1
|
Cai Y, Luo M, Yang W, Xu C, Wang P, Xue G, Jin X, Cheng R, Que J, Zhou W, Pang B, Xu S, Li Y, Jiang Q, Xu Z. The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood. Cancer Res 2024; 84:1915-1928. [PMID: 38536129 DOI: 10.1158/0008-5472.can-23-0860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/20/2023] [Accepted: 03/19/2024] [Indexed: 06/05/2024]
Abstract
T cells recognize tumor antigens and initiate an anticancer immune response in the very early stages of tumor development, and the antigen specificity of T cells is determined by the T-cell receptor (TCR). Therefore, monitoring changes in the TCR repertoire in peripheral blood may offer a strategy to detect various cancers at a relatively early stage. Here, we developed the deep learning framework iCanTCR to identify patients with cancer based on the TCR repertoire. The iCanTCR framework uses TCRβ sequences from an individual as an input and outputs the predicted cancer probability. The model was trained on over 2,000 publicly available TCR repertoires from 11 types of cancer and healthy controls. Analysis of several additional publicly available datasets validated the ability of iCanTCR to distinguish patients with cancer from noncancer individuals and demonstrated the capability of iCanTCR for the accurate classification of multiple cancers. Importantly, iCanTCR precisely identified individuals with early-stage cancer with an AUC of 86%. Altogether, this work provides a liquid biopsy approach to capture immune signals from peripheral blood for noninvasive cancer diagnosis. SIGNIFICANCE Development of a deep learning-based method for multicancer detection using the TCR repertoire in the peripheral blood establishes the potential of evaluating circulating immune signals for noninvasive early cancer detection.
Collapse
Affiliation(s)
- Yideng Cai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Meng Luo
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenyi Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Chang Xu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Pingping Wang
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, China
| | - Guangfu Xue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Xiyun Jin
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, China
| | - Rui Cheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jinhao Que
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenyang Zhou
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Boran Pang
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shouping Xu
- Department of Breast Cancer, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, China
| | - Zhaochun Xu
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, China
| |
Collapse
|
2
|
Ningoo M, Cruz-Encarnación P, Khilnani C, Heeger PS, Fribourg M. T-cell receptor sequencing reveals selected donor-reactive CD8 + T cell clones resist antithymocyte globulin depletion after kidney transplantation. Am J Transplant 2024; 24:755-764. [PMID: 38141722 PMCID: PMC11070313 DOI: 10.1016/j.ajt.2023.12.016] [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: 05/31/2023] [Revised: 11/21/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
High frequencies of donor-reactive memory T cells in the periphery of transplant candidates prior to transplantation are linked to the development of posttransplant acute rejection episodes and reduced allograft function. Rabbit antithymocyte globulin (rATG) effectively depletes naïve CD4+ and CD8+ T cells for >6 months posttransplant, but rATG's effects on human donor-reactive T cells have not been carefully determined. To address this, we performed T cell receptor β-chain sequencing on peripheral blood mononuclear cells aliquots collected pretransplant and serially posttransplant in 7 kidney transplant recipients who received rATG as induction therapy. We tracked the evolution of the donor-reactive CD4+ and CD8+ T cell repertoires and identified stimulated pretransplant, CTV-(surface dye)-labeled, peripheral blood mononuclear cells from each patient with donor cells or third-party cells. Our analyses showed that while rATG depleted CD4+ T cells in all tested subjects, a subset of donor-reactive CD8+ T cells that were present at high frequencies pretransplant, consistent with expanded memory cells, resisted rATG depletion, underwent posttransplant expansion and were functional. Together, our data support the conclusion that a subset of human memory CD8+ T cells specifically reactive to donor antigens expand in vivo despite induction therapy with rATG and thus have the potential to mediate allograft damage.
Collapse
Affiliation(s)
- Mehek Ningoo
- Translational Transplant Research Center, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pamela Cruz-Encarnación
- Translational Transplant Research Center, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Calla Khilnani
- Translational Transplant Research Center, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Peter S Heeger
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Miguel Fribourg
- Translational Transplant Research Center, Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Immunology Institute Icahn School of Medicine at Mount Sinai, New York, New York, USA.
| |
Collapse
|
3
|
Goldner Kabeli R, Zevin S, Abargel A, Zilberberg A, Efroni S. Self-supervised learning of T cell receptor sequences exposes core properties for T cell membership. SCIENCE ADVANCES 2024; 10:eadk4670. [PMID: 38669334 DOI: 10.1126/sciadv.adk4670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The T cell receptor (TCR) repertoire is an extraordinarily diverse collection of TCRs essential for maintaining the body's homeostasis and response to threats. In this study, we compiled an extensive dataset of more than 4200 bulk TCR repertoire samples, encompassing 221,176,713 sequences, alongside 6,159,652 single-cell TCR sequences from over 400 samples. From this dataset, we then selected a representative subset of 5 million bulk sequences and 4.2 million single-cell sequences to train two specialized Transformer-based language models for bulk (CVC) and single-cell (scCVC) TCR repertoires, respectively. We show that these models successfully capture TCR core qualities, such as sharing, gene composition, and single-cell properties. These qualities are emergent in the encoded TCR latent space and enable classification into TCR-based qualities such as public sequences. These models demonstrate the potential of Transformer-based language models in TCR downstream applications.
Collapse
Affiliation(s)
- Romi Goldner Kabeli
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sarit Zevin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avital Abargel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| |
Collapse
|
4
|
Silva BD, Viero FT, Rodrigues P, Trevisan G. Nitric oxide involvement in the disability and active disease of multiple sclerosis: Systematic review and meta-analysis. Nitric Oxide 2024; 145:8-20. [PMID: 38331311 DOI: 10.1016/j.niox.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic and immune-mediated disease of unknown etiology and leading to a physical and cognitive disability. Different studies suggest that nitrosative stress may play a pivotal role in the pathogenesis and disability in MS. Besides, reports evaluated NO and their metabolites, expressed by nitrite and nitrate (NOx) levels of MS patients compared with other pathologies, but did not evaluate disability and relapse/remission phases. OBJECTIVE Thus, this study aimed to conduct a systematic review and meta-analysis of NOx levels in MS patients in relapse/remission phases and its involvement in patient disability. METHODS The protocol was registered in PROSPERO (CRD42022327161). We used GRADE to estimate the articles' quality and evaluated the publication bias using Egger's and Begg's tests. RESULTS Here, through a search in the Pubmed, Scopus, and EMBASE databases, 5.276 studies were found, and after the selection process, 20 studies were included in this systematic review and meta-analysis. The studies included data from 1.474 MS patients and 1.717 healthy controls, 1.010 RRMS and 221 primary progressive MS (PPMS). CONCLUSION NOx levels are increased in relapsing-remitting MS (RRMS) patients in the relapse phase. Also, NOx levels were increased in MS patients with higher disability. However, further studies are still needed to control lifestyle habits, pain, and MS treatment effects in biased NOx levels.
Collapse
Affiliation(s)
- Brenda da Silva
- Graduate Program in Pharmacology, Federal University of Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil.
| | - Fernanda Tibolla Viero
- Graduate Program in Pharmacology, Federal University of Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil.
| | - Patrícia Rodrigues
- Graduate Program in Pharmacology, Federal University of Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil.
| | - Gabriela Trevisan
- Graduate Program in Pharmacology, Federal University of Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil.
| |
Collapse
|
5
|
Yin Y, Sheng Y, Gao S, Zhang J, Wang W, Liu Y, Xu T, Zhang Y. Profiling of T cell repertoire in peripheral blood of patients from type 2 diabetes with complication. BMC Immunol 2024; 25:10. [PMID: 38297222 PMCID: PMC10832173 DOI: 10.1186/s12865-024-00601-7] [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: 05/24/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
PURPOSE More than 90% of patients with diabetes worldwide are type 2 diabetes (T2D), which is caused by insulin resistance or impaired producing insulin by pancreatic β cells. T2D and its complications, mainly large cardiovascular (LCV) and kidney (Ne) complications, are the major cause of death in diabetes patients. Recently, the dysregulation of peripheral T cell immune homeostasis was found in most T2D patients. However, the characteristics of T-cell receptors (TCR) remain largely unexplored in T2D patients. PATIENTS AND METHODS Here we investigated the TCR repertoire using high-throughput sequencing in peripheral blood collected from T2D patient with (8 LCV and 7 Ne) or without complications. RESULTS Our analysis of TCR repertoires in peripheral blood samples showed that TCR profiles in T2D patients with complications tended to be single and specific compared to controls, according to the characteristics of TCR repertoire in V-J combination number, diversity, principal component analysis (PCA) and differential genes. And we identified some differentially expressed V-J gene segments and amino acid clonotypes, which had the potential to contribute to distinguishing T2D patient with or without complications. As the progression of the disease, we found that the profiling of TCR repertoire was also differential between T2D patients with LVD and Ne complications base on this pilot analysis. CONCLUSION This study demonstrated the protentional unique property of TCR repertoire in peripheral blood of T2D patient with and without complications, or T2D patients with LVD and Ne complications, which provided the possibility for future improvements in immune-related diagnosis and therapy for T2D complications.
Collapse
Affiliation(s)
- YongHui Yin
- Shandong University of Traditional Chinese Medicine Affiliated Hospital, Jinan, Shandong, 250014, China
| | - YingLi Sheng
- Shandong University of Traditional Chinese Medicine Affiliated Hospital, Jinan, Shandong, 250014, China
| | - Shuo Gao
- Shandong University of Traditional Chinese Medicine, 203, Administrative Building, 4655 University Road, Changqing District, Jinan, Shandong, 250035, China
| | - JinTao Zhang
- Shandong University of Traditional Chinese Medicine, 203, Administrative Building, 4655 University Road, Changqing District, Jinan, Shandong, 250035, China
| | - WenKuan Wang
- Shandong University of Traditional Chinese Medicine, 203, Administrative Building, 4655 University Road, Changqing District, Jinan, Shandong, 250035, China
| | - YingJun Liu
- Shandong University of Traditional Chinese Medicine, 203, Administrative Building, 4655 University Road, Changqing District, Jinan, Shandong, 250035, China
| | - TingTing Xu
- Shandong University of Traditional Chinese Medicine, 203, Administrative Building, 4655 University Road, Changqing District, Jinan, Shandong, 250035, China
| | - Yi Zhang
- Shandong University of Traditional Chinese Medicine, 203, Administrative Building, 4655 University Road, Changqing District, Jinan, Shandong, 250035, China.
| |
Collapse
|
6
|
Du Y, Zhang Y, Diao J, Fu P, Jiang R, Wang P, Yang H, Zheng X, Zhang L, Bi J, Zhou Q. Decoding the diagnostic potential of T cell repertoires in peripheral blood of patients from amnestic mild cognitive impairment to Alzheimer's disease. FASEB J 2024; 38:e23317. [PMID: 38095240 DOI: 10.1096/fj.202301485r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/13/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Alzheimer's disease (AD) is currently an incurable neurodegenerative disorder and is the most common etiological cause of dementia. Consequently, it has severe burden on its patients and on their caregivers and represents a global health concern. Clinical investigations have indicated that a dysregulation of peripheral T cell immune homeostasis may be involved in the pathogenesis of AD, as well as in the early stages of AD, characterized by mild cognitive impairment (MCI). However, the characteristics and concomitant feasibility of the use of T-cell receptor (TCR) typing for disease diagnosis remains largely unknown. We employed a high-throughput sequencing and multidimensional bioinformatics analyses for the identification of TCR repertoires present in peripheral blood samples of 10 patients with amnestic MCI (aMCI), 10 patients with AD, and 10 healthy controls (HCs). Based on the characteristics of the TCR repertoires in the amount and diversity of combinations of V-J, the spectrum of immune defense, and differentially expressed genes (DEGs), single and specific TCR profiles were observed in the patient samples of aMCI and AD compared to profiles of HCs. In particular, the diversity of TCR clonotypes manifested a pattern of "decreased first and then increased" pattern during the progression from aMCI to AD, a pattern that was not observed in HC samples. Additionally, a total of 46 and 35 amino acid CDR3 sequences with consistent and reverse expressive abundance with diversity of TCR clonotypes were identified, respectively. Taken together, we provide novel and essential preliminary evidence demonstrating the presence of diversity of T cell repertoires from differentially expressed V-J gene segments and amino acid clonotypes using peripheral blood samples from patients with AD, aMCI, and from HC. Such findings have the potential to reveal potential mechanisms through which aMCI progresses to AD and provide a reference for the future development of immune-related diagnoses and therapies for AD.
Collapse
Affiliation(s)
- Yansheng Du
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yichen Zhang
- Department of Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jiuzhou Diao
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Pengrui Fu
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Runze Jiang
- Department of Translational Medicine Research Institute, Shandong Jingwei Biotechnology Co. Ltd, Jinan, China
| | - Ping Wang
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hui Yang
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaolei Zheng
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Leisheng Zhang
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province & NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Radiation Technology and Biophysics, Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Jianzhong Bi
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qingbo Zhou
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| |
Collapse
|
7
|
Nozuma S, Matsuura E, Tanaka M, Kodama D, Matsuzaki T, Yoshimura A, Sakiyama Y, Nakahata S, Morishita K, Enose-Akahata Y, Jacoboson S, Kubota R, Takashima H. Identification and tracking of HTLV-1-infected T cell clones in virus-associated neurologic disease. JCI Insight 2023; 8:167422. [PMID: 37036006 PMCID: PMC10132145 DOI: 10.1172/jci.insight.167422] [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: 11/22/2022] [Accepted: 02/21/2023] [Indexed: 04/11/2023] Open
Abstract
Human T lymphotropic virus type 1-assoicated (HTLV-1-associated) myelopathy/tropical spastic paraparesis (HAM/TSP) is a neuroinflammatory disease caused by the persistent proliferation of HTLV-1-infected T cells. Here, we performed a T cell receptor (TCR) repertoire analysis focused on HTLV-1-infected cells to identify and track the infected T cell clones that are preserved in patients with HAM/TSP and migrate to the CNS. TCRβ repertoire analysis revealed higher clonal expansion in HTLV-1-infected cells compared with noninfected cells from patients with HAM/TSP and asymptomatic carriers (ACs). TCR clonality in HTLV-1-infected cells was similar in patients with HAM/TSP and ACs. Longitudinal analysis showed that the TCR repertoire signature in HTLV-1-infected cells remained stable, and highly expanded infected clones were preserved within each patient with HAM/TSP over years. Expanded HTLV-1-infected clones revealed different distributions between cerebrospinal fluid (CSF) and peripheral blood and were enriched in the CSF of patients with HAM/TSP. Cluster analysis showed similarity in TCRβ sequences in HTLV-1-infected cells, suggesting that they proliferate after common antigen stimulation. Our results indicate that exploring TCR repertoires of HTLV-1-infected cells can elucidate individual clonal dynamics and identify potential pathogenic clones expanded in the CNS.
Collapse
Affiliation(s)
- Satoshi Nozuma
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Eiji Matsuura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masakazu Tanaka
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Daisuke Kodama
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Toshio Matsuzaki
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Akiko Yoshimura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yusuke Sakiyama
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shingo Nakahata
- Division of HTLV-1/ATL Carcinogenesis and Therapeutics, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Kazuhiro Morishita
- Project for Advanced Medical Research and Development, Project Research Division, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Yoshimi Enose-Akahata
- Viral Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorder and Stroke, NIH, Bethesda, Maryland, USA
| | - Steven Jacoboson
- Viral Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorder and Stroke, NIH, Bethesda, Maryland, USA
| | - Ryuji Kubota
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| |
Collapse
|
8
|
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
|
9
|
Sorosina M, Santoro S, Ferrè L, Mascia E, Clarelli F, Giordano A, Cannizzaro M, Lucia M, Martinelli V, Filippi M, Esposito F. Risk HLA Variants Affect the T-Cell Repertoire in Multiple Sclerosis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2023; 10:10/3/e200093. [PMID: 36792371 PMCID: PMC9931183 DOI: 10.1212/nxi.0000000000200093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/14/2022] [Indexed: 02/17/2023]
Abstract
BACKGROUND AND OBJECTIVES The major histocompatibility complex (MHC) locus has a predominant role in the genetic predisposition to multiple sclerosis (MS), with 32 associations found to be involved. We aimed to investigate the impact of MHC MS-risk alleles on T-cell repertoire in patients with MS. METHODS We studied 161 untreated patients with relapsing-remitting MS for whom Class I and II human leukocyte antigen (HLA) alleles were inferred from whole-genome genotyping data, and T-cell receptor (TCR) CDR3 sequences were obtained through next-generation sequencing. T-cell repertoire features including diversity, public clones, and architecture were evaluated. RESULTS We identified 5 MS-risk loci associated with TCR diversity: HLA-DRB1*15:01 (7.65 × 10-3), rs9271366 (1.96 × 10-3), rs766848979 A (1.89 × 10-2), rs9277626 (2.95 × 10-2), and rs11751659 (1.92 × 10-2), with evidence of expanded clonotypes in carriers of risk alleles. Moreover, HLA-DRB1*15:01 (4.99 × 10-3), rs9271366 (6.54 × 10-3), rs1049079 C (4.37 × 10-2), AA DQΒ1 position -5 L (1.05 × 10-3), and AA DQΒ1 position 221 Q (9.39 × 10-4) showed an association with the CDR3 aminoacidic sequence architecture, suggesting an impact on the antigen recognition breadth as well. Evaluating the sharing of clones across MS-risk allele carrier individuals revealed the presence of highly shared clonotypes predicted to target viral antigens, including Epstein-Barr virus. DISCUSSION Our study supports the association between MHC-risk alleles and macrofeatures of the T-cell repertoire in the context of MS. Further studies are needed to understand the underlying molecular mechanisms.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Federica Esposito
- From the Laboratory of Neurological Complex Disorders (M.S., S.S., L.F., E.M., F.C., A.G., M.C., F.E.), Division of Neuroscience, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute; Neurology and Neurorehabilitation Unit (L.F., A.G., M.C., M.L., V.M., M.F., F.E.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University (M.F.); Neurophysiology Unit (M.F.), IRCCS San Raffaele Scientific Institute; and Neuroimaging Research Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE) (P.F.), IRCCS San Raffaele Scientific Institute, Milan, Italy.
| |
Collapse
|
10
|
Ruder J, Docampo MJ, Rex J, Obahor S, Naghavian R, Müller AM, Schanz U, Jelcic I, Martin R. Dynamics of T cell repertoire renewal following autologous hematopoietic stem cell transplantation in multiple sclerosis. Sci Transl Med 2022; 14:eabq1693. [DOI: 10.1126/scitranslmed.abq1693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Autologous hematopoietic stem cell transplantation (aHSCT) is a highly effective treatment of multiple sclerosis (MS). It depletes autoreactive cells and subsequently renews adaptive immune cells. The possible proinflammatory potential of surviving T cells early after aHSCT has not been studied. Here, we examined the dynamics of new and surviving T cells in 27 patients after aHSCT by multidimensional flow cytometry, T cell receptor (TCR) sequencing, specificity testing, telomere length profiling, and HLA genotyping. Early after aHSCT, naïve T cells are barely detectable, whereas effector memory (EM) T cells quickly reconstitute to pre-aHSCT values. EM CD4+T cells early after aHSCT have shorter telomeres, have higher expression of senescence and exhaustion markers, and proliferate less than those before aHSCT. We find a median TCR repertoire overlap of 26% between the early post-aHSCT EM CD4+T cells and pre-aHSCT, indicating persistence of EM CD4+T cells early after transplantation. The EM CD4+TCR repertoire overlap declines to 15% at 12 months after aHSCT, whereas the naïve TCR repertoire entirely renews. HLA-DR–associated EM CD4+T cell reactivity toward MS-related antigens decreased after aHSCT, whereas reactivity toward EBV increased. Our data show substantial survival of pre-aHSCT EM CD4+T cells early after transplantation but complete renewal of the T cell repertoire by nascent T cells later.
Collapse
Affiliation(s)
- Josefine Ruder
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - María José Docampo
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Jordan Rex
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Simon Obahor
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Reza Naghavian
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Antonia M.S. Müller
- Department of Medical Oncology and Hematology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Urs Schanz
- Department of Medical Oncology and Hematology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Ilijas Jelcic
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| |
Collapse
|
11
|
Garrido-Mesa J, Brown MA. T cell Repertoire Profiling and the Mechanism by which HLA-B27 Causes Ankylosing Spondylitis. Curr Rheumatol Rep 2022; 24:398-410. [PMID: 36197645 PMCID: PMC9666335 DOI: 10.1007/s11926-022-01090-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2022] [Indexed: 11/25/2022]
Abstract
Purpose of Review Ankylosing spondylitis (AS) is strongly associated with the HLA-B27 gene. The canonical function of HLA-B27 is to present antigenic peptides to CD8 lymphocytes, leading to adaptive immune responses. The ‘arthritogenic peptide’ theory as to the mechanism by which HLA-B27 induces ankylosing spondylitis proposes that HLA-B27 presents peptides derived from exogenous sources such as bacteria to CD8 lymphocytes, which subsequently cross-react with antigens at the site of inflammation of the disease, causing inflammation. This review describes findings of studies in AS involving profiling of T cell expansions and discusses future research opportunities based on these findings. Recent Findings Consistent with this theory, there is an expanding body of data showing that expansion of a restricted pool of CD8 lymphocytes is found in most AS patients yet only in a small proportion of healthy HLA-B27 carriers. Summary These exciting findings strongly support the theory that AS is driven by presentation of antigenic peptides to the adaptive immune system by HLA-B27. They point to new potential approaches to identify the exogenous and endogenous antigens involved and to potential therapies for the disease.
Collapse
Affiliation(s)
- Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England.
- Genomics England, Charterhouse Square, London, EC1M 6BQ, England.
| |
Collapse
|
12
|
Clauze A, Enose-Akahata Y, Jacobson S. T cell receptor repertoire analysis in HTLV-1-associated diseases. Front Immunol 2022; 13:984274. [PMID: 36189294 PMCID: PMC9520328 DOI: 10.3389/fimmu.2022.984274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Human T lymphotropic virus 1 (HTLV-1) is a human retrovirus identified as the causative agent in adult T-cell leukemia/lymphoma (ATL) and chronic-progressive neuroinflammatory disorder HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1 is estimated to infect between 5-20 million people worldwide, although most infected individuals remain asymptomatic. HTLV-1 infected persons carry an estimated lifetime risk of approximately 5% of developing ATL, and between 0.25% and 1.8% of developing HAM/TSP. Most HTLV-1 infection is detected in CD4+ T cells in vivo which causes the aggressive malignancy in ATL. In HAM/TSP, the increase of HTLV-1 provirus induces immune dysregulation to alter inflammatory milieu, such as expansion of HTLV-1-specific CD8+ T cells, in the central nervous system of the infected subjects, which have been suggested to underlie the pathogenesis of HAM/TSP. Factors contributing to the conversion from asymptomatic carrier to disease state remain poorly understood. As such, the identification and tracking of HTLV-1-specific T cell biomarkers that may be used to monitor the progression from primary infection to immune dysfunction and disease are of great interest. T cell receptor (TCR) repertoires have been extensively investigated as a mechanism of monitoring adaptive T cell immune response to viruses and tumors. Breakthrough technologies such as single-cell RNA sequencing have increased the specificity with which T cell clones may be characterized and continue to improve our understanding of TCR signatures in viral infection, cancer, and associated treatments. In HTLV-1-associated disease, sequencing of TCR repertoires has been used to reveal repertoire patterns, diversity, and clonal expansions of HTLV-1-specific T cells capable of immune evasion and dysregulation in ATL as well as in HAM/TSP. Conserved sequence analysis has further been used to identify CDR3 motif sequences and exploit disease- or patient-specificity and commonality in HTLV-1-associated disease. In this article we review current research on TCR repertoires and HTLV-1-specific clonotypes in HTLV-1-associated diseases ATL and HAM/TSP and discuss the implications of TCR clonal expansions on HTLV-1-associated disease course and treatments.
Collapse
|
13
|
Tanaka Y, Sato T, Yagishita N, Yamauchi J, Araya N, Aratani S, Takahashi K, Kunitomo Y, Nagasaka M, Kanda Y, Uchimaru K, Morio T, Yamano Y. Potential role of HTLV-1 Tax-specific cytotoxic t lymphocytes expressing a unique t-cell receptor to promote inflammation of the central nervous system in myelopathy associated with HTLV-1. Front Immunol 2022; 13:993025. [PMID: 36081501 PMCID: PMC9446235 DOI: 10.3389/fimmu.2022.993025] [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: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 01/09/2023] Open
Abstract
Human T-lymphotropic virus 1 (HTLV-1) infection causes two serious diseases: adult T-cell leukemia/lymphoma (ATL) and HTLV-1-associated myelopathy (HAM). Immunological studies have revealed that HTLV-1 Tax-specific CD8+ cytotoxic T-cells (Tax-CTLs) in asymptomatic carriers (ACs) and ATL patients play an important role in the elimination of HTLV-1-infected host cells, whereas Tax-CTLs in HAM patients trigger an excessive immune response against HTLV-1-infected host cells infiltrating the central nervous system (CNS), leading to local inflammation. Our previous evaluation of HTLV-1 Tax301-309 (SFHSLHLLF)-specific Tax-CTLs (Tax301-309-CTLs) revealed that a unique T-cell receptor (TCR) containing amino acid (AA)-sequence motif PDR, was shared among HLA-A*24:02+ ACs and ATL patients and behaved as an eliminator by strong activity against HTLV-1. However, it remains unclear whether PDR+Tax301-309-CTLs also exist in HLA-A*24:02+ HAM patients and are involved in the pathogenesis of HAM. In the present study, by high-throughput TCR repertoire analysis technology, we revealed TCR repertoires of Tax301-309-CTLs in peripheral blood (PB) of HLA-A*24:02+ HAM patients were skewed, and a unique TCR-motif PDR was conserved in HAM patients (10 of 11 cases). The remaining case dominantly expressed (-DR, P-R, and PD-), which differed by one AA from PDR. Overall, TCRs with unique AA-sequence motifs PDR, or (-DR, P-R, and PD-) accounted for a total of 0.3-98.1% of Tax301-309-CTLs repertoires of HLA-A*24:02+ HAM patients. Moreover, TCR repertoire analysis of T-cells in the cerebrospinal fluid (CSF) from four HAM patients demonstrated the possibility that PDR+Tax301-309-CTLs and (-DR, P-R, and PD-)+Tax301-309-CTLs efficiently migrated and accumulated in the CSF of HAM patients fostering increased inflammation, although we observed no clear significant correlation between the frequencies of them in PB and the levels of CSF neopterin, a known disease activity biomarker of HAM. Furthermore, to better understand the potential function of PDR+Tax301-309-CTLs, we performed immune profiling by single-cell RNA-sequencing of Tax301-309-CTLs, and the result showed that PDR+Tax301-309-CTLs up-regulated the gene expression of natural killer cell marker KLRB1 (CD161), which may be associated with T-cell activation and highly cytotoxic potential of memory T-cells. These findings indicated that unique and shared PDR+Tax301-309-CTLs have a potential role in promoting local inflammation within the CNS of HAM patients.
Collapse
Affiliation(s)
- Yukie Tanaka
- Department of Molecular Microbiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan,Research Core, Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomoo Sato
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan,Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoko Yagishita
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Junji Yamauchi
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan,Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Natsumi Araya
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Satoko Aratani
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan,Advanced Business Promotion Department, Business Development Segment, LSI Medience Corporation, Tokyo, Japan
| | - Katsunori Takahashi
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yasuo Kunitomo
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Misako Nagasaka
- Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan,Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, CA, United States
| | - Yoshinobu Kanda
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan,Division of Hematology, Department of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kaoru Uchimaru
- Department of Hematology and Oncology, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan,Laboratory of Tumor Cell Biology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yoshihisa Yamano
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Japan,Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan,*Correspondence: Yoshihisa Yamano,
| |
Collapse
|
14
|
Bierhansl L, Hartung HP, Aktas O, Ruck T, Roden M, Meuth SG. Thinking outside the box: non-canonical targets in multiple sclerosis. Nat Rev Drug Discov 2022; 21:578-600. [PMID: 35668103 PMCID: PMC9169033 DOI: 10.1038/s41573-022-00477-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 12/11/2022]
Abstract
Multiple sclerosis (MS) is an immune-mediated disease of the central nervous system that causes demyelination, axonal degeneration and astrogliosis, resulting in progressive neurological disability. Fuelled by an evolving understanding of MS immunopathogenesis, the range of available immunotherapies for clinical use has expanded over the past two decades. However, MS remains an incurable disease and even targeted immunotherapies often fail to control insidious disease progression, indicating the need for new and exceptional therapeutic options beyond the established immunological landscape. In this Review, we highlight such non-canonical targets in preclinical MS research with a focus on five highly promising areas: oligodendrocytes; the blood-brain barrier; metabolites and cellular metabolism; the coagulation system; and tolerance induction. Recent findings in these areas may guide the field towards novel targets for future therapeutic approaches in MS.
Collapse
Affiliation(s)
- Laura Bierhansl
- Department of Neurology, Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Hans-Peter Hartung
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Orhan Aktas
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- German Center of Diabetes Research, Partner Düsseldorf, Neuherberg, Germany
| | - Sven G Meuth
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| |
Collapse
|
15
|
Perdaens O, van Pesch V. Molecular Mechanisms of Immunosenescene and Inflammaging: Relevance to the Immunopathogenesis and Treatment of Multiple Sclerosis. Front Neurol 2022; 12:811518. [PMID: 35281989 PMCID: PMC8913495 DOI: 10.3389/fneur.2021.811518] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/27/2021] [Indexed: 12/18/2022] Open
Abstract
Aging is characterized, amongst other features, by a complex process of cellular senescence involving both innate and adaptive immunity, called immunosenescence and associated to inflammaging, a low-grade chronic inflammation. Both processes fuel each other and partially explain increasing incidence of cancers, infections, age-related autoimmunity, and vascular disease as well as a reduced response to vaccination. Multiple sclerosis (MS) is a lifelong disease, for which considerable progress in disease-modifying therapies (DMTs) and management has improved long-term survival. However, disability progression, increasing with age and disease duration, remains. Neurologists are now involved in caring for elderly MS patients, with increasing comorbidities. Aging of the immune system therefore has relevant implications for MS pathogenesis, response to DMTs and the risks mediated by these treatments. We propose to review current evidence regarding markers and molecular mechanisms of immunosenescence and their relevance to understanding MS pathogenesis. We will focus on age-related changes in the innate and adaptive immune system in MS and other auto-immune diseases, such as systemic lupus erythematosus and rheumatoid arthritis. The consequences of these immune changes on MS pathology, in interaction with the intrinsic aging process of central nervous system resident cells will be discussed. Finally, the impact of immunosenescence on disease evolution and on the safety and efficacy of current DMTs will be presented.
Collapse
Affiliation(s)
- Océane Perdaens
- Laboratory of Neurochemistry, Institute of Neuroscience, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Vincent van Pesch
- Laboratory of Neurochemistry, Institute of Neuroscience, Université catholique de Louvain (UCLouvain), Brussels, Belgium
- Department of Neurology, Cliniques universitaires Saint-Luc, Université catholique de Louvain (UCLouvain), Brussels, Belgium
- *Correspondence: Vincent van Pesch
| |
Collapse
|
16
|
Chen YT, Hsu HC, Lee YS, Liu H, Tan BCM, Chin CY, Chang IYF, Yang CY. Longitudinal High-Throughput Sequencing of the T-Cell Receptor Repertoire Reveals Dynamic Change and Prognostic Significance of Peripheral Blood TCR Diversity in Metastatic Colorectal Cancer During Chemotherapy. Front Immunol 2022; 12:743448. [PMID: 35095836 PMCID: PMC8789675 DOI: 10.3389/fimmu.2021.743448] [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] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancer (CRC) is a major cause of cancer mortality and morbidity. Despite advances in chemotherapy and targeted therapy, unsustainable clinical benefit was noted due to recurrence and therapy resistance. The immune status of the cancer patient may affect the effectiveness of disease treatments. The dynamic change in the T-cell receptor (TCR) repertoire might be a clinical parameter for monitoring treatment responses. In this study, we aimed to determine the characteristics and clinical significance of the TCR repertoire in patients with unresectable metastatic colorectal cancer (mCRC). Herein, we comprehensively profile 103 peripheral blood samples from 20 healthy controls and 16 CRC patients with a follow-up of 98 to 452 days to identify hypervariable rearrangements of the TCRα and TCRβ repertoires using high-throughput sequencing. We found that TCRα repertoires, TCRβ repertoires, and CDR3 clonotypes were altered in mCRC patients compared with healthy controls. The diversity of TCR repertoires and CDR3 clonotypes decreased in most mCRC patients after therapy. Furthermore, compared with baseline TCR diversity, patients whose TCR diversity dropped considerably during therapy had better treatment responses, including lower CEA and CA19-9 levels and smaller tumor sizes. TCR baseline diversity was also significantly associated with partial response (PR) status (odds ratio: 5.29, p = 0.04). In conclusion, the present study demonstrated the association between dynamic changes in TCR diversity during chemotherapy and clinical outcomes as well as the potential utility of the TCR repertoire in predicting the prognosis of cancer treatment.
Collapse
Affiliation(s)
- Yi-Tung Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Hung-Chih Hsu
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Tao-Yuan, Taiwan.,College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan
| | - Hsuan Liu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chia-Yin Chin
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chia-Yu Yang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| |
Collapse
|
17
|
Massey J, Jackson K, Singh M, Hughes B, Withers B, Ford C, Khoo M, Hendrawan K, Zaunders J, Charmeteau-De Muylder B, Cheynier R, Luciani F, Ma D, Moore J, Sutton I. Haematopoietic Stem Cell Transplantation Results in Extensive Remodelling of the Clonal T Cell Repertoire in Multiple Sclerosis. Front Immunol 2022; 13:798300. [PMID: 35197974 PMCID: PMC8859174 DOI: 10.3389/fimmu.2022.798300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Autologous haematopoietic stem cell transplantation (AHSCT) is a vital therapeutic option for patients with highly active multiple sclerosis (MS). Rates of remission suggest AHSCT is the most effective form of immunotherapy in controlling the disease. Despite an evolving understanding of the biology of immune reconstitution following AHSCT, the mechanism by which AHSCT enables sustained disease remission beyond the period of lymphopenia remains to be elucidated. Auto-reactive T cells are considered central to MS pathogenesis. Here, we analyse T cell reconstitution for 36 months following AHSCT in a cohort of highly active MS patients. Through longitudinal analysis of sorted naïve and memory T cell clones, we establish that AHSCT induces profound changes in the dominant T cell landscape of both CD4+ and CD8+ memory T cell clones. Lymphopenia induced homeostatic proliferation is followed by clonal attrition; with only 19% of dominant CD4 (p <0.025) and 13% of dominant CD8 (p <0.005) clones from the pre-transplant repertoire detected at 36 months. Recovery of a thymically-derived CD4 naïve T cell repertoire occurs at 12 months and is ongoing at 36 months, however diversity of the naïve populations is not increased from baseline suggesting the principal mechanism of durable remission from MS after AHSCT relates to depletion of putative auto-reactive clones. In a cohort of MS patients expressing the MS risk allele HLA DRB1*15:01, public clones are probed as potential biomarkers of disease. AHSCT appears to induce sustained periods of disease remission with dynamic changes in the clonal T cell repertoire out to 36 months post-transplant.
Collapse
Affiliation(s)
- Jennifer Massey
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- *Correspondence: Jennifer Massey,
| | - Katherine Jackson
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Mandeep Singh
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Brendan Hughes
- School of Medical Sciences and Kirby Institute for Infection and Immunity, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - Barbara Withers
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - Carole Ford
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Melissa Khoo
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Kevin Hendrawan
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - John Zaunders
- Immunology Laboratory, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | | | - Rémi Cheynier
- Université de Paris, INSERM, CNRS, Institut Cochin, Paris, France
| | - Fabio Luciani
- School of Medical Sciences and Kirby Institute for Infection and Immunity, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - David Ma
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - John Moore
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - Ian Sutton
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- Department of Neurology, St Vincent’s Clinic, Darlinghurst, NSW, Australia
| |
Collapse
|
18
|
Amoriello R, Mariottini A, Ballerini C. Immunosenescence and Autoimmunity: Exploiting the T-Cell Receptor Repertoire to Investigate the Impact of Aging on Multiple Sclerosis. Front Immunol 2021; 12:799380. [PMID: 34925384 PMCID: PMC8673061 DOI: 10.3389/fimmu.2021.799380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023] Open
Abstract
T-cell receptor (TCR) repertoire diversity is a determining factor for the immune system capability in fighting infections and preventing autoimmunity. During life, the TCR repertoire diversity progressively declines as a physiological aging progress. The investigation of TCR repertoire dynamics over life represents a powerful tool unraveling the impact of immunosenescence in health and disease. Multiple Sclerosis (MS) is a demyelinating, inflammatory, T-cell mediated autoimmune disease of the Central Nervous System in which age is crucial: it is the most widespread neurological disease among young adults and, furthermore, patients age may impact on MS progression and treatments outcome. Crossing knowledge on the TCR repertoire dynamics over MS patients' life is fundamental to investigate disease mechanisms, and the advent of high- throughput sequencing (HTS) has significantly increased our knowledge on the topic. Here we report an overview of current literature about the impact of immunosenescence and age-related TCR dynamics variation in autoimmunity, including MS.
Collapse
Affiliation(s)
- Roberta Amoriello
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Florence, Italy
| | - Alice Mariottini
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Clara Ballerini
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Florence, Italy
| |
Collapse
|
19
|
Subtypes of schizophrenia identified by multi-omic measures associated with dysregulated immune function. Mol Psychiatry 2021; 26:6926-6936. [PMID: 34588622 DOI: 10.1038/s41380-021-01308-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 08/08/2021] [Accepted: 09/14/2021] [Indexed: 02/05/2023]
Abstract
Epigenetic modifications are plausible molecular sources of phenotypic heterogeneity across schizophrenia patients. The current study investigated biological heterogeneity in schizophrenia using peripheral epigenetic profiles to delineate illness subtypes independent of their phenomenological manifestations. We applied epigenome-wide profiling with a DNA methylation array from blood samples of 63 schizophrenia patients and 59 healthy controls. Non-negative matrix factorization (NMF) and k-means clustering were performed to identify DNA methylation-related patient subtypes. The validity of the partition was tested by assessing the profile of the T cell receptor (TCR) repertoires. The uniqueness of the identified subtypes in relation to brain structural and clinical measures were evaluated. Two distinct patterns of DNA methylation profiles were identified in patients. One subtype (60.3% of patients) showed relatively limited changes in methylation levels and cell composition compared to controls, while a second subtype (39.7% of patients) exhibited widespread methylation level alterations among genes enriched in immune cell activity, as well as a higher proportion of neutrophils and lower proportion of lymphocytes. Differentiation of the two patient subtypes was validated by TCR repertoires, which paralleled the partition based on DNA methylation profiles. The subtype with widespread methylation modifications had higher symptom severity, performed worse on cognitive measures, and displayed greater reductions in fractional anisotropy of white matter tracts and evidence of gray matter thickening compared to the other subtype. Identification of a distinct subtype of schizophrenia with unique molecular, cerebral, and clinical features provide a novel parcellation of the schizophrenia syndrome with potential to guide development of individualized therapeutics.
Collapse
|
20
|
Salinas VH, Stüve O. Systems Approaches to Unravel T Cell Function and Therapeutic Potential in Autoimmune Disease. THE JOURNAL OF IMMUNOLOGY 2021; 206:669-675. [PMID: 33526601 DOI: 10.4049/jimmunol.2000954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022]
Abstract
Producing Ag-specific immune responses constrained to target tissues or cells that can be engaged or disengaged at will is predicated on understanding the network of genes governing immune cell function, defining the rules underlying Ag specificity, and synthesizing the tools to engineer them. The successes and limitations of chimeric Ag receptor (CAR) T cells emphasize this goal, and advances in high-throughput sequencing, large-scale genomic screens, single-cell profiling, and genetic modification are providing the necessary data to bring it to fruition-including a broader application into the treatment of autoimmune diseases. In this review, we delve into the implementation of these developments, survey the relevant works, and propose a framework for generating the next generation of synthetic T cells informed by the principles learned from these systems approaches.
Collapse
Affiliation(s)
- Victor H Salinas
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390; and
| | - Olaf Stüve
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390; and .,Neurology Section, Medical Service, U.S. Department of Veterans Affairs, North Texas Health Care System, Dallas, TX 75216
| |
Collapse
|
21
|
Dvorkin S, Levi R, Louzoun Y. Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors. PLoS Comput Biol 2021; 17:e1009225. [PMID: 34310600 PMCID: PMC8341707 DOI: 10.1371/journal.pcbi.1009225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/05/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
Recent advances in T cell repertoire (TCR) sequencing allow for the characterization of repertoire properties, as well as the frequency and sharing of specific TCR. However, there is no efficient measure for the local density of a given TCR. TCRs are often described either through their Complementary Determining region 3 (CDR3) sequences, or theirV/J usage, or their clone size. We here show that the local repertoire density can be estimated using a combined representation of these components through distance conserving autoencoders and Kernel Density Estimates (KDE). We present ELATE-an Encoder-based LocAl Tcr dEnsity and show that the resulting density of a sample can be used as a novel measure to study repertoire properties. The cross-density between two samples can be used as a similarity matrix to fully characterize samples from the same host. Finally, the same projection in combination with machine learning algorithms can be used to predict TCR-peptide binding through the local density of known TCRs binding a specific target.
Collapse
MESH Headings
- Algorithms
- Amino Acid Sequence
- Complementarity Determining Regions/classification
- Complementarity Determining Regions/genetics
- Computational Biology
- Databases, Genetic
- Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Humans
- Immunoglobulin Variable Region/genetics
- Machine Learning
- Receptors, Antigen, T-Cell/classification
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell, alpha-beta/classification
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Software
Collapse
Affiliation(s)
- Shirit Dvorkin
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Reut Levi
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| |
Collapse
|
22
|
Wu M, Zhao M, Wu H, Lu Q. Immune repertoire: Revealing the "real-time" adaptive immune response in autoimmune diseases. Autoimmunity 2021; 54:61-75. [PMID: 33650440 DOI: 10.1080/08916934.2021.1887149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The diversity of the immune repertoire (IR) enables the human immune system to distinguish multifarious antigens (Ags) that humans may encounter throughout life. At the same time, bias or abnormalities in the IR also pay a contribution to the pathogenesis of autoimmune diseases. Rapid advancements in high-throughput sequencing (HTS) technology have ushered in a new era of immune studies, revealing novel molecules and pathways that might result in autoimmunity. In the field of IR, HTS can monitor the immune response status and identify disease-specific immune repertoires. In this review, we summarize updated progress on the mechanisms of the IR and current related studies on four autoimmune diseases, particularly focusing on systemic lupus erythematosus (SLE). These autoimmune diseases can exhibit slightly or significantly skewed IRs and provide novel insights that inform our comprehending of disease pathogenesis and provide potential targets for diagnosis and treatment.
Collapse
Affiliation(s)
- Meiyu Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Ming Zhao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China.,Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| |
Collapse
|
23
|
Nozuma S, Enose-Akahata Y, Johnson KR, Monaco MC, Ngouth N, Elkahloun A, Ohayon J, Zhu J, Jacobson S. Immunopathogenic CSF TCR repertoire signatures in virus-associated neurologic disease. JCI Insight 2021; 6:144869. [PMID: 33616082 PMCID: PMC7934934 DOI: 10.1172/jci.insight.144869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/13/2021] [Indexed: 11/22/2022] Open
Abstract
In this study, we examined and characterized disease-specific TCR signatures in cerebrospinal fluid (CSF) of patients with HTLV-1–associated myelopathy/tropical spastic paraparesis (HAM/TSP). TCR β libraries using unique molecular identifier–based methodologies were sequenced in paired peripheral blood mononuclear cells (PBMCs) and CSF cells from HAM/TSP patients and normal healthy donors (NDs). The sequence analysis demonstrated that TCR β repertoires in CSF of HAM/TSP patients were highly expanded and contained both TCR clonotypes shared with PBMCs and uniquely enriched within the CSF. In addition, we analyzed TCR β repertoires of highly expanded and potentially immunopathologic HTLV-1 Tax11-19–specific CD8+ T cells from PBMCs of HLA-A*0201+ HAM/TSP and identified a conserved motif (PGLAG) in the CDR3 region. Importantly, TCR β clonotypes of expanded clones in HTLV-1 Tax11-19–specific CD8+ T cells were also expanded and enriched in the CSF of the same patient. These results suggest that exploring TCR repertoires of CSF and antigen-specific T cells may provide a TCR repertoire signature in virus-associated neurologic disorders.
Collapse
Affiliation(s)
| | | | - Kory R Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | | | - Nyater Ngouth
- Viral Immunology Section, Neuroimmunology Branch and
| | - Abdel Elkahloun
- Comparative Genomics and Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Joan Ohayon
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Jun Zhu
- Mokobio Biotechnology R&D Center, Rockville, Maryland, USA
| | | |
Collapse
|
24
|
Singhania A, Pham J, Dhanwani R, Frazier A, Rezende Dutra J, Marder KS, Phillips E, Mallal S, Amara AW, Standaert DG, Sulzer D, Peters B, Sette A, Lindestam Arlehamn CS. The TCR repertoire of α-synuclein-specific T cells in Parkinson's disease is surprisingly diverse. Sci Rep 2021; 11:302. [PMID: 33432042 PMCID: PMC7801678 DOI: 10.1038/s41598-020-79726-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/11/2020] [Indexed: 11/09/2022] Open
Abstract
The self-antigen α-synuclein (α-syn) was recently shown to be associated with Parkinson's disease (PD). Here we mapped the T cell receptor (TCR) repertoire of α-syn-specific T cells from six PD patients. The self-antigen α-syn-specific repertoire was compared to the repertoire of T cells specific for pertussis (PT), as a representative foreign antigen that most individuals are exposed to, revealing that the repertoire for α-syn was as diverse as the repertoire for PT. The diversity of PT-specific clonotypes was similar between individuals with PD diagnosis and age-matched healthy controls. We found that the TCR repertoire was specific to each PD patient, and no shared TCRs among patients were defined, likely due to differences in HLA expression that select for different subsets of epitope-specific TCR rearrangements. This study provides the first characterization of α-syn-specific TCR clonotypes in individuals with PD. Antigen-specific TCRs can serve as immunotherapeutics and diagnostics, and means to track longitudinal changes in specific T cells, and disease progression.
Collapse
Affiliation(s)
- Akul Singhania
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| | - John Pham
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| | - Rekha Dhanwani
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| | - April Frazier
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| | - Juliana Rezende Dutra
- grid.239585.00000 0001 2285 2675Department of Neurology, Columbia University Medical Center, New York, NY 10032 USA
| | - Karen S. Marder
- grid.239585.00000 0001 2285 2675Department of Neurology, Columbia University Medical Center, New York, NY 10032 USA
| | - Elizabeth Phillips
- grid.1025.60000 0004 0436 6763Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150 Australia ,grid.152326.10000 0001 2264 7217Vanderbilt University School of Medicine, Nashville, TN 37235 USA
| | - Simon Mallal
- grid.1025.60000 0004 0436 6763Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150 Australia ,grid.152326.10000 0001 2264 7217Vanderbilt University School of Medicine, Nashville, TN 37235 USA
| | - Amy W. Amara
- grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - David G. Standaert
- grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - David Sulzer
- grid.239585.00000 0001 2285 2675Department of Neurology, Columbia University Medical Center, New York, NY 10032 USA ,grid.239585.00000 0001 2285 2675Department of Psychiatry, Columbia University Medical Center, New York, NY 10032 USA ,grid.239585.00000 0001 2285 2675Department of Pharmacology, Columbia University Medical Center, New York, NY 10032 USA
| | - Bjoern Peters
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037 USA ,grid.266100.30000 0001 2107 4242Department of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Alessandro Sette
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037 USA ,grid.266100.30000 0001 2107 4242Department of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Cecilia S. Lindestam Arlehamn
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037 USA
| |
Collapse
|
25
|
Hayashi F, Isobe N, Glanville J, Matsushita T, Maimaitijiang G, Fukumoto S, Watanabe M, Masaki K, Kira JI. A new clustering method identifies multiple sclerosis-specific T-cell receptors. Ann Clin Transl Neurol 2021; 8:163-176. [PMID: 33400858 PMCID: PMC7818280 DOI: 10.1002/acn3.51264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE To characterize T-cell receptors (TCRs) and identify target epitopes in multiple sclerosis (MS). METHODS Peripheral blood mononuclear cells were obtained from 39 MS patients and 19 healthy controls (HCs). TCR repertoires for α/β/δ/γ chains, TCR diversity, and V/J usage were determined by next-generation sequencing. TCR β chain repertoires were compared with affectation status using a novel clustering method, Grouping of Lymphocyte Interactions by Paratope Hotspots (GLIPH). Cytomegalovirus (CMV)-IgG was measured in an additional 113 MS patients and 93 HCs. Regulatory T cells (Tregs) were measured by flow cytometry. RESULTS TCR diversity for all four chains decreased with age. TCRα and TCRβ diversity was higher in MS patients (P = 0.0015 and 0.024, respectively), even after age correction. TRAJ56 and TRBV4-3 were more prevalent in MS patients than in HCs (pcorr = 0.027 and 0.040, respectively). GLIPH consolidated 208,674 TCR clones from MS patients into 1,294 clusters, among which two candidate clusters were identified. The TRBV4-3 cluster was shared by HLA-DRB1*04:05-positive patients (87.5%) and predicted to recognize CMV peptides (CMV-TCR). MS Severity Score (MSSS) was lower in patients with CMV-TCR than in those without (P = 0.037). CMV-IgG-positivity was associated with lower MSSS in HLA-DRB1*04:05 carriers (P = 0.0053). HLA-DRB1*04:05-positive individuals demonstrated higher CMV-IgG titers than HLA-DRB1*04:05-negative individuals (P = 0.017). CMV-IgG-positive patients had more Tregs than CMV-IgG-negative patients (P = 0.054). INTERPRETATION High TCRα/TCRβ diversity, regardless of age, is characteristic of MS. Association of a CMV-recognizing TCR with mild disability indicates CMV's protective role in HLA-DRB1*04:05-positive MS.
Collapse
Affiliation(s)
- Fumie Hayashi
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Noriko Isobe
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jacob Glanville
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, California, USA
| | - Takuya Matsushita
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Shoko Fukumoto
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitsuru Watanabe
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuhisa Masaki
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jun-Ichi Kira
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| |
Collapse
|
26
|
Beshnova D, Ye J, Onabolu O, Moon B, Zheng W, Fu YX, Brugarolas J, Lea J, Li B. De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection. Sci Transl Med 2020; 12:eaaz3738. [PMID: 32817363 PMCID: PMC7887928 DOI: 10.1126/scitranslmed.aaz3738] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/05/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023]
Abstract
The adaptive immune system recognizes tumor antigens at an early stage to eradicate cancer cells. This process is accompanied by systemic proliferation of the tumor antigen-specific T lymphocytes. While detection of asymptomatic early-stage cancers is challenging due to small tumor size and limited somatic alterations, tracking peripheral T cell repertoire changes may provide an attractive solution to cancer diagnosis. Here, we developed a deep learning method called DeepCAT to enable de novo prediction of cancer-associated T cell receptors (TCRs). We validated DeepCAT using cancer-specific or non-cancer TCRs obtained from multiple major histocompatibility complex I (MHC-I) multimer-sorting experiments and demonstrated its prediction power for TCRs specific to cancer antigens. We blindly applied DeepCAT to distinguish over 250 patients with cancer from over 600 healthy individuals using blood TCR sequences and observed high prediction accuracy, with area under the curve (AUC) ≥ 0.95 for multiple early-stage cancers. This work sets the stage for using the peripheral blood TCR repertoire for noninvasive cancer detection.
Collapse
Affiliation(s)
- Daria Beshnova
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Oreoluwa Onabolu
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin Moon
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenxin Zheng
- Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jayanthi Lea
- Department of Obstetrics and Gynecology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA.
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
27
|
Nozuma S, Kubota R, Jacobson S. Human T-lymphotropic virus type 1 (HTLV-1) and cellular immune response in HTLV-1-associated myelopathy/tropical spastic paraparesis. J Neurovirol 2020; 26:652-663. [PMID: 32705480 PMCID: PMC7532128 DOI: 10.1007/s13365-020-00881-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 03/29/2020] [Accepted: 07/06/2020] [Indexed: 12/18/2022]
Abstract
Human T-lymphotropic virus type 1 (HTLV-1) is associated with adult T cell leukemia/lymphoma and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HAM/TSP is an inflammatory disease of the spinal cord and clinically characterized by progressive spastic paraparesis, urinary incontinence, and mild sensory disturbance. The interaction between the host immune response and HTLV-1-infected cells regulates the development of HAM/TSP. HTLV-1 preferentially infects CD4+ T cells and is maintained by proliferation of the infected T cells. HTLV-1-infected cells rarely express viral antigens in vivo; however, they easily express the antigens after short-term culture. Therefore, such virus-expressing cells may lead to activation and expansion of antigen-specific T cell responses. Infected T cells with HTLV-1 and HTLV-1-specific CD8+ cytotoxic T lymphocytes invade the central nervous system and produce various proinflammatory cytokines and chemokines, leading to neuronal damage and degeneration. Therefore, cellular immune responses to HTLV-1 have been considered to play important roles in disease development of HAM/TSP. Recent studies have clarified the viral strategy for persistence in the host through genetic and epigenetic changes by HTLV-1 and host immune responses including T cell function and differentiation. Newly developed animal models could provide the opportunity to uncover the precise pathogenesis and development of clinically effective treatment. Several molecular target drugs are undergoing clinical trials with promising efficacy. In this review, we summarize recent advances in the immunopathogenesis of HAM/TSP and discuss the perspectives of the research on this disease.
Collapse
MESH Headings
- Animals
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/virology
- Cell Proliferation/drug effects
- Cytokines/biosynthesis
- Cytokines/immunology
- Disease Models, Animal
- Host-Pathogen Interactions/immunology
- Human T-lymphotropic virus 1/drug effects
- Human T-lymphotropic virus 1/immunology
- Human T-lymphotropic virus 1/pathogenicity
- Humans
- Immunity, Cellular/drug effects
- Immunologic Factors/therapeutic use
- Leukemia-Lymphoma, Adult T-Cell/drug therapy
- Leukemia-Lymphoma, Adult T-Cell/immunology
- Leukemia-Lymphoma, Adult T-Cell/pathology
- Leukemia-Lymphoma, Adult T-Cell/virology
- Lymphocyte Activation/drug effects
- Neurons/drug effects
- Neurons/immunology
- Neurons/pathology
- Neurons/virology
- Neuroprotective Agents/therapeutic use
- Paraparesis, Tropical Spastic/drug therapy
- Paraparesis, Tropical Spastic/immunology
- Paraparesis, Tropical Spastic/pathology
- Paraparesis, Tropical Spastic/virology
- Spinal Cord/drug effects
- Spinal Cord/immunology
- Spinal Cord/virology
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/virology
- Urinary Incontinence/drug therapy
- Urinary Incontinence/immunology
- Urinary Incontinence/pathology
- Urinary Incontinence/virology
Collapse
Affiliation(s)
- Satoshi Nozuma
- Viral Immunology Section, Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ryuji Kubota
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Steven Jacobson
- Viral Immunology Section, Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
28
|
Song Z, Chen X, Shi Y, Huang R, Wang W, Zhu K, Lin S, Wang M, Tian G, Yang J, Chen G. Evaluating the Potential of T Cell Receptor Repertoires in Predicting the Prognosis of Resectable Non-Small Cell Lung Cancers. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:73-83. [PMID: 32995352 PMCID: PMC7488751 DOI: 10.1016/j.omtm.2020.05.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 01/07/2023]
Abstract
For resectable cancer patients, a method that could precisely predict the risk of postoperative recurrence would be crucial for guiding adjuvant treatment. Since T cell receptor (TCR) repertoires had been shown to be closely related to the dynamics of cancers, here we enrolled a cohort of patients to evaluate the potential of TCR repertoires in predicting the prognosis of resectable non-small cell lung cancers. Specifically, TCRβ repertoires were analyzed in surgical tumor tissues and matched adjacent non-tumor tissues from 39 patients enrolled with resectable non-small cell lung cancer, through target enrichment and high-throughput sequencing. As a result, there are significant differences between the TCR repertories of tumor samples and those of matched adjacent non-tumor samples as evaluated by criteria like the number of clonotypes. In addition, TCR repertoires were significantly associated with a few clinical features, as well as somatic mutations. Finally, certain TCRβ variable-joining (V-J) pairings were featured to build a logistic regression model in predicting postoperative recurrence of resectable non-small cell lung cancers with a testing area under the receiver operating characteristic curve (AUC) of around 0.9. Thus, we hypothesize that TCR repertoires could be potentially used to predict prognosis after curative surgery for non-small cell lung cancer patients.
Collapse
Affiliation(s)
- Zhengbo Song
- Department of Medical Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou 310022, China
| | | | - Yi Shi
- Department of Molecular Pathology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou 350014, China
| | - Rongfang Huang
- Department of Pathology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou 350014, China
| | - Wenxian Wang
- Department of Medical Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou 310022, China
| | - Kunshou Zhu
- Department of Thoracic Surgery, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou 350014, China
| | - Shaofeng Lin
- Department of Thoracic Surgery, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou 350014, China
| | - Minxian Wang
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Geng Tian
- Geneis Beijing, Beijing 100102, China
| | | | - Gang Chen
- Department of Pathology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou 350014, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
| |
Collapse
|
29
|
Kim BJ, Youn DH, Kim Y, Jeon JP. Characterization of the TCR β Chain CDR3 Repertoire in Subarachnoid Hemorrhage Patients with Delayed Cerebral Ischemia. Int J Mol Sci 2020; 21:ijms21093149. [PMID: 32365660 PMCID: PMC7246515 DOI: 10.3390/ijms21093149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
Little is known of the adaptive immune response to subarachnoid hemorrhage (SAH). This study was the first to investigate whether T cell receptor (TCR) immune repertoire may provide a better understanding of T cell immunology in delayed cerebral ischemia (DCI). We serially collected peripheral blood in five SAH patients with DCI. High-throughput sequencing was used to analyze the TCR β chain (TCRB) complimentary determining regions (CDR) 3 repertoire. We evaluated the compositions and variations of the repertoire between admission and the DCI period, for severe DCI and non-severe DCI patients. Clonality did not differ significantly between admission and DCI. Severe DCI patients had significantly lower clonality than non-severe DCI patients (p value = 0.019). A read frequency of 0.005% ≤ - < 0.05% dominated the clonal expansion in non-severe DCI patients. Regarding repertoire diversity, severe DCI had a higher diversity score on admission than non-severe DCI. The CDR3 lengths were similar between admission and DCI. Among 728 annotated V-J gene pairs, we found that the relative frequencies of two V-J pairs were different at the occurrence of DCI than at admission, with T cells increasing by over 15%. TCRB CDR3 repertoires may serve as biomarkers to identify severe DCI patients.
Collapse
Affiliation(s)
- Bong Jun Kim
- Institute of New Frontier Stroke Research, Hallym University College of Medicine, Chuncheon 24253, Korea; (B.J.K.); (D.H.Y.); (Y.K.)
| | - Dong Hyuk Youn
- Institute of New Frontier Stroke Research, Hallym University College of Medicine, Chuncheon 24253, Korea; (B.J.K.); (D.H.Y.); (Y.K.)
| | - Youngmi Kim
- Institute of New Frontier Stroke Research, Hallym University College of Medicine, Chuncheon 24253, Korea; (B.J.K.); (D.H.Y.); (Y.K.)
| | - Jin Pyeong Jeon
- Institute of New Frontier Stroke Research, Hallym University College of Medicine, Chuncheon 24253, Korea; (B.J.K.); (D.H.Y.); (Y.K.)
- Genetic and Research Inc., Chuncheon 24253, Korea
- Department of Neurosurgery, Hallym University College of Medicine, Chuncheon 24253, Korea
- Correspondence: ; Tel.: +82-33-240-5171; Fax: +82-33-240-9970
| |
Collapse
|
30
|
Amoriello R, Greiff V, Aldinucci A, Bonechi E, Carnasciali A, Peruzzi B, Repice AM, Mariottini A, Saccardi R, Mazzanti B, Massacesi L, Ballerini C. The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies. Front Immunol 2020; 11:559. [PMID: 32328061 PMCID: PMC7160336 DOI: 10.3389/fimmu.2020.00559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022] Open
Abstract
Natalizumab (NTZ) and autologous hematopoietic stem cell transplantation (AHSCT) are two successful treatments for relapsing-remitting multiple sclerosis (RRMS), an autoimmune T-cell-driven disorder affecting the central nervous system that is characterized by relapses interspersed with periods of complete or partial recovery. Both RRMS treatments have been documented to impact T-cell subpopulations and the T-cell receptor (TCR) repertoire in terms of clone frequency, but, so far, the link between T-cell naive and memory populations, autoimmunity, and treatment outcome has not yet been established hindering insight into the post-treatment TCR landscape of MS patients. To address this important knowledge gap, we tracked peripheral T-cell subpopulations (naïve and memory CD4+ and CD8+) across 15 RRMS patients before and after two years of continuous treatment (NTZ) and a single treatment course (AHSCT) by high-throughput TCRß sequencing. We found that the two MS treatments left treatment-specific multidimensional traces in patient TCRß repertoire dynamics with respect to clonal expansion, clonal diversity and repertoire architecture. Comparing MS TCR sequences with published datasets suggested that the majority of public TCRs belonged to virus-associated sequences. In summary, applying multi-dimensional computational immunology to a TCRß dataset of treated MS patients, we show that qualitative changes of TCRß repertoires encode treatment-specific information that may be relevant for future clinical trials monitoring and personalized MS follow-up, diagnosis and treatment regimes. Natalizumab (NTZ) and autologous hematopoietic stem cell transplantation (AHSCT) are two successful treatments for relapsing-remitting multiple sclerosis (RRMS), an autoimmune T-cell-driven disorder affecting the central nervous system that is characterized by relapses interspersed with periods of complete or partial recovery. Both RRMS treatments have been documented to impact T-cell subpopulations and the T-cell receptor (TCR) repertoire in terms of clone frequency, but, so far, the link between T-cell naive and memory populations, autoimmunity, and treatment outcome has not yet been established hindering insight into the posttreatment TCR landscape of MS patients. To address this important knowledge gap, we tracked peripheral T-cell subpopulations (naive and memory CD4+ and CD8+) across 15 RRMS patients before and after 2 years of continuous treatment (NTZ) and a single treatment course (AHSCT) by high-throughput TCRβ sequencing. We found that the two MS treatments left treatment-specific multidimensional traces in patient TCRβ repertoire dynamics with respect to clonal expansion, clonal diversity, and repertoire architecture. Comparing MS TCR sequences with published datasets suggested that the majority of public TCRs belonged to virus-associated sequences. In summary, applying multidimensional computational immunology to a TCRβ dataset of treated MS patients, we show that qualitative changes of TCRβ repertoires encode treatment-specific information that may be relevant for future clinical trials monitoring and personalized MS follow-up, diagnosis, and treatment regimens.
Collapse
Affiliation(s)
- Roberta Amoriello
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Alessandra Aldinucci
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Elena Bonechi
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Alberto Carnasciali
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Benedetta Peruzzi
- Centro Diagnostico di Citofluorimetria e Immunoterapia, Careggi University Hospital, Florence, Italy
| | - Anna Maria Repice
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Alice Mariottini
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Riccardo Saccardi
- SODc Terapie Cellulari e Medicina Trasfusionale, Careggi University Hospital, Florence, Italy
| | - Benedetta Mazzanti
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), University of Florence, Florence, Italy
| | - Luca Massacesi
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Clara Ballerini
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), University of Florence, Florence, Italy
| |
Collapse
|
31
|
Meyer Zu Hörste G, Gross CC, Klotz L, Schwab N, Wiendl H. Next-Generation Neuroimmunology: New Technologies to Understand Central Nervous System Autoimmunity. Trends Immunol 2020; 41:341-354. [PMID: 32147112 DOI: 10.1016/j.it.2020.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/11/2022]
Abstract
Understanding neuroimmunological disorders is essential for developing new diagnostic and therapeutic strategies. Rodent models have provided valuable insights, but are sometimes equated with their human counterparts. Here, we summarize how novel technologies may enable an improved human-focused view of immune mechanisms. Recent studies have applied these new technologies to the brain parenchyma, its surrounding cerebrospinal fluid, and peripheral immune compartments. Therapeutic interventions have also facilitated translational understanding in a reverse way. However, with improved technology, access to patient samples remains a rate-limiting step in translational research. We anticipate that next-generation neuroimmunology is likely to integrate, in the immediate future, diverse technical tools for optimal diagnosis, prognosis, and treatment of neuroimmunological disorders.
Collapse
Affiliation(s)
- Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany
| | - Catharina C Gross
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany
| | - Nicholas Schwab
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany.
| |
Collapse
|
32
|
Jorge NAN, Cruz JGV, Pretti MAM, Bonamino MH, Possik PA, Boroni M. Poor clinical outcome in metastatic melanoma is associated with a microRNA-modulated immunosuppressive tumor microenvironment. J Transl Med 2020; 18:56. [PMID: 32024530 PMCID: PMC7001250 DOI: 10.1186/s12967-020-02235-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/22/2020] [Indexed: 11/28/2022] Open
Abstract
Background Interaction between malignant cells and immune cells that reside within the tumor microenvironment (TME) modulate different aspects of tumor development and progression. Recent works showed the importance of miRNA-containing extracellular vesicles in this crosstalk. Methods Interested in understanding the interplay between melanoma and immune-related TME cells, we characterized the TCGA’s metastatic melanoma samples according to their tumor microenvironment profiles, HLA-I neoepitopes, transcriptome profile and classified them into three groups. Moreover, we combined our results with melanoma single-cell gene expression and public miRNA data to better characterize the regulatory network of circulating miRNAs and their targets related to immune evasion and microenvironment response. Results The group associated with a worse prognosis showed phenotypic characteristics that favor immune evasion, including a strong signature of suppressor cells and less stable neoantigen:HLA-I complexes. Conversely, the group with better prognosis was marked by enrichment in lymphocyte and MHC signatures. By analyzing publicly available melanoma single-cell RNA and microvesicle microRNAs sequencing data we identified circulating microRNAs potentially involved in the crosstalk between tumor and TME cells. Candidate miRNA/target gene pairs with previously reported roles in tumor progression and immune escape mechanisms were further investigated and demonstrated to impact patient’s overall survival not only in melanoma but across different tumor types. Conclusion Our results underscore the impact of tumor-microenvironment interactions on disease outcomes and reveal potential non-invasive biomarkers of prognosis and treatment response.
Collapse
Affiliation(s)
- Natasha A N Jorge
- Bioinformatics and Computational Biology Lab, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil
| | - Jéssica G V Cruz
- Bioinformatics and Computational Biology Lab, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil
| | - Marco Antônio M Pretti
- Bioinformatics and Computational Biology Lab, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil.,Program of Immunology and Tumor Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil
| | - Martín H Bonamino
- Program of Immunology and Tumor Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil.,Vice Presidency of Research and Biological Collections, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Patricia A Possik
- Program of Immunology and Tumor Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil.
| | - Mariana Boroni
- Bioinformatics and Computational Biology Lab, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro, RJ, 20231-050, Brazil.
| |
Collapse
|
33
|
Valpione S, Galvani E, Tweedy J, Mundra PA, Banyard A, Middlehurst P, Barry J, Mills S, Salih Z, Weightman J, Gupta A, Gremel G, Baenke F, Dhomen N, Lorigan PC, Marais R. Immune-awakening revealed by peripheral T cell dynamics after one cycle of immunotherapy. NATURE CANCER 2020; 1:210-221. [PMID: 32110781 PMCID: PMC7046489 DOI: 10.1038/s43018-019-0022-x] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 12/17/2019] [Indexed: 12/19/2022]
Abstract
Our understanding of how checkpoint inhibitors (CPI) affect T cell evolution is incomplete, limiting our ability to achieve full clinical benefit from these drugs. Here we analyzed peripheral T cell populations after one cycle of CPI and identified a dynamic awakening of the immune system revealed by T cell evolution in response to treatment. We sequenced T cell receptors (TCR) in plasma cell-free DNA (cfDNA) and peripheral blood mononuclear cells (PBMC) and performed phenotypic analysis of peripheral T cell subsets from metastatic melanoma patients treated with CPI. We found that early peripheral T cell turnover and TCR repertoire dynamics identified which patients would respond to treatment. Additionally, the expansion of a subset of immune-effector peripheral T cells we call TIE cells correlated with response. These events are prognostic and occur within 3 weeks of starting immunotherapy, raising the potential for monitoring patients responses using minimally invasive liquid biopsies."
Collapse
Affiliation(s)
- Sara Valpione
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Elena Galvani
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Joshua Tweedy
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Piyushkumar A Mundra
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Antonia Banyard
- Advanced Imaging and Flow Cytometry, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Philippa Middlehurst
- Manchester Cancer Research Centre Biobank, The Christie NHS Foundation Trust, Manchester, UK
| | - Jeff Barry
- Advanced Imaging and Flow Cytometry, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Sarah Mills
- Manchester Cancer Research Centre Biobank, The Christie NHS Foundation Trust, Manchester, UK
| | - Zena Salih
- The Christie NHS Foundation Trust, Manchester, UK
| | - John Weightman
- Molecular Biology Core Facility, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | | | - Gabriela Gremel
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
- Boehringer Ingelheim, Vienna, Austria
| | - Franziska Baenke
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
- German Cancer Consortium (DKTK), German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Nathalie Dhomen
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | | | - Richard Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK.
| |
Collapse
|
34
|
Enose-Akahata Y, Jacobson S. Immunovirological markers in HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Retrovirology 2019; 16:35. [PMID: 31783764 PMCID: PMC6884770 DOI: 10.1186/s12977-019-0499-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/23/2019] [Indexed: 02/06/2023] Open
Abstract
Human T cell lymphotropic virus 1 (HTLV-1) is a human retrovirus and infects approximately 10–20 million people worldwide. While the majority of infected people are asymptomatic carriers of HTLV-1, only 4% of infected people develop HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HAM/TSP is a chronic, progressive, neurological disease which usually progresses slowly without remission, and is characterized by perivascular inflammatory infiltrates in chronic inflammatory lesions of the central nervous system (CNS), primarily affecting the spinal cord. A high HTLV-1 proviral load, high levels of antibodies against HTLV-1 antigens, and elevated concentration of proteins are detected in cerebrospinal fluid (CSF) of HAM/TSP patients. These chronically activated immune responses against HTLV-1 and infiltration of inflammatory cells including HTLV-1 infected cells into the CNS contribute to clinical disability and underlie the pathogenesis of HAM/TSP. Since the disease development of HAM/TSP mainly occurs in adults, with a mean age at onset of 40–50 years, it is important for HTLV-1-infected carriers and HAM/TSP patients to be monitored throughout the disease process. Recent advances in technologies and findings provide new insights to virological and immunological aspects in both the CNS as well as in peripheral blood. In this review, we focus on understanding the inflammatory milieu in the CNS and discuss the immunopathogenic process in HTLV-1-associated neurologic diseases.
Collapse
Affiliation(s)
- Yoshimi Enose-Akahata
- Viral Immunology Section, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, 9000 Rockville Pike, Building 10 Room 5C-103, Bethesda, MD, USA
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, 9000 Rockville Pike, Building 10 Room 5C-103, Bethesda, MD, USA.
| |
Collapse
|