and behavior down to the clonal level. Although TCR repertoire sequencing is easily accessible today, it is important to deeply understand the available technologies for choosing the best fit for the specific experimental needs and questions. Here, we provide an updated overview of TCR repertoire sequencing strategies, providers and applications to infectious diseases and cancer to guide researchers’ choice through the multitude of available options. The possibility of extending the TCR repertoire to HLA characterization will be of pivotal importance in the near future to understand how specific HLA genes shape T-cell responses in different pathological contexts and will add a level of comprehension that was unthinkable just a few years ago.
Collapse
|
21
|
Katayama Y, Yokota R, Akiyama T, Kobayashi TJ. Machine Learning Approaches to TCR Repertoire Analysis. Front Immunol 2022; 13:858057. [PMID: 35911778 PMCID: PMC9334875 DOI: 10.3389/fimmu.2022.858057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.
Collapse
Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yotaro Katayama,
| | - Ryo Yokota
- National Research Institute of Police Science, Kashiwa, Chiba, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
22
|
Egri N, Olivé V, Hernández-Rodríguez J, Castro P, De Guzman C, Heredia L, Segura AC, Fernandez M, de Moner N, Torradeflot M, Ballús J, Martinez R, Vazquez M, Costa MV, Dobaño C, Mazza M, Mazzotti L, Pascal M, Juan M, González-Navarro EA, Calderón H. CoVITEST: A Fast and Reliable Method to Monitor Anti-SARS-CoV-2 Specific T Cells From Whole Blood. Front Immunol 2022; 13:848586. [PMID: 35865538 PMCID: PMC9295597 DOI: 10.3389/fimmu.2022.848586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/30/2022] [Indexed: 01/08/2023] Open
Abstract
Cellular and humoral immune responses are essential for COVID-19 recovery and protection against SARS-CoV-2 reinfection. To date, the evaluation of SARS-CoV-2 immune protection has mainly focused on antibody detection, generally disregarding the cellular response, or placing it in a secondary position. This phenomenon may be explained by the complex nature of the assays needed to analyze cellular immunity compared with the technically simple and automated detection of antibodies. Nevertheless, a large body of evidence supports the relevance of the T cell's role in protection against SARS-CoV-2, especially in vulnerable individuals with a weakened immune system (such as the population over 65 and patients with immunodeficiencies). Here we propose to use CoVITEST (Covid19 anti-Viral Immunity based on T cells for Evaluation in a Simple Test), a fast, affordable and accessible in-house assay that, together with a diagnostic matrix, allows us to determine those patients who might be protected with SARS-CoV-2-reactive T cells. The method was established using healthy SARS-CoV-2-naïve donors pre- and post-vaccination (n=30), and further validated with convalescent COVID-19 donors (n=51) in a side-by-side comparison with the gold standard IFN-γ ELISpot. We demonstrated that our CoVITEST presented reliable and comparable results to those obtained with the ELISpot technique in a considerably shorter time (less than 8 hours). In conclusion, we present a simple but reliable assay to determine cellular immunity against SARS-CoV-2 that can be used routinely during this pandemic to monitor the immune status in vulnerable patients and thereby adjust their therapeutic approaches. This method might indeed help to optimize and improve decision-making protocols for re-vaccination against SARS-CoV-2, at least for some population subsets.
Collapse
Affiliation(s)
- Natalia Egri
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Victoria Olivé
- Occupational Health Department, Hospital Clínic de Barcelona, Barcelona, Spain
| | - José Hernández-Rodríguez
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
- Vasculitis Research Unit and Autoinflammatory Diseases Clinical Unit, Department of Autoimmune Diseases, Hospital Clínic of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Pedro Castro
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Medical Intensive Care Unit, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Catherine De Guzman
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Libertad Heredia
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Ana Castellet Segura
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - M. Dolores Fernandez
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Noemi de Moner
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - María Torradeflot
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Judit Ballús
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Robert Martinez
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mario Vazquez
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marta Vidal Costa
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- CIBER Infectious Diseases (CIBERINFEC), Barcelona, Spain
| | - Massimiliano Mazza
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, FC, Italy
| | - Lucia Mazzotti
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, FC, Italy
| | - Mariona Pascal
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Allergy Network ARADyAL, Instituto de Salud Carlos III, Madrid, Spain
| | - Manel Juan
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Europa Azucena González-Navarro
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Hugo Calderón
- Department of Immunology, Centre de Diagnòstic Biomèdic, Hospital Clínic of Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| |
Collapse
|
23
|
Abadijoo H, Khayamian MA, Faramarzpour M, Ghaderinia M, Simaee H, Shalileh S, Yazdanparast SM, Ghabraie B, Makarem J, Sarrami-Forooshani R, Abdolahad M. Healing Field: Using Alternating Electric Fields to Prevent Cytokine Storm by Suppressing Clonal Expansion of the Activated Lymphocytes in the Blood Sample of the COVID-19 Patients. Front Bioeng Biotechnol 2022; 10:850571. [PMID: 35721862 PMCID: PMC9201910 DOI: 10.3389/fbioe.2022.850571] [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: 01/07/2022] [Accepted: 05/02/2022] [Indexed: 12/15/2022] Open
Abstract
In the case of the COVID-19 early diagnosis, numerous tech innovations have been introduced, and many are currently employed worldwide. But, all of the medical procedures for the treatment of this disease, up to now, are just limited to chemical drugs. All of the scientists believe that the major challenge toward the mortality of the COVID-19 patients is the out-of-control immune system activation and the subsequent cytokine production. During this process, the adaptive immune system is highly activated, and many of the lymphocytes start to clonally expand; hence many cytokines are also released. So, any attempt to harness this cytokine storm and calm down the immune outrage is appreciated. While the battleground for the immune hyperactivation is the lung ambient of the infected patients, the only medical treatment for suppressing the hypercytokinemia is based on the immunosuppressor drugs that systemically dampen the immunity with many unavoidable side effects. Here, we applied the alternating electric field to suppress the expansion of the highly activated lymphocytes, and by reducing the number of the renewed cells, the produced cytokines were also decreased. Applying this method to the blood of the COVID-19 patients in vitro showed ∼33% reduction in the average concentration of the three main cytokines after 4 days of stimulation. This method could carefully be utilized to locally suppress the hyperactivated immune cells in the lung of the COVID-19 patients without any need for systemic suppression of the immune system by the chemical drugs.
Collapse
Affiliation(s)
- Hamed Abadijoo
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Khayamian
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Mohammad Ali Khayamian, , ; Mohammad Abdolahad, ,
| | - Mahsa Faramarzpour
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Ghaderinia
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Simaee
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahriar Shalileh
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mojtaba Yazdanparast
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahman Ghabraie
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalil Makarem
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Sarrami-Forooshani
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Mohammad Abdolahad
- Nano Electronic Center of Excellence, Nano Bio Electronic Devices Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Nano Electronic Center of Excellence, Thin Film and Nano Electronics Lab, School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
- Institute of Cancer, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- UT and TUMS Cancer Electronics Research Center, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Mohammad Ali Khayamian, , ; Mohammad Abdolahad, ,
| |
Collapse
|
24
|
Richard D, Phillip S, Hosseinali A, Gracie DZ, Hai L, January W, Holtgrewe M, Charlotte T, Melina M, Xiaomin W, Zehra K, Jacopo S, Jan-Moritz D, Ralf-Harto H, Bernd H, Anja B, Sandra S, Dilduz T, Norbert S, Martin W, Stefan H, Carsten S, Wolfgang P, Leif E S, Dieter B, Florian K, Toumy G, Ulf L, Jan B, Khai L, Rubelt F, Bettina H. Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19. EClinicalMedicine 2022; 48:101438. [PMID: 35600330 PMCID: PMC9106482 DOI: 10.1016/j.eclinm.2022.101438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Disease progression of subjects with coronavirus disease 2019 (COVID-19) varies dramatically. Understanding the various types of immune response to SARS-CoV-2 is critical for better clinical management of coronavirus outbreaks and to potentially improve future therapies. Disease dynamics can be characterized by deciphering the adaptive immune response. METHODS In this cross-sectional study we analyzed 117 peripheral blood immune repertoires from healthy controls and subjects with mild to severe COVID-19 disease to elucidate the interplay between B and T cells. We used an immune repertoire Primer Extension Target Enrichment method (immunoPETE) to sequence simultaneously human leukocyte antigen (HLA) restricted T cell receptor beta chain (TRB) and unrestricted T cell receptor delta chain (TRD) and immunoglobulin heavy chain (IgH) immune receptor repertoires. The distribution was analyzed of TRB, TRD and IgH clones between healthy and COVID-19 infected subjects. Using McFadden's Adjusted R2 variables were examined for a predictive model. The aim of this study is to analyze the influence of the adaptive immune repertoire on the severity of the disease (value on the World Health Organization Clinical Progression Scale) in COVID-19. FINDINGS Combining clinical metadata with clonotypes of three immune receptor heavy chains (TRB, TRD, and IgH), we found significant associations between COVID-19 disease severity groups and immune receptor sequences of B and T cell compartments. Logistic regression showed an increase in shared IgH clonal types and decrease of TRD in subjects with severe COVID-19. The probability of finding shared clones of TRD clonal types was highest in healthy subjects (controls). Some specific TRB clones seems to be present in severe COVID-19 (Figure S7b). The most informative models (McFadden´s Adjusted R2=0.141) linked disease severity with immune repertoire measures across all three cell types, as well as receptor-specific cell counts, highlighting the importance of multiple lymphocyte classes in disease progression. INTERPRETATION Adaptive immune receptor peripheral blood repertoire measures are associated with COVID-19 disease severity. FUNDING The study was funded with grants from the Berlin Institute of Health (BIH).
Collapse
Affiliation(s)
| | - Suwalski Phillip
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | | | | | - Lin Hai
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Weiner January
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Thibeault Charlotte
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Müller Melina
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Wang Xiaomin
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Karadeniz Zehra
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Saccomanno Jacopo
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Doehn Jan-Moritz
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Hübner Ralf-Harto
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | | | - Blüher Anja
- Signature Diagnostics GmbH, DE 14473, Germany
| | | | - Telman Dilduz
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Suttorp Norbert
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Witzenrath Martin
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Hippenstiel Stefan
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Skurk Carsten
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Poller Wolfgang
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Sander Leif E
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Beule Dieter
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Kurth Florian
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | | | - Landmesser Ulf
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Germany
| | - Berka Jan
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Luong Khai
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | | | - Florian Rubelt
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Heidecker Bettina
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
- Corresponding authors.
| |
Collapse
|
25
|
Li J, Wu J, Zhang J, Tang L, Mei H, Hu Y, Li F. A multicompartment mathematical model based on host immunity for dissecting COVID-19 heterogeneity. Heliyon 2022; 8:e09488. [PMID: 35600458 PMCID: PMC9116108 DOI: 10.1016/j.heliyon.2022.e09488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 02/06/2023] Open
Abstract
The determinants underlying the heterogeneity of coronavirus disease 2019 (COVID-19) remain to be elucidated. To systemically analyze the immunopathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, we built a multicompartment mathematical model based on immunological principles and typical COVID-19-related characteristics. This model integrated the trafficking of immune cells and cytokines among the secondary lymphoid organs, peripheral blood and lungs. Our results suggested that early-stage lymphopenia was related to lymphocyte chemotaxis, while prolonged lymphopenia in critically ill patients was associated with myeloid-derived suppressor cells. Furthermore, our model predicted that insufficient SARS-CoV-2-specific naïve T/B cell pools and ineffective activation of antigen-presenting cells (APCs) would cause delayed immunity activation, resulting in elevated viral load, low immunoglobulin level, etc. Overall, we provided a comprehensive view of the dynamics of host immunity after SARS-CoV-2 infection that enabled us to understand COVID-19 heterogeneity from systemic perspective.
Collapse
Affiliation(s)
- Jianwei Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Jianghua Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
| | - Jingpeng Zhang
- School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Lu Tang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
| | - Heng Mei
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
- Corresponding author.
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Medical Center of Cell Therapy for Neoplastic Disease, Wuhan, 430022, China
- Corresponding author.
| | - Fangting Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
- Corresponding author.
| |
Collapse
|
26
|
Kockelbergh H, Evans S, Deng T, Clyne E, Kyriakidou A, Economou A, Luu Hoang KN, Woodmansey S, Foers A, Fowler A, Soilleux EJ. Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19. Diagnostics (Basel) 2022; 12:1222. [PMID: 35626377 PMCID: PMC9140453 DOI: 10.3390/diagnostics12051222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Measuring immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19), can rely on antibodies, reactive T cells and other factors, with T-cell-mediated responses appearing to have greater sensitivity and longevity. Because each T cell carries an essentially unique nucleic acid sequence for its T-cell receptor (TCR), we can interrogate sequence data derived from DNA or RNA to assess aspects of the immune response. This review deals with the utility of bulk, rather than single-cell, sequencing of TCR repertoires, considering the importance of study design, in terms of cohort selection, laboratory methods and analysis. The advances in understanding SARS-CoV-2 immunity that have resulted from bulk TCR repertoire sequencing are also be discussed. The complexity of sequencing data obtained by bulk repertoire sequencing makes analysis challenging, but simple descriptive analyses, clonal analysis, searches for specific sequences associated with immune responses to SARS-CoV-2, motif-based analyses, and machine learning approaches have all been applied. TCR repertoire sequencing has demonstrated early expansion followed by contraction of SARS-CoV-2-specific clonotypes, during active infection. Maintenance of TCR repertoire diversity, including the maintenance of diversity of anti-SARS-CoV-2 response, predicts a favourable outcome. TCR repertoire narrowing in severe COVID-19 is most likely a consequence of COVID-19-associated lymphopenia. It has been possible to follow clonotypic sequences longitudinally, which has been particularly valuable for clonotypes known to be associated with SARS-CoV-2 peptide/MHC tetramer binding or with SARS-CoV-2 peptide-induced cytokine responses. Closely related clonotypes to these previously identified sequences have been shown to respond with similar kinetics during infection. A possible superantigen-like effect of the SARS-CoV-2 spike protein has been identified, by means of observing V-segment skewing in patients with severe COVID-19, together with structural modelling. Such a superantigen-like activity, which is apparently absent from other coronaviruses, may be the basis of multisystem inflammatory syndrome and cytokine storms in COVID-19. Bulk TCR repertoire sequencing has proven to be a useful and cost-effective approach to understanding interactions between SARS-CoV-2 and the human host, with the potential to inform the design of therapeutics and vaccines, as well as to provide invaluable pathogenetic and epidemiological insights.
Collapse
Affiliation(s)
- Hannah Kockelbergh
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK;
| | - Shelley Evans
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Tong Deng
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Ella Clyne
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Anna Kyriakidou
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1QP, UK; (A.K.); (A.E.)
| | - Andreas Economou
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1QP, UK; (A.K.); (A.E.)
| | - Kim Ngan Luu Hoang
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Stephen Woodmansey
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
- Department of Respiratory Medicine, University Hospitals of Morecambe Bay, Kendal LA9 7RG, UK
| | - Andrew Foers
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7YF, UK;
| | - Anna Fowler
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK;
| | - Elizabeth J. Soilleux
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| |
Collapse
|
27
|
Budhraja A, Basu A, Gheware A, Abhilash D, Rajagopala S, Pakala S, Sumit M, Ray A, Subramaniam A, Mathur P, Nambirajan A, Kumar S, Gupta R, Wig N, Trikha A, Guleria R, Sarkar C, Gupta I, Jain D. Molecular signature of postmortem lung tissue from COVID-19 patients suggests distinct trajectories driving mortality. Dis Model Mech 2022; 15:dmm049572. [PMID: 35438176 PMCID: PMC9194484 DOI: 10.1242/dmm.049572] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/07/2022] [Indexed: 12/19/2022] Open
Abstract
To elucidate the molecular mechanisms that manifest lung abnormalities during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, we performed whole-transcriptome sequencing of lung autopsies from 31 patients with severe COVID-19 and ten uninfected controls. Using metatranscriptomics, we identified the existence of two distinct molecular signatures of lethal COVID-19. The dominant 'classical' signature (n=23) showed upregulation of the unfolded protein response, steroid biosynthesis and complement activation, supported by massive metabolic reprogramming leading to characteristic lung damage. The rarer signature (n=8) that potentially represents 'cytokine release syndrome' (CRS) showed upregulation of cytokines such as IL1 and CCL19, but absence of complement activation. We found that a majority of patients cleared SARS-CoV-2 infection, but they suffered from acute dysbiosis with characteristic enrichment of opportunistic pathogens such as Staphylococcus cohnii in 'classical' patients and Pasteurella multocida in CRS patients. Our results suggest two distinct models of lung pathology in severe COVID-19 patients, which can be identified through complement activation, presence of specific cytokines and characteristic microbiome. These findings can be used to design personalized therapy using in silico identified drug molecules or in mitigating specific secondary infections.
Collapse
Affiliation(s)
- Anshul Budhraja
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Anubhav Basu
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Atish Gheware
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Dasari Abhilash
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Seesandra Rajagopala
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman Pakala
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madhuresh Sumit
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Animesh Ray
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Arulselvi Subramaniam
- Department of Laboratory Medicine, JPNATC, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Purva Mathur
- Department of Laboratory Medicine, JPNATC, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sachin Kumar
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ritu Gupta
- Laboratory Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital (IRCH), All India Institute of Medical Sciences, New Delhi 110029, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Anjan Trikha
- Department of Anaesthesiology, Critical Care and Pain Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Randeep Guleria
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| |
Collapse
|
28
|
Immunology in COVID-19; more than diagnosis of infection or the basis of vaccination. MEDICINA CLINICA (ENGLISH ED.) 2022; 158:324-326. [PMID: 35233460 PMCID: PMC8872827 DOI: 10.1016/j.medcle.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
29
|
Qiao L, Cui X, Jia L, Gao Y, Wang W, Wei F, Zhang Z, Chen D, Ma Y, Zhang Y. Peripheral immune phenotypes and T cell receptor repertoire in pneumocystis pneumonia in HIV-1 infected patients. Clin Immunol 2022; 237:108985. [DOI: 10.1016/j.clim.2022.108985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 11/24/2022]
|
30
|
Ziemssen T, Groth M, Rauser B, Bopp T. Assessing the immune response to SARS-CoV-2 mRNA vaccines in siponimod-treated patients: a nonrandomized controlled clinical trial (AMA-VACC). Ther Adv Neurol Disord 2022; 15:17562864221135305. [PMID: 36381503 PMCID: PMC9647234 DOI: 10.1177/17562864221135305] [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: 06/24/2022] [Accepted: 10/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background: Systematic data are lacking on the immune response toward SARS-CoV-2 mRNA vaccination in SPMS patients on disease-modifying therapies (DMTs). Objective: The AMA-VACC clinical trial was designed to characterize immune responses to SARS-CoV-2 mRNA vaccines in siponimod-treated SPMS patients. Design: AMA-VACC is an ongoing three-cohort, multicenter, open-label, prospective clinical study. Methods: The study included patients at risk for SPMS or patients with SPMS diagnosis. Patients received SARS-CoV-2 mRNA vaccine as part of their clinical routine during ongoing siponimod treatment (cohort 1), during siponimod treatment interruption (cohort 2), or while on dimethyl fumarate, glatiramer acetate, beta-interferons, teriflunomide, or no current therapy (cohort 3). SARS-CoV-2-specific neutralizing antibodies and T-cell responses were measured 1 week and 1 month after the second dose of vaccination. Results: In total, 17 patients, 4 patients, and 20 patients were recruited into cohorts 1, 2, and 3, respectively. The primary endpoint of seroconversion for SARS-CoV-2-neutralizing antibodies at week 1 was reached by 52.9%, 75.0%, and 90.0% of patients in cohorts 1, 2, and 3, respectively. For 64.7% of patients in cohort 1, all patients in cohort 2, and 95% of patients in cohort 3, seroconversion was observed at either week 1 or month 1 or both time points. After 1 week, 71.4% of cohort 1, 75.0% of cohort 2, and 85.0% of cohort 3 were positive for either SARS-CoV-2-neutralizing antibodies or SARS-CoV-2-specific T-cells or both. After 1 month, the rates were 56.3%, 100.0%, and 95.0%, respectively. Conclusion: The study shows that the majority of siponimod patients mount humoral and cellular immune response under continuous siponimod treatment. The data do not sufficiently support interruption of treatment for the purpose of vaccination. Registration: EU Clinical Trials Register: EudraCT 2020-005752-38 (www.clinicaltrialsregister.eu); ClinicalTrials.gov: NCT04792567 (https://clinicaltrials.gov).
Collapse
Affiliation(s)
- Tjalf Ziemssen
- Department of Neurology, Center of Clinical Neuroscience, Carl Gustav Carus University Clinic, University Hospital of Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | | | | | - Tobias Bopp
- Institute for Immunology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| |
Collapse
|
31
|
Gededzha MP, Mampeule N, Gandini A, Mayne ES. SARS-CoV-2 Host Immunogenetic Biomarkers. Methods Mol Biol 2022; 2511:133-147. [PMID: 35838957 DOI: 10.1007/978-1-0716-2395-4_10] [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] [Indexed: 06/15/2023]
Abstract
SARS-CoV-2 causes generally mild symptoms, with approximately 10-20% of cases progressing to severe disease. The pathophysiologic mechanisms by which SARS-CoV-2 causes severe disease are largely unknown. Data have indicated the involvement of different immunogenetic markers such as HLA, T, and B cells, to be associated with disease outcome. This has led to interest in these genes as potential biomarkers of SARS-CoV-2 susceptibility and for predicting prognosis and response to vaccines and other therapeutic strategies. In this chapter, we discussed outline protocols for characterizing these potential biomarkers and methods for identifying SARS-CoV-2 biomarkers using the Luminex® 100/200 technology and next-generation sequencing.
Collapse
Affiliation(s)
- Maemu P Gededzha
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- National Health Laboratory Services, Johannesburg, South Africa.
| | - Nakampe Mampeule
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Anastasia Gandini
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Elizabeth S Mayne
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
32
|
Wan Z, Sun R, Liu YW, Li S, Sun J, Li J, Zhu J, Moharil P, Zhang B, Ren P, Ren G, Zhang M, Ma X, Dai S, Yang D, Lu B, Li S. Targeting metabotropic glutamate receptor 4 for cancer immunotherapy. SCIENCE ADVANCES 2021; 7:eabj4226. [PMID: 34890233 PMCID: PMC8664261 DOI: 10.1126/sciadv.abj4226] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/23/2021] [Indexed: 05/30/2023]
Abstract
In this study, we report a novel role of metabotropic glutamate receptor 4 (GRM4) in suppressing antitumor immunity. We revealed in three murine syngeneic tumor models (B16, MC38, and 3LL) that either genetic knockout (Grm4−/−) or pharmacological inhibition led to significant delay in tumor growth. Mechanistically, perturbation of GRM4 resulted in a strong antitumor immunity by promoting natural killer (NK), CD4+, and CD8+ T cells toward an activated, proliferative, and functional phenotype. Single-cell RNA sequencing and T cell receptor profiling further defined the clonal expansion and immune landscape changes in CD8+ T cells. We further showed that Grm4−/− intrinsically activated interferon-γ production in CD8+ T cells through cyclic adenosine 3′,5′-monophosphate (cAMP)/cAMP response element binding protein–mediated pathway. Our study appears to be of clinical significance as a signature of NKhigh-GRM4low and CD8high-GRM4low correlated with improved survival in patients with melanoma. Targeting GRM4 represents a new approach for cancer immunotherapy.
Collapse
Affiliation(s)
- Zhuoya Wan
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Runzi Sun
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Yang-Wuyue Liu
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sihan Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jingjing Sun
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jiang Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Junjie Zhu
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Pearl Moharil
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Bei Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Pengfei Ren
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Guolian Ren
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Min Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xiaochao Ma
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Shuangshuang Dai
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Binfeng Lu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Song Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| |
Collapse
|
33
|
Qin T, Guo E, Lu F, Fu Y, Liu S, Xiao R, Wu X, Liu C, He C, Wang Z, Qin X, Hu D, You L, Li F, Li X, Huang X, Ma D, Xu X, Yang B, Fan J. Impact of chemotherapy and immunotherapy on the composition and function of immune cells in COVID-19 convalescent with gynecological tumors. Aging (Albany NY) 2021; 13:24943-24962. [PMID: 34862879 PMCID: PMC8714165 DOI: 10.18632/aging.203739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/22/2021] [Indexed: 01/08/2023]
Abstract
Ongoing pandemic and potential resurgence of Coronavirus disease 2019 (COVID-19) has prompted urgent efforts to investigate the immunological memory of convalescent patients, especially in patients with active cancers. Here we performed single-cell RNA sequencing in peripheral blood samples of 3 healthy donors (HDs), 4 COVID-19 patients (Covs) and 4 COVID-19 patients with active gynecological tumor (TCs) pre- and post- anti-tumor treatment. All Covs patients had recovered from their acute infection. Interestingly, the molecular features of PBMCs in TCs are similar to that in Covs, suggesting that convalescent COVID-19 with gynecologic tumors do not have major immunological changes and may be protected against reinfection similar to COVID-19 patients without tumors. Moreover, the chemotherapy given to these patients mainly caused neutropenia, while having little effect on the proportion and functional phenotype of T and B cells, and T cell clonal expansion. Notably, anti-PD-L1 treatment massively increased cytotoxic scores of NK cells, and T cells, and facilitated clonal expansion of T cells in these patients. It is likely that T cells could protect patients from SARS-CoV-2 virus reinfection and anti-PD-L1 treatment can enhance the anti-viral activity of the T cells.
Collapse
Affiliation(s)
- Tianyu Qin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Funian Lu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Si Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xue Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chen Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chao He
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zizhuo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xu Qin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dianxing Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lixin You
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Fuxia Li
- Department of Gynecology, Foshan Women and Children’s Hospital Affiliated to Southern Medical University, Foshan 528000, China
| | - Xi Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Cell, Development and Cancer Biology, Oregon Health and Sciences University, Portland, OR 97201, USA
| | - Xiaoyuan Huang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoyan Xu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Bin Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| |
Collapse
|
34
|
Paul D, Pyne N, Paul S. Mutation profile of SARS-CoV-2 spike protein and identification of potential multiple epitopes within spike protein for vaccine development against SARS-CoV-2. Virusdisease 2021; 32:703-726. [PMID: 34754886 PMCID: PMC8569294 DOI: 10.1007/s13337-021-00747-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic worldwide has resulted in over 176 million cases and roughly 3.8 million deaths so far. We could analyze mutation dynamics across the genome from countries such as the USA, Italy, the UK, France, Brazil, and India considering the rapid mutations of the SARS-CoV-2 genome. The analysis would help us to understand the genome diversity, the implications of the mutations in protein stability, and viral transmission. Among the 11 genes, surface glycoprotein (S) was singled out because of its crucial function associated with the entry of virion into the human cell upon binding with the hACE2 receptor. 749 S protein sequences from India were retrieved from the NCBI database for our study. The S protein is an important antigenic component responsible for inducing host immune responses, neutralizing antibodies, and providing protective immunity against viral infection. During an epitope prediction from a mutation-prone S-protein region, it is necessary to ascertain how new mutations significantly change the S protein, such that our vaccine is effective against all the mutated strains as well. The S1 region of the S protein had been our prime focus for identifying immune epitopes against SARS-COV-2. Antigenic B- cell epitopes were YYPDKVF from NTD and LFRKSNLKP from RBD. Cytotoxic T-cell epitopes WTAGAAAYY (within NTD) and CVADYSVLY (within RBD) exhibited binding with a maximum number of MHC I alleles. The T-cell epitopes which showed a maximum affinity for MHC II alleles were FLPFFSNVT within NTD and YFPLQSYGF within RBD. Furthermore, the best epitopes were characterized in terms of their physicochemical properties to establish their potentiality.
Collapse
Affiliation(s)
- Debadrita Paul
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Nibedita Pyne
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Santanu Paul
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| |
Collapse
|
35
|
Egri N, Juan M. Immunology in COVID-19; more than diagnosis of infection or the basis of vaccination. Med Clin (Barc) 2021; 158:324-326. [PMID: 34872770 PMCID: PMC8590487 DOI: 10.1016/j.medcli.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Egri
- Servei d'Immunologia, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, España
| | - Manel Juan
- Servei d'Immunologia, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, España.
| |
Collapse
|
36
|
Mazzoni A, Salvati L, Maggi L, Annunziato F, Cosmi L. Hallmarks of immune response in COVID-19: Exploring dysregulation and exhaustion. Semin Immunol 2021; 55:101508. [PMID: 34728121 PMCID: PMC8547971 DOI: 10.1016/j.smim.2021.101508] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 01/08/2023]
Abstract
One and half year following the occurrence of COVID-19 pandemic, significant efforts from laboratories all over the world generated a huge amount of data describing the prototypical features of immunity in the course of SARS-CoV-2 infection. In this Review, we rationalize and organize the main observations, trying to define a “core” signature of immunity in COVID-19. We identified six hallmarks describing the main alterations occurring in the early infection phase and in the course of the disease, which predispose to severe illness. The six hallmarks are dysregulated type I IFN activity, hyperinflammation, lymphopenia, lymphocyte impairment, dysregulated myeloid response, and heterogeneous adaptive immunity to SARS-CoV-2. Dysregulation and exhaustion came out as the trait d’union, connecting abnormalities affecting both innate and adaptive immunity, humoral and cellular responses.
Collapse
Affiliation(s)
- Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lorenzo Salvati
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| |
Collapse
|
37
|
Hou X, Wang G, Fan W, Chen X, Mo C, Wang Y, Gong W, Wen X, Chen H, He D, Mo L, Jiang S, Ou M, Guo H, Liu H. T-cell receptor repertoires as potential diagnostic markers for patients with COVID-19. Int J Infect Dis 2021; 113:308-317. [PMID: 34688948 PMCID: PMC8530772 DOI: 10.1016/j.ijid.2021.10.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/25/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022] Open
Abstract
Objective Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global health emergency. T-cell receptors (TCRs) are crucial mediators of antiviral adaptive immunity. This study sought to comprehensively characterize the TCR repertoire changes in patients with COVID-19. Methods A large sample size multi-center randomized controlled trial was implemented to study the features of the TCR repertoire and identify COVID-19 disease-related TCR sequences. Results It was found that some T-cell receptor beta chain (TCRβ) features differed markedly between COVID-19 patients and healthy controls, including decreased repertoire diversity, longer complementarity-determining region 3 (CDR3) length, skewed utilization of the TCRβ variable gene/joining gene (TRBV/J), and a high degree of TCRβ sharing in COVID-19 patients. Moreover, this analysis showed that TCR repertoire diversity declines with aging, which may be a cause of the higher infection and mortality rates in elderly patients. Importantly, a set of TCRβ clones that can distinguish COVID-19 patients from healthy controls with high accuracy was identified. Notably, this diagnostic model demonstrates 100% specificity and 82.68% sensitivity at 0–3 days post diagnosis. Conclusions This study lays the foundation for immunodiagnosis and the development of medicines and vaccines for COVID-19 patients.
Collapse
Affiliation(s)
- Xianliang Hou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Guangyu Wang
- College of Laboratory Medicine, Guilin Medical University, Guilin, 541199, China
| | - Wentao Fan
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Xiaoyan Chen
- Department of State Owned Assets Management, Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Chune Mo
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Yongsi Wang
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Weiwei Gong
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Xuyan Wen
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, 541001, China
| | - Hui Chen
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Dan He
- Guangzhou Huayin Health Medical Group Co., Ltd, Guangzhou, China
| | - Lijun Mo
- Clinical Laboratory, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Shaofeng Jiang
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, 541199, China
| | - Minglin Ou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China
| | - Haonan Guo
- Department of Clinical Laboratory, The Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China.
| | - Hongbo Liu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, China.
| |
Collapse
|
38
|
Wellington D, Yin Z, Kessler BM, Dong T. Immunodominance complexity: lessons yet to be learned from dominant T cell responses to SARS-COV-2. Curr Opin Virol 2021; 50:183-191. [PMID: 34534732 PMCID: PMC8424056 DOI: 10.1016/j.coviro.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022]
Abstract
Immunodominance is a complex and highly debated topic of T cell biology. The current SARS-CoV-2 pandemic has provided the opportunity to profile adaptive immune responses and determine molecular factors contributing to emerging responses towards immunodominant viral epitopes. Here, we discuss parameters that alter the dynamics of CD8 viral epitope processing, generation and T-cell responses, and how immunodominance counteracts viral immune escape mechanisms that develop in the context of emerging SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Benedikt M Kessler
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Target Discovery Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
| |
Collapse
|
39
|
Simnica D, Schultheiß C, Mohme M, Paschold L, Willscher E, Fitzek A, Püschel K, Matschke J, Ciesek S, Sedding DG, Zhao Y, Gagliani N, Maringer Y, Walz JS, Heide J, Schulze-Zur-Wiesch J, Binder M. Landscape of T-cell repertoires with public COVID-19-associated T-cell receptors in pre-pandemic risk cohorts. Clin Transl Immunology 2021; 10:e1340. [PMID: 34484739 PMCID: PMC8401425 DOI: 10.1002/cti2.1340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/27/2021] [Accepted: 08/15/2021] [Indexed: 01/19/2023] Open
Abstract
Objectives T cells have an essential role in the antiviral defence. Public T-cell receptor (TCR) clonotypes are expanded in a substantial proportion of COVID-19 patients. We set out to exploit their potential use as read-out for COVID-19 T-cell immune responses. Methods We searched for COVID-19-associated T-cell clones with public TCRs, as defined by identical complementarity-determining region 3 (CDR3) beta chain amino acid sequence that can be reproducibly detected in the blood of COVID-19 patients. Of the different clonotype identification algorithms used in this study, deep sequencing of brain tissue of five patients with fatal COVID-19 delivered 68 TCR clonotypes with superior representation across 140 immune repertoires of unrelated COVID-19 patients. Results Mining of immune repertoires from subjects not previously exposed to the virus showed that these clonotypes can be found in almost 20% of pre-pandemic immune repertoires of healthy subjects, with lower representation in repertoires from risk groups like individuals above the age of 60 years or patients with cancer. Conclusion Together, our data show that at least a proportion of the SARS-CoV-2 T-cell response is mediated by public TCRs that are present in repertoires of unexposed individuals. The lower representation of these clones in repertoires of risk groups or failure to expand such clones may contribute to more unfavorable clinical COVID-19 courses.
Collapse
Affiliation(s)
- Donjete Simnica
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| | - Christoph Schultheiß
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| | - Malte Mohme
- Department of Neurosurgery University Medical Center Hamburg-Eppendorf (UKE) Hamburg Germany
| | - Lisa Paschold
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| | - Edith Willscher
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| | - Antonia Fitzek
- Institute of Legal Medicine University Medical Center Hamburg-Eppendorf (UKE) Hamburg Germany
| | - Klaus Püschel
- Institute of Legal Medicine University Medical Center Hamburg-Eppendorf (UKE) Hamburg Germany
| | - Jakob Matschke
- Department of Neuropathology University Medical Center Hamburg-Eppendorf (UKE) Hamburg Germany
| | - Sandra Ciesek
- Institute of Medical Virology University Hospital Frankfurt Frankfurt am Main Germany
| | - Daniel G Sedding
- Mid-German Heart Center Department of Cardiology and Intensive Care Medicine University Hospital Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Yu Zhao
- III. Department of Medicine Division of Translational Immunology University Medical Center Hamburg-Eppendorf Hamburg Germany.,Institute of Medical Systems Biology University Medical Center Hamburg-Eppendorf Hamburg Germany.,Hamburg Center for Translational Immunology (HCTI) University Medical Center Hamburg-Eppendorf Hamburg Germany.,Center for Biomedical AI University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Nicola Gagliani
- Hamburg Center for Translational Immunology (HCTI) University Medical Center Hamburg-Eppendorf Hamburg Germany.,I. Department of Medicine and Department for General Visceral and Thoracic Surgery Hamburg Germany.,Immunology and Allergy Unit Department of Medicine Solna Karolinska Institute and University Hospital Stockholm Sweden
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology German Cancer Consortium (DKTK) Department of Internal Medicine University Hospital Tübingen Tübingen Germany.,Institute for Cell Biology Department of Immunology University of Tübingen Tübingen Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies" University of Tübingen Tübingen Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology German Cancer Consortium (DKTK) Department of Internal Medicine University Hospital Tübingen Tübingen Germany.,Institute for Cell Biology Department of Immunology University of Tübingen Tübingen Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies" University of Tübingen Tübingen Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT) Stuttgart Germany
| | - Janna Heide
- I. Department of Medicine (with section Gastroenterology and Infectious Diseases) University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Julian Schulze-Zur-Wiesch
- I. Department of Medicine (with section Gastroenterology and Infectious Diseases) University Medical Center Hamburg-Eppendorf Hamburg Germany
| | - Mascha Binder
- Department of Internal Medicine IV Oncology/Hematology Martin-Luther-University Halle-Wittenberg Halle (Saale) Germany
| |
Collapse
|
40
|
Dhar S, Bhattacharjee P. Promising role of curcumin against viral diseases emphasizing COVID-19 management: A review on the mechanistic insights with reference to host-pathogen interaction and immunomodulation. J Funct Foods 2021; 82:104503. [PMID: 33897833 PMCID: PMC8057770 DOI: 10.1016/j.jff.2021.104503] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 02/07/2023] Open
Abstract
Curcumin has already acknowledged immense interest from both medical and scientific research because of its multifaceted activity. To date, the promising effects of curcumin were perceived against numerous inflammatory diseases. Besides, curcumin's role as a medicine has been studied in many virus infections like influenza, HIV, etc. There is a need to analyze the cellular mechanisms of curcumin including host-pathogen interaction and immunomodulatory effects, to explore the role of curcumin against COVID-19. With this background, our study suggests that curcumin can prevent COVID-19 infections by inhibiting the pathogen entry, viral genome replication and steps in the endosomal pathway along with inhibition of T-cell signalling by impairing the autophagy-mediated antigen-presenting pathway. This review explicit the possible mechanisms behind curcumin-induced cellular immunity and a therapeutive dosage of curcumin suggesting a preventive strategy against COVID-19.
Collapse
|
41
|
Comprehensive analysis of TCR repertoire in COVID-19 using single cell sequencing. Genomics 2021; 113:456-462. [PMID: 33383142 PMCID: PMC7833309 DOI: 10.1016/j.ygeno.2020.12.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/20/2020] [Accepted: 12/27/2020] [Indexed: 01/07/2023]
Abstract
T-cell receptor (TCR) is crucial in T cell-mediated virus clearance. To date, TCR bias has been observed in various diseases. However, studies on the TCR repertoire of COVID-19 patients are lacking. Here, we used single-cell V(D)J sequencing to conduct comparative analyses of TCR repertoire between 12 COVID-19 patients and 6 healthy controls, as well as other virus-infected samples. We observed distinct T cell clonal expansion in COVID-19. Further analysis of VJ gene combination revealed 6 VJ pairs significantly increased, while 139 pairs significantly decreased in COVID-19 patients. When considering the VJ combination of α and β chains at the same time, the combination with the highest frequency on COVID-19 was TRAV12-2-J27-TRBV7-9-J2-3. Besides, preferential usage of V and J gene segments was also observed in samples infected by different viruses. Our study provides novel insights on TCR in COVID-19, which contribute to our understanding of the immune response induced by SARS-CoV-2.
Collapse
|
42
|
Shkurnikov M, Nersisyan S, Jankevic T, Galatenko A, Gordeev I, Vechorko V, Tonevitsky A. Association of HLA Class I Genotypes With Severity of Coronavirus Disease-19. Front Immunol 2021; 12:641900. [PMID: 33732261 PMCID: PMC7959787 DOI: 10.3389/fimmu.2021.641900] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/02/2021] [Indexed: 01/11/2023] Open
Abstract
Human leukocyte antigen (HLA) class I molecules play a crucial role in the development of a specific immune response to viral infections by presenting viral peptides at the cell surface where they will be further recognized by T cells. In the present manuscript, we explored whether HLA class I genotypes can be associated with the critical course of Coronavirus Disease-19 by searching possible connections between genotypes of deceased patients and their age at death. HLA-A, HLA-B, and HLA-C genotypes of n = 111 deceased patients with COVID-19 (Moscow, Russia) and n = 428 volunteers were identified with next-generation sequencing. Deceased patients were split into two groups according to age at the time of death: n = 26 adult patients aged below 60 and n = 85 elderly patients over 60. With the use of HLA class I genotypes, we developed a risk score (RS) which was associated with the ability to present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides by the HLA class I molecule set of an individual. The resulting RS was significantly higher in the group of deceased adults compared to elderly adults [p = 0.00348, area under the receiver operating characteristic curve (AUC ROC = 0.68)]. In particular, presence of HLA-A*01:01 allele was associated with high risk, while HLA-A*02:01 and HLA-A*03:01 mainly contributed to low risk. The analysis of patients with homozygosity strongly highlighted these results: homozygosity by HLA-A*01:01 accompanied early deaths, while only one HLA-A*02:01 homozygote died before 60 years of age. Application of the constructed RS model to an independent Spanish patients cohort (n = 45) revealed that the score was also associated with the severity of the disease. The obtained results suggest the important role of HLA class I peptide presentation in the development of a specific immune response to COVID-19.
Collapse
Affiliation(s)
- Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Tatjana Jankevic
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan Gordeev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- O.M. Filatov City Clinical Hospital, Moscow, Russia
| | | | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
43
|
Mariën J, Ceulemans A, Michiels J, Heyndrickx L, Kerkhof K, Foque N, Widdowson MA, Mortgat L, Duysburgh E, Desombere I, Jansens H, Van Esbroeck M, Ariën KK. Evaluating SARS-CoV-2 spike and nucleocapsid proteins as targets for antibody detection in severe and mild COVID-19 cases using a Luminex bead-based assay. J Virol Methods 2021; 288:114025. [PMID: 33227340 PMCID: PMC7678438 DOI: 10.1016/j.jviromet.2020.114025] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 01/09/2023]
Abstract
Large-scale serosurveillance of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) will only be possible if serological tests are sufficiently reliable, rapid and affordable. Many assays are either labour-intensive and require specialised facilities (e.g. virus neutralization assays), or are expensive with suboptimal specificity (e.g. commercial ELISAs and RDTs). Bead-based assays offer a cost-effective alternative and allow for multiplexing to test for antibodies against multiple antigens and against other pathogens. Here, we compare the performance of spike (S) and nucleocapsid (NP) antigens for the detection of SARS-CoV-2 specific IgG, IgM and IgA antibodies in a panel of sera that includes recent (up to six weeks after symptom onset, severe n = 44; and mild cases n = 52) and old infections (five months after symptom onset, mild n = 104), using a Luminex-bead based assay and comparison to a virus neutralization test. While we show that neutralizing antibody levels are significantly lower in mild than in severe cases, we demonstrate that a combination of the recombinant nucleocapsid protein (NP) and receptor-binding domain (RBD) results in highly specific (99 %) IgG antibody detection five months after infection in 96 % of cases. Although most severe Covid-19 cases developed a clear IgM and IgA response, titers fell below the detection threshold in more than 20 % of mild cases in our bead-based assay. In conclusion, our data supports the use of RBD and NP for the development of SARS-CoV-2 serological IgG bead-based assays.
Collapse
Affiliation(s)
- Joachim Mariën
- Outbreak Research Team, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Ann Ceulemans
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Johan Michiels
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leo Heyndrickx
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Karen Kerkhof
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Nikki Foque
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Laure Mortgat
- Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Els Duysburgh
- Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | | | | | - Marjan Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kevin K Ariën
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; University of Antwerp, Antwerp, Belgium.
| |
Collapse
|
44
|
Oladejo BO, Adeboboye CF, Adebolu TT. Understanding the genetic determinant of severity in viral diseases: a case of SARS-Cov-2 infection. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020; 21:77. [PMID: 38624552 PMCID: PMC7773422 DOI: 10.1186/s43042-020-00122-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022] Open
Abstract
Background Numerous research studies have identified specific human gene variants that affect enhanced susceptibility to viral infections. More recently is the current pandemic where the SARS-CoV-2 infection has shown a high degree of person-to-person clinical variability. A wide range of disease severity occurs in the patients' experiences, from asymptomatic cases, mild infections to serious life threatening conditions requiring admission into the intensive care unit (ICU). Main body of the abstract Although, it is generally reported that age and co-morbidities contribute significantly to the variations in the clinical outcome of the scourge of COVID-19, a hypothetical question of the possibility of genetic involvement in the susceptibility and severity of the disease arose when some unique severe outcomes were seen among young patients with no co-morbidity. The role human genetics play in clinical response to the viral infections is scarcely understood; however, several ongoing researches all around the world are currently focusing on possible genetic factors. This review reports the possible genetic factors that have been widely studied in defining the severity of viral infections using SARS-CoV-2 as a case study. These involve the possible involvements of ACE2, HLA, and TLR genes such as TLR7 and TLR3 in the presentation of a more severe condition. Short conclusion Understanding these variations could help to inform efforts to identify people at increased risk of infection outbreaks through genetic diagnosis of infections by locating disease genes or mutations that predispose patients to severe infection. This will also suggest specific targets for therapy and prophylaxis.
Collapse
|
45
|
Akachar J, Bouricha EM, Hakmi M, Belyamani L, El Jaoudi R, Ibrahimi A. Identifying epitopes for cluster of differentiation and design of new peptides inhibitors against human SARS-CoV-2 spike RBD by an in-silico approach. Heliyon 2020; 6:e05739. [PMID: 33364503 PMCID: PMC7753134 DOI: 10.1016/j.heliyon.2020.e05739] [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: 08/28/2020] [Revised: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 12/23/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) is a highly contagious and rapidly spreading infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some cases, the disease can be fatal which resulted in more than one million deaths worldwide according the WHO. Currently, there is no effective vaccine or treatment for COVID-19, however many small-molecule inhibitors have shown potent antiviral activity against SARS-CoV-2 and some of them are now under clinical trials. Despite their promising activities, the development of these small molecules for the clinical use can be limited by many factors like the off-target effect, the poor stability, and the low bioavailability. The clusters of differentiation CD147, CD209, CD299 have been identified as essential entry co-receptors for SARS-CoV-2 species specificity to humans, although the underlying mechanisms are yet to be fully elucidated. In this paper, protein-protein docking was utilized for identifying the critical epitopes in CD147, CD209 and CD299 which are involved in the binding with SARS-CoV-2 Spike receptor binding domain (RBD). The results of binding free energies showed a high affinity of SARS-CoV-2 RBD to CD299 receptor which was used as a reference to derive hypothetical peptide sequences with specific binding activities to SARS-CoV-2 RBD. Molecular docking and molecular dynamics simulations of the newly designed peptides showed favorable binding features and stability with SARS-CoV-2 RBD and therefore can be further considered as potential candidates in future anti-SARS CoV-2 drug discovery studies.
Collapse
Affiliation(s)
- Jihane Akachar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - El Mehdi Bouricha
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Rachid El Jaoudi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed Vth University in Rabat, Morocco
| |
Collapse
|
46
|
Sauer K, Harris T. An Effective COVID-19 Vaccine Needs to Engage T Cells. Front Immunol 2020; 11:581807. [PMID: 33117391 PMCID: PMC7549399 DOI: 10.3389/fimmu.2020.581807] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/27/2020] [Indexed: 12/28/2022] Open
Affiliation(s)
- Karsten Sauer
- Repertoire Immune Medicines, Cambridge, MA, United States
| | - Tim Harris
- Repertoire Immune Medicines, Cambridge, MA, United States
| |
Collapse
|
47
|
Melenotte C, Silvin A, Goubet AG, Lahmar I, Dubuisson A, Zumla A, Raoult D, Merad M, Gachot B, Hénon C, Solary E, Fontenay M, André F, Maeurer M, Ippolito G, Piacentini M, Wang FS, Ginhoux F, Marabelle A, Kroemer G, Derosa L, Zitvogel L. Immune responses during COVID-19 infection. Oncoimmunology 2020; 9:1807836. [PMID: 32939324 PMCID: PMC7480812 DOI: 10.1080/2162402x.2020.1807836] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/05/2020] [Accepted: 08/05/2020] [Indexed: 02/09/2023] Open
Abstract
Over the past 16 years, three coronaviruses (CoVs), severe acute respiratory syndrome CoV (SARS-CoV) in 2002, Middle East respiratory syndrome CoV (MERS-CoV) in 2012 and 2015, and SARS-CoV-2 in 2020, have been causing severe and fatal human epidemics. The unpredictability of coronavirus disease-19 (COVID-19) poses a major burden on health care and economic systems across the world. This is caused by the paucity of in-depth knowledge of the risk factors for severe COVID-19, insufficient diagnostic tools for the detection of SARS-CoV-2, as well as the absence of specific and effective drug treatments. While protective humoral and cellular immune responses are usually mounted against these betacoronaviruses, immune responses to SARS-CoV2 sometimes derail towards inflammatory tissue damage, leading to rapid admissions to intensive care units. The lack of knowledge on mechanisms that tilt the balance between these two opposite outcomes poses major threats to many ongoing clinical trials dealing with immunostimulatory or immunoregulatory therapeutics. This review will discuss innate and cognate immune responses underlying protective or deleterious immune reactions against these pathogenic coronaviruses.
Collapse
Affiliation(s)
- Cléa Melenotte
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Infectious Diseases, IHU-Méditerranée Infection, Marseille, France
| | | | - Anne-Gaëlle Goubet
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Imran Lahmar
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Agathe Dubuisson
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Alimuddin Zumla
- Department of Infection, Division of Infection and Immunity, University College London, National Institute for Health Research Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Didier Raoult
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - Mansouria Merad
- Service de Urgences et de Permanence des Soins, Gustave Roussy Cancer Campus Grand Paris, Villejuif, France
| | | | | | - Eric Solary
- Immunology, Gustave Roussy, Villejuif, France
| | - Michaela Fontenay
- INSERM U1016, Centre National Recherche Scientifique (CNRS) UMR8104, Institut Cochin, Université de Paris, Paris, France
| | | | - Markus Maeurer
- Immunosurgery, Immunotherapy Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
- Med Clinic, University of Mainz, Mayence, Germany
| | - Giuseppe Ippolito
- Dipartimento di Epidemiologia Ricerca Pre-Clinica e Diagnostica Avanzata, National Institute for Infectious Diseases “Lazzaro Spallanzani” I.R.C.C.S., Rome, Italy
| | - Mauro Piacentini
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- Infectious Diseases Department, National Institute for Infectious Disease IRCCS “Lazzaro Spallanzani”, Rome, Italy
| | - Fu-Sheng Wang
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Aurélien Marabelle
- Infectious Diseases, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie,Pathologie – PUI – Hygiène, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Karolinska Institute, Department of Women’s and Children’s Health, Karolinska University Hospital, Stockholm, Sweden
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
| | - Lisa Derosa
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
| | - Laurence Zitvogel
- Immunology, Gustave Roussy, Villejuif, France
- Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Immunology, Institut National de la Santé Et de la Recherche Médicale (INSERM), U1015 Equipe Labellisée—Ligue Nationale contre le Cancer, Villejuif, France
- Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 1428, Villejuif, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
| |
Collapse
|