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Zha B, Pan L, Gao N. High-throughput sequencing reveals the change of TCR α chain CDR3 with Takayasu arteritis. Immun Inflamm Dis 2023; 11:e1122. [PMID: 38156386 PMCID: PMC10740332 DOI: 10.1002/iid3.1122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023] Open
Abstract
OBJECTIVE Takayasu arteritis (TAK) is an inflammatory disease of blood vessels, and its pathogenesis is not clear at present. In this study, we explored the immunological characteristics of T cell receptor (TCR) α-chain complementarity-determining region 3 (CDR3) in patients with TAK. METHODS Five untreated patients with TAK were collected from June 2019 to December 2019. Four healthy blood samples were matched as the control group. The blood mononuclear cells were separated, and RNA was extracted for reverse transcription to obtain complementary DNA. Then high-throughput sequencing was performed. The quality of samples was evaluated by principal component analysis. We compared the diversity and expression of TCR α-chain between TAK group and control group. R software was used for statistical analysis and drawing, and Mann-Whitney U test was used to analyze the differences between the two groups. RESULTS The results showed that there was a significant difference in the diversity of TCR α-chain CDR3 between the two groups. Three V region genes expression significantly higher in the TAK patients than in the control group. A total of 196 VJ rearrangement genes are significantly different between the two groups, of which 149 rearrangement genes in the TAK group are lower than those in the control group, and 47 rearrangement genes in the TAK group are higher than those in the control group. CONCLUSION Patients with TAK have a unique TCR α-chain CDR3 library. These characteristic genes may be a marker for early diagnosis and provide a new theoretical basis for treating TAK.
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Affiliation(s)
- Bowen Zha
- Department of EducationBeijing Anzhen Hospital, Capital Medical UniversityBeijingChina
| | - Lili Pan
- Department of RheumatologyBeijing Anzhen Hospital, Capital Medical UniversityBeijingChina
| | - Na Gao
- Department of RheumatologyBeijing Anzhen Hospital, Capital Medical UniversityBeijingChina
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2
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Kim T, Lim H, Jun S, Park J, Lee D, Lee JH, Lee JY, Bang D. Globally shared TCR repertoires within the tumor-infiltrating lymphocytes of patients with metastatic gynecologic cancer. Sci Rep 2023; 13:20485. [PMID: 37993659 PMCID: PMC10665396 DOI: 10.1038/s41598-023-47740-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023] Open
Abstract
Gynecologic cancer, including ovarian cancer and endometrial cancer, is characterized by morphological and molecular heterogeneity. Germline and somatic testing are available for patients to screen for pathogenic variants in genes such as BRCA1/2. Tissue expression levels of immunogenomic markers such as PD-L1 are also being used in clinical research. The basic therapeutic approach to gynecologic cancer combines surgery with chemotherapy. Immunotherapy, while not yet a mainstream treatment for gynecologic cancers, is advancing, with Dostarlimab recently receiving approval as a treatment for endometrial cancer. The goal remains to harness stimulated immune cells in the bloodstream to eradicate multiple metastases, a feat currently deemed challenging in a typical clinical setting. For the discovery of novel immunotherapy-based tumor targets, tumor-infiltrating lymphocytes (TILs) give a key insight on tumor-related immune activities by providing T cell receptor (TCR) sequences. Understanding the TCR repertoires of TILs in metastatic tissues and the circulation is important from an immunotherapy standpoint, as a subset of T cells in the blood have the potential to help kill tumor cells. To explore the relationship between distant tissue biopsy regions and blood circulation, we investigated the TCR beta chain (TCRβ) in bulk tumor and matched blood samples from 39 patients with gynecologic cancer. We found that the TCR clones of TILs at different tumor sites were globally shared within patients and had high overlap with the TCR clones in peripheral blood.
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Affiliation(s)
- Taehoon Kim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Hyeonseob Lim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Soyeong Jun
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Junsik Park
- Department of Obstetrics and Gynecology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Dongin Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
| | - Jung-Yun Lee
- Department of Obstetrics and Gynecology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Duhee Bang
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
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3
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Zou J, Li B, Li D, Bao HF, She CH, Ye JF, Cai JF, Guan JL. Comprehensive analysis of T-cell receptor repertoires reveals antigen-driven T-cell clusters in patients with Behçet's syndrome. Eur J Immunol 2023; 53:e2250181. [PMID: 36747316 DOI: 10.1002/eji.202250181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023]
Abstract
T lymphocytes are the major components of adaptive immunity in Behçet's syndrome (BS) pathology. However, the precise mechanism of T-cell-induced inflammatory condition remains to be determined. We applied bulk sequencing of the T-cell receptor (TCR) β chain in peripheral blood samples from 45 patients with BS and 10 healthy donors as controls. TCR repertoires in BS patients displayed more clonality and less diversity than in healthy donors. Male patients exhibited lower diversity metrics of TCR and had a larger proportion in the top 10 clones than females (p = 0.016). There were no TCR clonality differences in other clinical features, such as age, disease duration, organ involvement, disease severity, and activity. By "Grouping of Lymphocyte Interactions by Paratope Hotspots" (GLIPH2) for antigen prediction, we found distinct 2477 clusters of TCR-β sequences that potentially recognize similar antigens shared between BS patients. We observed clonal T-cell expansion in BS patients. Sexual differences in TCR clonal expansion and public TCR groups deserve further study to reveal the underline T-cell-mediated immunity in BS.
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Affiliation(s)
- Jun Zou
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Bin Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Hua-Fang Bao
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Chun-Hui She
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jing-Fen Ye
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jian-Fei Cai
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jian-Long Guan
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
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4
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Cui L, Zhang C, Ding H, Feng D, Huang H, Lu Z, Liu B. Clonal Distribution and Intratumor Heterogeneity of the TCR Repertoire in Papillary Thyroid Cancer With or Without Coexistent Hashimoto's Thyroiditis. Front Immunol 2022; 13:821601. [PMID: 35720279 PMCID: PMC9203861 DOI: 10.3389/fimmu.2022.821601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/11/2022] [Indexed: 12/24/2022] Open
Abstract
The intratumor heterogeneity (ITH) of the amount and TCR repertoires of tumor infiltrating lymphocytes (TILs) in PTC with and without coexistent Hashimoto's thyroiditis (HT) are unclear. Here, we investigated the amount of T cells in tumor and corresponding normal tissues by immunohistochemical staining on 80 tumor samples and 40 normal samples from 40 patients. The immune repertoire of T cells was identified on 24 tumor samples and 12 normal samples from 12 patients using TCR high-throughput sequencing. The results demonstrated that the numbers of CD3+, CD4+ and CD8+ T cells in PTC without coexistent HT (PTC-WO) were significantly lower than those in PTC with existing HT (PTC-W). In PTC-W, the density of CD4+ TILs were generally higher when compared with CD8+ TILs. Furthermore, we found that the numbers of CD3+ T cells and their CD4+, CD8+ subtypes in tumor samples were generally higher than those in normal tissue in PTC-WO and moreover, the number of CD3+ T cells was negatively associated with TCR clonality in PTC-WO. In addition, although ITH of the TCR repertoire truly existed in PTC-W and PTC-WO, the TCR repertoires between distinct regions of the non-adjacent tumor foci were presented with a higher degree of similarity than those between tumor and matched normal tissue in PTC-WO, yet the similarity of intratumor repertoires was not significantly higher than those between tumor and corresponding normal samples in PTC-W. This research comprehensively delineated the quantity and TCR repertoire ITH of T cells in PTC-W and PTC-WO, suggesting that TILs might be reactive to tumor antigens in PTC-WO. Moreover, multiregion biopsies should be performed to precisely identify the immune background in PTC-W and PTC-WO.
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Affiliation(s)
- Likun Cui
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Head & Neck Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Chaoting Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Huirong Ding
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Core Laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Dongdong Feng
- Department of Head and Neck Surgery, Center of Otolaryngology Head and Neck Surgery, Affiliated People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Hongying Huang
- Department of Pathology, New York University Langone Medical Center, New York, NY, United States
| | - Zheming Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Baoguo Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Head & Neck Surgery, Peking University Cancer Hospital & Institute, Beijing, China
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5
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Guo F, Hancock B, Griffith A, Lin H, Howard K, Keegan J, Zhang F, Chicoine A, Cahill L, Ng J, Lederer J. Distinct Injury Responsive Regulatory T Cells Identified by Multi-Dimensional Phenotyping. Front Immunol 2022; 13:833100. [PMID: 35634302 PMCID: PMC9135044 DOI: 10.3389/fimmu.2022.833100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/11/2022] [Indexed: 01/21/2023] Open
Abstract
CD4+ regulatory T cells (Tregs) activate and expand in response to different types of injuries, suggesting that they play a critical role in controlling the immune response to tissue and cell damage. This project used multi-dimensional profiling techniques to comprehensively characterize injury responsive Tregs in mice. We show that CD44high Tregs expand in response to injury and were highly suppressive when compared to CD44low Tregs. T cell receptor (TCR) repertoire analysis revealed that the CD44high Treg population undergo TCRαβ clonal expansion as well as increased TCR CDR3 diversity. Bulk RNA sequencing and single-cell RNA sequencing with paired TCR clonotype analysis identified unique differences between CD44high and CD44low Tregs and specific upregulation of genes in Tregs with expanded TCR clonotypes. Gene ontology analysis for molecular function of RNA sequencing data identified chemokine receptors and cell division as the most enriched functional terms in CD44high Tregs versus CD44low Tregs. Mass cytometry (CyTOF) analysis of Tregs from injured and uninjured mice verified protein expression of these genes on CD44high Tregs, with injury-induced increases in Helios, Galectin-3 and PYCARD expression. Taken together, these data indicate that injury triggers the expansion of a highly suppressive CD44high Treg population that is transcriptionally and phenotypically distinct from CD44low Tregs suggesting that they actively participate in controlling immune responses to injury and tissue damage.
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Affiliation(s)
- Fei Guo
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States,Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, China
| | - Brandon Hancock
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Alec Griffith
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Hui Lin
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States,Department of Pathophysiology, School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Kaitlyn Howard
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Joshua Keegan
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Fan Zhang
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States,Department of Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Adam Chicoine
- Human Immunology Center, Brigham and Women’s Hospital, Boston, MA, United States
| | - Laura Cahill
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Julie Ng
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - James Lederer
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States,*Correspondence: James Lederer,
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Jin A, Zhou J, Yu P, Zhou S, Chang C. High Expression of THBS1 Leads to a Poor Prognosis in Papillary Thyroid Cancer and Suppresses the Anti-Tumor Immune Microenvironment. Technol Cancer Res Treat 2022; 21:15330338221085360. [PMID: 35315710 PMCID: PMC8943644 DOI: 10.1177/15330338221085360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Objectives: To study the role of thrombospondin-1 (THBS1) in
papillary thyroid cancer (PTC) prognosis and the immune microenvironment.
Methods: A retrospective cohort study was designed, and data
from The Cancer Genome Atlas database and PTC tissues from Fudan University
Shanghai Cancer Center were used. Weighted gene co-expression network analysis
was performed to build a THBS1-immune-related gene prognostic
index (T-I index). Results: High THBS1 expression
was correlated with advanced TNM stage, higher recurrence risk, and shorter
progression-free interval. High THBS1 expression correlated
with MAPK and PD1 pathways indicating a tumor promoting and immunity-inhibiting
tendency. The T-I index showed a powerful capacity to predict progression-free
survival and immunotherapy benefit. Conclusion: High expression of
THBS1 leads to a poor prognosis in PTCs and suppresses the
anti-tumor immune microenvironment.
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Affiliation(s)
- Anqi Jin
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jin Zhou
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
| | - Pengcheng Yu
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
| | - Shichong Zhou
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
| | - Cai Chang
- 89667Fudan University Shanghai Cancer Center, Shanghai, China
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Arunkumar M, Zielinski CE. T-Cell Receptor Repertoire Analysis with Computational Tools-An Immunologist's Perspective. Cells 2021; 10:cells10123582. [PMID: 34944090 PMCID: PMC8700004 DOI: 10.3390/cells10123582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/25/2022] Open
Abstract
Over the last few years, there has been a rapid expansion in the application of information technology to biological data. Particularly the field of immunology has seen great strides in recent years. The development of next-generation sequencing (NGS) and single-cell technologies also brought forth a revolution in the characterization of immune repertoires. T-cell receptor (TCR) repertoires carry comprehensive information on the history of an individual’s antigen exposure. They serve as correlates of host protection and tolerance, as well as biomarkers of immunological perturbation by natural infections, vaccines or immunotherapies. Their interrogation yields large amounts of data. This requires a suite of highly sophisticated bioinformatics tools to leverage the meaning and complexity of the large datasets. Many different tools and methods, specifically designed for various aspects of immunological research, have recently emerged. Thus, researchers are now confronted with the issue of having to choose the right kind of approach to analyze, visualize and ultimately solve their task at hand. In order to help immunologists to choose from the vastness of available tools for their data analysis, this review addresses and compares commonly used bioinformatics tools for TCR repertoire analysis and illustrates the advantages and limitations of these tools from an immunologist’s perspective.
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Affiliation(s)
- Mahima Arunkumar
- Department of Infection Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, 07745 Jena, Germany;
- Department of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- Bioinformatics, Ludwig Maximilians University Munich, 80539 Munich, Germany
| | - Christina E. Zielinski
- Department of Infection Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, 07745 Jena, Germany;
- Department of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- Correspondence:
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8
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Huang J, Zhang W, Zhao Y, Li J, Xie M, Lu Y, Peng Q, Zhang J, Li P, Dai L. Deciphering the Intercellular Communication Network of Peripartum Decidua that Orchestrates Delivery. Front Cell Dev Biol 2021; 9:770621. [PMID: 34805176 PMCID: PMC8602332 DOI: 10.3389/fcell.2021.770621] [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: 09/04/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022] Open
Abstract
Intercellular communication in the decidua plays important roles in relaying information between the maternal and fetal systems in the maintenance of pregnancy and the transition to labor. To date, several studies have explored cell-cell communications in the decidua during different periods of pregnancy, but studies systematically decoding the intercellular communication network, its internal cascades, and their involvement in labor are still lacking. In this study, we reconstructed a decidual cell-cell communication network based on scRNA-seq of peripartum decidua via the CellCall method. The results showed that endometrial cells (EECs) and extravillous trophoblasts relayed most of the common intercellular signals in the decidua both before delivery (DBD) and after delivery (DAD). Endothelial cells and EECs controlled many WNT-signaling-related intercellular communication factors that differed between DBD and DAD, some of which could be candidate biomarkers for the diagnosis of labor. Analysis of intercellular communications related to T cells identified abundant maternal-fetal immune-tolerance-related communication, such as TNFSF14-TNFRSF14/LTBR and FASLG-FAS signalings. We further explored the characteristics of the B cell receptor (BCR) and T cell receptor (TCR) repertoires by single-cell BCR/TCR sequencing. The results showed no significant differences in clonal expansion of B/T cells between DAD and DBD, indicating there was no significant change to adaptive immunity at the maternal-fetal interface during delivery. In summary, the findings provide a comprehensive view of the intercellular communication landscape in the peripartum decidua and identified some key intercellular communications involved in labor and maternal-fetal immune tolerance. We believe that our study provides valuable clues for understanding the mechanisms of pregnancy and provides possible diagnostic strategies for the onset of labor.
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Affiliation(s)
- Jingrui Huang
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China
| | - Weishe Zhang
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China.,Hunan Engineering Research Center of Early Life Development and Disease Prevention, Changsha, China
| | - Yanhua Zhao
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China
| | - Jingzhi Li
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China
| | - Mingkun Xie
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China
| | - Yang Lu
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China
| | - Qiaozhen Peng
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China
| | - Jiejie Zhang
- Hunan Engineering Research Center of Early Life Development and Disease Prevention, Changsha, China
| | - Ping Li
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China
| | - Lei Dai
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China.,Hunan Engineering Research Center of Early Life Development and Disease Prevention, Changsha, China
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