Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation
Spectratyping assays are well recognized as the clinical gold standard for assessing the T cell receptor (TCR) repertoire in haematopoietic stem cell transplant (HSCT) recipients. These assays use length distributions of the hyper variable complementarity-determining region 3 (CDR3) to characterize...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-11-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fimmu.2018.02547/full |
| _version_ | 1818585405360963584 |
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| author | Athina Soragia Gkazi Ben K Margetts Ben K Margetts Ben K Margetts Teresa Attenborough Teresa Attenborough Lana Mhaldien Joseph F. Standing Joseph F. Standing Theres Oakes James M. Heather John Booth Marlene Pasquet Robert Chiesa Paul Veys Nigel Klein Nigel Klein Benny Chain Robin Callard Robin Callard Stuart P. Adams Stuart P. Adams |
| author_facet | Athina Soragia Gkazi Ben K Margetts Ben K Margetts Ben K Margetts Teresa Attenborough Teresa Attenborough Lana Mhaldien Joseph F. Standing Joseph F. Standing Theres Oakes James M. Heather John Booth Marlene Pasquet Robert Chiesa Paul Veys Nigel Klein Nigel Klein Benny Chain Robin Callard Robin Callard Stuart P. Adams Stuart P. Adams |
| author_sort | Athina Soragia Gkazi |
| collection | DOAJ |
| description | Spectratyping assays are well recognized as the clinical gold standard for assessing the T cell receptor (TCR) repertoire in haematopoietic stem cell transplant (HSCT) recipients. These assays use length distributions of the hyper variable complementarity-determining region 3 (CDR3) to characterize a patient's T cell immune reconstitution post-transplant. However, whilst useful, TCR spectratyping is notably limited by its resolution, with the technique unable to provide data on the individual clonotypes present in a sample. High-resolution clonotype data are necessary to provide quantitative clinical TCR assessments and to better understand clonotype dynamics during clinically relevant events such as viral infections or GvHD. In this study we developed and applied a CDR3 Next Generation Sequencing (NGS) methodology to assess the TCR repertoire in cord blood transplant (CBT) recipients. Using this, we obtained comprehensive TCR data from 16 CBT patients and 5 control cord samples at Great Ormond Street Hospital (GOSH). These were analyzed to provide a quantitative measurement of the TCR repertoire and its constituents in patients post-CBT. We were able to both recreate and quantify inferences typically drawn from spectratyping data. Additionally, we demonstrate that an NGS approach to TCR assessment can provide novel insights into the recovery of the immune system in these patients. We show that NGS can be used to accurately quantify TCR repertoire diversity and to provide valuable inference on clonotypes detected in a sample. We serially assessed the progress of T cell immune reconstitution demonstrating that there is dramatic variation in TCR diversity immediately following transplantation and that the dynamics of T cell immune reconstitution is perturbed by the presence of GvHD. These findings provide a proof of concept for the adoption of NGS TCR sequencing in clinical practice. |
| first_indexed | 2024-12-16T08:36:33Z |
| format | Article |
| id | doaj.art-56336d58687848308d44b7cd8222045f |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-16T08:36:33Z |
| publishDate | 2018-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-56336d58687848308d44b7cd8222045f2022-12-21T22:37:46ZengFrontiers Media S.A.Frontiers in Immunology1664-32242018-11-01910.3389/fimmu.2018.02547408770Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood TransplantationAthina Soragia Gkazi0Ben K Margetts1Ben K Margetts2Ben K Margetts3Teresa Attenborough4Teresa Attenborough5Lana Mhaldien6Joseph F. Standing7Joseph F. Standing8Theres Oakes9James M. Heather10John Booth11Marlene Pasquet12Robert Chiesa13Paul Veys14Nigel Klein15Nigel Klein16Benny Chain17Robin Callard18Robin Callard19Stuart P. Adams20Stuart P. Adams21Infection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United KingdomInfection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United KingdomDigital Research Environment, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United KingdomCentre for Computation, Mathematics, and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United KingdomInfection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United KingdomCentre for Computation, Mathematics, and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United KingdomSIHMDS-Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United KingdomInfection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United KingdomPharmacy Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United KingdomDivision of Infection and Immunity, University College London, London, United KingdomDivision of Infection and Immunity, University College London, London, United KingdomDigital Research Environment, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United KingdomLe Centre Hospitalier Universitaire de Toulouse, Toulouse, FranceDepartment of Blood and Marrow Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United KingdomDepartment of Blood and Marrow Transplantation, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United KingdomInfection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United KingdomInfectious Diseases Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United KingdomDivision of Infection and Immunity, University College London, London, United KingdomInfection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United KingdomCentre for Computation, Mathematics, and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United KingdomInfection, Immunity and Inflammation Section, Great Ormond Street Institute of Child Health, University College London, London, United KingdomSIHMDS-Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United KingdomSpectratyping assays are well recognized as the clinical gold standard for assessing the T cell receptor (TCR) repertoire in haematopoietic stem cell transplant (HSCT) recipients. These assays use length distributions of the hyper variable complementarity-determining region 3 (CDR3) to characterize a patient's T cell immune reconstitution post-transplant. However, whilst useful, TCR spectratyping is notably limited by its resolution, with the technique unable to provide data on the individual clonotypes present in a sample. High-resolution clonotype data are necessary to provide quantitative clinical TCR assessments and to better understand clonotype dynamics during clinically relevant events such as viral infections or GvHD. In this study we developed and applied a CDR3 Next Generation Sequencing (NGS) methodology to assess the TCR repertoire in cord blood transplant (CBT) recipients. Using this, we obtained comprehensive TCR data from 16 CBT patients and 5 control cord samples at Great Ormond Street Hospital (GOSH). These were analyzed to provide a quantitative measurement of the TCR repertoire and its constituents in patients post-CBT. We were able to both recreate and quantify inferences typically drawn from spectratyping data. Additionally, we demonstrate that an NGS approach to TCR assessment can provide novel insights into the recovery of the immune system in these patients. We show that NGS can be used to accurately quantify TCR repertoire diversity and to provide valuable inference on clonotypes detected in a sample. We serially assessed the progress of T cell immune reconstitution demonstrating that there is dramatic variation in TCR diversity immediately following transplantation and that the dynamics of T cell immune reconstitution is perturbed by the presence of GvHD. These findings provide a proof of concept for the adoption of NGS TCR sequencing in clinical practice.https://www.frontiersin.org/article/10.3389/fimmu.2018.02547/fullT cellhaematopoietic stem cell transplantnext generation sequencingT cell receptorCDR3clonotypes |
| spellingShingle | Athina Soragia Gkazi Ben K Margetts Ben K Margetts Ben K Margetts Teresa Attenborough Teresa Attenborough Lana Mhaldien Joseph F. Standing Joseph F. Standing Theres Oakes James M. Heather John Booth Marlene Pasquet Robert Chiesa Paul Veys Nigel Klein Nigel Klein Benny Chain Robin Callard Robin Callard Stuart P. Adams Stuart P. Adams Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation Frontiers in Immunology T cell haematopoietic stem cell transplant next generation sequencing T cell receptor CDR3 clonotypes |
| title | Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation |
| title_full | Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation |
| title_fullStr | Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation |
| title_full_unstemmed | Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation |
| title_short | Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation |
| title_sort | clinical t cell receptor repertoire deep sequencing and analysis an application to monitor immune reconstitution following cord blood transplantation |
| topic | T cell haematopoietic stem cell transplant next generation sequencing T cell receptor CDR3 clonotypes |
| url | https://www.frontiersin.org/article/10.3389/fimmu.2018.02547/full |
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