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Zuckerbrot-Schuldenfrei M, Aviel-Ronen S, Zilberberg A, Efroni S. Ovarian cancer is detectable from peripheral blood using machine learning over T-cell receptor repertoires. Brief Bioinform 2024; 25:bbae075. [PMID: 38483254 PMCID: PMC10938541 DOI: 10.1093/bib/bbae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/17/2024] [Accepted: 02/07/2024] [Indexed: 03/17/2024] Open
Abstract
The extraordinary diversity of T cells and B cells is critical for body maintenance. This diversity has an important role in protecting against tumor formation. In humans, the T-cell receptor (TCR) repertoire is generated through a striking stochastic process called V(D)J recombination, in which different gene segments are assembled and modified, leading to extensive variety. In ovarian cancer (OC), an unfortunate 80% of cases are detected late, leading to poor survival outcomes. However, when detected early, approximately 94% of patients live longer than 5 years after diagnosis. Thus, early detection is critical for patient survival. To determine whether the TCR repertoire obtained from peripheral blood is associated with tumor status, we collected blood samples from 85 women with or without OC and obtained TCR information. We then used machine learning to learn the characteristics of samples and to finally predict, over a set of unseen samples, whether the person is with or without OC. We successfully stratified the two groups, thereby associating the peripheral blood TCR repertoire with the formation of OC tumors. A careful study of the origin of the set of T cells most informative for the signature indicated the involvement of a specific invariant natural killer T (iNKT) clone and a specific mucosal-associated invariant T (MAIT) clone. Our findings here support the proposition that tumor-relevant signal is maintained by the immune system and is coded in the T-cell repertoire available in peripheral blood. It is also possible that the immune system detects tumors early enough for repertoire technologies to inform us near the beginning of tumor formation. Although such detection is made by the immune system, we might be able to identify it, using repertoire data from peripheral blood, to offer a pragmatic way to search for early signs of cancer with minimal patient burden, possibly with enhanced sensitivity.
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Affiliation(s)
| | - Sarit Aviel-Ronen
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel and Sheba Medical Center, Tel-Hashomer, Ramat Gan 526200, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
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2
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Paramithiotis E, Varaklis C, Pillet S, Shafiani S, Lancelotta MP, Steinhubl S, Sugden S, Clutter M, Montamat-Sicotte D, Chermak T, Crawford SY, Lambert BL, Mattison J, Murphy RL. Integrated antibody and cellular immunity monitoring are required for assessment of the long term protection that will be essential for effective next generation vaccine development. Front Immunol 2023; 14:1166059. [PMID: 38077383 PMCID: PMC10701527 DOI: 10.3389/fimmu.2023.1166059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
The COVID pandemic exposed the critical role T cells play in initial immunity, the establishment and maintenance of long term protection, and of durable responsiveness against novel viral variants. A growing body of evidence indicates that adding measures of cellular immunity will fill an important knowledge gap in vaccine clinical trials, likely leading to improvements in the effectiveness of the next generation vaccines against current and emerging variants. In depth cellular immune monitoring in Phase II trials, particularly for high risk populations such as the elderly or immune compromised, should result in better understanding of the dynamics and requirements for establishing effective long term protection. Such analyses can result in cellular immunity correlates that can then be deployed in Phase III studies using appropriate, scalable technologies. Measures of cellular immunity are less established than antibodies as correlates of clinical immunity, and some misconceptions persist about cellular immune monitoring usefulness, cost, complexity, feasibility, and scalability. We outline the currently available cellular immunity assays, review their readiness for use in clinical trials, their logistical requirements, and the type of information each assay generates. The objective is to provide a reliable source of information that could be leveraged to develop a rational approach for comprehensive immune monitoring during vaccine development.
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Affiliation(s)
| | | | | | | | | | - Steve Steinhubl
- Purdue University, West Lafayette, IN, United States
- PhysIQ, Chicago, IL, United States
| | - Scott Sugden
- Medical and Scientific Affairs, Infectious Diseases, Cepheid, Sunnyvale, CA, United States
| | - Matt Clutter
- Research and Development, CellCarta, Montreal, QC, Canada
| | | | - Todd Chermak
- Regulatory and Government Affairs, CellCarta, Montreal, QC, Canada
| | - Stephanie Y. Crawford
- Department of Pharmacy Systems, Outcomes and Policy, University of Illinois Chicago, Chicago, IL, United States
| | - Bruce L. Lambert
- Department of Communication Studies, Institute for Global Health, Northwestern University, Evanston, IL, United States
| | - John Mattison
- Health Technology Advisory Board, Arsenal Capital, New York, NY, United States
| | - Robert L. Murphy
- Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
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3
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Lang R, Welponer T, Richtig E, Wolf I, Hoeller C, Hafner C, Nguyen VA, Kofler J, Barta M, Koelblinger P, Hitzl W, Emberger M, Laimer M. Nivolumab for locally advanced and metastatic cutaneous squamous cell carcinoma (NIVOSQUACS study)-Phase II data covering impact of concomitant haematological malignancies. J Eur Acad Dermatol Venereol 2023; 37:1799-1810. [PMID: 37210651 DOI: 10.1111/jdv.19218] [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: 02/07/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Monoclonal antibodies, such as cemiplimab and pembrolizumab, against the programmed death receptor (PD)-1 have become the current standard of care and first-line treatment of advanced cutaneous squamous cell carcinoma (cSCC), proving remarkable clinical benefit and acceptable safety. OBJECTIVES To assess efficacy and safety of the anti-PD-1 antibody nivolumab in patients with locally advanced and metastatic cSCC. METHODS Patients received open-label nivolumab 240 mg intravenously every 2 weeks for up to 24 months. Patients with concomitant haematological malignancies (CHMs), either non-progressing or stable under active therapy, were eligible for inclusion. RESULTS Of 31 patients with a median age of 80 years, 22.6% of patients achieved an investigator assessed complete response, resulting in an objective response rate (ORR) of 61.3% and a disease control rate (DCR) of 64.5%. Progression-free survival (PFS) was 11.1 months, and the median overall survival (OS) was not reached after 24 weeks of therapy. Median follow-up was 23.82 months. Subgroup analysis of the CHM cohort (n = 11; 35%) revealed an ORR of 45.5%, a DCR of 54.5%, a median PFS of 10.9 months, and median OS of 20.7 months. Treatment related adverse events were reported in 58.1% of all patients (19.4% grade 3, the remaining grade 1 or 2). PD-L1 expression and CD-8+ T-cell infiltration did not significantly correlate with clinical response, although a trend towards a shorter PFS of 5.6 months was observed with PD-L1 negativity and low CD8+ intratumoral infiltration. CONCLUSION This study demonstrated robust clinical efficacy of nivolumab in patients with locally advanced and metastatic cSCCs and a tolerability comparable to data of other anti-PD-1 antibodies. Favourable outcomes were obtained despite involving the oldest hitherto reported study cohort for anti-PD-1 antibodies and a significant proportion of CHM patients prone to high risk tumours and an aggressive course otherwise typically excluded from clinical trials.
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Affiliation(s)
- R Lang
- Department of Dermatology and Allergology, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - T Welponer
- Department of Dermatology and Allergology, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - E Richtig
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - I Wolf
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - C Hoeller
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - C Hafner
- Department of Dermatology, University Hospital St. Pölten, Karl Landsteiner University of Health Sciences, St. Pölten, Austria
| | - V A Nguyen
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - J Kofler
- Department of Dermatology, Landeskrankenhaus Klagenfurt, Klagenfurt, Austria
| | - M Barta
- Department of Dermatology and Venereology, Hospital of Wels-Grieskirchen, Wels-Grieskirchen, Austria
| | - P Koelblinger
- Department of Dermatology and Allergology, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - W Hitzl
- Research and Innovation Management, Biostatistics and Publication of Clinical Trial Studies, Paracelsus Medical University Salzburg, Salzburg, Austria
- Department of Ophthalmology and Optometry, Paracelsus Medical University Salzburg, Salzburg, Austria
- Research Program Experimental Ophthalmology and Glaucoma Research, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - M Laimer
- Department of Dermatology and Allergology, Paracelsus Medical University Salzburg, Salzburg, Austria
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4
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Liu Y, Chen S, Liu S, Wallace KL, Zille M, Zhang J, Wang J, Jiang C. T-cell receptor signaling modulated by the co-receptors: Potential targets for stroke treatment. Pharmacol Res 2023; 192:106797. [PMID: 37211238 DOI: 10.1016/j.phrs.2023.106797] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/02/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
Stroke is a severe and life-threatening disease, necessitating more research on new treatment strategies. Infiltrated T lymphocytes, an essential adaptive immune cell with extensive effector function, are crucially involved in post-stroke inflammation. Immediately after the initiation of the innate immune response triggered by microglia/macrophages, the adaptive immune response associated with T lymphocytes also participates in the complex pathophysiology of stroke and partially informs the outcome of stroke. Preclinical and clinical studies have revealed the conflicting roles of T cells in post-stroke inflammation and as potential therapeutic targets. Therefore, exploring the mechanisms that underlie the adaptive immune response associated with T lymphocytes in stroke is essential. The T-cell receptor (TCR) and its downstream signaling regulate T lymphocyte differentiation and activation. This review comprehensively summarizes the various molecules that regulate TCR signaling and the T-cell response. It covers both the co-stimulatory and co-inhibitory molecules and their roles in stroke. Because immunoregulatory therapies targeting TCR and its mediators have achieved great success in some proliferative diseases, this article also summarizes the advances in therapeutic strategies related to TCR signaling in lymphocytes after stroke, which can facilitate translation. DATA AVAILABILITY: No data was used for the research described in the article.
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Affiliation(s)
- Yuanyuan Liu
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, P. R. China
| | - Shuai Chen
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, P. R. China
| | - Simon Liu
- Medical Genomics Unit, National Human Genome Research Institute, Bethesda, MD, 20814, USA
| | - Kevin L Wallace
- College of Mathematical and Natural Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Marietta Zille
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, A-1090 Vienna, Austria
| | - Jiewen Zhang
- Department of Neurology, People's Hospital of Zhengzhou University, 450000, Zhengzhou, P. R. China.
| | - Jian Wang
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, P. R. China; Department of Anatomy, School of Basic Medical Sciences, Zhengzhou University, 450001, Zhengzhou, P. R. China.
| | - Chao Jiang
- Department of Neurology, The Fifth Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, P. R. China.
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Andrade DS, Terrematte P, Rennó-Costa C, Zilberberg A, Efroni S. GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data. BMC Bioinformatics 2023; 24:32. [PMID: 36717789 PMCID: PMC9885559 DOI: 10.1186/s12859-023-05155-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND In the global effort to discover biomarkers for cancer prognosis, prediction tools have become essential resources. TCR (T cell receptor) repertoires contain important features that differentiate healthy controls from cancer patients or differentiate outcomes for patients being treated with different drugs. Considering, tools that can easily and quickly generate and identify important features out of TCR repertoire data and build accurate classifiers to predict future outcomes are essential. RESULTS This paper introduces GENTLE (GENerator of T cell receptor repertoire features for machine LEarning): an open-source, user-friendly web-application tool that allows TCR repertoire researchers to discover important features; to create classifier models and evaluate them with metrics; and to quickly generate visualizations for data interpretations. We performed a case study with repertoires of TRegs (regulatory T cells) and TConvs (conventional T cells) from healthy controls versus patients with breast cancer. We showed that diversity features were able to distinguish between the groups. Moreover, the classifiers built with these features could correctly classify samples ('Healthy' or 'Breast Cancer')from the TRegs repertoire when trained with the TConvs repertoire, and from the TConvs repertoire when trained with the TRegs repertoire. CONCLUSION The paper walks through installing and using GENTLE and presents a case study and results to demonstrate the application's utility. GENTLE is geared towards any researcher working with TCR repertoire data and aims to discover predictive features from these data and build accurate classifiers. GENTLE is available on https://github.com/dhiego22/gentle and https://share.streamlit.io/dhiego22/gentle/main/gentle.py .
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Affiliation(s)
- Dhiego Souto Andrade
- grid.411233.60000 0000 9687 399XBioinformatics Multidisciplinary Environment (BioME), Metropole Digital Institute (IMD), Federal University of Rio Grande Do Norte (UFRN), Natal, 59078-970 Brazil
| | - Patrick Terrematte
- grid.411233.60000 0000 9687 399XBioinformatics Multidisciplinary Environment (BioME), Metropole Digital Institute (IMD), Federal University of Rio Grande Do Norte (UFRN), Natal, 59078-970 Brazil
| | - César Rennó-Costa
- grid.411233.60000 0000 9687 399XBioinformatics Multidisciplinary Environment (BioME), Metropole Digital Institute (IMD), Federal University of Rio Grande Do Norte (UFRN), Natal, 59078-970 Brazil
| | - Alona Zilberberg
- grid.22098.310000 0004 1937 0503The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- grid.22098.310000 0004 1937 0503The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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6
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Barchi JJ. Glycoconjugate Nanoparticle-Based Systems in Cancer Immunotherapy: Novel Designs and Recent Updates. Front Immunol 2022; 13:852147. [PMID: 35432351 PMCID: PMC9006936 DOI: 10.3389/fimmu.2022.852147] [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: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 11/15/2022] Open
Abstract
For many years, cell-surface glycans (in particular, Tumor-Associated Carbohydrate Antigens, TACAs) have been the target of both passive and active anticancer immunotherapeutic design. Recent advances in immunotherapy as a treatment for a variety of malignancies has revolutionized anti-tumor treatment regimens. Checkpoint inhibitors, Chimeric Antigen Receptor T-cells, Oncolytic virus therapy, monoclonal antibodies and vaccines have been developed and many approvals have led to remarkable outcomes in a subset of patients. However, many of these therapies are very selective for specific patient populations and hence the search for improved therapeutics and refinement of techniques for delivery are ongoing and fervent research areas. Most of these agents are directed at protein/peptide epitopes, but glycans–based targets are gaining in popularity, and a handful of approved immunotherapies owe their activity to oligosaccharide targets. In addition, nanotechnology and nanoparticle-derived systems can help improve the delivery of these agents to specific organs and cell types based on tumor-selective approaches. This review will first outline some of the historical beginnings of this research area and subsequently concentrate on the last 5 years of work. Based on the progress in therapeutic design, predictions can be made as to what the future holds for increasing the percentage of positive patient outcomes for optimized systems.
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Affiliation(s)
- Joseph J Barchi
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
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7
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Gerdemann U, Fleming RA, Kaminski J, McGuckin C, Rui X, Lane JF, Keskula P, Cagnin L, Shalek AK, Tkachev V, Kean LS. Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform. Front Immunol 2022; 12:804932. [PMID: 35154078 PMCID: PMC8825351 DOI: 10.3389/fimmu.2021.804932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/22/2021] [Indexed: 01/14/2023] Open
Abstract
T cell receptor (TCR) clonotype tracking is a powerful tool for interrogating T cell mediated immune processes. New methods to pair a single cell's transcriptional program with its TCR identity allow monitoring of T cell clonotype-specific transcriptional dynamics. While these technologies have been available for human and mouse T cells studies, they have not been developed for Rhesus Macaques (RM), a critical translational organism for autoimmune diseases, vaccine development and transplantation. We describe a new pipeline, 'RM-scTCR-Seq', which, for the first time, enables RM specific single cell TCR amplification, reconstruction and pairing of RM TCR's with their transcriptional profiles. We apply this method to a RM model of GVHD, and identify and track in vitro detected alloreactive clonotypes in GVHD target organs and explore their GVHD driven cytotoxic T cell signature. This novel, state-of-the-art platform fundamentally advances the utility of RM to study protective and pathogenic T cell responses.
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Affiliation(s)
- Ulrike Gerdemann
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Ryan A Fleming
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - James Kaminski
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Department of Chemistry, Institute for Medical Engineering and Science (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Cambridge, MA, United States
| | - Connor McGuckin
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Xianliang Rui
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Jennifer F Lane
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Paula Keskula
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Lorenzo Cagnin
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Department of Chemistry, Institute for Medical Engineering and Science (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Cambridge, MA, United States
| | - Victor Tkachev
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Leslie S Kean
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
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8
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Nageswaran G, Byrne S, Veeriah S, Chain B. The Intra-Tumoral T Cell Receptor Repertoire: Steps Towards a Useful Clinical Biomarker. Methods Mol Biol 2022; 2574:135-158. [PMID: 36087200 DOI: 10.1007/978-1-0716-2712-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Adaptive immunity recognizes and responds to tumors, although they are part of the immunological "self." T cells, both CD4+ and CD8+, play a key role in the process, and the specific set of receptors which recognize tumor antigens therefore has the potential to provide prognostic biomarkers for tracking tumor growth after cancer therapy, including immunotherapy. Most published data on the T cell repertoire continue to rely on commercial proprietary methods, which often do not allow access to the raw data, and are difficult to validate. We describe an open-source protocol for amplifying, sequencing, and analyzing T cell receptors which is economical, robust, sensitive, and versatile. The key experimental step is the ligation of a single-stranded oligonucleotide to the 3' end of the T cell receptor cDNA, which allows easy amplification of all possible rearrangements using only a single set of primers per locus, while simultaneously introducing a unique molecular identifier to label each starting cDNA molecule. After sequencing, this molecular identifier can be used to correct both sequence errors and the effects of differential PCR amplification efficiency, thus producing a more accurate measure of the true T cell receptor frequency within the sample. Samples are then tagged with unique pairs of indices, facilitating robotic scale-up and significantly reducing cross-sample contamination from index hopping. This method has been applied to the analysis of tumor-infiltrating lymphocytes and matched peripheral blood samples from patients with a variety of solid tumors.
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Affiliation(s)
| | | | | | - Benny Chain
- Division of Infection and Immunity, UCL, London, UK.
- The Cancer Institute, UCL, London, UK.
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9
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Nakayama M, Michels AW. Using the T Cell Receptor as a Biomarker in Type 1 Diabetes. Front Immunol 2021; 12:777788. [PMID: 34868047 PMCID: PMC8635517 DOI: 10.3389/fimmu.2021.777788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022] Open
Abstract
T cell receptors (TCRs) are unique markers that define antigen specificity for a given T cell. With the evolution of sequencing and computational analysis technologies, TCRs are now prime candidates for the development of next-generation non-cell based T cell biomarkers, which provide a surrogate measure to assess the presence of antigen-specific T cells. Type 1 diabetes (T1D), the immune-mediated form of diabetes, is a prototypical organ specific autoimmune disease in which T cells play a pivotal role in targeting pancreatic insulin-producing beta cells. While the disease is now predictable by measuring autoantibodies in the peripheral blood directed to beta cell proteins, there is an urgent need to develop T cell markers that recapitulate T cell activity in the pancreas and can be a measure of disease activity. This review focuses on the potential and challenges of developing TCR biomarkers for T1D. We summarize current knowledge about TCR repertoires and clonotypes specific for T1D and discuss challenges that are unique for autoimmune diabetes. Ultimately, the integration of large TCR datasets produced from individuals with and without T1D along with computational 'big data' analysis will facilitate the development of TCRs as potentially powerful biomarkers in the development of T1D.
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Affiliation(s)
- Maki Nakayama
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Aaron W Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
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