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Li K, Zhuo Y, He Y, Lei F, He P, Lang Q, He D, Zuo S, Chen S, Yang X, Wen X, Zhang Z, Liu C. T cell receptor repertoire as a novel indicator for identification and immune surveillance of patients with severe obstructive sleep apnea. PeerJ 2023; 11:e15009. [PMID: 37051415 PMCID: PMC10084822 DOI: 10.7717/peerj.15009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/15/2023] [Indexed: 04/14/2023] Open
Abstract
Background Obstructive sleep apnea (OSA) is the most prevalent sleep disturbance that affects approximately 936 million people worldwide and leads to extensively increased incidence of cardiovascular disease, metabolic syndrome, neurological disorders, and traffic accidents. Severe OSA patients suffer a significantly higher risk of complications and worse comorbidity outcomes. Notwithstanding, with inadequate access to contact diagnosis based on polysomnography (PSG), numerous patients with severe sleep apnea have not been diagnosed, especially during the pandemic. Moreover, how the T cell immunity is impaired in OSA remains largely unknown. Methods We primarily investigated the T cell receptor (TCR) repertoires of 50 patients with severe OSA, 23 patients with mild-to-moderate OSA, 23 patients without OSA, and 157 healthy individuals, from their peripheral blood. Firstly, we compared the clinical characteristics, blood cell counts, the ratio of neutrophil-to-lymphocyte (NLR), platelet-to-lymphocyte (PLR), and CD4+/CD8+T cell count between groups. Then, we compared the diversity, clonotypes, unique VJ alleles in patients with different disease severity. Furthermore, by identifying a series of disease-associated amino acid sequences, we employed a repeated hold-out machine learning strategy to explore the optimal algorithm for calculating the TCR repertoire characteristic Index (OSA-TCI). We further confirmed its relation with clinical features by linear regression analysis. Moreover, in followup of severe OSA patients who accepted adherent non-invasive ventilation, we assessed the changes of TCR repertoires, OSA-TCI, ESS, NLR, PLR, and CD4+/CD8+T after therapy. Results We found an unexpected increase in diversity and clonotypes in the TCR repertoire of OSA patients. Furthermore, we successfully developed a novel indicator termed OSA-TCI to summarize the unique repertoire alteration, which provided 90% of sensitivity and 87% of specificity in distinguishing severe OSA. In rationalization, OSA-TCI was found correlated to AHI, BMI, hemoglobin, N1, N2 percentage of sleep, snoring, smoking and lowest oxygen saturation, but only independently related to AHI (R = 0.603) and smoking (R = 0.22). Finally, we observed OSA-TCI in the eight severe patients decreased significantly after home noninvasive ventilation for three months during follow-up, consistently in line with the TCR repertoire improvement. In contrast, NLR, PLR, and the ratio of CD4+/CD8+T cell count were found useless to diagnose and therapeutic surveillance of severe OSA. Conclusions Our study is the first to unveil the TCR repertoire alteration in OSA, indicates possible insidious autoimmune mechanisms underlying OSA, and suggests that TCR repertoires serve as a convenient peripheral blood biomarker for OSA assessment without long-time contact and facility/instrument occupation. It may shed light on future diagnostic, immunological, pathophysiological, and prognostic research on OSA.
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Affiliation(s)
- Kai Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, The Third People’s Hospital of Chengdu, Southwest Jiaotong University, Chengdu, China
- Department of Respiratory Medicine, The People’s Hospital of Pujiang County, Chengdu, China
| | - Yue Zhuo
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yue He
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, China
| | - Fei Lei
- Sleep Medicine Centre, West China Hospital, Sichuan University, Chengdu, China
| | - Pengming He
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Qin Lang
- Department of Pulmonary Diseases and Critical Care, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Dingxiu He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
- Department of Emergency Medicine, The People’s Hospital of Deyang, Deyang, China
| | - Suni Zuo
- Department of Respiratory Medicine, The People’s Hospital of Pujiang County, Chengdu, China
| | - Shan Chen
- Department of Respiratory and Critical Care Medicine, The Third People’s Hospital of Chengdu, Southwest Jiaotong University, Chengdu, China
| | - Xin Yang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xueping Wen
- Chengdu ExAb Biotechnology LTD, Chengdu, China
| | - Zhixin Zhang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chengdu ExAb Biotechnology LTD, Chengdu, China
| | - Chuntao Liu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
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Hong SB, Shin YW, Hong JB, Lee SK, Han B. Exploration of shared features of B cell receptor and T cell receptor repertoires reveals distinct clonotype clusters. Front Immunol 2022; 13:1006136. [PMID: 36341404 PMCID: PMC9632170 DOI: 10.3389/fimmu.2022.1006136] [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: 07/29/2022] [Accepted: 10/04/2022] [Indexed: 11/20/2022] Open
Abstract
Although B cells and T cells are integral players of the adaptive immune system and act in co-dependent ways to orchestrate immune responses, existing methods to study the immune repertoire have largely focused on separate analyses of B cell receptor (BCR) and T cell receptor (TCR) repertoires. Based on our hypothesis that the shared history of immune exposures and the shared cellular machinery for recombination result in similarities between BCR and TCR repertoires in an individual, we examine any commonalities and interrelationships between BCR and TCR repertoires. We find that the BCR and TCR repertoires have covarying clonal architecture and diversity, and that the pattern of correlations appears to be altered in immune-mediated diseases. Furthermore, hierarchical clustering of public B and T cell clonotypes in both health and disease based on correlation of clonal proportion revealed distinct clusters of B and T cell clonotypes that exhibit increased sequence similarity, share motifs, and have distinct amino acid characteristics. Our findings point to common principles governing memory formation, recombination, and clonal expansion to antigens in B and T cells within an individual. A significant proportion of public BCR and TCR repertoire can be clustered into nonoverlapping and correlated clusters, suggesting a novel way of grouping B and T cell clonotypes.
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Affiliation(s)
- Sang Bin Hong
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Yong-Won Shin
- Center for Hospital Medicine, Department of Neurosurgery, Seoul National University Hospital, Seoul, South Korea
| | - Ja Bin Hong
- Department of Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sang Kun Lee
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Buhm Han
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Brain Korea 21 (BK21) Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
- *Correspondence: Buhm Han,
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Nowicki TS, Farrell C, Morselli M, Rubbi L, Campbell KM, Macabali MH, Berent-Maoz B, Comin-Anduix B, Pellegrini M, Ribas A. Epigenetic Suppression of Transgenic T-cell Receptor Expression via Gamma-Retroviral Vector Methylation in Adoptive Cell Transfer Therapy. Cancer Discov 2020; 10:1645-1653. [PMID: 32699033 DOI: 10.1158/2159-8290.cd-20-0300] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/21/2020] [Accepted: 07/07/2020] [Indexed: 11/16/2022]
Abstract
Transgenic T-cell receptor (TCR) adoptive cell therapies recognizing tumor antigens are associated with robust initial response rates, but frequent disease relapse. This usually occurs in the setting of poor long-term persistence of cells expressing the transgenic TCR, generated using murine stem cell virus (MSCV) γ-retroviral vectors. Analysis of clinical transgenic adoptive cell therapy products in vivo revealed that despite strong persistence of the transgenic TCR DNA sequence over time, its expression was profoundly decreased over time at the RNA and protein levels. Patients with the greatest degrees of expression suppression displayed significant increases in DNA methylation over time within the MSCV promoter region, as well as progressive increases in DNA methylation within the entire MSCV vector over time. These increases in vector methylation occurred independently of its integration site within the host genomes. These results have significant implications for the design of future viral vector gene-engineered adoptive cell transfer therapies. SIGNIFICANCE: Cellular immunotherapies' reliance on retroviral vectors encoding foreign genetic material can be vulnerable to progressive acquisition of DNA methylation and subsequent epigenetic suppression of the transgenic product in TCR adoptive cell therapy. This must be considered in the design of future generations of cellular immunotherapies for cancer.This article is highlighted in the In This Issue feature, p. 1611.
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Affiliation(s)
- Theodore S Nowicki
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of California, Los Angeles, Los Angeles, California. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California
| | - Colin Farrell
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
| | - Marco Morselli
- Institute for Quantitative and Computational Biosciences - The Collaboratory, University of California, Los Angeles, Los Angeles, California.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California
| | - Liudmilla Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California
| | - Katie M Campbell
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Mignonette H Macabali
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Beata Berent-Maoz
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Begoña Comin-Anduix
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California.,Division of Surgical Oncology, Department of Surgery, University of California, Los Angeles, Los Angeles, California
| | - Matteo Pellegrini
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California.,Institute for Quantitative and Computational Biosciences - The Collaboratory, University of California, Los Angeles, Los Angeles, California.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California.,Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, California.,Division of Surgical Oncology, Department of Surgery, University of California, Los Angeles, Los Angeles, California.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California
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Fu Y, Li B, Li Y, Wang M, Yue Y, Xu L, Li S, Huang Q, Liu S, Dai Y. A comprehensive immune repertoire study for patients with pulmonary tuberculosis. Mol Genet Genomic Med 2019; 7:e00792. [PMID: 31173489 PMCID: PMC6625341 DOI: 10.1002/mgg3.792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 02/25/2019] [Accepted: 04/08/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major global health problem and has replaced HIV as the leading cause of death from a single infectious agent. METHODS Here, we applied high throughput sequencing to study the immune repertoire of nine pulmonary tuberculosis patients and nine healthy control samples. RESULTS Tuberculosis patients and healthy controls displayed significantly different high express clones and distinguishable sharing of CDR3 sequences. The TRBV and TRBJ gene usage showed higher expression clones in patients than in controls and we also found specific high express TRBV and TRBJ gene clones in different groups. In addition, six highly expressed TRBV/TRBJ combinations were detected in the CD4 group, 21 in the CD8 group and 32 in the tissue group. CONCLUSION In conclusion, we studied the patients with tuberculosis as well as healthy control individuals in order to understand the characteristics of immune repertoire. Sharing of CDR3 sequences and differential expression of genes was found among the patients with tuberculosis which could be used for the development of potential vaccine and targets treatment.
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Affiliation(s)
- Yingyun Fu
- Department of Respiratory and Critical Care Medicine, The Second Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China.,Shenzhen Key Laboratory of Respiratory Disease, Shenzhen, China
| | - Bo Li
- Department of Pediatrics, The Second Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Yazhen Li
- Department of Respiratory and Critical Care Medicine, The Second Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Minlian Wang
- Shenzhen Key Laboratory of Respiratory Disease, Shenzhen, China
| | - Yongjian Yue
- Shenzhen Key Laboratory of Respiratory Disease, Shenzhen, China
| | - Lan Xu
- Department of Respiratory and Critical Care Medicine, The Second Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Shulin Li
- Department of Respiratory and Critical Care Medicine, The Second Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Qijun Huang
- Department of Respiratory and Critical Care Medicine, The Second Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Song Liu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
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