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Smirnova AO, Miroshnichenkova AM, Olshanskaya YV, Maschan MA, Lebedev YB, Chudakov DM, Mamedov IZ, Komkov A. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. eLife 2023; 12:69157. [PMID: 36692004 PMCID: PMC9901932 DOI: 10.7554/elife.69157] [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: 04/06/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023] Open
Abstract
High-throughput sequencing of adaptive immune receptor repertoires is a valuable tool for receiving insights in adaptive immunity studies. Several powerful TCR/BCR repertoire reconstruction and analysis methods have been developed in the past decade. However, detecting and correcting the discrepancy between real and experimentally observed lymphocyte clone frequencies are still challenging. Here, we discovered a hallmark anomaly in the ratio between read count and clone count-based frequencies of non-functional clonotypes in multiplex PCR-based immune repertoires. Calculating this anomaly, we formulated a quantitative measure of V- and J-genes frequency bias driven by multiplex PCR during library preparation called Over Amplification Rate (OAR). Based on the OAR concept, we developed an original software for multiplex PCR-specific bias evaluation and correction named iROAR: immune Repertoire Over Amplification Removal (https://github.com/smiranast/iROAR). The iROAR algorithm was successfully tested on previously published TCR repertoires obtained using both 5' RACE (Rapid Amplification of cDNA Ends)-based and multiplex PCR-based approaches and compared with a biological spike-in-based method for PCR bias evaluation. The developed approach can increase the accuracy and consistency of repertoires reconstructed by different methods making them more applicable for comparative analysis.
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Affiliation(s)
- Anastasia O Smirnova
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
| | - Anna M Miroshnichenkova
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yulia V Olshanskaya
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Michael A Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
| | - Yuri B Lebedev
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Dmitriy M Chudakov
- Skolkovo Institute of Science and TechnologyMoscowRussian Federation
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
- Abu Dhabi Stem Cells CenterAbu DhabiUnited Arab Emirates
| | - Ilgar Z Mamedov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Pirogov Russian National Research Medical UniversityMoscowRussian Federation
| | - Alexander Komkov
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryMoscowRussian Federation
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and ImmunologyMoscowRussian Federation
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2
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Wong P, Cina DP, Sherwood KR, Fenninger F, Sapir-Pichhadze R, Polychronakos C, Lan J, Keown PA. Clinical application of immune repertoire sequencing in solid organ transplant. Front Immunol 2023; 14:1100479. [PMID: 36865546 PMCID: PMC9971933 DOI: 10.3389/fimmu.2023.1100479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Background Measurement of T cell receptor (TCR) or B cell receptor (BCR) gene utilization may be valuable in monitoring the dynamic changes in donor-reactive clonal populations following transplantation and enabling adjustment in therapy to avoid the consequences of excess immune suppression or to prevent rejection with contingent graft damage and to indicate the development of tolerance. Objective We performed a review of current literature to examine research in immune repertoire sequencing in organ transplantation and to assess the feasibility of this technology for clinical application in immune monitoring. Methods We searched MEDLINE and PubMed Central for English-language studies published between 2010 and 2021 that examined T cell/B cell repertoire dynamics upon immune activation. Manual filtering of the search results was performed based on relevancy and predefined inclusion criteria. Data were extracted based on study and methodology characteristics. Results Our initial search yielded 1933 articles of which 37 met the inclusion criteria; 16 of these were kidney transplant studies (43%) and 21 were other or general transplantation studies (57%). The predominant method for repertoire characterization was sequencing the CDR3 region of the TCR β chain. Repertoires of transplant recipients were found to have decreased diversity in both rejectors and non-rejectors when compared to healthy controls. Rejectors and those with opportunistic infections were more likely to have clonal expansion in T or B cell populations. Mixed lymphocyte culture followed by TCR sequencing was used in 6 studies to define an alloreactive repertoire and in specialized transplant settings to track tolerance. Conclusion Methodological approaches to immune repertoire sequencing are becoming established and offer considerable potential as a novel clinical tool for pre- and post-transplant immune monitoring.
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Affiliation(s)
- Paaksum Wong
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Davide P Cina
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Karen R Sherwood
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Franz Fenninger
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ruth Sapir-Pichhadze
- Department of Medicine, Division of Nephrology, McGill University, Montreal, QC, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Constantin Polychronakos
- Department of Pediatrics, The Research Institute of the McGill University Health Centre and the Montreal Children's Hospital, Montreal, QC, Canada
| | - James Lan
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Paul A Keown
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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3
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Louis K, Macedo C, Lefaucheur C, Metes D. Adaptive immune cell responses as therapeutic targets in antibody-mediated organ rejection. Trends Mol Med 2022; 28:237-250. [PMID: 35093288 PMCID: PMC8882148 DOI: 10.1016/j.molmed.2022.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 01/17/2023]
Abstract
Humoral alloimmunity of organ transplant recipient to donor can lead to antibody-mediated rejection (ABMR), causing thousands of organ transplants to fail each year worldwide. However, the mechanisms of adaptive immune cell responses at the basis of humoral alloimmunity have not been entirely understood. In this review, we discuss how recent investigations have uncovered the key contributions of T follicular helper (TFH) and B cells and their coordinated actions in driving donor-specific antibody generation and immune progression towards ABMR. We show how recognition of the role of TFH-B cell interactions may allow the elaboration of improved clinical strategies for immune monitoring and the identification of novel therapeutic targets to tackle ABMR that will ultimately improve organ transplant survival.
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Affiliation(s)
- Kevin Louis
- Kidney Transplant Department, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Human Immunology and Immunopathology, Institut National de la Santé et de la Recherche Médicale UMR 976, Université de Paris, Paris, France
| | - Camila Macedo
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Carmen Lefaucheur
- Kidney Transplant Department, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Paris Translational Research Center for Organ Transplantation, Institut National de la Santé et de la Recherche Médicale UMR 970, Université de Paris, Paris, France
| | - Diana Metes
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
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4
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Aschauer C, Jelencsics K, Hu K, Heinzel A, Gregorich MG, Vetter J, Schaller S, Winkler SM, Weinberger J, Pimenov L, Gualdoni GA, Eder M, Kainz A, Troescher AR, Regele H, Reindl-Schwaighofer R, Wekerle T, Huppa JB, Sykes M, Oberbauer R. Prospective Tracking of Donor-Reactive T-Cell Clones in the Circulation and Rejecting Human Kidney Allografts. Front Immunol 2021; 12:750005. [PMID: 34721420 PMCID: PMC8552542 DOI: 10.3389/fimmu.2021.750005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background Antigen recognition of allo-peptides and HLA molecules leads to the activation of donor-reactive T-cells following transplantation, potentially causing T-cell-mediated rejection (TCMR). Sequencing of the T-cell receptor (TCR) repertoire can be used to track the donor-reactive repertoire in blood and tissue of patients after kidney transplantation. Methods/Design In this prospective cohort study, 117 non-sensitized kidney transplant recipients with anti-CD25 induction were included. Peripheral mononuclear cells (PBMCs) were sampled pre-transplant and at the time of protocol or indication biopsies together with graft tissue. Next-generation sequencing (NGS) of the CDR3 region of the TCRbeta chain was performed after donor stimulation in mixed lymphocyte reactions to define the donor-reactive TCR repertoire. Blood and tissue of six patients experiencing a TCMR and six patients without rejection on protocol biopsies were interrogated for these TCRs. To elucidate common features of T-cell clonotypes, a network analysis of the TCR repertoires was performed. Results After transplantation, the frequency of circulating donor-reactive CD4 T-cells increased significantly from 0.86 ± 0.40% to 2.06 ± 0.40% of all CD4 cells (p < 0.001, mean dif.: -1.197, CI: -1.802, -0.593). The number of circulating donor-reactive CD4 clonotypes increased from 0.72 ± 0.33% to 1.89 ± 0.33% (p < 0.001, mean dif.: -1.168, CI: -1.724, -0.612). No difference in the percentage of donor-reactive T-cells in the circulation at transplant biopsy was found between subjects experiencing a TCMR and the control group [p = 0.64 (CD4+), p = 0.52 (CD8+)]. Graft-infiltrating T-cells showed an up to six-fold increase of donor-reactive T-cell clonotypes compared to the blood at the same time (3.7 vs. 0.6% and 2.4 vs. 1.5%), but the infiltrating TCR repertoire was not reflected by the composition of the circulating TCR repertoire despite some overlap. Network analysis showed a distinct segregation of the donor-reactive repertoire with higher modularity than the overall TCR repertoire in the blood. These findings indicate an unchoreographed process of diverse T-cell clones directed against numerous non-self antigens found in the allograft. Conclusion Donor-reactive T-cells are enriched in the kidney allograft during a TCMR episode, and dominant tissue clones are also found in the blood. Trial Registration Clinicaltrials.gov: NCT: 03422224 (https://clinicaltrials.gov/ct2/show/NCT03422224).
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Affiliation(s)
- Constantin Aschauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Kira Jelencsics
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Karin Hu
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Mariella Gloria Gregorich
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria.,Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Julia Vetter
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Stephan M Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Johannes Weinberger
- Research Laboratory of Infection Biology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | - Lisabeth Pimenov
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Guido A Gualdoni
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Michael Eder
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Alexander Kainz
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Heinz Regele
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Thomas Wekerle
- Department of General Surgery, Division of Transplantation, Section of Transplantation Immunology, Medical University of Vienna, Vienna, Austria
| | - Johannes Bernhard Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Megan Sykes
- Columbian Center for Translational Immunology, Department of Medicine, Columbia University, New York City, NY, United States
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
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5
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Louis K, Bailly E, Macedo C, Lau L, Ramaswami B, Chang A, Chandran U, Landsittel D, Gu X, Chalasani G, Zeevi A, Randhawa P, Singh H, Lefaucheur C, Metes D. T-bet+CD27+CD21- B cells poised for plasma cell differentiation during antibody-mediated rejection of kidney transplants. JCI Insight 2021; 6:148881. [PMID: 34032636 PMCID: PMC8262465 DOI: 10.1172/jci.insight.148881] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Alloimmune responses driven by donor-specific antibodies (DSAs) can lead to antibody-mediated rejection (ABMR) in organ transplantation. Yet, the cellular states underlying alloreactive B cell responses and the molecular components controlling them remain unclear. Using high-dimensional profiling of B cells in a cohort of 96 kidney transplant recipients, we identified expanded numbers of CD27+CD21– activated memory (AM) B cells that expressed the transcription factor T-bet in patients who developed DSAs and progressed to ABMR. Notably, AM cells were less frequent in DSA+ABMR– patients and at baseline levels in DSA– patients. RNA-Seq analysis of AM cells in patients undergoing ABMR revealed these cells to be poised for plasma cell differentiation and to express restricted IGHV sequences reflective of clonal expansion. In addition to T-bet, AM cells manifested elevated expression of interferon regulatory factor 4 and Blimp1, and upon coculture with autologous T follicular helper cells, differentiated into DSA-producing plasma cells in an IL-21–dependent manner. The frequency of AM cells was correlated with the timing and severity of ABMR manifestations. Importantly, T-bet+ AM cells were detected within kidney allografts along with their restricted IGHV sequences. This study delineates a pivotal role for AM cells in promoting humoral responses and ABMR in organ transplantation and highlights them as important therapeutic targets.
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Affiliation(s)
- Kevin Louis
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Human Immunology and Immunopathology, INSERM UMR 976, Université de Paris, Paris, France
| | - Elodie Bailly
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Human Immunology and Immunopathology, INSERM UMR 976, Université de Paris, Paris, France
| | - Camila Macedo
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Louis Lau
- Center for Systems Immunology.,Department of Immunology
| | - Bala Ramaswami
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | | | | | - Xinyan Gu
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Geetha Chalasani
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Department of Immunology.,Department of Medicine, and
| | - Adriana Zeevi
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Department of Immunology.,Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Parmjeet Randhawa
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Carmen Lefaucheur
- Human Immunology and Immunopathology, INSERM UMR 976, Université de Paris, Paris, France
| | - Diana Metes
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Department of Immunology
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6
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Kolovou K, Laskari K, Roumelioti M, Tektonidou MG, Panayiotidis P, Boletis JN, Marinaki S, Sfikakis PP. B-cell oligoclonal expansions in renal tissue of patients with immune-mediated glomerular disease. Clin Immunol 2020; 217:108488. [PMID: 32479988 DOI: 10.1016/j.clim.2020.108488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
B-cell clonal expansion has been sporadically described in the blood and/or renal tissue of patients with glomerulonephritides, albeit with unclear pathogenetic role. Herein, using spectratyping analysis, we observed oligoclonal intrarenal B-cell populations in 59% of glomerulonephritis patients with podocyte injury (6/7 with focal segmental glomerulosclerosis, 1/3 minimal change disease, 1/3 idiopathic membranous nephropathy, 3/4 IgA nephropathy, 2/5 membranous lupus nephritis), 20% of glomerulonephritis patients without podocyte involvement (4/13 with mesangial or proliferative lupus nephritis, 0/3 idiopathic membranoproliferative glomerulonephritis, 0/4 pauci-immune vasculitis) and 17% of control patients with renal cancer. In multivariate analysis, oligoclonal B-cells were associated with podocyte injury and the grade of glomerulosclerosis (both p = .009). B-cell oligoclonal expansions were not found in the paired peripheral blood samples. We postulate that B-cell expansion in the kidney results from local stimuli, including antigens expressed on podocytes. Further studies to unravel the role of oligoclonal B-cells in (auto)immune-mediated kidney disease are warranted.
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Affiliation(s)
- Kyriaki Kolovou
- Department of Nephrology and Renal Transplantation, National and Kapodistrian University of Athens Medical School, Laiko Hospital, Athens, Greece
| | - Katerina Laskari
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Laiko Hospital, Athens, Greece
| | - Maria Roumelioti
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Laiko Hospital, Athens, Greece
| | - Maria G Tektonidou
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Laiko Hospital, Athens, Greece
| | - Panayiotis Panayiotidis
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Laiko Hospital, Athens, Greece
| | - John N Boletis
- Department of Nephrology and Renal Transplantation, National and Kapodistrian University of Athens Medical School, Laiko Hospital, Athens, Greece
| | - Smaragdi Marinaki
- Department of Nephrology and Renal Transplantation, National and Kapodistrian University of Athens Medical School, Laiko Hospital, Athens, Greece
| | - Petros P Sfikakis
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Laiko Hospital, Athens, Greece.
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7
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Carmona SJ, Siddiqui I, Bilous M, Held W, Gfeller D. Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq. Oncoimmunology 2020; 9:1737369. [PMID: 32313720 PMCID: PMC7153840 DOI: 10.1080/2162402x.2020.1737369] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/09/2020] [Accepted: 01/25/2020] [Indexed: 01/08/2023] Open
Abstract
Recent studies have proposed that tumor-specific tumor-infiltrating CD8+ T lymphocytes (CD8 TIL) can be classified into two main groups: "exhausted" TILs, characterized by high expression of the inhibitory receptors PD-1 and TIM-3 and lack of transcription factor 1 (Tcf1); and "memory-like" TILs, with self-renewal capacity and co-expressing Tcf1 and PD-1. However, a comprehensive definition of the heterogeneity existing within CD8 TILs has yet to be clearly established. To investigate this heterogeneity at the transcriptomic level, we performed paired single-cell RNA and TCR sequencing of CD8 T cells infiltrating B16 murine melanoma tumors, including cells of known tumor specificity. Unsupervised clustering and gene-signature analysis revealed four distinct CD8 TIL states - exhausted, memory-like, naïve and effector memory-like (EM-like) - and predicted novel markers, including Ly6C for the EM-like cells, that were validated by flow cytometry. Tumor-specific PMEL T cells were predominantly found within the exhausted and memory-like states but also within the EM-like state. Further, T cell receptor sequencing revealed a large clonal expansion of exhausted, memory-like and EM-like cells with partial clonal relatedness between them. Finally, meta-analyses of public bulk and single-cell RNA-seq data suggested that anti-PD-1 treatment induces the expansion of EM-like cells. Our reference map of the transcriptomic landscape of murine CD8 TILs will help interpreting future bulk and single-cell transcriptomic studies and may guide the analysis of CD8IL subpopulations in response to therapeutic interventions.
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Affiliation(s)
- Santiago J Carmona
- Department of Oncology UNIL CHUV, University of Lausanne, Epalinges, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
| | - Imran Siddiqui
- Department of Oncology UNIL CHUV, University of Lausanne, Epalinges, Switzerland
| | - Mariia Bilous
- Department of Oncology UNIL CHUV, University of Lausanne, Epalinges, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Werner Held
- Department of Oncology UNIL CHUV, University of Lausanne, Epalinges, Switzerland
| | - David Gfeller
- Department of Oncology UNIL CHUV, University of Lausanne, Epalinges, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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8
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Van Loon E, Gazut S, Yazdani S, Lerut E, de Loor H, Coemans M, Noël LH, Thorrez L, Van Lommel L, Schuit F, Sprangers B, Kuypers D, Essig M, Gwinner W, Anglicheau D, Marquet P, Naesens M. Development and validation of a peripheral blood mRNA assay for the assessment of antibody-mediated kidney allograft rejection: A multicentre, prospective study. EBioMedicine 2019; 46:463-472. [PMID: 31378695 PMCID: PMC6710906 DOI: 10.1016/j.ebiom.2019.07.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Background Antibody-mediated rejection, a leading cause of renal allograft graft failure, is diagnosed by histological assessment of invasive allograft biopsies. Accurate non-invasive biomarkers are not available. Methods In the multicentre, prospective BIOMARGIN study, blood samples were prospectively collected at time of renal allograft biopsies between June 2011 and August 2016 and analyzed in three phases. The discovery and derivation phases of the study (N = 117 and N = 183 respectively) followed a case-control design and included whole genome transcriptomics and targeted mRNA expression analysis to construct and lock a multigene model. The primary end point was the diagnostic accuracy of the locked multigene assay for antibody-mediated rejection in a third validation cohort of serially collected blood samples (N = 387). This trial is registered with ClinicalTrials.gov, number NCT02832661. Findings We identified and locked an 8-gene assay (CXCL10, FCGR1A, FCGR1B, GBP1, GBP4, IL15, KLRC1, TIMP1) in blood samples from the discovery and derivation phases for discrimination between cases with (N = 49) and without (N = 134) antibody-mediated rejection. In the validation cohort, this 8-gene assay discriminated between cases with (N = 41) and without antibody-mediated rejection (N = 346) with good diagnostic accuracy (ROC AUC 79·9%; 95% CI 72·6 to 87·2, p < 0·0001). The diagnostic accuracy of the 8-gene assay was retained both at time of stable graft function and of graft dysfunction, within the first year and also later after transplantation. The 8-gene assay is correlated with microvascular inflammation and transplant glomerulopathy, but not with the histological lesions of T-cell mediated rejection. Interpretation We identified and validated a novel 8-gene expression assay that can be used for non-invasive diagnosis of antibody-mediated rejection. Funding The Seventh Framework Programme (FP7) of the European Commission.
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Affiliation(s)
- Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium
| | - Stéphane Gazut
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, Gif-sur-Yvette, France
| | - Saleh Yazdani
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Evelyne Lerut
- University Hospitals Leuven, Department of Morphology and Molecular Pathology, Leuven, Belgium
| | - Henriette de Loor
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Maarten Coemans
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium
| | - Laure-Hélène Noël
- Necker-Enfants Malades Institute, French National Institute of Health and Medical Research U1151, France
| | - Lieven Thorrez
- KU Leuven Department of Development and Regeneration, campus KULAK, Kortrijk, Belgium
| | - Leentje Van Lommel
- KU Leuven Gene Expression Unit, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frans Schuit
- KU Leuven Gene Expression Unit, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium; KU Leuven Laboratory of Molecular Immunology, Rega Institute, Leuven, Belgium
| | - Dirk Kuypers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium
| | - Marie Essig
- CHU Limoges, Department of Nephrology, Dialysis and Transplantation, Univ. Limoges, U850 INSERM, Limoges, France
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Dany Anglicheau
- Paris Descartes, Sorbonne Paris Cité University, INSERM U1151, Paris, France; Department of Nephrology and Kidney Transplantation, RTRS Centaure, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Pierre Marquet
- CHU Limoges, Univ. Limoges, U850 INSERM, Limoges, France
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, Leuven, Belgium; University Hospitals Leuven, Department of Nephrology and Renal Transplantation, Leuven, Belgium.
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9
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Natural protective immunity against grass pollen allergy is maintained by a diverse spectrum of response types. J Allergy Clin Immunol 2017; 140:1746-1749.e11. [PMID: 28867457 DOI: 10.1016/j.jaci.2017.07.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 07/15/2017] [Accepted: 07/24/2017] [Indexed: 12/24/2022]
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10
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Wekerle T, Segev D, Lechler R, Oberbauer R. Strategies for long-term preservation of kidney graft function. Lancet 2017; 389:2152-2162. [PMID: 28561006 DOI: 10.1016/s0140-6736(17)31283-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 12/21/2022]
Abstract
Kidney transplantation has become a routine procedure in the treatment of patients with kidney failure, and requires collaboration of experts from different disciplines, such as nephrology, surgery, immunology, pathology, infectious disease medicine, cardiology, and oncology. Grafts can be obtained from deceased or living donors, with different logistical requirements and implications for long-term graft patency. 1-year graft survival rates are greater than 95% in many centres but improvement of long-term function remains a challenge. New developments in molecular immunology and computational biology have increased precision of donor and recipient matching of HLA and non-HLA compatibility. Individual omics-wide molecular diagnostics, extracorporeal therapies, and drug developments allow for precise individual decision making and treatment. Tolerance induction by mixed chimerism without toxic conditioning and with a low risk of graft versus host disease is a visionary but realistic goal. Some of these innovations are already used in modern transplant centres and will allow advancement in long-term allograft preservation.
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Affiliation(s)
- Thomas Wekerle
- Department of Surgery, Section of Transplantation Immunology, Medical University of Vienna, Vienna, Austria
| | - Dorry Segev
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Robert Lechler
- MRC Centre for Transplantation, King's College London, London, UK
| | - Rainer Oberbauer
- Department of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria.
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