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Stamatopoulos K, Bruford E, Campo E, Lefranc MP. Immunogenetics in hematopathology and hematology: why a common language is important. Leukemia 2024; 38:1474-1476. [PMID: 38664547 PMCID: PMC11216993 DOI: 10.1038/s41375-024-02260-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 07/03/2024]
Affiliation(s)
- Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.
| | - Elspeth Bruford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elias Campo
- Hematopathology Section, Pathology Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
- Molecular Pathology of Lymphoid Neoplasms Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France.
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2
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van den Brand M, Möbs M, Otto F, Kroeze LI, Gonzalez de Castro D, Stamatopoulos K, Davi F, Bravetti C, Kolijn PM, Vlachonikola E, Stewart JP, Pott C, Hummel M, Darzentas N, Langerak AW, Fend F, Groenen PJTA. EuroClonality-NGS Recommendations for Evaluation of B-Cell Clonality Analysis by Next-Generation Sequencing: A Structured Approach with the DEPART Algorithm. J Mol Diagn 2023; 25:729-739. [PMID: 37467928 DOI: 10.1016/j.jmoldx.2023.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/16/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023] Open
Abstract
Next-generation sequencing (NGS)-based clonality analysis allows in-depth assessment of the clonal composition of a sample with high sensitivity for detecting small clones. Within the EuroClonality-NGS Working Group, a protocol for NGS Ig clonality analysis was developed and validated previously. This NGS-based approach was designed to generate small amplicons, making it suitable for samples with suboptimal DNA quality, especially material derived from formalin-fixed, paraffin-embedded tissue. Using expert assessment of NGS Ig clonality results as a reference, a structured algorithmic approach to the assessment of NGS-amplicon-based B-cell clonality analysis was developed. A structured approach with the Detection of clonality through Evaluation of sample quality and assessment of Pattern, Abundance and RaTio (DEPART) algorithm was proposed, which consecutively evaluates sample quality, the pattern of the clonotypes present, the abundance of the most dominant clonotypes, and the ratio between the dominant clonotypes and the background to evaluate the different Ig gene targets. Specific issues with respect to evaluation of the various Ig targets as well as the integration of results of individual targets into a molecular clonality conclusion are discussed and illustrated with case examples. Finally, the importance of interpretation of NGS-based clonality results in clinical and histopathologic contexts is discussed. It is expected that these recommendations will have clinical utility to facilitate proper evaluation of clonality assessment.
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Affiliation(s)
- Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Markus Möbs
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Franziska Otto
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David Gonzalez de Castro
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Frederic Davi
- Hematology Department, Hospital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - Clotilde Bravetti
- Hematology Department, Hospital Pitié-Salpêtrière, Sorbonne University, Paris, France
| | - P Martijn Kolijn
- Laboratory of Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - J Peter Stewart
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Christiane Pott
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anton W Langerak
- Laboratory of Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Patricia J T A Groenen
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
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3
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Couillez G, Morel P, Clichet V, Fourdrain L, Delette C, Harrivel V, Gubler B, Rottier C, Derreumaux S, Margat E, Garcon L, Marolleau JP, Boyer T. Flow cytometry as a fast, cost-effective tool to assess IGHV mutational status in CLL. Blood Adv 2023; 7:4701-4704. [PMID: 36287221 PMCID: PMC10468354 DOI: 10.1182/bloodadvances.2022008033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/28/2022] [Accepted: 10/02/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Guillaume Couillez
- Service d’Hématologie Biologique, Centre de Biologie Humaine, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - Pierre Morel
- Service d’Hématologie Clinique et de Thérapie Cellulaire, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - Valentin Clichet
- Service d’Hématologie Biologique, Centre de Biologie Humaine, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - Ludivine Fourdrain
- Service d’Hématologie Biologique, Centre de Biologie Humaine, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - Caroline Delette
- Service d’Hématologie Clinique et de Thérapie Cellulaire, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - Véronique Harrivel
- Service d’Hématologie Biologique, Centre de Biologie Humaine, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - Brigitte Gubler
- Laboratoire d’Oncobiologie Moléculaire, Centre de Biologie Humaine, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
- UR 4666, Université Picardie Jules Verne, Amiens, France
| | - Camille Rottier
- Laboratoire d’Oncobiologie Moléculaire, Centre de Biologie Humaine, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
| | - Sophie Derreumaux
- Laboratoire d’Hématologie, Centre Hospitalier de Valenciennes, Valenciennes, France
| | - Emilie Margat
- Laboratoire d’Hématologie, Centre Hospitalier de Lens, Lens, France
| | - Loic Garcon
- Service d’Hématologie Biologique, Centre de Biologie Humaine, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
- UR 4666, Université Picardie Jules Verne, Amiens, France
| | - Jean-Pierre Marolleau
- Service d’Hématologie Clinique et de Thérapie Cellulaire, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
- UR 4666, Université Picardie Jules Verne, Amiens, France
| | - Thomas Boyer
- Service d’Hématologie Biologique, Centre de Biologie Humaine, Centre Hospitalier Universitaire Amiens-Picardie, Amiens, France
- UR 4666, Université Picardie Jules Verne, Amiens, France
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4
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Bourbon E, Chabane K, Mosnier I, Bouvard A, Thonier F, Ferrant E, Michallet AS, Poulain S, Hayette S, Sujobert P, Huet S. Next-CLL: A New Next-Generation Sequencing-Based Method for Assessment of IGHV Gene Mutational Status in Chronic Lymphoid Leukemia. J Mol Diagn 2023; 25:274-283. [PMID: 36773701 DOI: 10.1016/j.jmoldx.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/27/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Current guidelines for patients with chronic lymphocytic leukemia (CLL) recommend mutation status determination of the clonotypic IGHV gene before treatment initiation to guide the choice of first-line therapy. Currently, commercially available next-generation sequencing (NGS) solutions have technical constraints, as they necessitate at least a 2 × 300 bp sequencing, which restricts their use for routine practice. The cost of the commercial kits also represents an important drawback. We present a new method called Next-CLL, a ready-to-use strategy to evaluate IGHV gene mutation status using any NGS device (including 2 × 150 bp sequencers) in routine diagnostic laboratories. The performance of Next-CLL was validated on genomic DNA and cDNA obtained from 80 patients with CLL at diagnosis. Next-CLL identified a productive clone in 100% of cases, whereas PCR with Sanger sequencing led to a 12.5% failure rate. Next-CLL had 100% concordance with the reference technique for IGHV gene identification and allowed assessment of the IGHV mutation status from the leader sequence, following international guidelines. Comparing a large retrospective series of samples, analyzed by using Sanger sequencing (n = 773) or Next-CLL (n = 352), showed no bias in IGHV usage or mutational status, further validating our strategy in the real-life setting. Next-CLL represents a straightforward workflow for IGHV analysis in routine practice to assess clonal architecture and prognosis of patients with CLL.
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Affiliation(s)
- Estelle Bourbon
- Hematology Laboratory, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Kaddour Chabane
- Hematology Laboratory, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Isabelle Mosnier
- Hematology Laboratory, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Anne Bouvard
- Hematology Laboratory, Hospices Civils de Lyon, Pierre-Bénite, France
| | | | - Emmanuelle Ferrant
- Department of Clinical Hematology, Hospices Civils de Lyon, Pierre-Bénite, France
| | | | - Stéphanie Poulain
- Hematology Laboratory, Biology and Pathology Center, University Clinical Center of Lille, Lille, France; Team "Factors of persistence of leukemic cells," CANTHER Laboratory, UMR 9020 CNRS-U1277 INSERM, ONCOLILLE Cancer Institute, University of Lille, Lille, France
| | - Sandrine Hayette
- Hematology Laboratory, Hospices Civils de Lyon, Pierre-Bénite, France; Team Lymphoma Immuno-Biology, Centre International de Recherche en Infectiologie U111 INSERM, Lyon, France
| | - Pierre Sujobert
- Hematology Laboratory, Hospices Civils de Lyon, Pierre-Bénite, France; Team Lymphoma Immuno-Biology, Centre International de Recherche en Infectiologie U111 INSERM, Lyon, France; University Claude Bernard Lyon I, Lyon, France
| | - Sarah Huet
- Hematology Laboratory, Hospices Civils de Lyon, Pierre-Bénite, France; Team Lymphoma Immuno-Biology, Centre International de Recherche en Infectiologie U111 INSERM, Lyon, France; University Claude Bernard Lyon I, Lyon, France.
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5
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Detecting measurable residual disease beyond 10-4 by an IGHV leader-based NGS approach improves prognostic stratification in CLL. Blood 2023; 141:519-528. [PMID: 36084320 DOI: 10.1182/blood.2022017411] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023] Open
Abstract
The sensitivity of conventional techniques for reliable quantification of minimal/measurable residual disease (MRD) in chronic lymphocytic leukemia (CLL) is limited to MRD 10-4. Measuring MRD <10-4 could help to further distinguish between patients with CLL with durable remission and those at risk of early relapse. We herein present an academically developed immunoglobulin heavy-chain variable (IGHV) leader-based next-generation sequencing (NGS) assay for the quantification of MRD in CLL. We demonstrate, based on measurements in contrived MRD samples, that the linear range of detection and quantification of our assay reaches beyond MRD 10-5. If provided with sufficient DNA input, MRD can be detected down to MRD 10-6. There was high interassay concordance between measurements of the IGHV leader-based NGS assay and allele-specific oligonucleotide quantitative polymerase chain reaction (PCR) (r = 0.92 [95% confidence interval {CI}, 0.86-0.96]) and droplet digital PCR (r = 0.93 [95% CI, 0.88-0.96]) on contrived MRD samples. In a cohort of 67 patients from the CLL11 trial, using MRD 10-5 as a cutoff, undetectable MRD was associated with superior progression-free survival (PFS) and time to next treatment. More important, deeper MRD measurement allowed for additional stratification of patients with MRD <10-4 but ≥10-5. PFS of patients in this MRD range was significantly shorter, compared with patients with MRD <10-5 (hazard ratio [HR], 4.0 [95% CI, 1.6-10.3]; P = .004), but significantly longer, compared with patients with MRD ≥10-4 (HR, 0.44 [95% CI, 0.23-0.87]; P = .018). These results support the clinical utility of the IGHV leader-based NGS assay.
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6
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Looking for a needle in the haystack of CLL. Blood 2023; 141:445-447. [PMID: 36729546 DOI: 10.1182/blood.2022018077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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7
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One-Step Next-Generation Sequencing of Immunoglobulin and T-Cell Receptor Gene Recombinations for MRD Marker Identification in Acute Lymphoblastic Leukemia. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:43-59. [PMID: 35622319 DOI: 10.1007/978-1-0716-2115-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Within the EuroClonality-NGS group, immune repertoire analysis for target identification in lymphoid malignancies was initially developed using two-stage amplicon approaches, essentially as a progressive modification of preceding methods developed for Sanger sequencing. This approach has, however, limitations with respect to sample handling, adaptation to automation, and risk of contamination by amplicon products. We therefore developed one-step PCR amplicon methods with individual barcoding for batched analysis for IGH, IGK, TRD, TRG, and TRB rearrangements, followed by Vidjil-based data analysis.
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Langlois de Septenville A, Boudjoghra M, Bravetti C, Armand M, Salson M, Giraud M, Davi F. Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:153-167. [PMID: 35622326 DOI: 10.1007/978-1-0716-2115-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
B cell receptor (BcR) immunoglobulins (IG) display a tremendous diversity due to complex DNA rearrangements, the V(D)J recombination, further enhanced by the somatic hypermutation process. In chronic lymphocytic leukemia (CLL), the mutational load of the clonal BcR IG expressed by the leukemic cells constitutes an important prognostic and predictive biomarker. Here, we provide a reliable methodology capable of determining the mutational status of IG genes in CLL using high-throughput sequencing, starting from leukemic cell DNA or RNA.
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Affiliation(s)
| | - Myriam Boudjoghra
- AP-HP, Pitié-Salpêtrière Hospital, Laboratory of Hematology, Paris, France
| | - Clotilde Bravetti
- AP-HP, Pitié-Salpêtrière Hospital, Laboratory of Hematology, Paris, France
- Sorbonne Université, Paris, France
| | - Marine Armand
- AP-HP, Pitié-Salpêtrière Hospital, Laboratory of Hematology, Paris, France
- Sorbonne Université, Paris, France
| | - Mikaël Salson
- Université de Lille, CNRS, UMR 9189-CRIStAL, Inria, Lille, France
| | - Mathieu Giraud
- Université de Lille, CNRS, UMR 9189-CRIStAL, Inria, Lille, France
| | - Frederic Davi
- AP-HP, Pitié-Salpêtrière Hospital, Laboratory of Hematology, Paris, France.
- Sorbonne Université, Paris, France.
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Langerak AW. The Advent of Precision Immunology: Immunogenetics at the Center of Immune Cell Analysis in Health and Disease. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:1-5. [PMID: 35622317 DOI: 10.1007/978-1-0716-2115-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune cells (i.e., lymphocytes of the B and T lineage) are equipped with unique antigen receptors, which collectively form a highly diverse repertoire. Within the lymphocytes, the antigen receptor diversity is created at the DNA level through recombination processes in the immunoglobulin (IG) and T cell receptor (TR) genes that encode these receptors. This gives rise to an enormous immune repertoire (a.k.a. the "immunome") that can be studied in health and disease, both in a scientific and clinical context. In fact, the inherent distinctiveness of the IG/TR rearrangements on a per cell basis allows their usage as unique DNA fingerprints, which enables precision medicine, or for that matter "precision immunology." The field of (fundamental and translational) research on IG/TR repertoire diversity is the topic of the Immunogenetics volume in the Methods in Molecular Biology series.
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Affiliation(s)
- Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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ARResT/Interrogate Immunoprofiling Platform: Concepts, Workflows, and Insights. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:571-584. [PMID: 35622342 DOI: 10.1007/978-1-0716-2115-8_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
ARResT/Interrogate was built within the EuroClonality-NGS working group to meet the challenge of developing and applying assays for the high-throughput sequence-based profiling of immunoglobulin (IG) and T-cell receptor (TR) repertoires. We herein present basic concepts, outline the main workflow, delve into EuroClonality-NGS-specific aspects, and share insights from our experiences with the platform.
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11
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Lefranc MP, Lefranc G. IMGT ®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies. Biomolecules 2022; 12:381. [PMID: 35327572 PMCID: PMC8945572 DOI: 10.3390/biom12030381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the adaptive immune responses. IMGT® is based on a standardized nomenclature of the immunoglobulin (IG) and T cell receptor (TR) genes and alleles from fish to humans and on the IMGT unique numbering for the variable (V) and constant (C) domains of the immunoglobulin superfamily (IgSF) of vertebrates and invertebrates, and for the groove (G) domain of the major histocompatibility (MH) and MH superfamily (MhSF) proteins. IMGT® comprises 7 databases, 17 tools and more than 25,000 pages of web resources for sequences, genes and structures, based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts. IMGT® reference directories are used for the analysis of the NGS high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences, two-dimensional (2D) and three-dimensional (3D) structures. This manuscript focuses on the IMGT®Homo sapiens IG and TR loci, gene order, copy number variation (CNV) and haplotypes new concepts, as a paradigm for jawed vertebrates genome assemblies.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d’Immuno Génétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), UMR 9002 CNRS-UM, 141 rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d’Immuno Génétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), UMR 9002 CNRS-UM, 141 rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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12
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Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community. Methods Mol Biol 2022; 2453:317-343. [PMID: 35622334 PMCID: PMC9374196 DOI: 10.1007/978-1-0716-2115-8_18] [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] [Indexed: 11/03/2022]
Abstract
In this method we illustrate how to amplify, sequence, and analyze antibody/immunoglobulin (IG) heavy-chain gene rearrangements from genomic DNA that is derived from bulk populations of cells by next-generation sequencing (NGS). We focus on human source material and illustrate how bulk gDNA-based sequencing can be used to examine clonal architecture and networks in different samples that are sequenced from the same individual. Although bulk gDNA-based sequencing can be performed on both IG heavy (IGH) or kappa/lambda light (IGK/IGL) chains, we focus here on IGH gene rearrangements because IG heavy chains are more diverse, tend to harbor higher levels of somatic hypermutations (SHM), and are more reliable for clone identification and tracking. We also provide a procedure, including code, and detailed instructions for processing and annotation of the NGS data. From these data we show how to identify expanded clones, visualize the overall clonal landscape, and track clonal lineages in different samples from the same individual. This method has a broad range of applications, including the identification and monitoring of expanded clones, the analysis of blood and tissue-based clonal networks, and the study of immune responses including clonal evolution.
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AIRR Community Guide to Planning and Performing AIRR-Seq Experiments. Methods Mol Biol 2022; 2453:261-278. [PMID: 35622331 PMCID: PMC9761540 DOI: 10.1007/978-1-0716-2115-8_15] [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: 10/18/2022]
Abstract
The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.
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14
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Wang Q, Zeng H, Zhu Y, Wang M, Zhang Y, Yang X, Tang H, Li H, Chen Y, Ma C, Lan C, Liu B, Yang W, Yu X, Zhang Z. Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire. Front Immunol 2021; 12:778298. [PMID: 35003093 PMCID: PMC8727365 DOI: 10.3389/fimmu.2021.778298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/25/2021] [Indexed: 12/03/2022] Open
Abstract
Antibody repertoire sequencing (Rep-seq) has been widely used to reveal repertoire dynamics and to interrogate antibodies of interest at single nucleotide-level resolution. However, polymerase chain reaction (PCR) amplification introduces extensive artifacts including chimeras and nucleotide errors, leading to false discovery of antibodies and incorrect assessment of somatic hypermutations (SHMs) which subsequently mislead downstream investigations. Here, a novel approach named DUMPArts, which improves the accuracy of antibody repertoires by labeling each sample with dual barcodes and each molecule with dual unique molecular identifiers (UMIs) via minimal PCR amplification to remove artifacts, is developed. Tested by ultra-deep Rep-seq data, DUMPArts removed inter-sample chimeras, which cause artifactual shared clones and constitute approximately 15% of reads in the library, as well as intra-sample chimeras with erroneous SHMs and constituting approximately 20% of the reads, and corrected base errors and amplification biases by consensus building. The removal of these artifacts will provide an accurate assessment of antibody repertoires and benefit related studies, especially mAb discovery and antibody-guided vaccine design.
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Affiliation(s)
- Qilong Wang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Huikun Zeng
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Zhu
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Minhui Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanfang Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiujia Yang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haipei Tang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hongliang Li
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Yuan Chen
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chunhong Lan
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Division of Nephrology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
| | - Zhenhai Zhang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
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15
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Agathangelidis A, Vlachonikola E, Davi F, Langerak AW, Chatzidimitriou A. High-Throughput immunogenetics for precision medicine in cancer. Semin Cancer Biol 2021; 84:80-88. [PMID: 34757183 DOI: 10.1016/j.semcancer.2021.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
Cancer is characterized by an extremely complex biological background, which hinders personalized therapeutic interventions. Precision medicine promises to overcome this obstacle through integrating information from different 'subsystems', including the host, the external environment, the tumor itself and the tumor micro-environment. Immunogenetics is an essential tool that allows dissecting both lymphoid cancer ontogeny at both a cell-intrinsic and a cell-extrinsic level, i.e. through characterizing micro-environmental interactions, with a view to precision medicine. This is particularly thanks to the introduction of powerful, high-throughput approaches i.e. next generation sequencing, which allow the comprehensive characterization of immune repertoires. Indeed, NGS immunogenetic analysis (Immune-seq) has emerged as key to both understanding cancer pathogenesis and improving the accuracy of clinical decision making in oncology. Immune-seq has applications in lymphoid malignancies, assisting in the diagnosis e.g. through differentiating from reactive conditions, as well as in disease monitoring through accurate assessment of minimal residual disease. Moreover, Immune-seq facilitates the study of T cell receptor clonal dynamics in critical clinical contexts, including transplantation as well as innovative immunotherapy for solid cancers. The clinical utility of Immune-seq represents the focus of the present contribution, where we highlight what can be achieved but also what must be addressed in order to maximally realize the promise of Immune-seq in precision medicine in cancer.
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Affiliation(s)
- Andreas Agathangelidis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Elisavet Vlachonikola
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Genetics and Molecular Biology, Faculty of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Frederic Davi
- Department of Hematology, APHP, Hôpital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, Rotterdam, the Netherlands
| | - Anastasia Chatzidimitriou
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75236, Sweden.
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16
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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.
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Ceppi F, Rizzati F, Colombini A, Conter V, Cazzaniga G. Utilizing the prognostic impact of minimal residual disease in treatment decisions for pediatric acute lymphoblastic leukemia. Expert Rev Hematol 2021; 14:795-807. [PMID: 34374613 DOI: 10.1080/17474086.2021.1967137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Acute lymphoblastic leukemia (ALL) is the first pediatric cancer where the assessment of early response to therapy by minimal residual disease (MRD) monitoring has demonstrated its importance to improve risk-based treatment approaches. The most standardized tools to study MRD in ALL are multiparametric flow cytometry and realtime-quantitative polymerase chain reaction amplification-based methods. In recent years, MRD measurement has reached greater levels of sensitivity and standardization through international laboratory networks collaboration. AREAS COVERED We herewith describe how to assess and apply the prognostic impact of MRD in treatment decisions, with specific focus on pediatric ALL. We also highlight the role of MRD monitoring in the context of genetically homogeneous subgroups of pediatric ALL. However, some queries remain to be addressed and emerging technologies hold the promise of improving MRD detection in ALL patients. EXPERT OPINION Emerging technologies, like next generation flow cytometry, droplet digital PCR, and next generation sequencing appear to be important methods for assessing MRD in pediatric ALL. These more specific and/or sensitive MRD monitoring methods may help to predict relapse with greater accuracy, and are currently being used in clinical trials to improve pediatric ALL outcome by optimizing patient stratification and earlier MRD-based interventional therapy.
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Affiliation(s)
- Francesco Ceppi
- Pediatric Hematology-Oncology Unit, Division of Pediatrics, Woman-Mother-Child Department, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Frida Rizzati
- Pediatric Hematology-Oncology Unit, Division of Pediatrics, Woman-Mother-Child Department, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
| | - Antonella Colombini
- Pediatric Hematology-Oncology, University Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Valentino Conter
- Pediatric Hematology-Oncology, University Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Pediatrics, School of Medicine, University of Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy.,Medical Genetics, School of Medicine, University of Milano Bicocca, Monza, Italy
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18
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Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders. Blood Adv 2021; 5:3188-3198. [PMID: 34424321 DOI: 10.1182/bloodadvances.2020004056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/20/2022] Open
Abstract
Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B- and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-to-end workflow for simultaneous detection of B- and T-cell clonality, translocations, CNAs, and sequence variants.
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19
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Kim M, Jeon K, Hutt K, Zlotnicki AM, Kim HJ, Lee J, Kim HS, Kang HJ, Lee YK. Immunoglobulin gene rearrangement in Koreans with multiple myeloma: Clonality assessment and repertoire analysis using next-generation sequencing. PLoS One 2021; 16:e0253541. [PMID: 34166440 PMCID: PMC8224885 DOI: 10.1371/journal.pone.0253541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/07/2021] [Indexed: 11/19/2022] Open
Abstract
Introduction We assessed the applicability of next-generation sequencing (NGS)-based IGH/IGK clonality testing and analyzed the repertoire of immunoglobulin heavy chain (IGH) or immunoglobulin kappa light chain (IGK) gene usage in Korean patients with multiple myeloma (MM) for the first time. Methods Fifty-nine bone marrow samples from 57 Korean patients with MM were analyzed, and NGS-based clonality testing that targeted the IGH and IGK genes was performed using IGH FR1 and IGK primer sets. Results Clonal IGH and IGK rearrangements were observed in 74.2% and 67.7% of samples from Korean patients with kappa-restricted MM, respectively (90.3% had one or both), and in 60.7% and 95.5% of samples from those with lambda-restricted MM, respectively (85.7% had one or both). In total, 88.1% of samples from Koreans with MM had clonal IGH and/or IGK rearrangement. Clonal rearrangement was not significantly associated with the bone marrow plasma cells as a proportion of all BM lymphoid cells. IGHV3-9 (11.63%) and IGHV4-31 (9.30%) were the most frequently reported IGHV genes and were more common in Koreans with MM than in Western counterparts. IGHD3-10 and IGHD3-3 (13.95% each) were the most frequent IGHD genes; IGHD3-3 was more common in Koreans with MM. No IGK rearrangement was particularly prevalent, but single IGKV-J rearrangements were less common in Koreans with kappa-restricted MM than in Western counterparts. IGKV4-1 was less frequent in Koreans regardless of light chain type. Otherwise, the usages of the IGH V, D, and J genes and of the IGK gene were like those observed in previous Western studies. Conclusion NGS-based IGH/IGK clonality testing ought to be applicable to most Koreans with MM. The overrepresentation of IGHV3-9, IGHV4-31, and IGHD3-3 along with the underrepresentation of IGKV4-1 and the differences in IGK gene rearrangement types suggest the existence of ethnicity-specific variations in this disease.
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Affiliation(s)
- Miyoung Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kibum Jeon
- Department of Laboratory Medicine, Hangang Sacred Heart Hospital, Seoul, South Korea
| | - Kasey Hutt
- Invivoscribe, Inc., San Diego, California, United States of America
| | | | - Hyo Jung Kim
- Department of Internal Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, South Korea
| | - Jiwon Lee
- Department of Laboratory Medicine, Green Cross Laboratories, Yongin, South Korea
| | - Han-Sung Kim
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, South Korea
| | - Hee Jung Kang
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, South Korea
| | - Young Kyung Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, South Korea
- * E-mail:
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20
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Navrkalova V, Plevova K, Hynst J, Pal K, Mareckova A, Reigl T, Jelinkova H, Vrzalova Z, Stranska K, Pavlova S, Panovska A, Janikova A, Doubek M, Kotaskova J, Pospisilova S. LYmphoid NeXt-Generation Sequencing (LYNX) Panel: A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. J Mol Diagn 2021; 23:959-974. [PMID: 34082072 DOI: 10.1016/j.jmoldx.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (≥6 Mb) and recurrent chromosomal aberrations (≥300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel represents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine II - Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrea Mareckova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Tomas Reigl
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Zuzana Vrzalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Andrea Janikova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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21
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Genuardi E, Romano G, Beccuti M, Alessandria B, Mannina D, Califano C, Rota Scalabrini D, Cortelazzo S, Ladetto M, Ferrero S, Calogero RA, Cordero F. Application of the Euro Clonality next-generation sequencing-based marker screening approach to detect immunoglobulin heavy chain rearrangements in mantle cell lymphoma patients: first data from the Fondazione Italiana Linfomi MCL0208 trial. Br J Haematol 2021; 194:378-381. [PMID: 34002365 PMCID: PMC8515379 DOI: 10.1111/bjh.17519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/06/2021] [Indexed: 01/09/2023]
Abstract
Minimal residual disease (MRD) determined by classic polymerase chain reaction (PCR) methods is a powerful outcome predictor in mantle cell lymphoma (MCL). Nevertheless, some technical pitfalls can reduce the rate of of molecular markers. Therefore, we applied the EuroClonality‐NGS IGH (next‐generation sequencing immunoglobulin heavy chain) method (previously published in acute lymphoblastic leukaemia) to 20 MCL patients enrolled in an Italian phase III trial sponsored by Fondazione Italiana Linfomi. Results from this preliminary investigation show that EuroClonality‐NGS IGH method is feasible in the MCL context, detecting a molecular IGH target in 19/20 investigated cases, allowing MRD monitoring also in those patients lacking a molecular marker for classical screening approaches.
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Affiliation(s)
- Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences - Hematology Division, University of Torino, Torino, Italy
| | - Greta Romano
- Department of Computer Sciences, University of Torino, Torino, Italy.,IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo (Torino), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Marco Beccuti
- Department of Computer Sciences, University of Torino, Torino, Italy
| | - Beatrice Alessandria
- Department of Molecular Biotechnologies and Health Sciences - Hematology Division, University of Torino, Torino, Italy
| | - Donato Mannina
- Azienda Ospedaliera Papardo- UOC di Ematologia, Messina, Italy
| | | | | | | | - Marco Ladetto
- Division of Hematology, Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Simone Ferrero
- Department of Molecular Biotechnologies and Health Sciences - Hematology Division, University of Torino, Torino, Italy.,Hematology Division, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Francesca Cordero
- Department of Computer Sciences, University of Torino, Torino, Italy
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22
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Hansen MH, Cédile O, Larsen TS, Abildgaard N, Nyvold CG. Perspective: sensitive detection of residual lymphoproliferative disease by NGS and clonal rearrangements-how low can you go? Exp Hematol 2021; 98:14-24. [PMID: 33823225 DOI: 10.1016/j.exphem.2021.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/12/2023]
Abstract
Malignant lymphoproliferative disorders collectively constitute a large fraction of the hematological cancers, ranging from indolent to highly aggressive neoplasms. Being a diagnostically important hallmark, clonal gene rearrangements of the immunoglobulins enable the detection of residual disease in the clinical course of patients down to a minute fraction of malignant cells. The introduction of next-generation sequencing (NGS) has provided unprecedented assay specificity, with a sensitivity matching that of polymerase chain reaction-based measurable residual disease (MRD) detection down to the 10-6 level. Although reaching 10-6 to 10-7 is theoretically feasible, employing a sufficient amount of DNA and sequencing coverage is placed in the perspective of the practical challenges when relying on clinical samples in contrast to controlled serial dilutions. As we discuss, the randomness of subsampling must be taken into account to accommodate the sensitivity threshold-in terms of both the required number of cells and sequencing coverage. As a substantial part of the reviewed studies do not state the depth of coverage or even amount of DNA in some cases, we call for increased transparency to enable critical assessment of the MRD assays for clinical implementation and feasibility.
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Affiliation(s)
- Marcus H Hansen
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark.
| | - Oriane Cédile
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Thomas S Larsen
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Niels Abildgaard
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Charlotte G Nyvold
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
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23
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Mendoza H, Tormey CA, Rinder HM, Howe JG, Siddon AJ. The utility and limitations of B- and T-cell gene rearrangement studies in evaluating lymphoproliferative disorders. Pathology 2020; 53:157-165. [PMID: 33358756 DOI: 10.1016/j.pathol.2020.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/05/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022]
Abstract
A hallmark of lymphoid malignancies is the presence of a monoclonal lymphocyte population. Monoclonality of B- and T-cell populations can be established through immunoglobulin (IG) or T-cell receptor (TCR) gene rearrangement analysis, respectively. The biological rationale of IG and TCR gene rearrangement analysis is that due to the extensive combinatorial repertoire made possible by V(D)J recombination in lymphocytes, it is unlikely that any substantive lymphocyte population would share the same IG or TCR gene rearrangement pattern unless there is an underlying neoplastic or reactive origin. Modern IG and TCR gene rearrangement analysis is typically performed by polymerase chain reaction (PCR) using commercially available primer sets followed by gel capillary electrophoresis. This process is highly sensitive in the detection of nearly all lymphoid malignancies. Several pitfalls and limitations, both biological and technical, apply to IG/TCR gene rearrangement analysis, but these can be minimised with high quality controls, performance of assays in duplicate, and adherence to strict criteria for interpreting and reporting results. Next generation sequencing (NGS) will likely replace PCR based methods of IG/TCR gene rearrangement analysis but is not yet widespread due to the absence of standardised protocols and multicentre validation.
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Affiliation(s)
- Hadrian Mendoza
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Henry M Rinder
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Hematology Section, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - John G Howe
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Alexa J Siddon
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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24
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Reading the B-cell receptor immunome in chronic lymphocytic leukemia: revelations and applications. Exp Hematol 2020; 93:14-24. [PMID: 32976948 DOI: 10.1016/j.exphem.2020.09.194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/25/2020] [Accepted: 09/19/2020] [Indexed: 12/19/2022]
Abstract
B-Cell receptor (BCR) sequencing has been the force driving many recent advances in chronic lymphocytic leukemia (CLL) research. Here, we discuss the general principles, revelations, and applications of reading the BCR immunome in the context of CLL. First, IGHV mutational status, obtained by measuring the mutational imprint on the IGHV gene of the CLL clonotype, is the cornerstone of CLL risk stratification. Furthermore, the discovery of "BCR-stereotyped" groups of unrelated patients that share not only a highly similar BCR on their leukemic clone, but also certain clinical characteristics has provided insights key to understanding disease ontogeny. Additionally, whereas the BCR repertoire of most CLL patients is characterized by a single dominant rearrangement, next-generation sequencing (NGS) has revealed a rich subclonal landscape in a larger than previously expected proportion of CLL patients. We review the mechanisms underlying these "multiple dominant" cases, including V(D)J-recombination errors, failure of allelic exclusion, intraclonal diversification, and "true" bi- or oligoclonality, and their implications, in detail. Finally, BCR repertoire sequencing can be used for sensitive quantification of minimal residual disease to potentially unprecedented depth. To surmount pitfalls inherent to this approach and develop internationally harmonized protocols, the EuroClonality-NGS Working Group has been established.
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25
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Lefranc MP, Lefranc G. Immunoglobulins or Antibodies: IMGT ® Bridging Genes, Structures and Functions. Biomedicines 2020; 8:E319. [PMID: 32878258 PMCID: PMC7555362 DOI: 10.3390/biomedicines8090319] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as 'genes' as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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26
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Immunoglobulin gene analysis in chronic lymphocytic leukemia in the era of next generation sequencing. Leukemia 2020; 34:2545-2551. [PMID: 32561841 PMCID: PMC7515836 DOI: 10.1038/s41375-020-0923-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 12/19/2022]
Abstract
Twenty years after landmark publications, there is a consensus that the somatic hypermutation (SHM) status of the clonotypic immunoglobulin heavy variable (IGHV) gene is an important cornerstone for accurate risk stratification and therapeutic decision-making in patients with chronic lymphocytic leukemia (CLL). The IGHV SHM status has traditionally been determined by conventional Sanger sequencing. However, NGS has heralded a new era in medical diagnostics and immunogenetic analysis is following this trend. There is indeed a growing demand for shifting practice and using NGS for IGHV gene SHM assessment, although it is debatable whether it is always justifiable, at least taking into account financial considerations for laboratories with limited resources. Nevertheless, as this analysis impacts on treatment decisions, standardization of both technical aspects, and data interpretation becomes essential. Also, the need for establishing new recommendations and providing dedicated education and training on NGS-based immunogenetics is greater than ever before. Here we address potential and challenges of NGS-based immunogenetics in CLL. We are convinced that this perspective helps the hematological community to better understand the pros and cons of this new technological development for CLL patient management.
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Capture-based Next-Generation Sequencing Improves the Identification of Immunoglobulin/T-Cell Receptor Clonal Markers and Gene Mutations in Adult Acute Lymphoblastic Leukemia Patients Lacking Molecular Probes. Cancers (Basel) 2020; 12:cancers12061505. [PMID: 32526928 PMCID: PMC7352935 DOI: 10.3390/cancers12061505] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/23/2020] [Accepted: 06/05/2020] [Indexed: 01/08/2023] Open
Abstract
The monitoring of minimal residual disease (MRD) in Philadelphia-negative acute lymphoblastic leukemia (ALL) requires the identification at diagnosis of immunoglobulin/T-cell receptor (Ig/TCR) rearrangements as clonality markers. Aiming to simplify and possibly improve the patients' initial screening, we designed a capture-based next-generation sequencing (NGS) panel combining the Ig/TCR rearrangement detection with the profiling of relevant leukemia-related genes. The validation of the assay on well-characterized samples allowed us to identify all the known Ig/TCR rearrangements as well as additional clonalities, including rare rearrangements characterized by uncommon combinations of variable, diversity, and joining (V-D-J) gene segments, oligoclonal rearrangements, and low represented clones. Upon validation, the capture NGS approach allowed us to identify Ig/TCR clonal markers in 87% of a retrospective cohort (MRD-unknown within the Northern Italy Leukemia Group (NILG)-ALL 09/00 clinical trial) and in 83% of newly-diagnosed ALL cases in which conventional method failed, thus proving its prospective applicability. Finally, we identified gene variants in 94.7% of patients analyzed for mutational status with the same implemented capture assay. The prospective application of this technology could simplify clonality assessment and improve standard assay development for leukemia monitoring, as well as provide information about the mutational status of selected leukemia-related genes, potentially representing new prognostic elements, MRD markers, and targets for specific therapies.
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Wang Y, Wen FQ. [Latest advances in minimal residual disease evaluation in B-cell lymphoproliferative disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:667-671. [PMID: 32571470 PMCID: PMC7390215 DOI: 10.7499/j.issn.1008-8830.1912034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
The clearance of cancer cells is closely associated with the prognosis of various hematologic malignancies. Clinical studies have shown that minimal residual disease (MRD) can directly reflect the clearance of cancer cells, but the tools for MRD detection need to be improved. This article reviews the latest advances in the MRD detection by digital polymerase chain reaction and next-generation sequencing in B-cell lymphoproliferative disease.
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Affiliation(s)
- Yan Wang
- Department of Pediatric Hematology and Oncology, Shenzhen Children's Hospital, China Medical University, Shenzhen, Guangdong 518031, China.
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Amoriello R, Greiff V, Aldinucci A, Bonechi E, Carnasciali A, Peruzzi B, Repice AM, Mariottini A, Saccardi R, Mazzanti B, Massacesi L, Ballerini C. The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies. Front Immunol 2020; 11:559. [PMID: 32328061 PMCID: PMC7160336 DOI: 10.3389/fimmu.2020.00559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022] Open
Abstract
Natalizumab (NTZ) and autologous hematopoietic stem cell transplantation (AHSCT) are two successful treatments for relapsing-remitting multiple sclerosis (RRMS), an autoimmune T-cell-driven disorder affecting the central nervous system that is characterized by relapses interspersed with periods of complete or partial recovery. Both RRMS treatments have been documented to impact T-cell subpopulations and the T-cell receptor (TCR) repertoire in terms of clone frequency, but, so far, the link between T-cell naive and memory populations, autoimmunity, and treatment outcome has not yet been established hindering insight into the post-treatment TCR landscape of MS patients. To address this important knowledge gap, we tracked peripheral T-cell subpopulations (naïve and memory CD4+ and CD8+) across 15 RRMS patients before and after two years of continuous treatment (NTZ) and a single treatment course (AHSCT) by high-throughput TCRß sequencing. We found that the two MS treatments left treatment-specific multidimensional traces in patient TCRß repertoire dynamics with respect to clonal expansion, clonal diversity and repertoire architecture. Comparing MS TCR sequences with published datasets suggested that the majority of public TCRs belonged to virus-associated sequences. In summary, applying multi-dimensional computational immunology to a TCRß dataset of treated MS patients, we show that qualitative changes of TCRß repertoires encode treatment-specific information that may be relevant for future clinical trials monitoring and personalized MS follow-up, diagnosis and treatment regimes. Natalizumab (NTZ) and autologous hematopoietic stem cell transplantation (AHSCT) are two successful treatments for relapsing-remitting multiple sclerosis (RRMS), an autoimmune T-cell-driven disorder affecting the central nervous system that is characterized by relapses interspersed with periods of complete or partial recovery. Both RRMS treatments have been documented to impact T-cell subpopulations and the T-cell receptor (TCR) repertoire in terms of clone frequency, but, so far, the link between T-cell naive and memory populations, autoimmunity, and treatment outcome has not yet been established hindering insight into the posttreatment TCR landscape of MS patients. To address this important knowledge gap, we tracked peripheral T-cell subpopulations (naive and memory CD4+ and CD8+) across 15 RRMS patients before and after 2 years of continuous treatment (NTZ) and a single treatment course (AHSCT) by high-throughput TCRβ sequencing. We found that the two MS treatments left treatment-specific multidimensional traces in patient TCRβ repertoire dynamics with respect to clonal expansion, clonal diversity, and repertoire architecture. Comparing MS TCR sequences with published datasets suggested that the majority of public TCRs belonged to virus-associated sequences. In summary, applying multidimensional computational immunology to a TCRβ dataset of treated MS patients, we show that qualitative changes of TCRβ repertoires encode treatment-specific information that may be relevant for future clinical trials monitoring and personalized MS follow-up, diagnosis, and treatment regimens.
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Affiliation(s)
- Roberta Amoriello
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Alessandra Aldinucci
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Elena Bonechi
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Alberto Carnasciali
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Benedetta Peruzzi
- Centro Diagnostico di Citofluorimetria e Immunoterapia, Careggi University Hospital, Florence, Italy
| | - Anna Maria Repice
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Alice Mariottini
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Riccardo Saccardi
- SODc Terapie Cellulari e Medicina Trasfusionale, Careggi University Hospital, Florence, Italy
| | - Benedetta Mazzanti
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), University of Florence, Florence, Italy
| | - Luca Massacesi
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Clara Ballerini
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), University of Florence, Florence, Italy
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Matsuyama A, Bienzle D, Richardson D, Deravi N, Hwang MH, Darzentas N, Keller SM. Composite lymphoma of concurrent T zone lymphoma and large cell B cell lymphoma in a dog. BMC Vet Res 2019; 15:413. [PMID: 31733649 PMCID: PMC6858704 DOI: 10.1186/s12917-019-2154-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/23/2019] [Indexed: 01/22/2023] Open
Abstract
Background Evolution of indolent to aggressive lymphoma has been described in dogs but is difficult to distinguish from the de novo development of a second, clonally distinct lymphoma. Differentiation of these scenarios can be aided by next generation sequencing (NGS)-based assessment of clonality of lymphocyte antigen receptor genes. Case presentation An 8-year-old male intact Mastiff presented with generalized lymphadenomegaly was diagnosed with nodal T zone lymphoma (TZL) based on cytology, histopathology, immunohistochemistry and flow cytometry. Thirteen months later, the dog re-presented with progressive lymphadenomegaly, and based on cytology and flow cytometry, a large B cell lymphoma (LBCL) was diagnosed. Sequencing-based clonality testing confirmed the de novo development of a LBCL and the persistence of a TZL. Conclusions The occurrence of two distinct lymphoid neoplasms should be considered if patient features and tumor cytomorphology or immunophenotype differ among sequential samples. Sequencing-based clonality testing may provide conclusive evidence of two concurrent and distinct clonal lymphocyte populations, termed most appropriately “composite lymphoma”.
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Affiliation(s)
- Arata Matsuyama
- Departments of Biomedical Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Dorothee Bienzle
- Departments of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Danielle Richardson
- Departments of Clinical Studies, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Nariman Deravi
- Departments of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Present address: Idexx Laboratories, 1345 Denison St., Markham, ON, L3R 5V2, Canada
| | - Mei-Hua Hwang
- Departments of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Nikos Darzentas
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany/Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Stefan M Keller
- Departments of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada. .,Present address: Department of Pathology, Microbiology, Immunology, University of California, Davis, USA.
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31
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Komkov A, Miroshnichenkova A, Nugmanov G, Popov A, Pogorelyy M, Zapletalova E, Jelinkova H, Pospisilova S, Lebedev Y, Chudakov D, Olshanskaya Y, Plevova K, Maschan M, Mamedov I. High‐throughput sequencing of T‐cell receptor alpha chain clonal rearrangements at the DNA level in lymphoid malignancies. Br J Haematol 2019; 188:723-731. [DOI: 10.1111/bjh.16230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Alexander Komkov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Anna Miroshnichenkova
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Gaiaz Nugmanov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
| | - Alexander Popov
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Mikhail Pogorelyy
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
| | - Eva Zapletalova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Yuri Lebedev
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
| | - Dmitriy Chudakov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Yulia Olshanskaya
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Karla Plevova
- Department of Internal Medicine, Haematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic
- Central European Institute of Technology Masaryk University Brno Czech Republic
| | - Michael Maschan
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
| | - Ilgar Mamedov
- Department of Genomics of Adaptive Immunity Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Moscow Russia
- Laboratory of Cytogenetics and Molecular Genetics Dmitry Rogachev National Medical and Research Centre of Paediatric Haematology, Oncology and Immunology Moscow Russia
- Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia
- Central European Institute of Technology Masaryk University Brno Czech Republic
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32
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Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study. Leukemia 2019; 33:2241-2253. [PMID: 31243313 PMCID: PMC6756028 DOI: 10.1038/s41375-019-0496-7] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/20/2019] [Indexed: 01/09/2023]
Abstract
Amplicon-based next-generation sequencing (NGS) of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements for clonality assessment, marker identification and quantification of minimal residual disease (MRD) in lymphoid neoplasms has been the focus of intense research, development and application. However, standardization and validation in a scientifically controlled multicentre setting is still lacking. Therefore, IG/TR assay development and design, including bioinformatics, was performed within the EuroClonality-NGS working group and validated for MRD marker identification in acute lymphoblastic leukaemia (ALL). Five EuroMRD ALL reference laboratories performed IG/TR NGS in 50 diagnostic ALL samples, and compared results with those generated through routine IG/TR Sanger sequencing. A central polytarget quality control (cPT-QC) was used to monitor primer performance, and a central in-tube quality control (cIT-QC) was spiked into each sample as a library-specific quality control and calibrator. NGS identified 259 (average 5.2/sample, range 0–14) clonal sequences vs. Sanger-sequencing 248 (average 5.0/sample, range 0–14). NGS primers covered possible IG/TR rearrangement types more completely compared with local multiplex PCR sets and enabled sequencing of bi-allelic rearrangements and weak PCR products. The cPT-QC showed high reproducibility across all laboratories. These validated and reproducible quality-controlled EuroClonality-NGS assays can be used for standardized NGS-based identification of IG/TR markers in lymphoid malignancies.
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33
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Knecht H, Reigl T, Kotrová M, Appelt F, Stewart P, Bystry V, Krejci A, Grioni A, Pal K, Stranska K, Plevova K, Rijntjes J, Songia S, Svatoň M, Froňková E, Bartram J, Scheijen B, Herrmann D, García-Sanz R, Hancock J, Moppett J, van Dongen JJM, Cazzaniga G, Davi F, Groenen PJTA, Hummel M, Macintyre EA, Stamatopoulos K, Trka J, Langerak AW, Gonzalez D, Pott C, Brüggemann M, Darzentas N. Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS. Leukemia 2019; 33:2254-2265. [PMID: 31227779 PMCID: PMC6756032 DOI: 10.1038/s41375-019-0499-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/23/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022]
Abstract
Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.
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Affiliation(s)
- Henrik Knecht
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Tomas Reigl
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Kotrová
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Franziska Appelt
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Peter Stewart
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Vojtech Bystry
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Adam Krejci
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andrea Grioni
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Karol Pal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jos Rijntjes
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simona Songia
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Michael Svatoň
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Eva Froňková
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Jack Bartram
- Department of Paediatric Haematology, Great Ormond Street Hospital, London, UK
| | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dietrich Herrmann
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ramón García-Sanz
- IBMCC-CSIC, Hospital Universitario de Salamanca-IBSAL, Salamanca, Spain
| | - Jeremy Hancock
- Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | - John Moppett
- Department of Pediatric Haematology, Bristol Royal Hospital for Children, Bristol, UK
| | - Jacques J M van Dongen
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center, Leiden, The Netherlands
| | | | - Frédéric Davi
- Department of Hematology, Hopital Pitié-Salpêtrière, Paris, France
| | | | - Michael Hummel
- Insititute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Elizabeth A Macintyre
- Department of Hematology, APHP Necker-Enfants Malades and Paris Descartes University, Paris, France
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Jan Trka
- CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University, University Hospital Motol, Prague, Czech Republic
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - David Gonzalez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Christiane Pott
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Monika Brüggemann
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nikos Darzentas
- Department of Hematology, University Hospital Schleswig-Holstein, Kiel, Germany.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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34
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Monter A, Nomdedéu JF. ClonoSEQ assay for the detection of lymphoid malignancies. Expert Rev Mol Diagn 2019; 19:571-578. [DOI: 10.1080/14737159.2019.1627877] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Anna Monter
- Laboratori d´Hematologia. Department of Hematology, Hospital de la Santa Creu i Sant Pau, IIB Sant Pau. Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep F. Nomdedéu
- Laboratori d´Hematologia. Department of Hematology, Hospital de la Santa Creu i Sant Pau, IIB Sant Pau. Universitat Autònoma de Barcelona, Barcelona, Spain
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35
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Sánchez R, Ayala R, Martínez-López J. Minimal Residual Disease Monitoring with Next-Generation Sequencing Methodologies in Hematological Malignancies. Int J Mol Sci 2019; 20:ijms20112832. [PMID: 31185671 PMCID: PMC6600313 DOI: 10.3390/ijms20112832] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/15/2022] Open
Abstract
Ultra-deep next-generation sequencing has emerged in recent years as an important diagnostic tool for the detection and follow-up of tumor burden in most of the known hematopoietic malignancies. Meticulous and high-throughput methods for the lowest possible quantified disease are needed to address the deficiencies of more classical techniques. Precision-based approaches will allow us to correctly stratify each patient based on the minimal residual disease (MRD) after a treatment cycle. In this review, we consider the most prominent ways to approach next-generation sequencing methodologies to follow-up MRD in hematological neoplasms.
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Affiliation(s)
- Ricardo Sánchez
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
| | - Rosa Ayala
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
- Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain.
| | - Joaquín Martínez-López
- Servicio de Hematología y Hemoterapia. Hospital Universitario 12 de Octubre, 28041 Madrid, Spain.
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain.
- Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain.
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Galardy PJ, Bedekovics T, Macintyre E, Miles RR. Lymphoma diagnostics: getting more from less. Br J Haematol 2019; 185:1136-1141. [PMID: 30784044 DOI: 10.1111/bjh.15788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In the modern era, clinicians and pathologists increasingly make challenging diagnoses in patients with suspected lymphoma using minimal amounts of diagnostic material. The increase in utilization of minimally invasive procedures, such as fine needle aspiration or needle core biopsies, lead to challenges in our ability to make accurate histopathological assessments of disease, including the integration of new diagnostic and prognostic testing, with smaller amounts of material. The trend towards minimally invasive diagnostics is also often in conflicting interest with researchers seeking to study tissue specimens to better understand the biology and genetics of these diseases to move the field forward. Thankfully, there are emerging fields which seek to extract large amounts of diagnostic and prognostic data out of material that is circulating in the blood of patients with lymphoma. Here we will review recent exciting data regarding the use of circulating tumour cells, circulating tumour DNA, and the detection and utility of circulating exosomes and how it can assist in diagnosis, prognosis and therapeutic monitoring. These advances hold the promise to enable continued safe patient care while also advancing discovery, translational and clinical research.
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Affiliation(s)
- Paul J Galardy
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.,Division of Pediatric Haematology-Oncology, Mayo Clinic, Rochester, MN, USA
| | - Tibor Bedekovics
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth Macintyre
- Diagnostic Haematology, Necker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris, Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, Paris, France
| | - Rodney R Miles
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
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Agathangelidis A, Psomopoulos F, Stamatopoulos K. Stereotyped B Cell Receptor Immunoglobulins in B Cell Lymphomas. Methods Mol Biol 2019; 1956:139-155. [PMID: 30779034 DOI: 10.1007/978-1-4939-9151-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Comprehensive analysis of the clonotypic B cell receptor immunoglobulin (BcR IG) gene rearrangement sequences in patients with mature B cell neoplasms has led to the identification of significant repertoire restrictions, culminating in the discovery of subsets of patients expressing highly similar, stereotyped BcR IG. This finding strongly supports selection by common epitopes or classes of structurally similar epitopes in the ontogeny of these tumors. BcR IG stereotypy was initially described in chronic lymphocytic leukemia (CLL), where the stereotyped fraction of the disease accounts for a remarkable one-third of patients. However, subsequent studies showed that stereotyped BcR IG are also present in other neoplasms of mature B cells, including mantle cell lymphoma (MCL) and splenic marginal zone lymphoma (SMZL). Subsequent cross-entity comparisons led to the conclusion that stereotyped IG are mostly "disease-specific," implicating distinct immunopathogenetic processes. Interestingly, mounting evidence suggests that a molecular subclassification of lymphomas based on BcR IG stereotypy is biologically and clinically relevant. Indeed, particularly in CLL, patients assigned to the same subset due to expressing a particular stereotyped BcR IG display remarkably consistent biological background and clinical course, at least for major and well-studied subsets. Thus, the robust assignment to stereotyped subsets may assist in the identification of mechanisms underlying disease onset and progression, while also refining risk stratification. In this book chapter, we provide an overview of the recent BcR IG stereotypy studies in mature B cell malignancies and outline previous and current methodological approaches used for the identification of stereotyped IG.
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Affiliation(s)
- Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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Rettig TA, Pecaut MJ, Chapes SK. A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing. FASEB Bioadv 2019; 1:6-17. [PMID: 32123808 PMCID: PMC6996338 DOI: 10.1096/fba.1017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/09/2018] [Accepted: 08/17/2018] [Indexed: 11/26/2022] Open
Abstract
Sequencing antibody repertoires has steadily become cheaper and easier. Sequencing methods usually rely on some form of amplification, often a massively multiplexed PCR prior to sequencing. To eliminate potential biases and create a data set that could be used for other studies, our laboratory compared unamplified sequencing results from the splenic heavy-chain repertoire in the mouse to those processed through two commercial applications. We also compared the use of mRNA vs total RNA, reverse transcriptase, and primer usage for cDNA synthesis and submission. The use of mRNA for cDNA synthesis resulted in higher read counts but reverse transcriptase and primer usage had no statistical effects on read count. Although most of the amplified data sets contained more antibody reads than the unamplified data set, we detected more unique variable (V)-gene segments in the unamplified data set. Although unique CDR3 detection was much lower in the unamplified data set, RNASeq detected 98% of the high-frequency CDR3s. We have shown that unamplified profiling of the antibody repertoire is possible, detects more V-gene segments, and detects high-frequency clones in the repertoire.
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Affiliation(s)
| | - Michael J. Pecaut
- Division of Biomedical Engineering Sciences (BMES)Loma Linda UniversityLoma LindaCalifornia
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Arcila ME, Yu W, Syed M, Kim H, Maciag L, Yao J, Ho C, Petrova K, Moung C, Salazar P, Rijo I, Baldi T, Zehir A, Landgren O, Park J, Roshal M, Dogan A, Nafa K. Establishment of Immunoglobulin Heavy (IGH) Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms. J Mol Diagn 2018; 21:330-342. [PMID: 30590126 DOI: 10.1016/j.jmoldx.2018.10.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/09/2018] [Accepted: 10/26/2018] [Indexed: 01/03/2023] Open
Abstract
Immunoglobulin heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the assessment of B-cell lineage neoplasms. Clinical use remains limited because assays are not standardized and validation/implementation guidelines are not yet developed. Herein, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1 was validated using commercially available kits. Data were analyzed by commercial and in-house-developed bioinformatics pipelines. Performance characteristics were evaluated directly comparing with capillary electrophoresis (CE) assays (BIOMED-2 primers). Assays were monitored after implementation (>1.5 years), concurrently testing by CE methods. A total of 1189 clinical samples were studied (94 validation, 1095 postimplementation). NGS showed superior performance compared with CE assays. For initial assessment, clonality detection rate was >97% for all malignancy types. Concordance with CE was 96%; discordances were related to higher sensitivity/resolution of NGS and improved detection in cases with high somatic hypermutation. Routine NGS clonality assessment is feasible and superior to existing assays, enabling accurate and specific index clone assessment and future tracking of all rearrangements in a patient sample. Successful implementation requires new standardization, validation, and implementation processes, which should be performed as a multicenter and multidisciplinary collaboration.
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Affiliation(s)
- Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Wayne Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mustafa Syed
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hannah Kim
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lidia Maciag
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinJuan Yao
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Caleb Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine Moung
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ivelise Rijo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tessara Baldi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ola Landgren
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jae Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mikhail Roshal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Considerations for monitoring minimal residual disease using immunoglobulin clonality in patients with precursor B-cell lymphoblastic leukemia. Clin Chim Acta 2018; 488:81-89. [PMID: 30389459 DOI: 10.1016/j.cca.2018.10.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 10/08/2018] [Accepted: 10/29/2018] [Indexed: 11/23/2022]
Abstract
BACKGROUND Minimal residual disease (MRD) monitoring is a powerful tool to predict the risk of relapse. Herein, we present an MRD monitoring strategy for B-cell lymphoblastic leukemia (B-ALL) using high-throughput sequencing (HTS) of immunoglobulin (Ig) clonality before implementation into routine practice. METHODS We selected 74 bone marrow (BM) specimens from 47 patients who were diagnosed with B-ALL. Ig clonality was analyzed using both fragment analysis and HTS. The performance of Ig clonality was evaluated through comparison of the results from real-time quantitative polymerase chain reaction (qPCR) of leukemia-specific fusion transcripts and flow cytometry. RESULTS IGH clonality was observed in all patients, and the sum of clonal burden varied (9.47%-96.77%). IGK clonality was identified in 70% of patients and availed in cases with low IGH clonal burden. The total IGH clonal burden was significantly correlated with the proportion of leukemic blasts, leukemia-specific fusion transcripts, and flow cytometry. We recognized the different responses of each clone and emerging clones originating from the trace of Ig rearrangement presented in the initial specimen. IGH clonal burden after chemotherapy represented patient outcomes well. IGH assay also provided information of repertoire diversity of IGH rearrangement. CONCLUSION The Ig clonality assay via HTS will be a promising tool for MRD monitoring of B-ALL through an adequate strategy to identify and monitor individual clones and determine repertoire diversity.
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41
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Theunissen PMJ, de Bie M, van Zessen D, de Haas V, Stubbs AP, van der Velden VHJ. Next-generation antigen receptor sequencing of paired diagnosis and relapse samples of B-cell acute lymphoblastic leukemia: Clonal evolution and implications for minimal residual disease target selection. Leuk Res 2018; 76:98-104. [PMID: 30389174 DOI: 10.1016/j.leukres.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/01/2018] [Accepted: 10/18/2018] [Indexed: 11/26/2022]
Abstract
Antigen receptor gene rearrangements are frequently applied as molecular targets for detection of minimal residual disease (MRD) in B-cell precursor acute lymphoblastic leukemia patients. Since such targets may be lost at relapse, appropriate selection of antigen receptor genes as MRD-PCR target is critical. Recently, next-generation sequencing (NGS) - much more sensitive and quantitative than classical PCR-heteroduplex approaches - has been introduced for identification of MRD-PCR targets. We evaluated 42 paired diagnosis-relapse samples by NGS (IGH, IGK, TRG, TRD, and TRB) to evaluate clonal evolution patterns and to design an algorithm for selection of antigen receptor gene rearrangements most likely to remain stable at relapse. Overall, only 393 out of 1446 (27%) clonal rearrangements were stable between diagnosis and relapse. If only index clones with a frequency >5% at diagnosis were taken into account, this number increased to 65%; including only index clones with an absolute read count >10,000, indicating truly major clones, further increased the stability to 84%. Over 90% of index clones at relapse were also present as index clone at diagnosis. Our data provide detailed information about the stability of antigen receptor gene rearrangements, based on which we propose an algorithm for selecting stable MRD-PCR targets, successful in >97% of patients.
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Affiliation(s)
- Prisca M J Theunissen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Maaike de Bie
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - David van Zessen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | | | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
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42
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Derrieux C, Trinquand A, Bruneau J, Verkarre V, Lhermitte L, Alcantara M, Villarese P, Meresse B, Sibon D, Hermine O, Brousse N, Molina T, Cellier C, Cerf-Bensussan N, Malamut G, Macintyre E. A Single-Tube, EuroClonality-Inspired, TRG Clonality Multiplex PCR Aids Management of Patients with Enteropathic Diseases, including from Formaldehyde-Fixed, Paraffin-Embedded Tissues. J Mol Diagn 2018; 21:111-122. [PMID: 30268943 DOI: 10.1016/j.jmoldx.2018.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/09/2018] [Accepted: 08/16/2018] [Indexed: 01/06/2023] Open
Abstract
Celiac disease is a chronic inflammation of the small intestine with villous atrophy that can become refractory to a gluten-free diet. Two categories of refractory celiac disease can be distinguished by the phenotype of intraepithelial lymphocytes and the status of TRG genes. Their distinction is important because 30% to 50% of type II but only 0% to 14% of type I evolve to an aggressive enteropathy-associated T-cell lymphoma and therefore require intensive treatment. Currently, differential diagnosis integrates immunohistochemistry, immunophenotyping, and TRG clonality analyses, but each has limitations. A single-tube multiplex TRG PCR (ECN) was prospectively compared to an in-house two-tube TRG PCR (N2T) in 73 samples, including 67 cryopreserved intestine tissues. Thirteen formalin-fixed, paraffin-embedded (FFPE) samples were also analyzed retrospectively. The ECN PCR had comparable efficiency to detect major clonal rearrangements in highly infiltrated tissues from T-cell lymphoproliferative disorders and type II refractory celiac disease and to detect the persistence of minor clones in type II refractory celiac disease follow-up samples. The ECN PCR abolished the risk of amplification of false-positive weak clonal rearrangements in cryopreserved specimens and allowed improved detection of clonal rearrangements in DNA from FFPE samples. The ECN PCR allows robust assessment of cryopreserved and FFPE digestive tissues at diagnosis and follow-up of enteropathies with villous atrophy, thus guiding therapeutic management.
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Affiliation(s)
- Coralie Derrieux
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Hematology Laboratory, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; INSERM UMR1151 and Institut Necker-Enfants Malades, Paris, France
| | - Amélie Trinquand
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Hematology Laboratory, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; INSERM UMR1151 and Institut Necker-Enfants Malades, Paris, France; INSERM UMR1163 Laboratory of Intestinal Immunity, Imagine Institute, Paris, France; Centre national Expert des Lymphomes Associés à la maladie Coeliaque, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Julie Bruneau
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Centre national Expert des Lymphomes Associés à la maladie Coeliaque, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; Department of Pathology, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Virginie Verkarre
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Department of Pathology, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Ludovic Lhermitte
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Hematology Laboratory, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; INSERM UMR1151 and Institut Necker-Enfants Malades, Paris, France; Centre national Expert des Lymphomes Associés à la maladie Coeliaque, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Marion Alcantara
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Hematology Laboratory, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; INSERM UMR1151 and Institut Necker-Enfants Malades, Paris, France
| | - Patrick Villarese
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Hematology Laboratory, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; INSERM UMR1151 and Institut Necker-Enfants Malades, Paris, France
| | - Bertrand Meresse
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; INSERM UMR1163 Laboratory of Intestinal Immunity, Imagine Institute, Paris, France; INSERM UMR995, Lille Inflammation Research International Center (LIRIC), Lille, France
| | - David Sibon
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; INSERM UMR1151 and Institut Necker-Enfants Malades, Paris, France; Department of Clinical Hematology, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Olivier Hermine
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Department of Clinical Hematology, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; INSERM UMR1163, CNRS ERL 8254, Imagine Institute, Paris, France
| | - Nicole Brousse
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Centre national Expert des Lymphomes Associés à la maladie Coeliaque, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; Department of Pathology, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Thierry Molina
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Department of Pathology, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Christophe Cellier
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Centre national Expert des Lymphomes Associés à la maladie Coeliaque, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; Department of Gastroenterology, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Nadine Cerf-Bensussan
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; INSERM UMR1163 Laboratory of Intestinal Immunity, Imagine Institute, Paris, France; Centre national Expert des Lymphomes Associés à la maladie Coeliaque, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Georgia Malamut
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Centre national Expert des Lymphomes Associés à la maladie Coeliaque, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; Department of Gastroenterology, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Elizabeth Macintyre
- Hematology Laboratory, Necker-Enfants Malades Hosptial and Paris Descartes, Sorbonne Paris Cité University, Paris, France; Hematology Laboratory, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France; INSERM UMR1151 and Institut Necker-Enfants Malades, Paris, France; Centre national Expert des Lymphomes Associés à la maladie Coeliaque, Hôpital Necker-Enfants Malades, Assistance Publique des Hôpitaux de Paris, Paris, France.
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New Molecular Technologies for Minimal Residual Disease Evaluation in B-Cell Lymphoid Malignancies. J Clin Med 2018; 7:jcm7090288. [PMID: 30231510 PMCID: PMC6162632 DOI: 10.3390/jcm7090288] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022] Open
Abstract
The clearance of malignant clonal cells significantly correlates with clinical outcomes in many hematologic malignancies. Accurate and high throughput tools for minimal residual disease (MRD) detection are needed to overcome some drawbacks of standard molecular techniques; such novel tools have allowed for higher sensitivity analyses and more precise stratification of patients, based on molecular response to therapy. In this review, we depict the recently introduced digital PCR and next-generation sequencing technologies, describing their current application for MRD monitoring in lymphoproliferative disorders. Moreover, we illustrate the feasibility of these new technologies to test less invasive and more patient-friendly tissues sources, such as "liquid biopsy".
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44
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Wang HW, Raffeld M. Molecular assessment of clonality in lymphoid neoplasms. Semin Hematol 2018; 56:37-45. [PMID: 30573043 DOI: 10.1053/j.seminhematol.2018.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/08/2018] [Indexed: 02/03/2023]
Abstract
Molecular clonality assays in B- and T-cell lymphoproliferative disorders often provide critical information in establishing a diagnosis of a lymphoproliferative disorder. These assays rely on the unique genetic structures that serve as assay targets, created in the process of generating immunoglobulin and T-cell receptors during B- and T-cell development. Molecular clonality assays are generally used when flow cytometry or immunohistochemistry has not sufficiently clarified the benign or malignant nature of a lymphoid proliferation. Additionally, since molecular clonality assays are tumor specific, they allow the clinician to distinguish recurrences from second tumors, and have the sensitivity to monitor minimal residual disease. In this review, we discuss the principles underlying these tests, the current approaches to clonality testing, some of the pitfalls in their interpretation, and the future applications of next generation sequencing technology to clonality testing.
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Affiliation(s)
- Hao-Wei Wang
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Mark Raffeld
- Molecular Diagnostics Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD.
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45
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Chaara W, Gonzalez-Tort A, Florez LM, Klatzmann D, Mariotti-Ferrandiz E, Six A. RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy. Front Immunol 2018; 9:1038. [PMID: 29868003 PMCID: PMC5962720 DOI: 10.3389/fimmu.2018.01038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/25/2018] [Indexed: 12/30/2022] Open
Abstract
High-throughput sequencing (HTS) has the potential to decipher the diversity of T cell repertoires and their dynamics during immune responses. Applied to T cell subsets such as T effector and T regulatory cells, it should help identify novel biomarkers of diseases. However, given the extreme diversity of TCR repertoires, understanding how the sequencing conditions, including cell numbers, biological and technical sampling and sequencing depth, impact the experimental outcome is critical to proper use of these data. Here, we assessed the representativeness and robustness of TCR repertoire diversity assessment according to experimental conditions. By comparative analyses of experimental datasets and computer simulations, we found that (i) for small samples, the number of clonotypes recovered is often higher than the number of cells per sample, even after removing the singletons; (ii) high-sequencing depth for small samples alters the clonotype distributions, which can be corrected by filtering the datasets using Shannon entropy as a threshold; and (iii) a single sequencing run at high depth does not ensure a good coverage of the clonotype richness in highly polyclonal populations, which can be better covered using multiple sequencing. Altogether, our results warrant better understanding and awareness of the limitation of TCR diversity analyses by HTS and justify the development of novel computational tools for improved modeling of the highly complex nature of TCR repertoires.
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Affiliation(s)
- Wahiba Chaara
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Ariadna Gonzalez-Tort
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Laura-Maria Florez
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
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Ichinohe T, Miyama T, Kawase T, Honjo Y, Kitaura K, Sato H, Shin-I T, Suzuki R. Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host-Gut Microbiome Interactions. Front Immunol 2018; 9:668. [PMID: 29666626 PMCID: PMC5891584 DOI: 10.3389/fimmu.2018.00668] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 03/19/2018] [Indexed: 12/23/2022] Open
Abstract
The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype. Over the past several years, high-throughput next-generation sequencing has been developed as a powerful tool to profile T- and B-cell receptor repertoires in a given individual at the single-cell level. Sophisticated immuno-bioinformatic analyses by use of this innovative methodology have been already implemented in clinical development of antibody engineering, vaccine design, and cellular immunotherapy. In this article, we aim to discuss the possible application of high-throughput immune receptor sequencing in the field of nutritional and intestinal immunology. Although there are still unsolved caveats, this emerging technology combined with single-cell transcriptomics/proteomics provides a critical tool to unveil the previously unrecognized principle of host–microbiome immune homeostasis. Accumulation of such knowledge will lead to the development of effective ways for personalized immune modulation through deeper understanding of the mechanisms by which the intestinal environment affects our immune ecosystem.
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Affiliation(s)
- Tatsuo Ichinohe
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Takahiko Miyama
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Takakazu Kawase
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Yasuko Honjo
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | | | | | | | - Ryuji Suzuki
- Repertoire Genesis Incorporation, Ibaraki, Japan.,Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, National Hospital Organization Sagamihara Hospital, Sagamihara, Japan
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47
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Ho C, Arcila ME. Minimal residual disease detection of myeloma using sequencing of immunoglobulin heavy chain gene VDJ regions. Semin Hematol 2018; 55:13-18. [DOI: 10.1053/j.seminhematol.2018.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 02/21/2018] [Indexed: 01/29/2023]
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48
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Kotrova M, Trka J, Kneba M, Brüggemann M. Is Next-Generation Sequencing the way to go for Residual Disease Monitoring in Acute Lymphoblastic Leukemia? Mol Diagn Ther 2017; 21:481-492. [DOI: 10.1007/s40291-017-0277-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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49
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Boyer F, Boutouil H, Dalloul I, Dalloul Z, Cook-Moreau J, Aldigier JC, Carrion C, Herve B, Scaon E, Cogné M, Péron S. CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing. THE JOURNAL OF IMMUNOLOGY 2017; 198:4148-4155. [PMID: 28416601 DOI: 10.4049/jimmunol.1601924] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/19/2017] [Indexed: 11/19/2022]
Abstract
B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study.
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Affiliation(s)
- François Boyer
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Hend Boutouil
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Iman Dalloul
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Zeinab Dalloul
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Jeanne Cook-Moreau
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Jean-Claude Aldigier
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Claire Carrion
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
| | - Bastien Herve
- Université de Limoges,plateforme Biologie Intégrative Santé Chimie Environnement, F-87000 Limoges, France; and
| | - Erwan Scaon
- Université de Limoges,plateforme Biologie Intégrative Santé Chimie Environnement, F-87000 Limoges, France; and
| | - Michel Cogné
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.,Institut Universitaire de France, F-75000 Paris, France
| | - Sophie Péron
- Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France; .,CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France
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50
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IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Stubbs AP, van der Burg M. Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data. THE JOURNAL OF IMMUNOLOGY 2017; 198:4156-4165. [PMID: 28416602 DOI: 10.4049/jimmunol.1601921] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/13/2017] [Indexed: 11/19/2022]
Abstract
Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest. The demultiplex tool allows data trimming and demultiplexing, whereas with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published ImmunoGlobulin Galaxy (IGGalaxy) virtual machine that was developed to visualize V(D)J gene usage. It allows analysis of both BCR and TCR rearrangements, visualizes CDR3 characteristics (length and amino acid usage) and junction characteristics, and calculates the diversity of the immune repertoire. Finally, ARGalaxy includes the newly developed SHM and CSR pipeline to analyze SHM and/or CSR in BCR rearrangements. It analyzes the frequency and patterns of SHM, Ag selection (including BASELINe), clonality (Change-O), and CSR. The functionality of the ARGalaxy tool is illustrated in several clinical examples of patients with primary immunodeficiencies. In conclusion, ARGalaxy is a novel tool for the analysis of the complete immune repertoire, which is applicable to many patient groups with disturbances in the immune repertoire such as autoimmune diseases, allergy, and leukemia, but it can also be used to address basic research questions in repertoire formation and selection.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
| | | | - David van Zessen
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and.,Department of Bioinformatics, Erasmus University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
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