1
|
van der Velden VHJ, Dombrink I, Alten J, Cazzaniga G, Clappier E, Drandi D, Eckert C, Fronkova E, Hancock J, Kotrova M, Kraemer R, Montonen M, Pfeifer H, Pott C, Raff T, Trautmann H, Cavé H, Schäfer BW, van Dongen JJM, Trka J, Brüggemann M. Analysis of measurable residual disease by IG/TR gene rearrangements: quality assurance and updated EuroMRD guidelines. Leukemia 2024; 38:1315-1322. [PMID: 38744919 PMCID: PMC11147754 DOI: 10.1038/s41375-024-02272-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024]
Abstract
Minimal/measurable residual disease (MRD) diagnostics using real-time quantitative PCR analysis of rearranged immunoglobulin and T-cell receptor gene rearrangements are nowadays implemented in most treatment protocols for patients with acute lymphoblastic leukemia (ALL). Within the EuroMRD Consortium, we aim to provide comparable, high-quality MRD diagnostics, allowing appropriate risk-group classification for patients and inter-protocol comparisons. To this end, we set up a quality assessment scheme, that was gradually optimized and updated over the last 20 years, and that now includes participants from around 70 laboratories worldwide. We here describe the design and analysis of our quality assessment scheme. In addition, we here report revised data interpretation guidelines, based on our newly generated data and extensive discussions between experts. The main novelty is the partial re-definition of the "positive below quantitative range" category by two new categories, "MRD low positive, below quantitative range" and "MRD of uncertain significance". The quality assessment program and revised guidelines will ensure reproducible and accurate MRD data for ALL patients. Within the Consortium, similar programs and guidelines have been introduced for other lymphoid diseases (e.g., B-cell lymphoma), for new technological platforms (e.g., digital droplet PCR or Next-Generation Sequencing), and for other patient-specific MRD PCR-based targets (e.g., fusion genes).
Collapse
Affiliation(s)
- Vincent H J van der Velden
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Isabel Dombrink
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Julia Alten
- Department of Pediatrics, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Giovanni Cazzaniga
- Centro Tettamanti, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- School of Medicine, University of Milano-Bicocca, Monza, Italy
| | - Emmanuelle Clappier
- Hematology Laboratory, Saint-Louis Hospital, Paris Cité University, Paris, France
- Université Paris-Cité, Paris, France
| | - Daniela Drandi
- Department of Molecular Biotechnology and health sciences, Hematology Division, University of Torino, Torino, Italy
| | - Cornelia Eckert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eva Fronkova
- CLIP, Department of Pediatric Hematology and Oncology, Second Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Jeremy Hancock
- Bristol MRD Group, Bristol Genetics Laboratory, Southmead Hospital, Bristol, UK
| | - Michaela Kotrova
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rebekka Kraemer
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Mirkka Montonen
- Tyks Laboratories, Genomics Department, Turku University Hospital, Turku, Finland
| | - Heike Pfeifer
- Department of Hematology, University Hospital Frankfurt, Frankfurt, Germany
| | - Christiane Pott
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Thorsten Raff
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
- Military Medical City Hospital, Doha, Qatar
| | - Heiko Trautmann
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Hélène Cavé
- Hematology Laboratory, Saint-Louis Hospital, Paris Cité University, Paris, France
- Department of Genetics, University Hospital Robert Debré, Paris, France
| | | | - Jacques J M van Dongen
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC, USAL-CSIC-FICUS) and Department of Medicine, University of Salamanca, Salamanca, Spain
- European Scientific foundation for Laboratory Hemato Oncology (ESLHO), Zutphen, The Netherlands
- Department of Immunology, LUMC, Leiden, The Netherlands
| | - Jan Trka
- CLIP, Department of Pediatric Hematology and Oncology, Second Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Monika Brüggemann
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| |
Collapse
|
2
|
Ashouri K, Nittur V, Ginosyan AA, Hwang J, Adnani B, Chen D, Savitala-Damerla L, Schiff K, Chaudhary P, Kovach AE, Ladha A, Siddiqi I, Ali A, Woan K, Tam E, Yaghmour G. Concordance of Next-Generation Sequencing and Multiparametric Flow Cytometry Methods for Detecting Measurable Residual Disease in Adult Acute Lymphoblastic Leukemia: Optimizing Prediction of Clinical Outcomes From a Single-Center Study. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2024; 24:e59-e66.e2. [PMID: 38061959 DOI: 10.1016/j.clml.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 03/01/2024]
Abstract
INTRODUCTION Detection of measurable residual disease (MRD) in adults with acute lymphoblastic leukemia (ALL) is a vital biomarker in risk prediction and treatment selection. Next-generation sequencing (NGS) offers greater sensitivity relative to multiparametric flow cytometry (MFC) and may be a better predictive tool for identifying ALL patients at risk of relapse. PATIENTS AND METHODS This single-center retrospective study compares MRD detection by NGS versus MFC in 52 adult B- and T-ALL patients treated at our institution between 2018 and 2023. Pretreatment bone marrow samples were used for assay calibration, while post-treatment MRD assessment was completed up to 4.5 months after the first complete remission (CR1) using an MRD cutoff of 10-6 for distinguishing relapse risk. RESULTS The 2-year cumulative incidence of relapse (CIR) among patients who were MRD positive using MFC and NGS was 39.5% and 46.2%, respectively. Unlike MFC, post-CR1 MRD positivity with NGS significantly predicted CIR (HR = 9.47, P = .028). In patients who were MRD negative by MFC, low levels of MRD detected by NGS distinguished patients at high risk of relapse (HR 10.3, P = .026, 2-year CIR 51.6%). CONCLUSION Our data suggests that assessment of post-CR1 MRD using a highly sensitive NGS assay can identify ALL patients undergoing frontline therapy at increased risk of relapse and guide the use of adjuvant therapy.
Collapse
Affiliation(s)
- Karam Ashouri
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Vinay Nittur
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Anush A Ginosyan
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jennifer Hwang
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Blake Adnani
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Denaly Chen
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Lakshmi Savitala-Damerla
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Kimberly Schiff
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Preet Chaudhary
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Alexandra E Kovach
- Keck School of Medicine, University of Southern California, Los Angeles, CA; Hematopathology, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
| | - Abdullah Ladha
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Imran Siddiqi
- Keck School of Medicine, University of Southern California, Los Angeles, CA; Division of Pathology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Amir Ali
- Department of Pharmacy, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Karrune Woan
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Eric Tam
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - George Yaghmour
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA.
| |
Collapse
|
3
|
Antigen Receptors Gene Analysis for Minimal Residual Disease Detection in Acute Lymphoblastic Leukemia: The Role of High Throughput Sequencing. HEMATO 2023. [DOI: 10.3390/hemato4010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The prognosis of adult acute lymphoblastic leukemia (ALL) is variable but more often dismal. Indeed, its clinical management is challenging, current therapies inducing complete remission in 65–90% of cases, but only 30–40% of patients being cured. The major determinant of treatment failure is relapse; consequently, measurement of residual leukemic blast (minimal residual disease, MRD) has become a powerful independent prognostic indicator in adults. Numerous evidences have also supported the clinical relevance of MRD assessment for risk class assignment and treatment selection. MRD can be virtually evaluated in all ALL patients using different technologies, such as polymerase chain reaction amplification of fusion transcripts and clonal rearrangements of antigen receptor genes, flow cytometric study of leukemic immunophenotypes and, the most recent, high throughput sequencing (HTS). In this review, the authors focused on the latest developments on MRD monitoring with emphasis on the use of HTS, as well as on the clinical impact of MRD monitoring.
Collapse
|
4
|
Immunophenotype of Measurable Residual Blast Cells as an Additional Prognostic Factor in Adults with B-Cell Acute Lymphoblastic Leukemia. Diagnostics (Basel) 2022; 13:diagnostics13010021. [PMID: 36611312 PMCID: PMC9818326 DOI: 10.3390/diagnostics13010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Measurable residual disease (MRD) is a well-known independent prognostic factor in acute leukemias, and multicolor flow cytometry (MFC) is widely used to detect MRD. MFC is able not only to enumerate MRD accurately but also to describe an antigen expression profile of residual blast cells. However, the relationship between MRD immunophenotype and patient survival probability has not yet been studied. We determined the prognostic impact of MRD immunophenotype in adults with B-cell acute lymphoblastic leukemia (B-ALL). In a multicenter study RALL-2016 (NCT03462095), 267 patients were enrolled from 2016 to 2022. MRD was assessed at the end of induction (day 70) in 94 patients with B-ALL by six- or 10-color flow cytometry in the bone marrow specimens. The 4 year relapse-free survival (RFS) was lower in MRD-positive B-ALL patients [37% vs. 78% (p < 0.0001)]. The absence of CD10, positive expression of CD38, and high expression of CD58 on MRD cells worsened the 4 year RFS [19% vs. 51% (p = 0.004), 0% vs. 51% (p < 0.0001), and 21% vs. 40% (p = 0.02), respectively]. The MRD immunophenotype is associated with RFS and could be an additional prognostic factor for B-ALL patients.
Collapse
|
5
|
Schwinghammer C, Koopmann J, Chitadze G, Karawajew L, Brüggemann M, Eckert C. Droplet Digital PCR: A New View on Minimal Residual Disease Quantification in Acute Lymphoblastic Leukemia. J Mol Diagn 2022; 24:856-866. [PMID: 35691569 DOI: 10.1016/j.jmoldx.2022.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/05/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022] Open
Abstract
Real-time quantitative PCR (qPCR) using immunoglobulin/T-cell receptor gene rearrangements has been used as the gold standard for minimal residual disease (MRD) monitoring in acute lymphoblastic leukemia (ALL) for >20 years. Recently, new PCR-based technologies have emerged, such as droplet digital PCR (ddPCR), which could offer several methodologic advances for MRD monitoring. In the current work, qPCR and ddPCR were compared in an unbiased blinded prospective study (n = 88 measurements) and in a retrospective study with selected critical low positive samples (n = 65 measurements). The former included flow cytometry (Flow; n = 31 measurements) as a third MRD detection method. Published guidelines (qPCR) and the latest, revised evaluation criteria (ie, ddPCR, Flow) have been applied for data analysis. The prospective study shows that ddPCR outperforms qPCR with a significantly better quantitative limit of detection and sensitivity. The number of critical MRD estimates below quantitative limit was reduced by sixfold and by threefold in the retrospective and prospective cohorts, respectively. Furthermore, the concordance of quantitative values between ddPCR and Flow was higher than between ddPCR and qPCR, probably because ddPCR and Flow are absolute quantification methods independent of the diagnostic sample, unlike qPCR. In summary, our data highlight the advantages of ddPCR as a more precise and sensitive technology that could be used to refine response monitoring in ALL.
Collapse
Affiliation(s)
- Claudia Schwinghammer
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Koopmann
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Guranda Chitadze
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Leonid Karawajew
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Brüggemann
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Cornelia Eckert
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.
| |
Collapse
|
6
|
High-sensitivity next-generation sequencing MRD assessment in ALL identifies patients at very low risk of relapse. Blood Adv 2022; 6:4006-4014. [PMID: 35533262 PMCID: PMC9278301 DOI: 10.1182/bloodadvances.2022007378] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Abstract
Measurable residual disease (MRD) is highly prognostic for relapse and overall survival (OS) in acute lymphoblastic leukemia (ALL), although many patients with apparent "MRD negativity" by standard assays still relapse. We evaluated the clinical impact of a highly sensitive next-generation sequencing (NGS) MRD assay in 74 adults with ALL undergoing frontline therapy. Among remission samples that were MRD negative by multiparameter flow cytometry (MFC), 46% were MRD positive by the NGS assay. After one cycle of induction chemotherapy, MRD negativity by MFC at a sensitivity of 1x10-4 and NGS at a sensitivity of 1x10-6 was achieved in 66% and 23% of patients, respectively. The 5-year cumulative incidence of relapse (CIR) among patients who achieved MRD negativity by MFC at CR was 29%; in contrast, no patients who achieved early MRD negativity by NGS relapsed, and their 5-year OS was 90%. NGS MRD negativity at CR was associated with significantly decreased risk of relapse compared with MRD positivity (5-year CIR: 0% versus 45%, respectively, P=0.04). Among patients who were MRD negative by MFC, detection of low levels of MRD by NGS identified patients who still had a significant risk of relapse (5-year CIR: 39%). Early assessment of MRD using a highly sensitive NGS assay adds clinically relevant prognostic information to standard MFC-based approaches and can identify patients with ALL undergoing frontline therapy who have a very low risk of relapse and excellent long-term survival.
Collapse
|
7
|
Kuiper RP, Hoogeveen PG, Bladergroen R, van Dijk F, Sonneveld E, van Leeuwen FN, Boer J, Sergeeva I, Feitsma H, den Boer ML, van der Velden VHJ. Minimal residual disease (MRD) detection in acute lymphoblastic leukaemia based on fusion genes and genomic deletions: towards MRD for all. Br J Haematol 2021; 194:888-892. [PMID: 34337744 PMCID: PMC9291030 DOI: 10.1111/bjh.17744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/18/2021] [Indexed: 12/16/2022]
Abstract
Minimal residual disease (MRD) diagnostics are implemented in most clinical protocols for patients with acute lymphoblastic leukaemia (ALL) and are mostly performed using rearranged immunoglobulin (IG) and/or T-cell receptor (TR) gene rearrangements as molecular polymerase chain reaction targets. Unfortunately, in 5-10% of patients no or no sensitive IG/TR targets are available, and patients therefore cannot be stratified appropriately. In the present study, we used fusion genes and genomic deletions as alternative MRD targets in these patients, which retrospectively revealed appropriate MDR stratification in 79% of patients with no (sensitive) IG/TR target, and a different risk group stratification in more than half of the cases.
Collapse
Affiliation(s)
- Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patricia G Hoogeveen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Reno Bladergroen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Freerk van Dijk
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Judith Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | | | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands.,Department of Pediatric Oncology, Erasmus MC - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Vincent H J van der Velden
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| |
Collapse
|
8
|
Immune Gene Rearrangements: Unique Signatures for Tracing Physiological Lymphocytes and Leukemic Cells. Genes (Basel) 2021; 12:genes12070979. [PMID: 34198966 PMCID: PMC8329920 DOI: 10.3390/genes12070979] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
The tremendous diversity of the human immune repertoire, fundamental for the defense against highly heterogeneous pathogens, is based on the ingenious mechanism of immune gene rearrangements. Rearranged immune genes encoding the immunoglobulins and T-cell receptors and thus determining each lymphocyte's antigen specificity are very valuable molecular markers for tracing malignant or physiological lymphocytes. One of their most significant applications is tracking residual leukemic cells in patients with lymphoid malignancies. This so called 'minimal residual disease' (MRD) has been shown to be the most important prognostic factor across various leukemia subtypes and has therefore been given enormous attention. Despite the current rapid development of the molecular methods, the classical real-time PCR based approach is still being regarded as the standard method for molecular MRD detection due to the cumbersome standardization of the novel approaches currently in progress within the EuroMRD and EuroClonality NGS Consortia. Each of the molecular methods, however, poses certain benefits and it is therefore expectable that none of the methods for MRD detection will clearly prevail over the others in the near future.
Collapse
|
9
|
B-cell acute lymphoblastic leukemia in patients with chronic lymphocytic leukemia treated with lenalidomide. Blood 2021; 137:2267-2271. [PMID: 33512465 DOI: 10.1182/blood.2020008609] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
|
10
|
Crook OM, Gatto L, Kirk PD. Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics. Stat Appl Genet Mol Biol 2019; 18:/j/sagmb.ahead-of-print/sagmb-2018-0065/sagmb-2018-0065.xml. [PMID: 31829970 PMCID: PMC7614016 DOI: 10.1515/sagmb-2018-0065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Dirichlet Process (DP) mixture model has become a popular choice for model-based clustering, largely because it allows the number of clusters to be inferred. The sequential updating and greedy search (SUGS) algorithm (Wang & Dunson, 2011) was proposed as a fast method for performing approximate Bayesian inference in DP mixture models, by posing clustering as a Bayesian model selection (BMS) problem and avoiding the use of computationally costly Markov chain Monte Carlo methods. Here we consider how this approach may be extended to permit variable selection for clustering, and also demonstrate the benefits of Bayesian model averaging (BMA) in place of BMS. Through an array of simulation examples and well-studied examples from cancer transcriptomics, we show that our method performs competitively with the current state-of-the-art, while also offering computational benefits. We apply our approach to reverse-phase protein array (RPPA) data from The Cancer Genome Atlas (TCGA) in order to perform a pan-cancer proteomic characterisation of 5157 tumour samples. We have implemented our approach, together with the original SUGS algorithm, in an open-source R package named sugsvarsel, which accelerates analysis by performing intensive computations in C++ and provides automated parallel processing. The R package is freely available from: https://github.com/ococrook/sugsvarsel.
Collapse
Affiliation(s)
- Oliver M. Crook
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK,Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK,MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Paul D.W. Kirk
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK,University of Cambridge, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge Biomedical Campus Cambridge, United Kingdom of Great Britain and Northern Ireland
| |
Collapse
|
11
|
Wenzinger C, Williams E, Gru AA. Updates in the Pathology of Precursor Lymphoid Neoplasms in the Revised Fourth Edition of the WHO Classification of Tumors of Hematopoietic and Lymphoid Tissues. Curr Hematol Malig Rep 2018; 13:275-288. [PMID: 29951888 DOI: 10.1007/s11899-018-0456-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Acute lymphoblastic leukemias (ALL) are malignant disorders of immature B or T cells that occur characteristically in children, usually under the age of 6 (75%). Approximately 6000 new cases of ALL are diagnosed each year in the USA, 80-85% of which represent B-ALL forms. Most presentations of B-ALL are leukemic, whereas T-ALL presents with a mediastinal mass, with or without leukemic involvement. The revised fourth edition of the World Health Organization (WHO) classification (2017) has introduced some changes in both B and T-ALL. Here, we summarize the categories of lymphoblastic leukemia/lymphomas as defined by the WHO and recent developments in the understanding of this group of hematologic malignancy. RECENT FINDINGS Two provisional categories of B-ALL have now been identified including B-ALL, BCR-ABL1-like, and B-ALL with iAMP21. The Philadelphia chromosome-like B-ALL includes forms of the disease that shares the expression profiling of B-ALL with t(9;22) but lack such rearrangement. The second one shows amplification of part of the chromosome 21. Both entities are associated with worse prognosis. Within the T-ALL group, an early precursor T cell form has now been introduced as a provisional category. Such group demonstrates expression of stem cell and myeloid markers in conjunction with the T cell antigens. The current review summarizes the recent updates to the WHO classification.
Collapse
MESH Headings
- Child, Preschool
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Chromosomes, Human, Pair 9/genetics
- Chromosomes, Human, Pair 9/metabolism
- Female
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Hematopoiesis
- Humans
- Infant
- Lymphoid Tissue/metabolism
- Lymphoid Tissue/pathology
- Male
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/classification
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/classification
- Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Translocation, Genetic
- World Health Organization
Collapse
Affiliation(s)
| | - Eli Williams
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Alejandro A Gru
- Departments of Pathology & Dermatology, University of Virginia, 415 Lane Road, Hospital Expansion Bldg Room 3024, Charlottesville, VA, 22908, USA.
| |
Collapse
|
12
|
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.
Collapse
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
| | | |
Collapse
|
13
|
Theunissen PMJ, van Zessen D, Stubbs AP, Faham M, Zwaan CM, van Dongen JJM, Van Der Velden VHJ. Antigen receptor sequencing of paired bone marrow samples shows homogeneous distribution of acute lymphoblastic leukemia subclones. Haematologica 2017; 102:1869-1877. [PMID: 28860343 PMCID: PMC5664391 DOI: 10.3324/haematol.2017.171454] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/24/2017] [Indexed: 01/30/2023] Open
Abstract
In B-cell precursor acute lymphoblastic leukemia, the initial leukemic cells share the same antigen receptor gene rearrangements. However, due to ongoing rearrangement processes, leukemic cells with different gene rearrangement patterns can develop, resulting in subclone formation. We studied leukemic subclones and their distribution in the bone marrow and peripheral blood at diagnosis. Antigen receptor gene rearrangements (IGH, IGK, TRG, TRD, TRB) were analyzed by next-generation sequencing in seven paired bone marrow samples and five paired bone marrow-peripheral blood samples. Background-thresholds were defined, which enabled identification of leukemic gene rearrangements down to very low levels. Paired bone marrow analysis showed oligoclonality in all 7 patients and up to 34 leukemic clones per patient. Additional analysis of evolutionary-related IGH gene rearrangements revealed up to 171 leukemic clones per patient. Interestingly, overall 86% of all leukemic gene rearrangements, including small subclones, were present in both bone marrow samples (range per patient: 72–100%). Paired bone marrow-peripheral blood analysis showed that 83% of all leukemic gene rearrangements in bone marrow were also found in peripheral blood (range per patient: 81–100%). Remarkably, in the paired bone marrow samples and paired bone marrow-peripheral blood samples the vast majority of leukemic gene rearrangements had a similar frequency (<5-fold frequency difference) (96% and 96% of leukemic rearrangements, respectively). Together, these results indicate that B-cell precursor acute lymphoblastic leukemia is generally highly oligoclonal. Nevertheless, the vast majority of leukemic clones, even the minor antigen receptor-defined subclones, are homogeneously distributed throughout the bone marrow and peripheral blood compartment.
Collapse
Affiliation(s)
- Prisca M J Theunissen
- 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
| | - Malek Faham
- Adaptive Biotechnologies Corp., South San Francisco, CA, USA
| | - Christian M Zwaan
- Department of Pediatric Oncology, Sophia Children's Hospital/Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | - Jacques J M van Dongen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, the Netherlands
| | | |
Collapse
|
14
|
Ikoma MRV, Beltrame MP, Ferreira SIACP, Souto EX, Malvezzi M, Yamamoto M. Proposal for the standardization of flow cytometry protocols to detect minimal residual disease in acute lymphoblastic leukemia. Rev Bras Hematol Hemoter 2015; 37:406-13. [PMID: 26670404 PMCID: PMC4678914 DOI: 10.1016/j.bjhh.2015.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 01/26/2023] Open
Abstract
Minimal residual disease is the most powerful predictor of outcome in acute leukemia and is useful in therapeutic stratification for acute lymphoblastic leukemia protocols. Nowadays, the most reliable methods for studying minimal residual disease in acute lymphoblastic leukemia are multiparametric flow cytometry and polymerase chain reaction. Both provide similar results at a minimal residual disease level of 0.01% of normal cells, that is, detection of one leukemic cell in up to 10,000 normal nucleated cells. Currently, therapeutic protocols establish the minimal residual disease threshold value at the most informative time points according to the appropriate methodology employed. The expertise of the laboratory in a cancer center or a cooperative group could be the most important factor in determining which method should be used. In Brazil, multiparametric flow cytometry laboratories are available in most leukemia treatment centers, but multiparametric flow cytometry processes must be standardized for minimal residual disease investigations in order to offer reliable and reproducible results that ensure quality in the clinical application of the method. The Minimal Residual Disease Working Group of the Brazilian Society of Bone Marrow Transplantation (SBTMO) was created with that aim. This paper presents recommendations for the detection of minimal residual disease in acute lymphoblastic leukemia based on the literature and expertise of the laboratories who participated in this consensus, including pre-analytical and analytical methods. This paper also recommends that both multiparametric flow cytometry and polymerase chain reaction are complementary methods, and so more laboratories with expertise in immunoglobulin/T cell receptor (Ig/TCR) gene assays are necessary in Brazil.
Collapse
Affiliation(s)
| | | | | | | | | | - Mihoko Yamamoto
- Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | | |
Collapse
|
15
|
Gazzola A, Mannu C, Rossi M, Laginestra MA, Sapienza MR, Fuligni F, Etebari M, Melle F, Sabattini E, Agostinelli C, Bacci F, Sagramoso Sacchetti CA, Pileri SA, Piccaluga PP. The evolution of clonality testing in the diagnosis and monitoring of hematological malignancies. Ther Adv Hematol 2014; 5:35-47. [PMID: 24688753 PMCID: PMC3949299 DOI: 10.1177/2040620713519729] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Currently, distinguishing between benign and malignant lymphoid proliferations is based on a combination of clinical characteristics, cyto/histomorphology, immunophenotype and the identification of well-defined chromosomal aberrations. However, such diagnoses remain challenging in 10-15% of cases of lymphoproliferative disorders, and clonality assessments are often required to confirm diagnostic suspicions. In recent years, the development of new techniques for clonality detection has allowed researchers to better characterize, classify and monitor hematological neoplasms. In the past, clonality was primarily studied by performing Southern blotting analyses to characterize rearrangements in segments of the IG and TCR genes. Currently, the most commonly used method in the clinical molecular diagnostic laboratory is polymerase chain reaction (PCR), which is an extremely sensitive technique for detecting nucleic acids. This technique is rapid, accurate, specific, and sensitive, and it can be used to analyze small biopsies as well as formalin-fixed paraffin-embedded samples. These advantages make PCR-based approaches the current gold standard for IG/TCR clonality testing. Since the completion of the first human genome sequence, there has been a rapid development of technologies to facilitate high-throughput sequencing of DNA. These techniques have been applied to the deep characterization and classification of various diseases, patient stratification, and the monitoring of minimal residual disease. Furthermore, these novel approaches have the potential to significantly improve the sensitivity and cost of clonality assays and post-treatment monitoring of B- and T-cell malignancies. However, more studies will be required to demonstrate the utility, sensitivity, and benefits of these methods in order to warrant their adoption into clinical practice. In this review, recent developments in clonality testing are examined with an emphasis on highly sensitive systems for improving diagnostic workups and minimal residual disease assessments.
Collapse
Affiliation(s)
- Anna Gazzola
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Claudia Mannu
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Maura Rossi
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Maria Antonella Laginestra
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Maria Rosaria Sapienza
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Fabio Fuligni
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Maryam Etebari
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Federica Melle
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Elena Sabattini
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Claudio Agostinelli
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Francesco Bacci
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Carlo Alberto Sagramoso Sacchetti
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Stefano Aldo Pileri
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Pier Paolo Piccaluga
- Molecular Pathology Laboratory, Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Via Massarenti 9, 40138 Bologna, Italy
| |
Collapse
|
16
|
Logan AC, Vashi N, Faham M, Carlton V, Kong K, Buño I, Zheng J, Moorhead M, Klinger M, Zhang B, Waqar A, Zehnder JL, Miklos DB. Immunoglobulin and T cell receptor gene high-throughput sequencing quantifies minimal residual disease in acute lymphoblastic leukemia and predicts post-transplantation relapse and survival. Biol Blood Marrow Transplant 2014; 20:1307-13. [PMID: 24769317 DOI: 10.1016/j.bbmt.2014.04.018] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 04/17/2014] [Indexed: 01/11/2023]
Abstract
Minimal residual disease (MRD) quantification is an important predictor of outcome after treatment for acute lymphoblastic leukemia (ALL). Bone marrow ALL burden ≥ 10(-4) after induction predicts subsequent relapse. Likewise, MRD ≥ 10(-4) in bone marrow before initiation of conditioning for allogeneic (allo) hematopoietic cell transplantation (HCT) predicts transplantation failure. Current methods for MRD quantification in ALL are not sufficiently sensitive for use with peripheral blood specimens and have not been broadly implemented in the management of adults with ALL. Consensus-primed immunoglobulin (Ig), T cell receptor (TCR) amplification and high-throughput sequencing (HTS) permit use of a standardized algorithm for all patients and can detect leukemia at 10(-6) or lower. We applied the LymphoSIGHT HTS platform (Sequenta Inc., South San Francisco, CA) to quantification of MRD in 237 samples from 29 adult B cell ALL patients before and after allo-HCT. Using primers for the IGH-VDJ, IGH-DJ, IGK, TCRB, TCRD, and TCRG loci, MRD could be quantified in 93% of patients. Leukemia-associated clonotypes at these loci were identified in 52%, 28%, 10%, 35%, 28%, and 41% of patients, respectively. MRD ≥ 10(-4) before HCT conditioning predicted post-HCT relapse (hazard ratio [HR], 7.7; 95% confidence interval [CI], 2.0 to 30; P = .003). In post-HCT blood samples, MRD ≥10(-6) had 100% positive predictive value for relapse with median lead time of 89 days (HR, 14; 95% CI, 4.7 to 44, P < .0001). The use of HTS-based MRD quantification in adults with ALL offers a standardized approach with sufficient sensitivity to quantify leukemia MRD in peripheral blood. Use of this approach may identify a window for clinical intervention before overt relapse.
Collapse
Affiliation(s)
- Aaron C Logan
- Division of Hematology and Blood and Marrow Transplantation, Department of Medicine, University of California, San Francisco, San Francisco, California.
| | - Nikita Vashi
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Malek Faham
- Sequenta Inc., South San Francisco, California
| | | | | | - Ismael Buño
- Department of Hematology, Hospital G.U. Gregorio Maranon, Madrid, Spain
| | | | | | | | - Bing Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Amna Waqar
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - David B Miklos
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, California
| |
Collapse
|
17
|
Poopak B, Saki N, Purfatholah AA, Najmabadi H, Mortazavi Y, Arzanian MT, Khosravipour G, Haghnejad F, Salari F, Shahjahani M. Pattern of immunoglobulin and T-cell receptor-δ/γ gene rearrangements in Iranian children with B-precursor acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2014; 19:259-66. [PMID: 24620952 DOI: 10.1179/1607845413y.0000000126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Acute lymphoblastic leukemia (ALL) cells have unique rearranged immunoglobulin heavy chain (IgH), immunoglobulin light chain (IgK), and T-cell receptor (TCR) genes, which can be used as markers for clonality assay and evaluation of minimal residual disease. In this study, we have evaluated the pattern of IgH, IgK chains, and TCRG/D gene rearrangements in precursor-B ALL. MATERIALS AND METHODS In our prospective study, hyper-variable regions (CDRI and III) of IgH, TCRD (Vδ2-Dδ3 and Dδ2-Dδ3), TCRG (Vγ, VγI, and VγII), and IgK (Vκ-Kde) were studied in 126 cases with diagnosis of B-precursor ALL. RESULTS One hundred and fourteen (90.5%) out of 126 patients had clonal rearrangements of IgH using consensus primers for CDRI and/or CDRIII regions. Monoclonal, biclonal, and oligoclonal patterns were observed in 63 (57.8%), 38 (34.9%), and 6 (5.5%) patients with IgH (CDRIII) rearrangements, respectively. Clonal rearrangements of TCRG (Vγ) and VγI/II were present in 79.3 and 64.9% of patients, respectively, and only 5% of cases showed biclonal pattern. The VγII rearrangement was the most common (46.8%) type in TCRG. Vδ2-Dδ3 and Dδ2-Dδ3 partial gene rearrangements were observed in 47 (45.2%; n = 104) and 11 (16.6%; n = 66) patients, respectively. Biclonal/oligoclonal patterns were present in 13 (27.7%) and 2 (4.3%) cases with Vδ2-Dδ3 rearrangement, respectively. Only one patient had biclonal Dδ2-Dδ3 rearrangement. Clonal pattern of IgK-Kde was detected in 59 cases (67%; n = 88). CONCLUSION Our findings showed that clonal rearrangements of IgH and TCRD (Vδ2-Dδ3 and Dδ2-Dδ3) genes had similar patterns to other studies. Frequency of TCRG (VγI and VγII) and IgK rearrangements was found to be slightly higher than previous reports. Among the IgK rearrangements, VKI (25%) was the most common.
Collapse
|
18
|
Brüggemann M, Gökbuget N, Kneba M. Acute Lymphoblastic Leukemia: Monitoring Minimal Residual Disease as a Therapeutic Principle. Semin Oncol 2012; 39:47-57. [DOI: 10.1053/j.seminoncol.2011.11.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
19
|
Bonzheim I, Fröhlich F, Adam P, Colak S, Metzler G, Quintanilla-Martinez L, Fend F. A comparative analysis of protocols for detection of T cell clonality in formalin-fixed, paraffin-embedded tissue—implications for practical use. J Hematop 2011. [DOI: 10.1007/s12308-011-0128-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
20
|
Nakazawa Y, Huye LE, Salsman VS, Leen AM, Ahmed N, Rollins L, Dotti G, Gottschalk SM, Wilson MH, Rooney CM. PiggyBac-mediated cancer immunotherapy using EBV-specific cytotoxic T-cells expressing HER2-specific chimeric antigen receptor. Mol Ther 2011; 19:2133-43. [PMID: 21772253 DOI: 10.1038/mt.2011.131] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Epstein-Barr virus (EBV)-specific cytotoxic T lymphocytes (CTLs) can be modified to function as heterologous tumor directed effector cells that survive longer in vivo than tumor directed T cells without virus specificity, due to chronic stimulation by viral antigens expressed during persistent infection in seropositive individuals. We evaluated the nonviral piggyBac (PB) transposon system as a platform for modifying EBV-CTLs to express a functional human epidermal growth factor receptor 2-specific chimeric antigen receptor (HER2-CAR) thereby directing virus-specific, gene modified CTLs towards HER2-positive cancer cells. Peripheral blood mononuclear cells (PBMCs) were nucleofected with transposons encoding a HER2-CAR and a truncated CD19 molecule for selection followed by specific activation and expansion of EBV-CTLs. HER2-CAR was expressed in ~40% of T cells after CD19 selection with retention of immunophenotype, polyclonality, and function. HER2-CAR-modified EBV-CTLs (HER2-CTLs) killed HER2-positive brain tumor cell lines in vitro, exhibited transient and reversible increases in HER2-CAR expression following antigen-specific stimulation, and stably expressed HER2-CAR beyond 120 days. Adoptive transfer of PB-modified HER2-CTLs resulted in tumor regression in a murine xenograft model. Our results demonstrate that PB can be used to redirect virus-specific CTLs to tumor targets, which should prolong tumor-specific T cell survival in vivo producing more efficacious immunotherapy.
Collapse
Affiliation(s)
- Yozo Nakazawa
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Eckert C, Flohr T, Koehler R, Hagedorn N, Moericke A, Stanulla M, Kirschner-Schwabe R, Cario G, Stackelberg A, Bartram CR, Henze G, Schrappe M, Schrauder A. Very early/early relapses of acute lymphoblastic leukemia show unexpected changes of clonal markers and high heterogeneity in response to initial and relapse treatment. Leukemia 2011; 25:1305-13. [DOI: 10.1038/leu.2011.89] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
22
|
Immunologic minimal residual disease detection in acute lymphoblastic leukemia: a comparative approach to molecular testing. Best Pract Res Clin Haematol 2010; 23:347-58. [PMID: 21112034 DOI: 10.1016/j.beha.2010.07.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The generation of antisera directed against leukocyte differentiation antigens opened the possibility of studying minimal residual disease (MRD) in patients with acute lymphoblastic leukemia (ALL). During the three decades that followed the pioneering studies in this field, great progress has been made in the development of a wide array of monoclonal antibodies and of flow cytometric techniques for rare event detection. This advance was accompanied by an increasingly greater understanding of the immunophenotypic features of leukemic and normal lymphoid cells, and of the antigenic differences that make MRD studies possible. In parallel, molecular methods for MRD detection were established. The systematic application of immunologic and molecular techniques to study MRD in clinical samples has demonstrated the clinical significance of MRD in patients, leading to the use of MRD to regulate treatment intensity in many contemporary protocols. In this article, we discuss methodologic issues related to the immunologic monitoring of MRD and the evidence supporting its clinical significance, and compare the advantages and limitations of this approach to those of molecular monitoring of MRD.
Collapse
|
23
|
Campana D. Role of minimal residual disease monitoring in adult and pediatric acute lymphoblastic leukemia. Hematol Oncol Clin North Am 2010; 23:1083-98, vii. [PMID: 19825454 DOI: 10.1016/j.hoc.2009.07.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Assays that measure minimal residual disease (MRD) can determine the response to treatment in patients with acute lymphoblastic leukemia (ALL) much more precisely than morphologic screening of bone marrow smears. The clinical significance of MRD, detected by flow cytometry or polymerase chain reaction-based methods in childhood ALL, has been established. Hence, MRD is being used in several clinical trials to adjust treatment intensity. Similar findings have been gathered in adult patients with ALL, making MRD one of the most powerful and informative parameters to guide clinical management. This article discusses practical issues related to MRD methodologies and the evidence supporting the use of MRD for risk assignment in clinical trials.
Collapse
Affiliation(s)
- Dario Campana
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| |
Collapse
|
24
|
Standardized MRD quantification in European ALL trials: proceedings of the Second International Symposium on MRD assessment in Kiel, Germany, 18-20 September 2008. Leukemia 2009; 24:521-35. [PMID: 20033054 DOI: 10.1038/leu.2009.268] [Citation(s) in RCA: 264] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Assessment of minimal residual disease (MRD) has acquired a prominent position in European treatment protocols for patients with acute lymphoblastic leukemia (ALL), on the basis of its high prognostic value for predicting outcome and the possibilities for implementation of MRD diagnostics in treatment stratification. Therefore, there is an increasing need for standardization of methodologies and harmonization of terminology. For this purpose, a panel of representatives of all major European study groups on childhood and adult ALL and of international experts on PCR- and flow cytometry-based MRD assessment was built in the context of the Second International Symposium on MRD assessment in Kiel, Germany, 18-20 September 2008. The panel summarized the current state of MRD diagnostics in ALL and developed recommendations on the minimal technical requirements that should be fulfilled before implementation of MRD diagnostics into clinical trials. Finally, a common terminology for a standard description of MRD response and monitoring was established defining the terms 'complete MRD response', 'MRD persistence' and 'MRD reappearance'. The proposed MRD terminology may allow a refined and standardized assessment of response to treatment in adult and childhood ALL, and provides a sound basis for the comparison of MRD results between different treatment protocols.
Collapse
|
25
|
Thörn I, Forestier E, Thuresson B, Wasslavik C, Malec M, Li A, Lindström-Eriksson E, Botling J, Barbany G, Jacobsson S, Olofsson T, Porwit A, Sundström C, Rosenquist R. Applicability of IG/TCR gene rearrangements as targets for minimal residual disease assessment in a population-based cohort of Swedish childhood acute lymphoblastic leukaemia diagnosed 2002-2006. Eur J Haematol 2009; 84:117-27. [PMID: 19895569 DOI: 10.1111/j.1600-0609.2009.01374.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minimal residual disease (MRD) detection during the early treatment phase has become an important stratification parameter in many childhood acute lymphoblastic leukaemia (ALL) treatment protocols. Here, we aimed to address the applicability of rearranged antigen-receptor genes as potential MRD markers using real-time quantitative polymerase chain reaction (RQ-PCR) in a Swedish population-based cohort. From 334 childhood ALL cases diagnosed during 2002-2006, we analysed 279 diagnostic samples (84%) by screening for rearranged immunoglobulin (IG) and T-cell receptor (TCR) genes. Allele-specific oligonucleotides were designed, and the sensitivity and quantitative level was determined for each target. Overall, clonal IG/TCR rearrangements were detected in 97% (236/244) of B-cell precursor ALL (BCP ALL) and 94% (33/35) of T-ALL. A sensitive RQ-PCR analysis (< or = 10(-4)) was obtained in 89% (216/244) of BCP ALL and in 74% (26/35) of T-ALL, whereas two sensitive targets were only available in 47% (115/244) of BCP ALL and 29% (10/35) of T-ALL cases. With the stratification threshold of > or = 10(-3), which is applied in the current Nordic treatment protocol (NOPHO-ALL 2008) for the identification of high-risk patients, 93% of BCP ALL and 86% of T-ALL reached this quantitative range by at least one target gene. Taken together, this national retrospective study demonstrates that an IG/TCR target for MRD monitoring can be identified in the majority of childhood ALL cases, whereas identification of a second sensitive target gene needs to be improved.
Collapse
Affiliation(s)
- Ingrid Thörn
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
|
27
|
Abstract
In patients with acute lymphoblastic leukemia (ALL), monitoring of minimal residual disease (MRD) offers a way to precisely assess early treatment response and detect relapse. Established methods to study MRD are flow cytometric detection of abnormal immunophenotypes, polymerase chain reaction (PCR) amplification of antigen-receptor genes, and PCR amplification of fusion transcripts. The strong correlation between MRD levels and risk of relapse in childhood ALL is well demonstrated; studies in adult patients also support its prognostic value. Hence, results of MRD studies can be used to select treatment intensity and duration, and to estimate the optimal timing for hematopoietic stem cell transplantation. Practical issues in the implementation of MRD assays in clinical studies include determining the most informative time point to study MRD and the levels of MRD that will trigger changes in treatment intensity, as well as the relative cost and informative power of different methodologies. The identification of new markers of leukemia and the use of increasingly refined assays should further facilitate routine monitoring of MRD and help to clarify the cellular and biologic features of leukemic cells that resist chemotherapy in vivo.
Collapse
Affiliation(s)
- Dario Campana
- Department of Oncology, St. Jude Children's Research Hospital, and Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38105, USA.
| |
Collapse
|
28
|
van der Velden VHJ, van Dongen JJM. MRD detection in acute lymphoblastic leukemia patients using Ig/TCR gene rearrangements as targets for real-time quantitative PCR. Methods Mol Biol 2009; 538:115-50. [PMID: 19277574 DOI: 10.1007/978-1-59745-418-6_7] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Minimal residual disease (MRD) diagnostics has proven to be clinically relevant for evaluation of treatment effectiveness in patients with acute lymphoblastic leukemia (ALL). In most ALL treatment protocols, MRD diagnostics is performed by real-time quantitative PCR (RQ-PCR) analysis of the junctional regions of rearranged immunoglobulin (Ig) and T-cell receptor (TCR) genes.MRD diagnostics via Ig/TCR genes is broadly applicable (>95% of ALL patients) and can reach a good sensitivity (< or =10 (-4)). However, the technique is complex and requires extensive knowledge and experience, because the junctional regions of each leukemia have to be identified before the patient-specific RQ-PCR assays can be designed for MRD monitoring. This chapter provides all relevant background information and technical aspects for the complete laboratory process from detection of the clonal Ig/TCR gene rearrangements in ALL cells at diagnosis to the actual MRD measurements in clinical follow-up samples. This information aims at facilitating the PCR-based MRD diagnostics in ALL patients. However, it should be noted that MRD diagnostics for clinical treatment protocols has to be accompanied by regular international quality control rounds to ensure the reproducibility and reliability of the MRD results.
Collapse
|
29
|
Dawidowska M, Jółkowska J, Szczepański T, Derwich K, Wachowiak J, Witt M. Implementation of the standard strategy for identification of Ig/TCR targets for minimal residual disease diagnostics in B-cell precursor ALL pediatric patients: Polish experience. Arch Immunol Ther Exp (Warsz) 2008; 56:409-18. [PMID: 19043668 PMCID: PMC2805919 DOI: 10.1007/s00005-008-0045-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 10/20/2008] [Indexed: 12/04/2022]
Abstract
Introduction: Minimal residual disease (MRD), detected based on immunoglobulin and T-cell receptor (Ig/TCR) gene rearrangements as markers of residual leukemic cells, is currently the most reliable prognostic factor in acute lymphoblastic leukemia (ALL). A feasibility study is presented of the standard strategy for the identification of Ig/TCR targets for MRD diagnostics in Polish ALL patients by identifying Ig/TCR gene rearrangement pattern using standard primer sets and protocols. Materials and Methods: The PCR-heteroduplex approach based on BIOMED-1 and BIOMED-2 protocols (recommended as the European standard) was used to detect IGH, IGK-Kde, TCRD, TCRG, and TCRB rearrangements in 58 Polish B-cell precursor ALL patients. Sequencing and homology analysis between the obtained and germline Ig/TCR sequences enabled identification of the rearrangements. The U-Gauss test was used for statistical analysis of the Ig/TCR rearrangement pattern in Polish patients compared with relevant data on other nationalities. Results: The following pattern was identified: IGH: 83% (VH-JH: 74%, DH-JH: 9%), IGK-Kde: 41%, TCRD: 78% (incomplete TCRD: 55%, Vδ2-Dδ3: 45%, Dδ2-Dδ3: 21%, Vδ2-Jα: 35%), TCRG: 50%, and TCRB: 13%. Considerable convergence of the Ig/TCR pattern in Polish patients and those of other nationalities (mainly West Europeans) was demonstrated. Statistically relevant differences were only found between the incidence of DH-JH in Polish (9%) and Dutch patients (24%; p<0.05) and Polish and Italian patients (19%; p<0.05), VH-JH in Polish (74%) and Chilean patients (100%; p<0.05), and TCRG in Polish (50%) and Brazilian patients (69%; p<0.05). Conclusions: The convergence of Ig/TCR patterns in Polish and European patients indicates that the strategy for Ig/TCR target identification based on standard primers and protocols might be directly used for the construction of Polish standards and recommendations for MRD diagnostics.
Collapse
Affiliation(s)
- Małgorzata Dawidowska
- Department of Molecular and Clinical Genetics, Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland.
| | | | | | | | | | | |
Collapse
|
30
|
The pattern of clonal immunoglobulin and T-cell receptor (Ig/TCR) gene rearrangements in Chinese adult acute lymphoblastic leukemia patients. Leuk Res 2008; 32:1735-40. [DOI: 10.1016/j.leukres.2008.03.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2007] [Revised: 03/24/2008] [Accepted: 03/25/2008] [Indexed: 11/22/2022]
|
31
|
Campana D. Status of minimal residual disease testing in childhood haematological malignancies. Br J Haematol 2008; 143:481-9. [PMID: 18710378 DOI: 10.1111/j.1365-2141.2008.07350.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In children with acute leukaemia, measurements of minimal residual disease (MRD) provide unique information on treatment response and have become a crucial component of contemporary treatment protocols. In acute lymphoblastic leukaemia (ALL), the most useful MRD assays are based on polymerase chain reaction (PCR) amplification of antigen-receptor genes, and on flow cytometric detection of abnormal immunophenotypes. The latter is the only MRD assay available for most patients with acute myeloid leukaemia (AML). PCR amplification of chromosomal breakpoints and fusion transcripts can also be used to track MRD in a minority of patients with ALL or AML. Because of the strong correlation between MRD levels and risk of relapse, several ongoing regimens include treatment intensification for children with higher MRD. Treatment de-intensification for patients with early MRD clearance is also being tested. In addition to their direct clinical application, MRD measurements can be used to better understand the molecular and cellular mechanisms of drug resistance in vivo. The identification of new markers of leukaemia and the use of increasingly sophisticated technologies for detection of rare cells should further facilitate routine monitoring of MRD and elucidate the features of drug-resistant leukaemic cells.
Collapse
Affiliation(s)
- Dario Campana
- Department of Oncology, St. Jude Children's Research Hospital, and Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38105, USA.
| |
Collapse
|
32
|
Flohr T, Schrauder A, Cazzaniga G, Panzer-Grümayer R, van der Velden V, Fischer S, Stanulla M, Basso G, Niggli FK, Schäfer BW, Sutton R, Koehler R, Zimmermann M, Valsecchi MG, Gadner H, Masera G, Schrappe M, van Dongen JJM, Biondi A, Bartram CR. Minimal residual disease-directed risk stratification using real-time quantitative PCR analysis of immunoglobulin and T-cell receptor gene rearrangements in the international multicenter trial AIEOP-BFM ALL 2000 for childhood acute lymphoblastic leukemia. Leukemia 2008; 22:771-82. [PMID: 18239620 DOI: 10.1038/leu.2008.5] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Detection of minimal residual disease (MRD) is the most sensitive method to evaluate treatment response and one of the strongest predictors of outcome in childhood acute lymphoblastic leukemia (ALL). The 10-year update on the I-BFM-SG MRD study 91 demonstrates stable results (event-free survival), that is, standard risk group (MRD-SR) 93%, intermediate risk group (MRD-IR) 74%, and high risk group (MRD-HR) 16%. In multicenter trial AIEOP-BFM ALL 2000, patients were stratified by MRD detection using quantitative PCR after induction (TP1) and consolidation treatment (TP2). From 1 July 2000 to 31 October 2004, PCR target identification was performed in 3341 patients: 2365 (71%) patients had two or more sensitive targets (< or =10(-4)), 671 (20%) patients revealed only one sensitive target, 217 (6%) patients had targets with lower sensitivity, and 88 (3%) patients had no targets. MRD-based risk group assignment was feasible in 2594 (78%) patients: 40% were classified as MRD-SR (two sensitive targets, MRD negativity at both time points), 8% as MRD-HR (MRD > or =10(-3) at TP2), and 52% as MRD-IR. The remaining 823 patients were stratified according to clinical risk features: HR (n=108) and IR (n=715). In conclusion, MRD-PCR-based stratification using stringent criteria is feasible in almost 80% of patients in an international multicenter trial.
Collapse
Affiliation(s)
- T Flohr
- Department of Pediatrics, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Jansen MWJC, Corral L, van der Velden VHJ, Panzer-Grümayer R, Schrappe M, Schrauder A, Marschalek R, Meyer C, den Boer ML, Hop WJC, Valsecchi MG, Basso G, Biondi A, Pieters R, van Dongen JJM. Immunobiological diversity in infant acute lymphoblastic leukemia is related to the occurrence and type of MLL gene rearrangement. Leukemia 2007; 21:633-41. [PMID: 17268512 DOI: 10.1038/sj.leu.2404578] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The aim of this study was to identify immunobiological subgroups in 133 infant acute lymphoblastic leukemia (ALL) cases as assessed by their immunophenotype, immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangement pattern, and the presence of mixed lineage leukemia (MLL) rearrangements. About 70% of cases showed the pro-B-ALL immunophenotype, whereas the remaining cases were common ALL and pre-B-ALL. MLL translocations were found in 79% of infants, involving MLL-AF4 (41%), MLL-ENL (18%), MLL-AF9 (11%) or another MLL partner gene (10%). Detailed analysis of Ig/TCR rearrangement patterns revealed IGH, IGK and IGL rearrangements in 91, 21 and 13% of infants, respectively. Cross-lineage TCRD, TCRG and TCRB rearrangements were found in 46, 17 and 10% of cases, respectively. As compared to childhood precursor-B-ALL, Ig/TCR rearrangements in infant ALL were less frequent and more oligoclonal. MLL-AF4 and MLL-ENL-positive infants demonstrated immature rearrangements, whereas in MLL-AF9-positive leukemias more mature rearrangements predominated. The immature Ig/TCR pattern in infant ALL correlated with young age at diagnosis, CD10 negativity and predominantly with the presence and the type of MLL translocation. The high frequency of immature and oligoclonal Ig/TCR rearrangements is probably caused by early (prenatal) oncogenic transformation in immature B-lineage progenitor cells with germline Ig/TCR genes combined with a short latency period.
Collapse
Affiliation(s)
- M W J C Jansen
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Evans PAS, Pott C, Groenen PJTA, Salles G, Davi F, Berger F, Garcia JF, van Krieken JHJM, Pals S, Kluin P, Schuuring E, Spaargaren M, Boone E, González D, Martinez B, Villuendas R, Gameiro P, Diss TC, Mills K, Morgan GJ, Carter GI, Milner BJ, Pearson D, Hummel M, Jung W, Ott M, Canioni D, Beldjord K, Bastard C, Delfau-Larue MH, van Dongen JJM, Molina TJ, Cabeçadas J. Significantly improved PCR-based clonality testing in B-cell malignancies by use of multiple immunoglobulin gene targets. Report of the BIOMED-2 Concerted Action BHM4-CT98-3936. Leukemia 2006; 21:207-14. [PMID: 17170731 DOI: 10.1038/sj.leu.2404479] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polymerase chain reaction (PCR) assessment of clonal immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements is an important diagnostic tool in mature B-cell neoplasms. However, lack of standardized PCR protocols resulting in a high level of false negativity has hampered comparability of data in previous clonality studies. In order to address these problems, 22 European laboratories investigated the Ig/TCR rearrangement patterns as well as t(14;18) and t(11;14) translocations of 369 B-cell malignancies belonging to five WHO-defined entities using the standardized BIOMED-2 multiplex PCR tubes accompanied by international pathology panel review. B-cell clonality was detected by combined use of the IGH and IGK multiplex PCR assays in all 260 definitive cases of B-cell chronic lymphocytic leukemia (n=56), mantle cell lymphoma (n=54), marginal zone lymphoma (n=41) and follicular lymphoma (n=109). Two of 109 cases of diffuse large B-cell lymphoma showed no detectable clonal marker. The use of these techniques to assign cell lineage should be treated with caution as additional clonal TCR gene rearrangements were frequently detected in all disease categories. Our study indicates that the BIOMED-2 multiplex PCR assays provide a powerful strategy for clonality assessment in B-cell malignancies resulting in high Ig clonality detection rates particularly when IGH and IGK strategies are combined.
Collapse
MESH Headings
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 18
- Gene Rearrangement
- Genes, Immunoglobulin
- Genotype
- Humans
- Immunoglobulin Heavy Chains/genetics
- Leukemia, B-Cell/diagnosis
- Leukemia, B-Cell/genetics
- Leukemia, B-Cell/immunology
- Lymphoma, B-Cell/diagnosis
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Polymerase Chain Reaction/methods
- Receptors, Antigen, T-Cell/genetics
- Translocation, Genetic
Collapse
Affiliation(s)
- P A S Evans
- Haematological Malignancy Diagnostic Service, The General Infirmary at Leeds, Leeds, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Brüggemann M, White H, Gaulard P, Garcia-Sanz R, Gameiro P, Oeschger S, Jasani B, Ott M, Delsol G, Orfao A, Tiemann M, Herbst H, Langerak AW, Spaargaren M, Moreau E, Groenen PJTA, Sambade C, Foroni L, Carter GI, Hummel M, Bastard C, Davi F, Delfau-Larue MH, Kneba M, van Dongen JJM, Beldjord K, Molina TJ. Powerful strategy for polymerase chain reaction-based clonality assessment in T-cell malignancies Report of the BIOMED-2 Concerted Action BHM4 CT98-3936. Leukemia 2006; 21:215-21. [PMID: 17170730 DOI: 10.1038/sj.leu.2404481] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Polymerase chain reaction (PCR) assessment of clonal T-cell receptor (TCR) and immunoglobulin (Ig) gene rearrangements is an important diagnostic tool in mature T-cell neoplasms. However, lack of standardized primers and PCR protocols has hampered comparability of data in previous clonality studies. To obtain reference values for Ig/TCR rearrangement patterns, 19 European laboratories investigated 188 T-cell malignancies belonging to five World Health Organization-defined entities. The TCR/Ig spectrum of each sample was analyzed in duplicate in two different laboratories using the standardized BIOMED-2 PCR multiplex tubes accompanied by international pathology panel review. TCR clonality was detected in 99% (143/145) of all definite cases of T-cell prolymphocytic leukemia, T-cell large granular lymphocytic leukemia, peripheral T-cell lymphoma (unspecified) and angioimmunoblastic T-cell lymphoma (AILT), whereas nine of 43 anaplastic large cell lymphomas did not show clonal TCR rearrangements. Combined use of TCRB and TCRG genes revealed two or more clonal signals in 95% of all TCR clonal cases. Ig clonality was mostly restricted to AILT. Our study indicates that the BIOMED-2 multiplex PCR tubes provide a powerful strategy for clonality assessment in T-cell malignancies assisting the firm diagnosis of T-cell neoplasms. The detected TCR gene rearrangements can also be used as PCR targets for monitoring of minimal residual disease.
Collapse
MESH Headings
- Gene Amplification
- Gene Rearrangement
- Genes, Immunoglobulin
- Genotype
- Humans
- Immunohistochemistry
- Leukemia, Prolymphocytic/genetics
- Leukemia, Prolymphocytic/immunology
- Leukemia, Prolymphocytic/pathology
- Leukemia, T-Cell/genetics
- Leukemia, T-Cell/immunology
- Leukemia, T-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/immunology
- Lymphoma, T-Cell/pathology
- Polymerase Chain Reaction/methods
- Receptors, Antigen, T-Cell/genetics
- T-Lymphocytes/immunology
Collapse
Affiliation(s)
- M Brüggemann
- Medical Clinic II, University of Kiel, Kiel, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Raff T, Gökbuget N, Lüschen S, Reutzel R, Ritgen M, Irmer S, Böttcher S, Horst HA, Kneba M, Hoelzer D, Brüggemann M. Molecular relapse in adult standard-risk ALL patients detected by prospective MRD monitoring during and after maintenance treatment: data from the GMALL 06/99 and 07/03 trials. Blood 2006; 109:910-5. [PMID: 17023577 DOI: 10.1182/blood-2006-07-037093] [Citation(s) in RCA: 201] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Although levels of minimal residual disease (MRD) decrease below the detection limit in most adult patients with standard-risk acute lymphoblastic leukemia (ALL) after consolidation treatment, about 30% of these patients will ultimately relapse. To evaluate the power of MRD monitoring as an indicator of impending relapse, we prospectively analyzed postconsolidation samples of 105 patients enrolled in the German Multicenter ALL (GMALL) trial by real-time quantitative polymerase chain reaction (PCR) of clonal immune gene rearrangements. All patients were in hematologic remission, had completed first-year polychemotherapy, and tested MRD negative prior to study entry. Twenty-eight of 105 patients (27%) converted to MRD positivity thereafter, and 17 of 28 (61%) relapsed so far. Median time from molecular (MRD-positive) to clinical relapse was 9.5 months. In 15 of these patients, MRD within the quantitative range of PCR was measured in hematologic remission, and 13 of these patients (89%) relapsed after a median interval of 4.1 months. Of the 77 continuously MRD-negative patients, only 5 (6%) have relapsed. We conclude that conversion to MRD positivity during the early postconsolidation phase in adult standard-risk ALL patients is highly predictive of subsequent hematologic relapse. As a result of the study, as of spring 2006, salvage treatment in the ongoing GMALL trial is intended to be started at the time of recurrence of quantifiable MRD.
Collapse
Affiliation(s)
- Thorsten Raff
- Second Medical Department, University Schleswig-Holstein, Campus Kiel, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Jabeen R, Payne D, Wiktorowicz J, Mohammad A, Petersen J. Capillary electrophoresis and the clinical laboratory. Electrophoresis 2006; 27:2413-38. [PMID: 16718719 DOI: 10.1002/elps.200500948] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Over the past 15 years, CE as an analytical tool has shown great promise in replacing many conventional clinical laboratory methods, such as electrophoresis and HPLC. CE's appeal was that it was fast, used very small amounts of sample and reagents, was extremely versatile, and was able to separate large and small analytes, whether neutral or charged. Because of this versatility, numerous methods have been developed for analytes that are of clinical interest. Other than molecular diagnostic and forensic laboratories CE has not been able to make a major impact in the United States. In contrast, in Europe and Japan an increasing number of clinical laboratories are using CE. Now that automated multicapillary instruments are commercially available along with cost-effective test kits, CE may yet be accepted as an instrument that will be routinely used in the clinical laboratories. This review will focus on areas where CE has the potential to have the greatest impact on the clinical laboratory. These include analyses of proteins found in serum and urine, hemoglobin (A1c and variants), carbohydrate-deficient transferrin, forensic and therapeutic drug screening, and molecular diagnostics.
Collapse
Affiliation(s)
- Rukhsana Jabeen
- University of Texas Medical Branch--Pathology, Galveston, TX 77555-0551, USA
| | | | | | | | | |
Collapse
|
38
|
Dawidowska M, Derwich K, Szczepański T, Jółkowska J, van der Velden VHJ, Wachowiak J, Witt M. Pattern of immunoglobulin and T-cell receptor (Ig/TCR) gene rearrangements in Polish pediatric acute lymphoblastic leukemia patients—implications for RQ-PCR-based assessment of minimal residual disease. Leuk Res 2006; 30:1119-25. [PMID: 16476479 DOI: 10.1016/j.leukres.2006.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Revised: 12/30/2005] [Accepted: 01/02/2006] [Indexed: 11/20/2022]
Abstract
We studied 23 Polish children with precursor-B-ALL, using PCR-heteroduplex analysis and DNA sequencing, to determine the availability of Ig/TCR gene rearrangements as patient-specific MRD-RQ-PCR targets. We found IGH, IGK-Kde, incomplete TCRD, Vdelta2-Jalpha, TCRG and TCRB rearrangements in 83%, 39%, 61%, 35%, 61% and 13% of patients, respectively. Comparison of Ig/TCR gene rearrangements pattern (frequency and characteristics of rearrangements) in Polish patients with those reported for patients of other European nationalities did not show major differences. These results are the first promising step for further development of MRD study in Polish patients according to current diagnostic standards.
Collapse
Affiliation(s)
- Małgorzata Dawidowska
- Institute of Human Genetics, Polish Academy of Sciences, Department of Molecular and Clinical Genetics, Strzeszyńska 32, 60 479 Poznań, Poland.
| | | | | | | | | | | | | |
Collapse
|
39
|
Panzer-Grümayer ER, Cazzaniga G, van der Velden VHJ, del Giudice L, Peham M, Mann G, Eckert C, Schrauder A, Germano G, Harbott J, Basso G, Biondi A, van Dongen JJM, Gadner H, Haas OA. Immunogenotype changes prevail in relapses of young children with TEL-AML1-positive acute lymphoblastic leukemia and derive mainly from clonal selection. Clin Cancer Res 2006; 11:7720-7. [PMID: 16278392 DOI: 10.1158/1078-0432.ccr-05-1239] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Variations of the immunogenotype and TEL deletions in children with TEL-AML1+ acute lymphoblastic leukemia support the hypothesis that relapses derive from a persistent TEL-AML1+ preleukemic/leukemic clone rather than a resistant leukemia. We aimed at elucidating the relationship between the immunogenotype patterns at diagnosis and relapse as well as their clinical and biological relevance. PATIENTS AND METHODS Immunoglobulin and T-cell receptor gene rearrangements were analyzed in 41 children with a TEL-AML1+ acute lymphoblastic leukemia and an early (up to 30 months after diagnosis; n = 12) or late (at 30 months or later; n = 29) disease recurrence by a standardized PCR approach. RESULTS In 68% of the patients (group I), we identified differences in the immunogenotype patterns, whereas no changes were observed in the remaining 32% (group II). The divergence resulted more often from clonal selection than clonal evolution and consisted predominantly of losses (0-6, median 5) and/or gains (0-4, median 1) of rearrangements. The frequency and number of clonal immunoglobulin/T-cell receptor rearrangements in group I was higher at diagnosis (2-13, median 5) than at relapse (2-7, median 4), whereas it was the lowest in group II (1-5, median 3). Although group I children were younger at diagnosis, there was no correlation between particular immunogenotype patterns and remission duration. CONCLUSION These findings imply that the clonal heterogeneity in younger children most likely reflects an ongoing high recombinatorial activity in the preleukemic/leukemic cells, whereas the more uniform repertoire observed in older children mirrors end-stage rearrangement patterns of selected cell clones that evolved during the prolonged latency period.
Collapse
|
40
|
Baak JPA, Janssen EAM, Soreide K, Heikkilae R. Genomics and proteomics—the way forward. Ann Oncol 2005; 16 Suppl 2:ii30-44. [PMID: 15958472 DOI: 10.1093/annonc/mdi728] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- J P A Baak
- Department of Pathology, Stavanger University Hospital, Stavanger, Gade Institute, University of Bergen, Norway
| | | | | | | |
Collapse
|