1
|
Aterido A, López-Lasanta M, Blanco F, Juan-Mas A, García-Vivar ML, Erra A, Pérez-García C, Sánchez-Fernández SÁ, Sanmartí R, Fernández-Nebro A, Alperi-López M, Tornero J, Ortiz AM, Fernández-Cid CM, Palau N, Pan W, Byrne-Steele M, Starenki D, Weber D, Rodriguez-Nunez I, Han J, Myers RM, Marsal S, Julià A. Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes. Genome Biol 2024; 25:68. [PMID: 38468286 PMCID: PMC10926600 DOI: 10.1186/s13059-024-03210-0] [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: 03/04/2022] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven chains that comprise the adaptive immune receptor repertoire (AIRR) in RA. RESULTS In comparison to controls, we show that RA patients have multiple and strong differences in the B cell receptor repertoire including reduced diversity as well as altered isotype, chain, and segment frequencies. We demonstrate that therapeutic tumor necrosis factor inhibition partially restores this alteration but find a profound difference in the underlying biochemical reactivities between responders and non-responders. Combining the AIRR with HLA typing, we identify the specific T cell receptor repertoire associated with disease risk variants. Integrating these features, we further develop a molecular classifier that shows the utility of the AIRR as a diagnostic tool. CONCLUSIONS Simultaneous sequencing of the seven chains of the human AIRR reveals novel features associated with the disease and clinically relevant phenotypes, including response to therapy. These findings show the unique potential of AIRR to address precision medicine in immune-related diseases.
Collapse
Affiliation(s)
- Adrià Aterido
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - María López-Lasanta
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - Francisco Blanco
- Rheumatology Department, Hospital Juan Canalejo, A Coruña, Spain
| | | | | | - Alba Erra
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
- Rheumatology Department, Hospital Sant Rafael, Barcelona, Spain
| | | | | | - Raimon Sanmartí
- Rheumatology Department, Hospital Clínic de Barcelona and IDIBAPS, Barcelona, Spain
| | | | | | - Jesús Tornero
- Rheumatology Department, Hospital Universitario Guadalajara, Guadalajara, Spain
| | - Ana María Ortiz
- Rheumatology Department, Hospital Universitario La Princesa, IIS La Princesa, Madrid, Spain
| | | | - Núria Palau
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | | | | | | | | | | | - Jian Han
- iRepertoire Inc, Huntsville, AL, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sara Marsal
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain.
| |
Collapse
|
2
|
Serebrovskaya EO, Bryushkova EA, Lukyanov DK, Mushenkova NV, Chudakov DM, Turchaninova MA. Toolkit for mapping the clonal landscape of tumor-infiltrating B cells. Semin Immunol 2024; 72:101864. [PMID: 38301345 DOI: 10.1016/j.smim.2024.101864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Our current understanding of whether B cell involvement in the tumor microenvironment benefits the patient or the tumor - in distinct cancers, subcohorts and individual patients - is quite limited. Both statements are probably true in most cases: certain clonal B cell populations contribute to the antitumor response, while others steer the immune response away from the desired mechanics. To step up to a new level of understanding and managing B cell behaviors in the tumor microenvironment, we need to rationally discern these roles, which are cumulatively defined by B cell clonal functional programs, specificities of their B cell receptors, specificities and isotypes of the antibodies they produce, and their spatial interactions within the tumor environment. Comprehensive analysis of these characteristics of clonal B cell populations is now becoming feasible with the development of a whole arsenal of advanced technical approaches, which include (1) methods of single-cell and spatial transcriptomics, genomics, and proteomics; (2) methods of massive identification of B cell specificities; (3) methods of deep error-free profiling of B cell receptor repertoires. Here we overview existing techniques, summarize their current application for B cells studies and propose promising future directions in advancing B cells exploration.
Collapse
Affiliation(s)
- E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, 119049, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| |
Collapse
|
3
|
Gallo E. Current advancements in B-cell receptor sequencing fast-track the development of synthetic antibodies. Mol Biol Rep 2024; 51:134. [PMID: 38236361 DOI: 10.1007/s11033-023-08941-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 01/19/2024]
Abstract
Synthetic antibodies (Abs) are a class of engineered proteins designed to mimic the functions of natural Abs. These are produced entirely in vitro, eliminating the need for an immune response. As such, synthetic Abs have transformed the traditional methods of raising Abs. Likewise, deep sequencing technologies have revolutionized genomics and molecular biology. These enable the rapid and cost-effective sequencing of DNA and RNA molecules. They have allowed for accurate and inexpensive analysis of entire genomes and transcriptomes. Notably, via deep sequencing it is now possible to sequence a person's entire B-cell receptor immune repertoire, termed BCR sequencing. This procedure allows for big data explorations of natural Abs associated with an immune response. Importantly, the identified sequences have the ability to improve the design and engineering of synthetic Abs by offering an initial sequence framework for downstream optimizations. Additionally, machine learning algorithms can be introduced to leverage the vast amount of BCR sequencing datasets to rapidly identify patterns hidden in big data to effectively make in silico predictions of antigen selective synthetic Abs. Thus, the convergence of BCR sequencing, machine learning, and synthetic Ab development has effectively promoted a new era in Ab therapeutics. The combination of these technologies is driving rapid advances in precision medicine, diagnostics, and personalized treatments.
Collapse
Affiliation(s)
- Eugenio Gallo
- Avance Biologicals, Department of Medicinal Chemistry, 950 Dupont Street, Toronto, ON, M6H 1Z2, Canada.
- RevivAb, Department of Protein Engineering, Av. Ipiranga, 6681, Partenon, Porto Alegre, RS, 90619-900, Brazil.
| |
Collapse
|
4
|
Rediti M, Fernandez-Martinez A, Venet D, Rothé F, Hoadley KA, Parker JS, Singh B, Campbell JD, Ballman KV, Hillman DW, Winer EP, El-Abed S, Piccart M, Di Cosimo S, Symmans WF, Krop IE, Salgado R, Loi S, Pusztai L, Perou CM, Carey LA, Sotiriou C. Immunological and clinicopathological features predict HER2-positive breast cancer prognosis in the neoadjuvant NeoALTTO and CALGB 40601 randomized trials. Nat Commun 2023; 14:7053. [PMID: 37923752 PMCID: PMC10624889 DOI: 10.1038/s41467-023-42635-2] [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: 12/01/2022] [Accepted: 10/16/2023] [Indexed: 11/06/2023] Open
Abstract
The identification of prognostic markers in patients receiving neoadjuvant therapy is crucial for treatment optimization in HER2-positive breast cancer, with the immune microenvironment being a key factor. Here, we investigate the complexity of B and T cell receptor (BCR and TCR) repertoires in the context of two phase III trials, NeoALTTO and CALGB 40601, evaluating neoadjuvant paclitaxel with trastuzumab and/or lapatinib in women with HER2-positive breast cancer. BCR features, particularly the number of reads and clones, evenness and Gini index, are heterogeneous according to hormone receptor status and PAM50 subtypes. Moreover, BCR measures describing clonal expansion, namely evenness and Gini index, are independent prognostic factors. We present a model developed in NeoALTTO and validated in CALGB 40601 that can predict event-free survival (EFS) by integrating hormone receptor and clinical nodal status, breast pathological complete response (pCR), stromal tumor-infiltrating lymphocyte levels (%) and BCR repertoire evenness. A prognostic score derived from the model and including those variables, HER2-EveNT, allows the identification of patients with 5-year EFS > 90%, and, in those not achieving pCR, of a subgroup of immune-enriched tumors with an excellent outcome despite residual disease.
Collapse
Affiliation(s)
- Mattia Rediti
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - David Venet
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jordan D Campbell
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Karla V Ballman
- Alliance Statistics and Data Management Center, Weill Cornell Medicine, New York, NY, USA
| | - David W Hillman
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Eric P Winer
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | - Martine Piccart
- Medical Oncology Department, Institut Jules Bordet and l'Université Libre de Bruxelles (U.L.B.), Brussels, Belgium
| | - Serena Di Cosimo
- Integrated biology platform unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - William Fraser Symmans
- Department of Pathology, University of Texas, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ian E Krop
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Ziekenhuizen, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Lajos Pusztai
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Lisa A Carey
- Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Hôpital Universitaire de Bruxelles (H.U.B), Université Libre de Bruxelles (ULB), Brussels, Belgium.
| |
Collapse
|
5
|
Min Q, Csomos K, Li Y, Dong L, Hu Z, Meng X, Yu M, Walter JE, Wang JY. B cell abnormalities and autoantibody production in patients with partial RAG deficiency. Front Immunol 2023; 14:1155380. [PMID: 37475856 PMCID: PMC10354446 DOI: 10.3389/fimmu.2023.1155380] [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: 01/31/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Mutations in the recombination activating gene 1 (RAG1) and RAG2 in humans are associated with a broad spectrum of clinical phenotypes, from severe combined immunodeficiency to immune dysregulation. Partial (hypomorphic) RAG deficiency (pRD) in particular, frequently leads to hyperinflammation and autoimmunity, with several underlying intrinsic and extrinsic mechanisms causing a break in tolerance centrally and peripherally during T and B cell development. However, the relative contributions of these processes to immune dysregulation remain unclear. In this review, we specifically focus on the recently described tolerance break and B cell abnormalities, as well as consequent molecular and cellular mechanisms of autoantibody production in patients with pRD.
Collapse
Affiliation(s)
- Qing Min
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Krisztian Csomos
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children's Hospital, St. Petersburg, FL, United States
| | - Yaxuan Li
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lulu Dong
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ziying Hu
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xin Meng
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Meiping Yu
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jolan E Walter
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children's Hospital, St. Petersburg, FL, United States
- Division of Pediatric Allergy/Immunology, Massachusetts General Hospital for Children, Boston, MA, United States
| | - Ji-Yang Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China
| |
Collapse
|
6
|
Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. BMC Genomics 2023; 24:349. [PMID: 37365517 DOI: 10.1186/s12864-023-09424-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
T cell receptor repertoires can be profiled using next generation sequencing (NGS) to measure and monitor adaptive dynamical changes in response to disease and other perturbations. Genomic DNA-based bulk sequencing is cost-effective but necessitates multiplex target amplification using multiple primer pairs with highly variable amplification efficiencies. Here, we utilize an equimolar primer mixture and propose a single statistical normalization step that efficiently corrects for amplification bias post sequencing. Using samples analyzed by both our open protocol and a commercial solution, we show high concordance between bulk clonality metrics. This approach is an inexpensive and open-source alternative to commercial solutions.
Collapse
Affiliation(s)
- Burcu Gurun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- School of Medicine, Oregon Health and Science University, Portland, OR, USA.
| | - Wesley Horton
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Dhaarini Murugan
- Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Biqing Zhu
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Patrick Leyshock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Sushil Kumar
- Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Katelyn T Byrne
- Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert H Vonderheide
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Motomi Mori
- Department of Biostatistics, St. Jude's Children's Research Hospital, Memphis, TN, USA
| | - Paul T Spellman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Lisa M Coussens
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
7
|
Moulana A, Dupic T, Phillips AM, Desai MM. Genotype-phenotype landscapes for immune-pathogen coevolution. Trends Immunol 2023; 44:384-396. [PMID: 37024340 PMCID: PMC10147585 DOI: 10.1016/j.it.2023.03.006] [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: 02/03/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/07/2023]
Abstract
Our immune systems constantly coevolve with the pathogens that challenge them, as pathogens adapt to evade our defense responses, with our immune repertoires shifting in turn. These coevolutionary dynamics take place across a vast and high-dimensional landscape of potential pathogen and immune receptor sequence variants. Mapping the relationship between these genotypes and the phenotypes that determine immune-pathogen interactions is crucial for understanding, predicting, and controlling disease. Here, we review recent developments applying high-throughput methods to create large libraries of immune receptor and pathogen protein sequence variants and measure relevant phenotypes. We describe several approaches that probe different regions of the high-dimensional sequence space and comment on how combinations of these methods may offer novel insight into immune-pathogen coevolution.
Collapse
Affiliation(s)
- Alief Moulana
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Dupic
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Angela M Phillips
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA; Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
8
|
Xu AM, Chour W, DeLucia DC, Su Y, Pavlovitch-Bedzyk AJ, Ng R, Rasheed Y, Davis MM, Lee JK, Heath JR. Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities. Cell Syst 2023; 14:273-284.e5. [PMID: 37001518 PMCID: PMC10355346 DOI: 10.1016/j.cels.2023.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 09/01/2022] [Accepted: 03/01/2023] [Indexed: 04/22/2023]
Abstract
Antigen-specific T cell receptor (TCR) sequences can have prognostic, predictive, and therapeutic value, but decoding the specificity of TCR recognition remains challenging. Unlike DNA strands that base pair, TCRs bind to their targets with different orientations and different lengths, which complicates comparisons. We present scanning parametrized by normalized TCR length (SPAN-TCR) to analyze antigen-specific TCR CDR3 sequences and identify patterns driving TCR-pMHC specificity. Using entropic analysis, SPAN-TCR identifies 2-mer motifs that decrease the diversity (entropy) of CDR3s. These motifs are the most common patterns that can predict CDR3 composition, and we identify "essential" motifs that decrease entropy in the same CDR3 α or β chain containing the 2-mer, and "super-essential" motifs that decrease entropy in both chains. Molecular dynamics analysis further suggests that these motifs may play important roles in binding. We then employ SPAN-TCR to resolve similarities in TCR repertoires against different antigens using public databases of TCR sequences.
Collapse
Affiliation(s)
- Alexander M Xu
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 91125, USA
| | - Diana C DeLucia
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Rachel Ng
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yusuf Rasheed
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Mark M Davis
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA 98109, USA.
| |
Collapse
|
9
|
Vujović M, Marcatili P, Chain B, Kaplinsky J, Andresen TL. Signatures of T cell immunity revealed using sequence similarity with TCRDivER algorithm. Commun Biol 2023; 6:357. [PMID: 37002292 PMCID: PMC10066310 DOI: 10.1038/s42003-023-04702-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Changes in the T cell receptor (TCR) repertoires have become important markers for monitoring disease or therapy progression. With the rise of immunotherapy usage in cancer, infectious and autoimmune disease, accurate assessment and comparison of the "state" of the TCR repertoire has become paramount. One important driver of change within the repertoire is T cell proliferation following immunisation. A way of monitoring this is by investigating large clones of individual T cells believed to bind epitopes connected to the disease. However, as a single target can be bound by many different TCRs, monitoring individual clones cannot fully account for T cell cross-reactivity. Moreover, T cells responding to the same target often exhibit higher sequence similarity, which highlights the importance of accounting for TCR similarity within the repertoire. This complexity of binding relationships between a TCR and its target convolutes comparison of immune responses between individuals or comparisons of TCR repertoires at different timepoints. Here we propose TCRDivER algorithm (T cell Receptor Diversity Estimates for Repertoires), a global method of T cell repertoire comparison using diversity profiles sensitive to both clone size and sequence similarity. This approach allowed for distinction between spleen TCR repertoires of immunised and non-immunised mice, showing the need for including both facets of repertoire changes simultaneously. The analysis revealed biologically interpretable relationships between sequence similarity and clonality. These aid in understanding differences and separation of repertoires stemming from different biological context. With the rise of availability of sequencing data we expect our tool to find broad usage in clinical and research applications.
Collapse
Affiliation(s)
- Milena Vujović
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Paolo Marcatili
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Benny Chain
- UCL Division of Infection and Immunity, University College London, London, UK.
| | - Joseph Kaplinsky
- Ludwig Institute for Cancer Research Ltd, University of Oxford, Nuffield Department of Medicine, Oxford, UK.
| | - Thomas Lars Andresen
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
| |
Collapse
|
10
|
García-Valiente R, Merino Tejero E, Stratigopoulou M, Balashova D, Jongejan A, Lashgari D, Pélissier A, Caniels TG, Claireaux MAF, Musters A, van Gils MJ, Rodríguez Martínez M, de Vries N, Meyer-Hermann M, Guikema JEJ, Hoefsloot H, van Kampen AHC. Understanding repertoire sequencing data through a multiscale computational model of the germinal center. NPJ Syst Biol Appl 2023; 9:8. [PMID: 36927990 PMCID: PMC10019394 DOI: 10.1038/s41540-023-00271-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Sequencing of B-cell and T-cell immune receptor repertoires helps us to understand the adaptive immune response, although it only provides information about the clonotypes (lineages) and their frequencies and not about, for example, their affinity or antigen (Ag) specificity. To further characterize the identified clones, usually with special attention to the particularly abundant ones (dominant), additional time-consuming or expensive experiments are generally required. Here, we present an extension of a multiscale model of the germinal center (GC) that we previously developed to gain more insight in B-cell repertoires. We compare the extent that these simulated repertoires deviate from experimental repertoires established from single GCs, blood, or tissue. Our simulations show that there is a limited correlation between clonal abundance and affinity and that there is large affinity variability among same-ancestor (same-clone) subclones. Our simulations suggest that low-abundance clones and subclones, might also be of interest since they may have high affinity for the Ag. We show that the fraction of plasma cells (PCs) with high B-cell receptor (BcR) mRNA content in the GC does not significantly affect the number of dominant clones derived from single GCs by sequencing BcR mRNAs. Results from these simulations guide data interpretation and the design of follow-up experiments.
Collapse
Affiliation(s)
- Rodrigo García-Valiente
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Elena Merino Tejero
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Maria Stratigopoulou
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Daria Balashova
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Danial Lashgari
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aurélien Pélissier
- IBM Research Zurich, 8803, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Tom G Caniels
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Mathieu A F Claireaux
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Anne Musters
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | | | - Niek de Vries
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Michael Meyer-Hermann
- Department for Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jeroen E J Guikema
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Pathology, Lymphoma and Myeloma Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Huub Hoefsloot
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Antoine H C van Kampen
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands.
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
11
|
Park M, de Villavicencio Diaz TN, Lange V, Wu L, Le Bihan T, Ma B. Exploring the sheep (Ovis aries) immunoglobulin repertoire by next generation sequencing. Mol Immunol 2023; 156:20-30. [PMID: 36867981 DOI: 10.1016/j.molimm.2023.02.008] [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: 12/15/2022] [Revised: 02/10/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the way we determine the antibody repertoires encoded by B cells in the blood or lymphoid organs and transformed our understanding of adaptive immune responses in many species. Sheep (Ovis aries) have been widely used as a host for therapeutic antibody production since the early 1980s, however, little is known about their immune repertoires or immunological processes affecting the antibody generation. The objective of this study was to employ NGS for a comprehensive analysis of immunoglobulin heavy and light chain repertoires in four healthy sheep. We obtained > 90 % complete antibody sequences and nearly 130,000, 48,000 and 218,000 unique CDR3 reads for the heavy chain (IGH), kappa chain (IGK), and lambda chain (IGL) loci, respectively. Consistent with other species, we observed biased usage of germline variable (V), diversity (D) and joining (J) genes in the heavy and kappa loci, but not in the lambda loci. Moreover, the enormous diversity of CDR3 sequences was observed through sequence clustering and convergent recombination. These data will build a foundation for future studies investigating immune repertoires in health and disease as well as contribute to further refinement of ovine-derived therapeutic antibody drugs.
Collapse
Affiliation(s)
| | | | | | - Lin Wu
- Rapid Novor Inc., Kitchener, Ontario, Canada
| | | | - Bin Ma
- Rapid Novor Inc., Kitchener, Ontario, Canada
| |
Collapse
|
12
|
Gurun B, Horton W, Murugan D, Zhu B, Leyshock P, Kumar S, Byrne KT, Vonderheide RH, Margolin AA, Mori M, Spellman PT, Coussens LM, Speed TP. An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. RESEARCH SQUARE 2023:rs.3.rs-2140339. [PMID: 36824803 PMCID: PMC9949261 DOI: 10.21203/rs.3.rs-2140339/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
T cell receptor repertoires can be profiled using next generation sequencing (NGS) to measure and monitor adaptive dynamical changes in response to disease and other perturbations. Genomic DNA-based bulk sequencing is cost-effective but necessitates multiplex target amplification using multiple primer pairs with highly variable amplification efficiencies. Here, we utilize an equimolar primer mixture and propose a single statistical normalization step that efficiently corrects for amplification bias post sequencing. Using samples analyzed by both our open protocol and a commercial solution, we show high concordance between bulk clonality metrics. This approach is an inexpensive and open-source alternative to commercial solutions.
Collapse
|
13
|
Ge H, Ferris RL, Wang JH. Cetuximab Responses in Patients with HNSCC Correlate to Clonal Expansion Feature of Peripheral and Tumor-Infiltrating T Cells with Top T-Cell Receptor Clonotypes. Clin Cancer Res 2023; 29:647-658. [PMID: 36315045 PMCID: PMC9898159 DOI: 10.1158/1078-0432.ccr-22-2355] [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: 07/29/2022] [Revised: 09/21/2022] [Accepted: 10/27/2022] [Indexed: 12/23/2022]
Abstract
PURPOSE Cetuximab is a standard-of-care treatment for head and neck squamous cell carcinoma (HNSCC). Well-defined correlative markers of therapeutic responses are still lacking. Characterizing dynamic changes of T-cell receptor (TCR) repertoire in peripheral blood and tumor tissue may facilitate developing markers for cetuximab response in HNSCCs. EXPERIMENTAL DESIGN We analyzed high-throughput TCRβ sequencing data generated with ImmunoSEQ platform using peripheral blood mononuclear cells (PBMC) and tumor-infiltrating lymphocytes (TIL) from patients with HNSCC before and after cetuximab treatment (pre-/post-PBMC vs. pre-/post-TIL). Multiple analytic approaches were employed to normalize sequencing data. RESULTS Normalized TCR richness was significantly lower in post-TIL than pre-TIL, suggesting that cetuximab reduced TCR diversity and promoted TCR expansion in TIL samples, regardless of response status. The magnitude of clonal expansion (defined as expansion rate) in top 20 TCR clonotypes was significantly higher in responder PBMC with or without normalization, and in responder TIL upon normalization, than nonresponder ones. Notably, the expanded top 20 or top 50 TCR clonotypes overlapped between PBMC and TIL samples, which occurred significantly more frequently in responders than nonresponders. CONCLUSIONS Patients with cetuximab-treated HNSCC harbor dynamic changes of TCR repertoires correlative to therapeutic responses. The expansion rate of top TCR clonotypes in peripheral blood may serve as a minimally invasive, readily accessible, and feasible marker for predicting cetuximab responses in HNSCCs and beyond, and the expansion rate of top TCR clonotypes in TILs and their overlapping probability between PBMC and TIL may serve as additional predictive markers. Our study also highlights the importance of data normalization for TCR repertoire analysis.
Collapse
Affiliation(s)
- Huaibin Ge
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Robert L. Ferris
- UPMC Hillman Cancer Center, Department of Otolaryngology, University of Pittsburgh, Pittsburgh, Pennsylvania, PA 15213.,Correspondence should be addressed to Robert L. Ferris, UPMC Hillman Cancer Center Cancer Pavilion, Suite 500, 5150 Centre Avenue, Pittsburgh, PA 15232; Tel: 412-623-3205; or Jing H Wang, UPMC Hillman Cancer Center Research Pavilion, 5117 Centre Ave, Suite 1.16, Pittsburgh, PA, 15213, Tel: 412-864-7728;
| | - Jing H Wang
- UPMC Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213.,Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213.,Correspondence should be addressed to Robert L. Ferris, UPMC Hillman Cancer Center Cancer Pavilion, Suite 500, 5150 Centre Avenue, Pittsburgh, PA 15232; Tel: 412-623-3205; or Jing H Wang, UPMC Hillman Cancer Center Research Pavilion, 5117 Centre Ave, Suite 1.16, Pittsburgh, PA, 15213, Tel: 412-864-7728;
| |
Collapse
|
14
|
Hayashi S, Ishikawa S. Analyzing Antibody Repertoire Using Next-Generation Sequencing and Machine Learning. Methods Mol Biol 2023; 2552:465-473. [PMID: 36346609 DOI: 10.1007/978-1-0716-2609-2_26] [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] [Indexed: 06/16/2023]
Abstract
Advances in high-throughput sequencing technologies have enabled comprehensive sequencing of the immune repertoire. Since repertoire analysis can help to explain the relationship between the immune system and diseases, several methods have been developed for repertoire analysis. Here, using simulated and real-world datasets, we describe how to use DeepRC, a method that applies cutting-edge machine learning techniques.
Collapse
Affiliation(s)
- Shuto Hayashi
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
15
|
Katoh H, Komura D, Furuya G, Ishikawa S. Immune repertoire profiling for disease pathobiology. Pathol Int 2023; 73:1-11. [PMID: 36342353 PMCID: PMC10099665 DOI: 10.1111/pin.13284] [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: 05/24/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Lymphocytes consist of highly heterogeneous populations, each expressing a specific cell surface receptor corresponding to a particular antigen. Lymphocytes are both the cause and regulator of various diseases, including autoimmune/allergic diseases, lifestyle diseases, neurodegenerative diseases, and cancers. Recently, immune repertoire sequencing has attracted much attention because it helps obtain global profiles of the immune receptor sequences of infiltrating T and B cells in specimens. Immune repertoire sequencing not only helps deepen our understanding of the molecular mechanisms of immune-related pathology but also assists in discovering novel therapeutic modalities for diseases, thereby shedding colorful light on otherwise tiny monotonous cells when observed under a microscope. In this review article, we introduce and detail the background and methodology of immune repertoire sequencing and summarize recent scientific achievements in association with human diseases. Future perspectives on this genetic technique in the field of histopathological research will also be discussed.
Collapse
Affiliation(s)
- Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genta Furuya
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
16
|
Kanduri C, Scheffer L, Pavlović M, Rand KD, Chernigovskaya M, Pirvandy O, Yaari G, Greiff V, Sandve GK. simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods. Gigascience 2022; 12:giad074. [PMID: 37848619 PMCID: PMC10580376 DOI: 10.1093/gigascience/giad074] [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: 02/21/2023] [Revised: 07/20/2023] [Accepted: 08/29/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Machine learning (ML) has gained significant attention for classifying immune states in adaptive immune receptor repertoires (AIRRs) to support the advancement of immunodiagnostics and therapeutics. Simulated data are crucial for the rigorous benchmarking of AIRR-ML methods. Existing approaches to generating synthetic benchmarking datasets result in the generation of naive repertoires missing the key feature of many shared receptor sequences (selected for common antigens) found in antigen-experienced repertoires. RESULTS We demonstrate that a common approach to generating simulated AIRR benchmark datasets can introduce biases, which may be exploited for undesired shortcut learning by certain ML methods. To mitigate undesirable access to true signals in simulated AIRR datasets, we devised a simulation strategy (simAIRR) that constructs antigen-experienced-like repertoires with a realistic overlap of receptor sequences. simAIRR can be used for constructing AIRR-level benchmarks based on a range of assumptions (or experimental data sources) for what constitutes receptor-level immune signals. This includes the possibility of making or not making any prior assumptions regarding the similarity or commonality of immune state-associated sequences that will be used as true signals. We demonstrate the real-world realism of our proposed simulation approach by showing that basic ML strategies perform similarly on simAIRR-generated and real-world experimental AIRR datasets. CONCLUSIONS This study sheds light on the potential shortcut learning opportunities for ML methods that can arise with the state-of-the-art way of simulating AIRR datasets. simAIRR is available as a Python package: https://github.com/KanduriC/simAIRR.
Collapse
Affiliation(s)
- Chakravarthi Kanduri
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0373 Oslo, Norway
- UiORealArt Convergence Environment, University of Oslo, 0373 Oslo, Norway
| | - Lonneke Scheffer
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0373 Oslo, Norway
| | - Milena Pavlović
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0373 Oslo, Norway
- UiORealArt Convergence Environment, University of Oslo, 0373 Oslo, Norway
| | - Knut Dagestad Rand
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0373 Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology and Oslo University Hospital, University of Oslo, 0373 Oslo, Norway
| | - Oz Pirvandy
- Faculty of Engineering, Bar-Ilan University, 5290002, Israel
| | - Gur Yaari
- Faculty of Engineering, Bar-Ilan University, 5290002, Israel
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, 0373 Oslo, Norway
| | - Geir K Sandve
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0373 Oslo, Norway
- UiORealArt Convergence Environment, University of Oslo, 0373 Oslo, Norway
| |
Collapse
|
17
|
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: 17] [Impact Index Per Article: 8.5] [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
|
18
|
Zhuo Y, Yang X, Shuai P, Yang L, Wen X, Zhong X, Yang S, Xu S, Liu Y, Zhang Z. Evaluation and comparison of adaptive immunity through analyzing the diversities and clonalities of T-cell receptor repertoires in the peripheral blood. Front Immunol 2022; 13:916430. [PMID: 36159829 PMCID: PMC9493076 DOI: 10.3389/fimmu.2022.916430] [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: 04/20/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
The adaptive immune system plays an important role in defending against different kinds of diseases, including infection and cancer. There has been a longtime need for a simple method to quantitatively evaluate the potency of adaptive immunity in our bodies. The tremendously diversified T-cell receptor (TCR) repertoires are the foundation of the adaptive immune system. In this study, we analyzed the expressed TCRβ repertoires in the peripheral blood of 582 healthy donors and 60 cancer patients. The TCR repertoire in each individual is different, with different usages of TCR Vβ and Jβ genes. Importantly, the TCR diversity and clonality change along with age and disease situation. Most elder individuals and cancer patients have elevated numbers of large TCRβ clones and reduced numbers of shared common clones, and thus, they have very low TCR diversity index (D50) values. These results reveal the alteration of the expressed TCRβ repertoire with aging and oncogenesis, and thus, we hypothesize that the TCR diversity and clonality in the peripheral blood might be used to evaluate and compare the adaptive immunities among different individuals in clinical practice.
Collapse
Affiliation(s)
- Yue Zhuo
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xin Yang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Ping Shuai
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Liangliang Yang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xueping Wen
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Xuemei Zhong
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Shihan Yang
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Shaoxian Xu
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuping Liu
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Zhixin Zhang, ; Yuping Liu,
| | - Zhixin Zhang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Zhixin Zhang, ; Yuping Liu,
| |
Collapse
|
19
|
Lan X, Ruminy P, Bohers E, Marchand V, Viennot M, Viailly PJ, Etancelin P, Tilly H, Mihailescu S, Bouclet F, Leprêtre S, Jardin F. 5’ Rapid amplification of cDNA ends (5’RACE): A simpler method to analyze immunoglobulin genes and discover the value of the light chain in chronic lymphocytic leukemia. Leuk Res 2022; 123:106952. [DOI: 10.1016/j.leukres.2022.106952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/04/2022] [Accepted: 09/15/2022] [Indexed: 12/01/2022]
|
20
|
T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer. Int J Mol Sci 2022; 23:ijms23158590. [PMID: 35955721 PMCID: PMC9369427 DOI: 10.3390/ijms23158590] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
The immune system is a dynamic feature of each individual and a footprint of our unique internal and external exposures. Indeed, the type and level of exposure to physical and biological agents shape the development and behavior of this complex and diffuse system. Many pathological conditions depend on how our immune system responds or does not respond to a pathogen or a disease or on how the regulation of immunity is altered by the disease itself. T-cells are important players in adaptive immunity and, together with B-cells, define specificity and monitor the internal and external signals that our organism perceives through its specific receptors, TCRs and BCRs, respectively. Today, high-throughput sequencing (HTS) applied to the TCR repertoire has opened a window of opportunity to disclose T-cell repertoire development and behavior down to the clonal level. Although TCR repertoire sequencing is easily accessible today, it is important to deeply understand the available technologies for choosing the best fit for the specific experimental needs and questions. Here, we provide an updated overview of TCR repertoire sequencing strategies, providers and applications to infectious diseases and cancer to guide researchers’ choice through the multitude of available options. The possibility of extending the TCR repertoire to HLA characterization will be of pivotal importance in the near future to understand how specific HLA genes shape T-cell responses in different pathological contexts and will add a level of comprehension that was unthinkable just a few years ago.
Collapse
|
21
|
Exploring the Immunomodulatory Aspect of Mesenchymal Stem Cells for Treatment of Severe Coronavirus Disease 19. Cells 2022; 11:cells11142175. [PMID: 35883618 PMCID: PMC9322532 DOI: 10.3390/cells11142175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/06/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an enveloped, positive sense, single stranded RNA (+ssRNA) virus, belonging to the genus Betacoronavirus and family Coronaviridae. It is primarily transmitted from infected persons to healthy ones through inhalation of virus-laden respiratory droplets. After an average incubation period of 2–14 days, the majority of infected individuals remain asymptomatic and/or mildly symptomatic, whereas the remaining individuals manifest a myriad of clinical symptoms, including fever, sore throat, dry cough, fatigue, chest pain, and breathlessness. SARS-CoV-2 exploits the angiotensin converting enzyme 2 (ACE-2) receptor for cellular invasion, and lungs are amongst the most adversely affected organs in the body. Thereupon, immune responses are elicited, which may devolve into a cytokine storm characterized by enhanced secretion of multitude of inflammatory cytokines/chemokines and growth factors, such as interleukin (IL)-2, IL-6, IL-7, IL-8, IL-9, tumor necrosis factor alpha (TNF-α), granulocyte colony-stimulating factor (GCSF), basic fibroblast growth factor 2 (bFGF2), monocyte chemotactic protein-1 (MCP1), interferon-inducible protein 10 (IP10), macrophage inflammatory protein 1A (MIP1A), platelet-derived growth factor subunit B (PDGFB), and vascular endothelial factor (VEGF)-A. The systemic persistence of inflammatory molecules causes widespread histological injury, leading to functional deterioration of the infected organ(s). Although multiple treatment modalities with varying effectiveness are being employed, nevertheless, there is no curative COVID-19 therapy available to date. In this regard, one plausible supportive therapeutic modality may involve administration of mesenchymal stem cells (MSCs) and/or MSC-derived bioactive factors-based secretome to critically ill COVID-19 patients with the intention of accomplishing better clinical outcome owing to their empirically established beneficial effects. MSCs are well established adult stem cells (ASCs) with respect to their immunomodulatory, anti-inflammatory, anti-oxidative, anti-apoptotic, pro-angiogenic, and pro-regenerative properties. The immunomodulatory capabilities of MSCs are not constitutive but rather are highly dependent on a holistic niche. Following intravenous infusion, MSCs are known to undergo considerable histological trapping in the lungs and, therefore, become well positioned to directly engage with lung infiltrating immune cells, and thereby mitigate excessive inflammation and reverse/regenerate damaged alveolar epithelial cells and associated tissue post SARS-CoV-2 infection. Considering the myriad of abovementioned biologically beneficial properties and emerging translational insights, MSCs may be used as potential supportive therapy to counteract cytokine storms and reduce disease severity, thereby facilitating speedy recovery and health restoration.
Collapse
|
22
|
Kanduri C, Pavlović M, Scheffer L, Motwani K, Chernigovskaya M, Greiff V, Sandve GK. Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification. Gigascience 2022; 11:6593147. [PMID: 35639633 PMCID: PMC9154052 DOI: 10.1093/gigascience/giac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 12/23/2021] [Accepted: 04/08/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Machine learning (ML) methodology development for the classification of immune states in adaptive immune receptor repertoires (AIRRs) has seen a recent surge of interest. However, so far, there does not exist a systematic evaluation of scenarios where classical ML methods (such as penalized logistic regression) already perform adequately for AIRR classification. This hinders investigative reorientation to those scenarios where method development of more sophisticated ML approaches may be required. RESULTS To identify those scenarios where a baseline ML method is able to perform well for AIRR classification, we generated a collection of synthetic AIRR benchmark data sets encompassing a wide range of data set architecture-associated and immune state-associated sequence patterns (signal) complexity. We trained ≈1,700 ML models with varying assumptions regarding immune signal on ≈1,000 data sets with a total of ≈250,000 AIRRs containing ≈46 billion TCRβ CDR3 amino acid sequences, thereby surpassing the sample sizes of current state-of-the-art AIRR-ML setups by two orders of magnitude. We found that L1-penalized logistic regression achieved high prediction accuracy even when the immune signal occurs only in 1 out of 50,000 AIR sequences. CONCLUSIONS We provide a reference benchmark to guide new AIRR-ML classification methodology by (i) identifying those scenarios characterized by immune signal and data set complexity, where baseline methods already achieve high prediction accuracy, and (ii) facilitating realistic expectations of the performance of AIRR-ML models given training data set properties and assumptions. Our study serves as a template for defining specialized AIRR benchmark data sets for comprehensive benchmarking of AIRR-ML methods.
Collapse
Affiliation(s)
- Chakravarthi Kanduri
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo 0373, Norway
| | - Milena Pavlović
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo 0373, Norway
| | - Lonneke Scheffer
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo 0373, Norway
| | - Keshav Motwani
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, FL 32610, USA
| | - Maria Chernigovskaya
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, 0372, Norway
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, 0372, Norway
| | - Geir K Sandve
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo 0373, Norway
| |
Collapse
|
23
|
Xu AM, Li D, Ebinger JE, Mengesha E, Elyanow R, Gittelman RM, Chapman H, Joung S, Botwin GJ, Pozdnyakova V, Debbas P, Mujukian A, Prostko JC, Frias EC, Stewart JL, Horizon AA, Merin N, Sobhani K, Figueiredo JC, Cheng S, Kaplan IM, McGovern DPB, Merchant A, Melmed GY, Braun J. Differences in SARS-CoV-2 Vaccine Response Dynamics Between Class-I- and Class-II-Specific T-Cell Receptors in Inflammatory Bowel Disease. Front Immunol 2022; 13:880190. [PMID: 35464463 PMCID: PMC9024211 DOI: 10.3389/fimmu.2022.880190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/18/2022] [Indexed: 12/01/2022] Open
Abstract
T-cells specifically bind antigens to induce adaptive immune responses using highly specific molecular recognition, and a diverse T-cell repertoire with expansion of antigen-specific clones can indicate robust immune responses after infection or vaccination. For patients with inflammatory bowel disease (IBD), a spectrum of chronic intestinal inflammatory diseases usually requiring immunomodulatory treatment, the T-cell response has not been well characterized. Understanding the patient factors that result in strong vaccination responses is critical to guiding vaccination schedules and identifying mechanisms of T-cell responses in IBD and other immune-mediated conditions. Here we used T-cell receptor sequencing to show that T-cell responses in an IBD cohort were influenced by demographic and immune factors, relative to a control cohort of health care workers (HCWs). Subjects were sampled at the time of SARS-CoV-2 vaccination, and longitudinally afterwards; TCR Vβ gene repertoires were sequenced and analyzed for COVID-19-specific clones. We observed significant differences in the overall strength of the T-cell response by age and vaccine type. We further stratified the T-cell response into Class-I- and Class-II-specific responses, showing that Ad26.COV2.S vector vaccine induced Class-I-biased T-cell responses, whereas mRNA vaccine types led to different responses, with mRNA-1273 vaccine inducing a more Class-I-deficient T-cell response compared to BNT162b2. Finally, we showed that these T-cell patterns were consistent with antibody levels from the same patients. Our results account for the surprising success of vaccination in nominally immuno-compromised IBD patients, while suggesting that a subset of IBD patients prone to deficiencies in T-cell response may warrant enhanced booster protocols.
Collapse
Affiliation(s)
- Alexander M. Xu
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | | | | | - Heidi Chapman
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Gregory J. Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Philip Debbas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - John C. Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - Edwin C. Frias
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - James L. Stewart
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - Arash A. Horizon
- Center for Rheumatology Medical Group, Los Angeles, CA, United States
| | - Noah Merin
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jane C. Figueiredo
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Ian M. Kaplan
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Dermot P. B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Akil Merchant
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Gil Y. Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| |
Collapse
|
24
|
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
|
25
|
Baldwin J, Piplani S, Sakala IG, Honda-Okubo Y, Li L, Petrovsky N. Rapid development of analytical methods for evaluating pandemic vaccines: a COVID-19 perspective. Bioanalysis 2021; 13:1805-1826. [PMID: 34645288 PMCID: PMC8516068 DOI: 10.4155/bio-2021-0096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022] Open
Abstract
Vaccines are key in charting a path out of the COVID-19 pandemic. However, development of new vaccines is highly dependent on availability of analytical methods for their design and evaluation. This paper highlights the challenges presented in having to rapidly develop vaccine analytical tools during an ongoing pandemic, including the need to address progressive virus mutation and adaptation which can render initial assays unreliable or redundant. It also discusses the potential of new computational modeling techniques to model and analyze key viral proteins and their attributes to assist vaccine production and assay design. It then reviews the current range of analytical tools available for COVID-19 vaccine application, ranging from in vitro assays for immunogen characterization to assays to measure vaccine responses in vivo. Finally, it provides a future perspective for COVID-19 vaccine analytical tools and attempts to predict how the field might evolve over the next 5-10 years.
Collapse
Affiliation(s)
- Jeremy Baldwin
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
| | - Sakshi Piplani
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Isaac G Sakala
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Yoshikazu Honda-Okubo
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Lei Li
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| | - Nikolai Petrovsky
- Vaxine Pty Ltd, 11 Walkley Avenue, Adelaide, 5046, Australia
- College of Medicine & Public Health, Flinders University, Adelaide, 5042, Australia
| |
Collapse
|
26
|
Kos IA, Thurner L, Bittenbring JT, Christofyllakis K, Kaddu-Mulindwa D. Advances in Lymphoma Molecular Diagnostics. Diagnostics (Basel) 2021; 11:diagnostics11122174. [PMID: 34943410 PMCID: PMC8699850 DOI: 10.3390/diagnostics11122174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Lymphomas encompass a diverse group of malignant lymphoid neoplasms. Over recent years much scientific effort has been undertaken to identify and understand molecular changes in lymphomas, resulting in a wide range of genetic alterations that have been reported across all types of lymphomas. As many of these changes are now incorporated into the World Health Organization’s defined criteria for the diagnostic evaluation of patients with lymphoid neoplasms, their accurate identification is crucial. Even if many alterations are not routinely evaluated in daily clinical practice, they may still have implications in risk stratification, treatment, prognosis or disease monitoring. Moreover, some alterations can be used for targeted treatment. Therefore, these advances in lymphoma molecular diagnostics in some cases have led to changes in treatment algorithms. Here, we give an overview of and discuss advances in molecular techniques in current clinical practice, as well as highlight some of them in a clinical context.
Collapse
|
27
|
The Value of Flow Cytometry Clonality in Large Granular Lymphocyte Leukemia. Cancers (Basel) 2021; 13:cancers13184513. [PMID: 34572739 PMCID: PMC8468916 DOI: 10.3390/cancers13184513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Large granular lymphocyte (LGL) leukemia, a lymphoproliferative disease, is characterized by an increased frequency of large-sized lymphocytes with typical expression of T-cell receptor (TCR) αβ, CD3, CD8, CD16, CD45RA, and CD57, and with the expansion of one to three subfamilies of the TCR variable β chain reflecting gene rearrangements. Molecular analysis remains the gold standard for confirmation of TCR clonality; however, flow cytometry is time and labor saving, and can be associated with simultaneous investigation of other surface markers. Moreover, Vβ usage by flow cytometry can be employed for monitoring clonal kinetics during treatment and follow-up of LGL leukemia patients. Abstract Large granular lymphocyte (LGL) leukemia is a lymphoproliferative disorder of mature T or NK cells frequently associated with autoimmune disorders and other hematological conditions, such as myelodysplastic syndromes. Immunophenotype of LGL cells is similar to that of effector memory CD8+ T cells with T-cell receptor (TCR) clonality defined by molecular and/or flow cytometric analysis. Vβ usage by flow cytometry can identify clonal TCR rearrangements at the protein level, and is fast, sensitive, and almost always available in every Hematology Center. Moreover, Vβ usage can be associated with immunophenotypic characterization of LGL clone in a multiparametric staining, and clonal kinetics can be easily monitored during treatment and follow-up. Finally, Vβ usage by flow cytometry might identify LGL clones silently underlying other hematological conditions, and routine characterization of Vβ skewing might identify recurrent TCR rearrangements that might trigger aberrant immune responses during hematological or autoimmune conditions.
Collapse
|
28
|
Liu H, Pan W, Tang C, Tang Y, Wu H, Yoshimura A, Deng Y, He N, Li S. The methods and advances of adaptive immune receptors repertoire sequencing. Theranostics 2021; 11:8945-8963. [PMID: 34522220 PMCID: PMC8419057 DOI: 10.7150/thno.61390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.
Collapse
Affiliation(s)
- Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Congli Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Yujie Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hu-nan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| |
Collapse
|
29
|
Natali EN, Babrak LM, Miho E. Prospective Artificial Intelligence to Dissect the Dengue Immune Response and Discover Therapeutics. Front Immunol 2021; 12:574411. [PMID: 34211454 PMCID: PMC8239437 DOI: 10.3389/fimmu.2021.574411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Dengue virus (DENV) poses a serious threat to global health as the causative agent of dengue fever. The virus is endemic in more than 128 countries resulting in approximately 390 million infection cases each year. Currently, there is no approved therapeutic for treatment nor a fully efficacious vaccine. The development of therapeutics is confounded and hampered by the complexity of the immune response to DENV, in particular to sequential infection with different DENV serotypes (DENV1-5). Researchers have shown that the DENV envelope (E) antigen is primarily responsible for the interaction and subsequent invasion of host cells for all serotypes and can elicit neutralizing antibodies in humans. The advent of high-throughput sequencing and the rapid advancements in computational analysis of complex data, has provided tools for the deconvolution of the DENV immune response. Several types of complex statistical analyses, machine learning models and complex visualizations can be applied to begin answering questions about the B- and T-cell immune responses to multiple infections, antibody-dependent enhancement, identification of novel therapeutics and advance vaccine research.
Collapse
Affiliation(s)
- Eriberto N. Natali
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Lmar M. Babrak
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
| |
Collapse
|
30
|
Gadot M, Gal M, Dobosz P, Dotan Z, Ramon J, Berger R, Avni D, Fridman E, Leibowitz R. Associations between T cell infiltration, T cell receptor clonality, histology and recurrence in renal cell carcinoma. Clin Exp Immunol 2021; 205:160-168. [PMID: 33899933 DOI: 10.1111/cei.13608] [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: 08/30/2020] [Revised: 03/14/2021] [Accepted: 03/28/2021] [Indexed: 11/29/2022] Open
Abstract
Renal cell carcinoma (RCC) is comprised of clear-cell (ccRCC) and non-clear-cell (nccRCC) tumors. Despite definitive surgical resection in localized disease, recurrence often occurs. A commercial method based on a multiplex polymerase chain reaction (PCR) assay exclusively targets rearranged T cell receptor (TCR) genes to generate high-throughput sequencing-based data, allowing characterization of the immune repertoire within tumors. In this study we performed a retrospective analysis on archived tumor samples from patients with recurring versus non-recurring T3 ccRCC and on samples from early nccRCC versus ccRCC. Following genomic DNA extraction and multiplex PCR, the fraction of T cells within tumors, the number of unique receptors ('richness') and their relative abundances ('clonality') were calculated. Statistical significance and correlations were calculated using Student's t-test and Spearman's rho, respectively. Average fraction and clonality of T cells in tumors from non-recurring patients was 2.5- and 4.3-fold higher than in recurring patients (P = 0.025 and P = 0.043, respectively). A significant positive correlation was found between T cell fraction and clonality (Spearman's rho = 0.78, P = 0.008). The average fraction of T cells in ccRCC tumors was 2.8-fold higher than in nccRCC tumors (P = 0.015). Clonality and estimated richness were similar between ccRCC and nccRCC tumors. In summary, recurrence of ccRCC is associated with a lower fraction and clonality of T cells within tumors; nccRCC tumors are more 'deserted' than ccRCC, but similar in their ability to generate a clonal T cell repertoire. Our work suggests associations between the characteristics of T cell infiltrate, histology and tumor recurrence.
Collapse
Affiliation(s)
- Moran Gadot
- Oncology Institute, Sheba Medical Center, Tel-Hashomer, Israel
| | - Mordechay Gal
- Faculty of Life Science, Bar Ilan University, Ramat-Gan, Israel
| | - Paula Dobosz
- Department of Hematology, Oncology and Internal Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Zohar Dotan
- Department of Urology, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel
| | - Jacob Ramon
- Department of Urology, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel
| | - Raanan Berger
- Oncology Institute, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel
| | - Dror Avni
- Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel.,Laboratory of Molecular Cell Biology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Eduard Fridman
- Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel.,Pathology Institute, Sheba Medical Center, Tel-Hashomer, Israel
| | - Raya Leibowitz
- Faculty of Medicine, Tel-Aviv university, Tel-Aviv, Israel.,Oncology Institute, Shamir Medical Center, Zerifin, Israel
| |
Collapse
|
31
|
Trück J, Eugster A, Barennes P, Tipton CM, Luning Prak ET, Bagnara D, Soto C, Sherkow JS, Payne AS, Lefranc MP, Farmer A, Bostick M, Mariotti-Ferrandiz E. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife 2021; 10:66274. [PMID: 34037521 PMCID: PMC8154019 DOI: 10.7554/elife.66274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community’s Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.
Collapse
Affiliation(s)
- Johannes Trück
- University Children's Hospital and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Anne Eugster
- CRTD Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Pierre Barennes
- Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi), Paris, France
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, United States
| | - Eline T Luning Prak
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Davide Bagnara
- University of Genoa, Department of Experimental Medicine, Genoa, Italy
| | - Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, United States
| | - Jacob S Sherkow
- College of Law, University of Illinois, Champaign, United States.,Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of Law, Copenhagen, Denmark.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States
| | - Aimee S Payne
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France.,Laboratoire d'ImmunoGénétique Moléculaire (LIGM) CNRS, University of Montpellier, Montpellier, France.,Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
| | | | | | | | | |
Collapse
|
32
|
Kuzich JA, Kankanige Y, Guinto J, Ryland G, McBean M, Wong E, Koldej R, Collins J, Westerman D, Ritchie D, Blombery P. T cell receptor beta locus sequencing early post-allogeneic stem cell transplant identifies patients at risk of initial and recurrent cytomegalovirus infection. Bone Marrow Transplant 2021; 56:2582-2590. [PMID: 34031553 DOI: 10.1038/s41409-021-01354-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/29/2021] [Accepted: 05/10/2021] [Indexed: 11/09/2022]
Abstract
Identification of patients at risk of initial & recurrent cytomegalovirus (CMV) reactivation following allogeneic stem cell transplant (alloSCT) may help guide prophylactic strategies. T-cell receptor beta (TRB) deep sequencing was used to identify and enumerate the T-cell repertoire harbouring TRB sequences with annotated specificity to CMV (pubCMVrep), as well as the overall T-cell receptor (TCR) repertoire diversity at day +30 & day +60 post-alloSCT for 65 patients. T-cells harbouring TRB sequences with annotated specificity for CMV were identifiable in all patients. 56% of patients required CMV treatment and 23% of the cohort developed recurrent CMV. PubCMVrep size at day +30 was not associated with reactivation, however amongst patients with antecedent CMV viremia a low day +60 pubCMVrep was associated with a greater incidence of recurrent CMV (75% vs. 21%, HR 6.16, 95% CI 1.29-29.40, P = 0.0008). Moreover, patients with high pubCMVrep only developed recurrent CMV in the setting of GVHD. Low TCR diversity at day +30 was associated with a greater incidence of initial CMV reactivation (71% vs. 22%, HR 5.39, 95% CI 1.70-17.09, p = 0.0002). pubCMVrep and TCR diversity are promising biomarkers to identify patients at risk of initial & recurrent CMV who may benefit from novel prophylactic strategies.
Collapse
Affiliation(s)
- James A Kuzich
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
| | - Yamuna Kankanige
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,University of Melbourne, Parkville, VIC, Australia
| | - Jerick Guinto
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Georgina Ryland
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,University of Melbourne, Parkville, VIC, Australia
| | - Michelle McBean
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Eric Wong
- University of Melbourne, Parkville, VIC, Australia.,Clinical Haematology, Peter MacCallum Cancer Centre & the Royal Melbourne Hospital, Melbourne, VIC, Australia.,ACRF Translational Research Laboratory, Royal Melbourne Hospital, Parkville, VIC, Australia.,Department of Clinical Haematology, Austin Hospital, Heidelberg, VIC, Australia
| | - Rachel Koldej
- University of Melbourne, Parkville, VIC, Australia.,ACRF Translational Research Laboratory, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Jenny Collins
- Clinical Haematology, Peter MacCallum Cancer Centre & the Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - David Westerman
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,University of Melbourne, Parkville, VIC, Australia.,Clinical Haematology, Peter MacCallum Cancer Centre & the Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - David Ritchie
- University of Melbourne, Parkville, VIC, Australia.,Clinical Haematology, Peter MacCallum Cancer Centre & the Royal Melbourne Hospital, Melbourne, VIC, Australia.,ACRF Translational Research Laboratory, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,University of Melbourne, Parkville, VIC, Australia.,Clinical Haematology, Peter MacCallum Cancer Centre & the Royal Melbourne Hospital, Melbourne, VIC, Australia
| |
Collapse
|
33
|
Baptista MJ, Baskar S, Gaglione EM, Keyvanfar K, Ahn IE, Wiestner A, Sun C. Select Antitumor Cytotoxic CD8 + T Clonotypes Expand in Patients with Chronic Lymphocytic Leukemia Treated with Ibrutinib. Clin Cancer Res 2021; 27:4624-4633. [PMID: 33875521 DOI: 10.1158/1078-0432.ccr-20-4894] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/15/2021] [Accepted: 04/15/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE In chronic lymphocytic leukemia (CLL), the T-cell receptor (TCR) repertoire is skewed and tumor-derived antigens are hypothesized as drivers of oligoclonal expansion. Ibrutinib, a standard treatment for CLL, inhibits not only Bruton tyrosine kinase of the B-cell receptor signaling pathway, but also IL2-inducible kinase of the TCR signaling pathway. T-cell polarization and activation are affected by ibrutinib, but it is unknown whether T cells contribute to clinical response. EXPERIMENTAL DESIGN High-throughput TCRβ sequencing was performed in 77 longitudinal samples from 26 patients with CLL treated with ibrutinib. TCRβ usage in CD4+ and CD8+ T cells and granzyme B expression were assessed by flow cytometric analysis. Antitumor cytotoxicity of T cells expanded with autologous CLL cells or with antigen-independent anti-CD3/CD28/CD137 beads was tested. RESULTS The clonality of the TCR repertoire increased at the time of response. With extended treatment, TCR clonality remained stable in patients with sustained remission and decreased in patients with disease progression. Expanded clonotypes were rarely shared between patients, indicating specificity for private antigens. Flow cytometry demonstrated a predominance of CD8+ cells among expanded clonotypes. Importantly, bulk T cells from responding patients were cytotoxic against autologous CLL cells in vitro and selective depletion of major expanded clonotypes reduced CLL cell killing. CONCLUSIONS In patients with CLL, established T-cell responses directed against tumor are suppressed by disease and reactivated by ibrutinib.See related commentary by Zent, p. 4465.
Collapse
Affiliation(s)
- Maria Joao Baptista
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland.,Lymphoid Neoplasms, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | | | - Erika M Gaglione
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Keyvan Keyvanfar
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Inhye E Ahn
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland.
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland.
| |
Collapse
|
34
|
Chronister WD, Crinklaw A, Mahajan S, Vita R, Koşaloğlu-Yalçın Z, Yan Z, Greenbaum JA, Jessen LE, Nielsen M, Christley S, Cowell LG, Sette A, Peters B. TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors. Front Immunol 2021; 12:640725. [PMID: 33777034 PMCID: PMC7991084 DOI: 10.3389/fimmu.2021.640725] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
The adaptive immune system in vertebrates has evolved to recognize non-self antigens, such as proteins expressed by infectious agents and mutated cancer cells. T cells play an important role in antigen recognition by expressing a diverse repertoire of antigen-specific receptors, which bind epitopes to mount targeted immune responses. Recent advances in high-throughput sequencing have enabled the routine generation of T-cell receptor (TCR) repertoire data. Identifying the specific epitopes targeted by different TCRs in these data would be valuable. To accomplish that, we took advantage of the ever-increasing number of TCRs with known epitope specificity curated in the Immune Epitope Database (IEDB) since 2004. We compared seven metrics of sequence similarity to determine their power to predict if two TCRs have the same epitope specificity. We found that a comprehensive k-mer matching approach produced the best results, which we have implemented into TCRMatch, an openly accessible tool (http://tools.iedb.org/tcrmatch/) that takes TCR β-chain CDR3 sequences as an input, identifies TCRs with a match in the IEDB, and reports the specificity of each match. We anticipate that this tool will provide new insights into T cell responses captured in receptor repertoire and single cell sequencing experiments and will facilitate the development of new strategies for monitoring and treatment of infectious, allergic, and autoimmune diseases, as well as cancer.
Collapse
Affiliation(s)
| | - Austin Crinklaw
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Swapnil Mahajan
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Randi Vita
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | | | - Zhen Yan
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Jason A Greenbaum
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Leon E Jessen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina
| | - Scott Christley
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Lindsay G Cowell
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
| |
Collapse
|
35
|
Dynamic blood single-cell immune responses in patients with COVID-19. Signal Transduct Target Ther 2021; 6:110. [PMID: 33677468 PMCID: PMC7936231 DOI: 10.1038/s41392-021-00526-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
The 2019 coronavirus disease (COVID-19) outbreak caused by the SARS-CoV-2 virus is an ongoing global health emergency. However, the virus’ pathogenesis remains unclear, and there is no cure for the disease. We investigated the dynamic changes of blood immune response in patients with COVID-19 at different stages by using 5’ gene expression, T cell receptor (TCR), and B cell receptors (BCR) V(D)J transcriptome analysis at a single-cell resolution. We obtained single-cell mRNA sequencing (scRNA-seq) data of 341,420 peripheral blood mononuclear cells (PBMCs) and 185,430 clonotypic T cells and 28,802 clonotypic B cells from 25 samples of 16 patients with COVID-19 for dynamic studies. In addition, we used three control samples. We found expansion of dendritic cells (DCs), CD14+ monocytes, and megakaryocytes progenitor cells (MP)/platelets and a reduction of naïve CD4+ T lymphocytes in patients with COVID-19, along with a significant decrease of CD8+ T lymphocytes, and natural killer cells (NKs) in patients in critical condition. The type I interferon (IFN-I), mitogen-activated protein kinase (MAPK), and ferroptosis pathways were activated while the disease was active, and recovered gradually after patient conditions improved. Consistent with this finding, the mRNA level of IFN-I signal-induced gene IFI27 was significantly increased in patients with COVID-19 compared with that of the controls in a validation cohort that included 38 patients and 35 controls. The concentration of interferon-α (IFN-α) in the serum of patients with COVID-19 increased significantly compared with that of the controls in an additional cohort of 215 patients with COVID-19 and 106 controls, further suggesting the important role of the IFN-I pathway in the immune response of COVID-19. TCR and BCR sequences analyses indicated that patients with COVID-19 developed specific immune responses against SARS-CoV-2 antigens. Our study reveals a dynamic landscape of human blood immune responses to SARS-CoV-2 infection, providing clues for therapeutic potentials in treating COVID-19.
Collapse
|
36
|
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
|
37
|
Liang Q, Zhang M, Hu Y, Zhang W, Zhu P, Chen Y, Xue P, Li Q, Wang K. Gut Microbiome Contributes to Liver Fibrosis Impact on T Cell Receptor Immune Repertoire. Front Microbiol 2020; 11:571847. [PMID: 33329430 PMCID: PMC7729130 DOI: 10.3389/fmicb.2020.571847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota (GM) modifies the intrahepatic immune microenvironment, but the underlying mechanisms remain poorly understood. Liver fibrosis-associated imprinting is predicted to be reflected in GM. This study investigated the link between GM and the intrahepatic T cell receptor (TCR) immune repertoire (IR), and whether GM modulates the intrahepatic immune microenvironment via TCR IR during liver fibrosis. We analyzed the correlation between GM and TCR IR during liver fibrogenesis. Accordingly, 16S rRNA gene sequencing (16S-seq) and bulk immune repertoire sequencing (IR-seq) were performed to characterize GM and intrahepatic TCR IR. Fecal microbial transplant (FMT) and TCRβ knockout (TcrbKO) mouse models were employed to determine the biological link between GM and TCR IR in liver fibrosis. We found that GM and intrahepatic TCR IR are highly correlated, with both showing reduced diversity and centralized distribution during liver fibrosis. The restoration of normal intestinal microbiota may reshape intrahepatic TCR IR and delay liver fibrosis. Interestingly, TCR IR ablation abrogated the impact of GM on liver fibrogenesis. Furthermore, GM modulated hepatic stellate cell (HSC) activation via TCR IR-mediated intrahepatic immune milieu. Our study demonstrates that GM, which exhibits cross-talk with the intrahepatic TCR IR, influences the intrahepatic immune microenvironment and liver fibrosis progression.
Collapse
Affiliation(s)
- Qing Liang
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Meina Zhang
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Yudi Hu
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Wei Zhang
- Department of Pathology, The 971 Hospital of People's Liberation Army Navy, Qingdao, China
| | - Ping Zhu
- Department of Gynecology and Obstetrics, The 971 Hospital of People's Liberation Army Navy, Qingdao, China
| | - Yujie Chen
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Pengxin Xue
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Qiyuan Li
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Kejia Wang
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| |
Collapse
|
38
|
Wijetunga NA, Yu Y, Morris LG, Lee N, Riaz N. The head and neck cancer genome in the era of immunotherapy. Oral Oncol 2020; 112:105040. [PMID: 33197752 DOI: 10.1016/j.oraloncology.2020.105040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/04/2020] [Accepted: 10/04/2020] [Indexed: 12/19/2022]
Abstract
The recent success of immunotherapy in head and neck squamous cell carcinoma (HNSCC) has necessitated a new perspective on the cancer genome. Here we review recent advances in the carcinogenesis and molecular genetics of HNSCC with an eye on their implications for cancer immunity. Newer sequencing technologies have recently facilitated dissection of the complex interaction between the HPV virus, tumor, host factors, and the tumor microenvironment (TME) that help shed light on how the immune system interacts with head and neck malignancies.
Collapse
Affiliation(s)
- N Ari Wijetunga
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yao Yu
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc G Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Lee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
39
|
Luo G, Gao Q, Zhang S, Yan B. Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives. Comput Struct Biotechnol J 2020; 18:2962-2971. [PMID: 33106757 PMCID: PMC7577221 DOI: 10.1016/j.csbj.2020.10.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
The increasing application of single-cell RNA sequencing (scRNA-seq) technology in life science and biomedical research has significantly increased our understanding of the cellular heterogeneities in immunology, oncology and developmental biology. This review will summarize the development of various scRNA-seq technologies; primarily discussing the application of scRNA-seq on infectious diseases, and exploring the current development, challenges, and potential applications of scRNA-seq technology in the future.
Collapse
Key Words
- 3C, Chromosome Conformation Capture
- ACE2, Angiotensin-Converting Enzyme 2
- ARDS, acute respiratory distress syndrome
- ATAC-seq, Assay for Transposase-Accessible Chromatin using sequencing
- BCR, B cell receptor
- CEL-seq, Cell Expression by Linear amplification and Sequencing
- CLU, clusterin
- COVID-19, corona virus disease 2019
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- CytoSeq, gene expression cytometry
- DENV, dengue virus
- FACS, fluorescence-activated cell sorting
- GNLY, granulysin
- GO analysis, Gene Ontology analysis
- HIV, Human Immunodeficiency Virus
- IAV, Influenza A virus
- IGHV/HD/HJ/HC, Immune globulin heavy V/D/J/C/ region
- IGLV/LJ/LC, Immune globulin light V/J/C/ region
- ILC, Innate Lymphoid Cell
- Infectious diseases
- LIGER, Linked Inference of Genomics Experimental Relationships
- MAGIC, Markov Affinity-based Graph Imputation of Cells
- MARS-seq, Massively parallel single-cell RNA sequencing
- MATCHER, Manifold Alignment To CHaracterize Experimental Relationships
- MCMV, mouse cytomegalovirus
- MERFISH, Multiplexed, Error Robust Fluorescent In Situ Hybridization
- MLV, Moloney Murine Leukemia Virus
- MOFA, Multi-Omics Factor Analysis
- MOI, multiplicity of infection
- PBMCs, peripheral blood mononuclear cells
- PLAC8, placenta-associated 8
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SAVER, Single-cell Analysis Via Expression Recovery
- SPLit-seq, split pool ligation-based tranome sequencing
- STARTRAC, Single T-cell Analysis by RNA sequencing and TCR TRACking
- STRT-seq, Single-cell Tagged Reverse Transcription sequencing
- Single-cell RNA sequencing
- TCR, T cell receptor
- TSLP, thymic stromal lymphopoietin
- UMAP, Uniform Manifold Approximation and Projection
- UMI, Unique Molecular Identifier
- mcSCRB-seq, molecular crowding single-cell RNA barcoding and sequencing
- pDCs, plasmacytoid dendritic cells
- scRNA-seq, single cell RNA sequencing technology
- sci-RNA-seq, single-cell combinatorial indexing RNA sequencing
- seqFISH, sequential Fluorescent In Situ Hybridization
- smart-seq, switching mechanism at 5′ end of the RNA transcript sequencing
- t-SNE, t-Distributed stochastic neighbor embedding
Collapse
Affiliation(s)
- Geyang Luo
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qian Gao
- Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Bo Yan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| |
Collapse
|
40
|
Yang X, Tipton CM, Woodruff MC, Zhou E, Lee FEH, Sanz I, Qiu P. GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data. BMC Genomics 2020; 21:583. [PMID: 32900378 PMCID: PMC7488003 DOI: 10.1186/s12864-020-06936-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background B cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind antigens. Lineage trees are used to describe this microevolution of B cell immunoglobulin genes. In a lineage tree, each node is one BCR sequence that mutated from the germinal center and each directed edge represents a single base mutation, insertion or deletion. In BCR sequencing data, the observed data only contains a subset of BCR sequences in this microevolution process. Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. Results We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree nodes. Through comparison using simulated and real data, GLaMST outperforms existing algorithms in simulations with high rates of mutation, insertion and deletion, and generates lineage trees with smaller size and closer to ground truth according to tree features that highly correlated with selection pressure. Conclusions GLaMST outperforms state-of-art in reconstruction of the BCR lineage tree in both efficiency and accuracy. Integrating it into existing BCR sequencing analysis frameworks can significant improve lineage tree reconstruction aspect of the analysis.
Collapse
Affiliation(s)
- Xingyu Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Christopher M Tipton
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, USA
| | - Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, USA
| | - Enlu Zhou
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, USA
| | | | - Inãki Sanz
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, USA
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, USA.
| |
Collapse
|
41
|
Kury P, Führer M, Fuchs S, Lorenz MR, Giorgetti OB, Bakhtiar S, Frei AP, Fisch P, Boehm T, Schwarz K, Speckmann C, Ehl S. Long-term robustness of a T-cell system emerging from somatic rescue of a genetic block in T-cell development. EBioMedicine 2020; 59:102961. [PMID: 32841837 PMCID: PMC7452388 DOI: 10.1016/j.ebiom.2020.102961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGOUND The potential of a single progenitor cell to establish and maintain long-term protective T-cell immunity in humans is unknown. For genetic disorders disabling T-cell immunity, somatic reversion was shown to support limited T-cell development attenuating the clinical phenotype. However, the cases reported so far deteriorated over time leaving unanswered the important question of long-term activity of revertant precursors and the robustness of the resulting T-cell system. METHODS We applied TCRβ-CDR3 sequencing and mass cytometry on serial samples of a now 18 year-old SCIDX1 patient with somatic reversion to analyse the longitudinal diversification and stability of a T-cell system emerging from somatic gene rescue. FINDINGS We detected close to 105 individual CDR3β sequences in the patient. Blood samples of equal size contained about 10-fold fewer unique CDR3β sequences compared to healthy donors, indicating a surprisingly broad repertoire. Despite dramatic expansions and contractions of individual clonotypes representing up to 30% of the repertoire, stable diversity indices revealed that these transient clonal distortions did not cause long-term repertoire imbalance. Phenotypically, the T-cell system did not show evidence for progressive exhaustion. Combined with immunoglobulin substitution, the limited T-cell system in this patient supported an unremarkable clinical course over 18 years. INTERPRETATION Genetic correction in the appropriate cell type, in our patient most likely in a T-cell biased self-renewing hematopoietic progenitor, can yield a diverse T-cell system that provides long-term repertoire stability, does not show evidence for progressive exhaustion and is capable of providing protective and regulated T-cell immunity for at least two decades. FUNDING DFG EH 145/9-1, DFG SCHW 432/4-1 and the German Research Foundation under Germany's Excellence Strategy-EXC-2189-Project ID: 390939984.
Collapse
Affiliation(s)
- Patrick Kury
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Straße 115, 79106 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany
| | - Marita Führer
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service, Baden-Wuerttemberg - Hessen, Ulm, Germany
| | - Sebastian Fuchs
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Myriam R Lorenz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Orlando Bruno Giorgetti
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics Freiburg, Freiburg, Germany
| | - Shahrzad Bakhtiar
- Division for Pediatric Stem-Cell Transplantation, Immunology and Intensive Medicine, University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Andreas P Frei
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel, Switzerland
| | - Paul Fisch
- Department of Pathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics Freiburg, Freiburg, Germany
| | - Klaus Schwarz
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service, Baden-Wuerttemberg - Hessen, Ulm, Germany; Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Straße 115, 79106 Freiburg, Germany; Center for Pediatrics, Department of Pediatric Hematology and Oncology, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Straße 115, 79106 Freiburg, Germany; CIBBS -Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
42
|
Dissecting efficiency of a 5' rapid amplification of cDNA ends (5'-RACE) approach for profiling T-cell receptor beta repertoire. PLoS One 2020; 15:e0236366. [PMID: 32702062 PMCID: PMC7377388 DOI: 10.1371/journal.pone.0236366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/02/2020] [Indexed: 01/21/2023] Open
Abstract
Deep sequencing of T-cell receptor (TCR) genes is powerful at profiling immune repertoire. To prepare a TCR sequencing library, multiplex polymerase chain reaction (mPCR) is widely applied and is highly efficient. That is, most mPCR products contain the region critical for antigen recognition, which also indicates regular V(D)J recombination. Multiplex PCR, however, may suffer from primer bias. A promising alternative is 5'-RACE, which avoids primer bias by applying only one primer pair. In 5'-RACE data, however, non-regular V(D)J recombination (e.g., TCR sequences without a V gene segment) has been observed and the frequency varies (30-80%) between studies. This suggests that the cause of or how to reduce non-regular TCR sequences is not yet well known by the science community. Although it is possible to speculate the cause by comparing the 5'-RACE protocols, careful experimental confirmation is needed and such a systematic study is still not available. Here, we examined the 5'-RACE protocol of a commercial kit and demonstrated how a modification increased the fraction of regular TCR-β sequences to >85%. We also found a strong linear correlation between the fraction of short DNA fragments and the percentage of non-regular TCR-β sequences, indicating that the presence of short DNA fragments in the library was the main cause of non-regular TCR-β sequences. Therefore, thorough removal of short DNA fragments from a 5'-RACE library is the key to high data efficiency. We highly recommend conducting a fragment length analysis before sequencing, and the fraction of short DNA fragments can be used to estimate the percentage of non-regular TCR sequences. As deep sequencing of TCR genes is still relatively expensive, good quality control should be valuable.
Collapse
|
43
|
Teraguchi S, Saputri DS, Llamas-Covarrubias MA, Davila A, Diez D, Nazlica SA, Rozewicki J, Ismanto HS, Wilamowski J, Xie J, Xu Z, Loza-Lopez MDJ, van Eerden FJ, Li S, Standley DM. Methods for sequence and structural analysis of B and T cell receptor repertoires. Comput Struct Biotechnol J 2020; 18:2000-2011. [PMID: 32802272 PMCID: PMC7366105 DOI: 10.1016/j.csbj.2020.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.
Collapse
Affiliation(s)
- Shunsuke Teraguchi
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Dianita S. Saputri
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Mara Anais Llamas-Covarrubias
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Mexico
| | - Ana Davila
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Diego Diez
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Sedat Aybars Nazlica
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - John Rozewicki
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Hendra S. Ismanto
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Jan Wilamowski
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Jiaqi Xie
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Zichang Xu
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | | | - Floris J. van Eerden
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Songling Li
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| | - Daron M. Standley
- Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Japan
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Japan
| |
Collapse
|
44
|
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
|
45
|
Moritz CP, Paul S, Stoevesandt O, Tholance Y, Camdessanché JP, Antoine JC. Autoantigenomics: Holistic characterization of autoantigen repertoires for a better understanding of autoimmune diseases. Autoimmun Rev 2020; 19:102450. [DOI: 10.1016/j.autrev.2019.102450] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
|
46
|
Shi X, Shao T, Huo F, Zheng C, Li W, Jiang Z. An analysis of abnormalities in the B cell receptor repertoire in patients with systemic sclerosis using high-throughput sequencing. PeerJ 2020; 8:e8370. [PMID: 31988805 PMCID: PMC6968515 DOI: 10.7717/peerj.8370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/09/2019] [Indexed: 11/30/2022] Open
Abstract
Systemic sclerosis is a chronic multisystem autoimmune disease that is associated with polyclonal B cell hyperreactivity. The CDR3 of BCRs is the major site of antigen recognition. Therefore, we analyzed the BCR repertoire of patients with SSc. The BCR repertoires in 12 subjects including eight SSc patients and four healthy controls were characterized by high-throughput sequencing, and bioinformatics analysis were studied. The average CDR3 length in the SSc group was significantly shorter. The SSc patient displayed more diverse BCR. Moreover, SSc patients with mild skin sclerosis, anti-Scl70, interstitial lung disease or female sex were more diversified. B cells from the SSc patients showed a differential V and J gene usage. SSc patients had distinct BCR repertoires.These findings reflected the differences of BCR repertoires between SSc patients and controls. The higher-usage genes for the BCR sequence might be potential biomarkers of B cell-targeted therapies or diagnosis for SSc.
Collapse
Affiliation(s)
- Xiaodong Shi
- Rheumatology, First Hospital of Jilin University, Changchun, The People's Republic of China
| | - Tihong Shao
- Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, The People's Republic of China
| | - Feifei Huo
- Intensive Care Unit, First hospital of Jilin university, Changchun, The People's Republic of China
| | - Chenqing Zheng
- Shenzhen RealOmics (Biotech) Co.Ltd, Shenzhen, The People's Republic of China
| | - Wanyu Li
- Hepatology, First hospital of Jilin university, Changchun, The People's Republic of China
| | - Zhenyu Jiang
- Rheumatology, First Hospital of Jilin University, Changchun, The People's Republic of China
| |
Collapse
|
47
|
Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
Collapse
Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
48
|
Schonhoff AM, Williams GP, Wallen ZD, Standaert DG, Harms AS. Innate and adaptive immune responses in Parkinson's disease. PROGRESS IN BRAIN RESEARCH 2019; 252:169-216. [PMID: 32247364 DOI: 10.1016/bs.pbr.2019.10.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD) has classically been defined as a movement disorder, in which motor symptoms are explained by the aggregation of alpha-synuclein (α-syn) and subsequent death of dopaminergic neurons of the substantia nigra pars compacta (SNpc). More recently, the multisystem effects of the disease have been investigated, with the immune system being implicated in a number of these processes in the brain, the blood, and the gut. In this review, we highlight the dysfunctional immune system found in both human PD and animal models of the disease, and discuss how genetic risk factors and risk modifiers are associated with pro-inflammatory immune responses. Finally, we emphasize evidence that the immune response drives the pathogenesis and progression of PD, and discuss key questions that remain to be investigated in order to identify immunomodulatory therapies in PD.
Collapse
Affiliation(s)
- Aubrey M Schonhoff
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gregory P Williams
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zachary D Wallen
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - David G Standaert
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ashley S Harms
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States.
| |
Collapse
|
49
|
Ko TM, Kiyotani K, Chang JS, Park JH, Yin Yew P, Chen YT, Wu JY, Nakamura Y. Immunoglobulin profiling identifies unique signatures in patients with Kawasaki disease during intravenous immunoglobulin treatment. Hum Mol Genet 2019; 27:2671-2677. [PMID: 29771320 PMCID: PMC6048982 DOI: 10.1093/hmg/ddy176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/01/2018] [Accepted: 05/01/2018] [Indexed: 12/18/2022] Open
Abstract
Identifying the causes of high fever syndromes such as Kawasaki disease (KD) remains challenging. To investigate pathogen exposure signatures in suspected pathogen-mediated diseases such as KD, we performed immunoglobulin (Ig) profiling using a next-generation sequencing method. After intravenous Ig (IVIG) treatment, we observed disappearance of clonally expanded IgM clonotypes, which were dominantly observed in acute-phase patients. The complementary-determining region 3 (CDR3) sequences of dominant IgM clonotypes in acute-phase patients were commonly observed in other Ig isotypes. In acute-phase KD patients, we identified 32 unique IgM CDR3 clonotypes shared in three or more cases. Furthermore, before the IVIG treatment, the sums of dominant IgM clonotypes in IVIG-resistant KD patients were significantly higher than those of IVIG-sensitive KD patients. Collectively, we demonstrate a novel approach for identifying certain Ig clonotypes for potentially interacting with pathogens involved in KD; this approach could be applied for a wide variety of fever-causing diseases of unknown origin.
Collapse
Affiliation(s)
- Tai-Ming Ko
- Department of Medicine, University of Chicago, Chicago, Illinois, USA.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Kazuma Kiyotani
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Jeng-Sheng Chang
- Department of Pediatrics, China Medical University Hospital, Taichung, Taiwan.,College of Medicine, China Medical University, Taichung, Taiwan
| | - Jae-Hyun Park
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Poh Yin Yew
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Yusuke Nakamura
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| |
Collapse
|
50
|
Abstract
Immune repertoire is a collection of enormously diverse adaptive immune cells within an individual. As the repertoire shapes and represents immunological conditions, identification of clones and characterization of diversity are critical for understanding how to protect ourselves against various illness such as infectious diseases and cancers. Over the past several years, fast growing technologies for high throughput sequencing have facilitated rapid advancement of repertoire research, enabling us to observe the diversity of repertoire at an unprecedented level. Here, we focus on B cell receptor (BCR) repertoire and review approaches to B cell isolation and sequencing library construction. These experiments should be carefully designed according to BCR regions to be interrogated, such as heavy chain full length, complementarity determining regions, and isotypes. We also highlight preprocessing steps to remove sequencing and PCR errors with unique molecular index and bioinformatics techniques. Due to the nature of massive sequence variation in BCR, caution is warranted when interpreting repertoire diversity from error-prone sequencing data. Furthermore, we provide a summary of statistical frameworks and bioinformatics tools for clonal evolution and diversity. Finally, we discuss limitations of current BCR-seq technologies and future perspectives on advances in repertoire sequencing.
Collapse
Affiliation(s)
- Daeun Kim
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, Korea
| | - Daechan Park
- Department of Biological Sciences, College of Natural Sciences, Ajou University, Suwon 16499, Korea
| |
Collapse
|