1
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Yu P, Lian Y, Zuleger CL, Albertini RJ, Albertini MR, Newton MA. SURROGATE SELECTION OVERSAMPLES EXPANDED T CELL CLONOTYPES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548950. [PMID: 37503118 PMCID: PMC10369934 DOI: 10.1101/2023.07.13.548950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Inference from immunological data on cells in the adaptive immune system may benefit from modeling specifications that describe variation in the sizes of various clonal sub-populations. We develop one such specification in order to quantify the effects of surrogate selection assays, which we confirm may lead to an enrichment for amplified, potentially disease-relevant T cell clones. Our specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We examine statistical properties of immunological samples governed by the coupled model specification, and we illustrate calculations in surrogate selection studies of melanoma and in single-cell genomic studies of T cell repertoires.
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Affiliation(s)
- Peng Yu
- Department of Statistics, University of Wisconsin, Madison
| | - Yumin Lian
- Department of Chemistry, Laboratory of Genetics, University of Wisconsin, Madison
| | - Cindy L. Zuleger
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison
- Carbone Cancer Center, University of Wisconsin, Madison
| | | | - Mark R. Albertini
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison
- Carbone Cancer Center, University of Wisconsin, Madison
- Medical Service, William S. Middleton Memorial Veterans Hospital, Madison
| | - Michael A. Newton
- Department of Statistics, University of Wisconsin, Madison
- Carbone Cancer Center, University of Wisconsin, Madison
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison
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2
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Inferring the T cell repertoire dynamics of healthy individuals. Proc Natl Acad Sci U S A 2023; 120:e2207516120. [PMID: 36669107 PMCID: PMC9942919 DOI: 10.1073/pnas.2207516120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The adaptive immune system is a diverse ecosystem that responds to pathogens by selecting cells with specific receptors. While clonal expansion in response to particular immune challenges has been extensively studied, we do not know the neutral dynamics that drive the immune system in the absence of strong stimuli. Here, we learn the parameters that underlie the clonal dynamics of the T cell repertoire in healthy individuals of different ages, by applying Bayesian inference to longitudinal immune repertoire sequencing (RepSeq) data. Quantifying the experimental noise accurately for a given RepSeq technique allows us to disentangle real changes in clonal frequencies from noise. We find that the data are consistent with clone sizes following a geometric Brownian motion and show that its predicted steady state is in quantitative agreement with the observed power-law behavior of the clone-size distribution. The inferred turnover time scale of the repertoire increases with patient age and depends on the clone size in some individuals.
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3
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Katayama Y, Yokota R, Akiyama T, Kobayashi TJ. Machine Learning Approaches to TCR Repertoire Analysis. Front Immunol 2022; 13:858057. [PMID: 35911778 PMCID: PMC9334875 DOI: 10.3389/fimmu.2022.858057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yotaro Katayama,
| | - Ryo Yokota
- National Research Institute of Police Science, Kashiwa, Chiba, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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4
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Dessalles R, Pan Y, Xia M, Maestrini D, D'Orsogna MR, Chou T. How Naive T-Cell Clone Counts Are Shaped By Heterogeneous Thymic Output and Homeostatic Proliferation. Front Immunol 2022; 12:735135. [PMID: 35250963 PMCID: PMC8891377 DOI: 10.3389/fimmu.2021.735135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
The specificity of T cells is that each T cell has only one T cell receptor (TCR). A T cell clone represents a collection of T cells with the same TCR sequence. Thus, the number of different T cell clones in an organism reflects the number of different T cell receptors (TCRs) that arise from recombination of the V(D)J gene segments during T cell development in the thymus. TCR diversity and more specifically, the clone abundance distribution, are important factors in immune functions. Specific recombination patterns occur more frequently than others while subsequent interactions between TCRs and self-antigens are known to trigger proliferation and sustain naive T cell survival. These processes are TCR-dependent, leading to clone-dependent thymic export and naive T cell proliferation rates. We describe the heterogeneous steady-state population of naive T cells (those that have not yet been antigenically triggered) by using a mean-field model of a regulated birth-death-immigration process. After accounting for random sampling, we investigate how TCR-dependent heterogeneities in immigration and proliferation rates affect the shape of clone abundance distributions (the number of different clones that are represented by a specific number of cells, or “clone counts”). By using reasonable physiological parameter values and fitting predicted clone counts to experimentally sampled clone abundances, we show that realistic levels of heterogeneity in immigration rates cause very little change to predicted clone-counts, but that modest heterogeneity in proliferation rates can generate the observed clone abundances. Our analysis provides constraints among physiological parameters that are necessary to yield predictions that qualitatively match the data. Assumptions of the model and potentially other important mechanistic factors are discussed.
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Affiliation(s)
- Renaud Dessalles
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Yunbei Pan
- Department of Mathematics, California State University at Northridge, Los Angeles, CA, United States
| | - Mingtao Xia
- Department of Mathematics, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Davide Maestrini
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
| | - Maria R D'Orsogna
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States.,Department of Mathematics, California State University at Northridge, Los Angeles, CA, United States
| | - Tom Chou
- Department of Computational Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, United States.,Department of Mathematics, University of California at Los Angeles (UCLA), Los Angeles, CA, United States
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5
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Snyder ME, Moghbeli K, Bondonese A, Craig A, Popescu I, Fan L, Tabib T, Lafyatis R, Chen K, Trejo Bittar HE, Lendermon E, Pilewski J, Johnson B, Kilaru S, Zhang Y, Sanchez PG, Alder JK, Sims PA, McDyer JF. Modulation of tissue resident memory T cells by glucocorticoids after acute cellular rejection in lung transplantation. J Exp Med 2022; 219:e20212059. [PMID: 35285873 PMCID: PMC8924935 DOI: 10.1084/jem.20212059] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/13/2021] [Accepted: 02/04/2022] [Indexed: 01/01/2023] Open
Abstract
Acute cellular rejection is common after lung transplantation and is associated with an increased risk of early chronic rejection. We present combined single-cell RNA and TCR sequencing on recipient-derived T cells obtained from the bronchoalveolar lavage of three lung transplant recipients with rejection and compare them with T cells obtained from the same patients after treatment of rejection with high-dose systemic glucocorticoids. At the time of rejection, we found an oligoclonal expansion of cytotoxic CD8+ T cells that all persisted as tissue resident memory T cells after successful treatment. Persisting CD8+ allograft-resident T cells have reduced gene expression for cytotoxic mediators after therapy with glucocorticoids but accumulate around airways. This clonal expansion is discordant with circulating T cell clonal expansion at the time of rejection, suggesting in situ expansion. We thus highlight the accumulation of cytotoxic, recipient-derived tissue resident memory T cells within the lung allograft that persist despite the administration of high-dose systemic glucocorticoids. The long-term clinical consequences of this persistence have yet to be characterized.
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Affiliation(s)
- Mark E Snyder
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA
- Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA
| | - Kaveh Moghbeli
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Anna Bondonese
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Andrew Craig
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Iulia Popescu
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Li Fan
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Tracy Tabib
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Robert Lafyatis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Kong Chen
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Joseph Pilewski
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Bruce Johnson
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Silpa Kilaru
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Pablo G Sanchez
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA
| | - Jonathan K Alder
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY
| | - John F McDyer
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA
- Starzl Transplantation Institute, University of Pittsburgh, Pittsburgh, PA
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6
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Cheon IS, Li C, Son YM, Goplen NP, Wu Y, Cassmann T, Wang Z, Wei X, Tang J, Li Y, Marlow H, Hughes S, Hammel L, Cox TM, Goddery E, Ayasoufi K, Weiskopf D, Boonyaratanakornkit J, Dong H, Li H, Chakraborty R, Johnson AJ, Edell E, Taylor JJ, Kaplan MH, Sette A, Bartholmai BJ, Kern R, Vassallo R, Sun J. Immune signatures underlying post-acute COVID-19 lung sequelae. Sci Immunol 2021; 6:eabk1741. [PMID: 34591653 DOI: 10.1126/sciimmunol.abk1741] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- I S Cheon
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - C Li
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y M Son
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - N P Goplen
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y Wu
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - T Cassmann
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Z Wang
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - X Wei
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - J Tang
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y Li
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - H Marlow
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - S Hughes
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - L Hammel
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - T M Cox
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - E Goddery
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - K Ayasoufi
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - D Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - J Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - H Dong
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - H Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - R Chakraborty
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - A J Johnson
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - E Edell
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - J J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - M H Kaplan
- Department of Microbiology and Immunology, Indiana University of School of Medicine, Indianapolis, IN 46202, USA
| | - A Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego (UCSD), La Jolla, CA 92037, USA
| | - B J Bartholmai
- Department of Radiology, Mayo Clinic, Rochester, MN 5590, USA
| | - R Kern
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - R Vassallo
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - J Sun
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.,Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA.,Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA.,Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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7
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Escobar G, Mangani D, Anderson AC. T cell factor 1: A master regulator of the T cell response in disease. Sci Immunol 2021; 5:5/53/eabb9726. [PMID: 33158974 DOI: 10.1126/sciimmunol.abb9726] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
Recent advances have redefined a role for T cell factor 1 (TCF1) that goes beyond T cell development and T memory formation and encompasses new functions in the regulation of T cell biology. Here, we discuss the multifaceted and context-dependent role of TCF1 in peripheral T cells, particularly during disease-induced inflammatory states such as autoimmunity, cancer, and chronic infections. Understanding how TCF1 fine-tunes peripheral T cell biology holds the potential to tailor improved immune-targeted therapies.
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Affiliation(s)
- Giulia Escobar
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital Mass General Brigham, Boston, MA 02115, USA
| | - Davide Mangani
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital Mass General Brigham, Boston, MA 02115, USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital Mass General Brigham, Boston, MA 02115, USA.
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8
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Wang S, Wang L, Liu Y, Zhu Y, Liu Y. Characteristics of T-cell receptor repertoire of stem cell-like memory CD4+ T cells. PeerJ 2021; 9:e11987. [PMID: 34527440 PMCID: PMC8401816 DOI: 10.7717/peerj.11987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
Stem cell-like memory T cells (Tscm) combine phenotypes of naïve and memory. However, it remains unclear how T cell receptor (TCR) characteristics contribute to heterogeneity in Tscm and other memory T cells. We compared the TCR-beta (TRB) repertoire characteristics of CD4+ Tscm with those of naïve and other CD4+ memory (Tm) in 16 human subjects. Compared with Tm, Tscm had an increased diversity across all stretches of TRB repertoire structure, a skewed gene usage, and a shorter length distribution of CDR3 region. These distinctions between Tscm and Tm were enlarged in top1000 abundant clonotypes. Furthermore, top1000 clonotypes in Tscm were more public than those in Tm and grouped in more clusters, implying more epitope types recognized by top1000 clonotypes in Tscm. Importantly, self-reactive clonotypes were public and enriched in Tscm rather than Tm, of type one diabetes patients. Therefore, this study highlights the unique features of Tscm different from those of other memory subsets and provides clues to understand the physiological and pathological functions of Tscm.
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Affiliation(s)
- Shiyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Longlong Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yang Liu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yonggang Zhu
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen, China
| | - Ya Liu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, China
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9
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Recipient-specific T-cell repertoire reconstitution in the gut following murine hematopoietic cell transplant. Blood Adv 2021; 4:4232-4243. [PMID: 32898248 DOI: 10.1182/bloodadvances.2019000977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/27/2020] [Indexed: 01/12/2023] Open
Abstract
Graft-versus-host disease (GVHD) is a complication of hematopoietic cell transplantation (HCT) caused by alloreactive T cells. Murine models of HCT are used to understand GVHD and T-cell reconstitution in GVHD target organs, most notably the gastrointestinal (GI) tract where the disease contributes most to patient mortality. T-cell receptor (TCR) repertoire sequencing was used to measure T-cell reconstitution from the same donor graft (C57BL/6 H-2b) in the GI tract of different recipients across a spectrum of matching, from syngeneic (C57BL/6), to minor histocompatibility (MHC) antigen mismatch BALB.B (H-2b), to major MHC mismatched B10.BR (H-2k) and BALB/c (H-2d). Although the donor T-cell pools had highly similar TCR, the TCR repertoire after HCT was very specific to recipients in each experiment independent of geography. A single invariant natural killer T clone was identifiable in every recipient group and was enriched in syngeneic recipients according to clonal count and confirmatory flow cytometry. Using a novel cluster analysis of the TCR repertoire, we could classify recipient groups based only on their CDR3 size distribution or TCR repertoire relatedness. Using a method for evaluating the contribution of common TCR motifs to relatedness, we found that reproducible sets of clones were associated with specific recipient groups within each experiment and that relatedness did not necessarily depend on the most common clones in allogeneic recipients. This finding suggests that TCR reconstitution is highly stochastic and likely does not depend on the evaluation of the most expanded TCR clones in any individual recipient but instead depends on a complex polyclonal architecture.
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10
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Lucca LE, Axisa PP, Lu B, Harnett B, Jessel S, Zhang L, Raddassi K, Zhang L, Olino K, Clune J, Singer M, Kluger HM, Hafler DA. Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells. J Exp Med 2021; 218:e20200921. [PMID: 33651881 PMCID: PMC7933991 DOI: 10.1084/jem.20200921] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/14/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Understanding the relationship between tumor and peripheral immune environments could allow longitudinal immune monitoring in cancer. Here, we examined whether T cells that share the same TCRαβ and are found in both tumor and blood can be interrogated to gain insight into the ongoing tumor T cell response. Paired transcriptome and TCRαβ repertoire of circulating and tumor-infiltrating T cells were analyzed at the single-cell level from matched tumor and blood from patients with metastatic melanoma. We found that in circulating T cells matching clonally expanded tumor-infiltrating T cells (circulating TILs), gene signatures of effector functions, but not terminal exhaustion, reflect those observed in the tumor. In contrast, features of exhaustion are displayed predominantly by tumor-exclusive T cells. Finally, genes associated with a high degree of blood-tumor TCR sharing were overexpressed in tumor tissue after immunotherapy. These data demonstrate that circulating TILs have unique transcriptional patterns that may have utility for the interrogation of T cell function in cancer immunotherapy.
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Affiliation(s)
- Liliana E. Lucca
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Pierre-Paul Axisa
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Benjamin Lu
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Brian Harnett
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Shlomit Jessel
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Le Zhang
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Khadir Raddassi
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Lin Zhang
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Kelly Olino
- Department of Surgery, Yale School of Medicine, New Haven, CT
| | - James Clune
- Department of Surgery, Yale School of Medicine, New Haven, CT
| | - Meromit Singer
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | | | - David A. Hafler
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
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11
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D’Ippolito E, Wagner KI, Busch DH. Needle in a Haystack: The Naïve Repertoire as a Source of T Cell Receptors for Adoptive Therapy with Engineered T Cells. Int J Mol Sci 2020; 21:E8324. [PMID: 33171940 PMCID: PMC7664211 DOI: 10.3390/ijms21218324] [Citation(s) in RCA: 4] [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: 09/29/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022] Open
Abstract
T cell engineering with antigen-specific T cell receptors (TCRs) has allowed the generation of increasingly specific, reliable, and versatile T cell products with near-physiological features. However, a broad applicability of TCR-based therapies in cancer is still limited by the restricted number of TCRs, often also of suboptimal potency, available for clinical use. In addition, targeting of tumor neoantigens with TCR-engineered T cell therapy moves the field towards a highly personalized treatment, as tumor neoantigens derive from somatic mutations and are extremely patient-specific. Therefore, relevant TCRs have to be de novo identified for each patient and within a narrow time window. The naïve repertoire of healthy donors would represent a reliable source due to its huge diverse TCR repertoire, which theoretically entails T cells for any antigen specificity, including tumor neoantigens. As a challenge, antigen-specific naïve T cells are of extremely low frequency and mostly of low functionality, making the identification of highly functional TCRs finding a "needle in a haystack." In this review, we present the technological advancements achieved in high-throughput mapping of patient-specific neoantigens and corresponding cognate TCRs and how these platforms can be used to interrogate the naïve repertoire for a fast and efficient identification of rare but therapeutically valuable TCRs for personalized adoptive T cell therapy.
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MESH Headings
- Antigens, Neoplasm/genetics
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Immunotherapy, Adoptive/trends
- Neoplasms/genetics
- Precision Medicine/methods
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/physiology
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
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Affiliation(s)
- Elvira D’Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Karolin I. Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Focus Group ‘‘Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München (TUM), 81675 Munich, Germany
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T-cell repertoire analysis and metrics of diversity and clonality. Curr Opin Biotechnol 2020; 65:284-295. [PMID: 32889231 DOI: 10.1016/j.copbio.2020.07.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022]
Abstract
The recent developments of high-throughput bulk and single-cell sequencing technologies accelerated the understanding of the complexity of immune repertoire dynamics combined to transcriptomics. Also, profiling of cellular repertoires in health or disease requires statistical metrics to capture clonal diversity characterized by clones frequency, repertoire richness and convergence. Here we present the common technologies of bulk and single-cell sequencing of T-cell receptors (TCRs), discuss current knowledge regarding computational tools clustering and predicting specificity of TCR repertoires based on shared structural motifs and review main indices for repertoire diversity and convergence analyses. These tools represent potential biomarkers to decipher the fitness of immune repertoires in diseased or treated patients but also the presages and promises of computational approaches to revolutionize personalized immunotherapy.
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Abstract
Single-cell sequencing is an emerging technology in the field of immunology and oncology that allows researchers to couple RNA quantification and other modalities, like immune cell receptor profiling at the level of an individual cell. A number of workflows and software packages have been created to process and analyze single-cell transcriptomic data. These packages allow users to take the vast dimensionality of the data generated in single-cell-based experiments and distill the data into novel insights. Unlike the transcriptomic field, there is a lack of options for software that allow for single-cell immune receptor profiling. Enabling users to easily combine mRNA and immune profiling, scRepertoire was built to process data derived from 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with a number of popular R packages for single-cell expression, such as Seurat. The scRepertoire R package and processed data are open source and available on GitHub and provides in-depth tutorials on the capability of the package.
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Affiliation(s)
- Nicholas Borcherding
- Department of Pathology, University of Iowa, Iowa City, IA, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
- Cancer Biology Graduate Program, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | | | - Gloria Kraus
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
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