1
|
Chen W, Huang J, Zhao Y, Huang L, Yuan Z, Gu M, Xu X, Shi J, Luo Y, Yu J, Lai X, Liu L, Fu H, Bao C, Huang X, Zheng Z, Huang H, Hu X, Zhao Y. Measurable residual disease monitoring by ddPCR in the early posttransplant period complements the traditional MFC method to predict relapse after HSCT in AML/MDS: a multicenter retrospective study. J Transl Med 2024; 22:410. [PMID: 38689269 PMCID: PMC11061929 DOI: 10.1186/s12967-024-05114-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Droplet digital PCR (ddPCR) is widely applied to monitor measurable residual disease (MRD). However, there are limited studies on the feasibility of ddPCR-MRD monitoring after allogeneic hematopoietic stem cell transplantation (allo-HSCT), especially targeting multiple molecular markers simultaneously. METHODS Our study collected samples from patients with acute myeloid leukemia (AML) or high-risk myelodysplastic syndrome (MDS) in complete remission after allo-HSCT between January 2018 and August 2021 to evaluate whether posttransplant ddPCR-MRD monitoring can identify patients at high risk of relapse. RESULTS Of 152 patients, 58 (38.2%) were MRD positive by ddPCR within 4 months posttransplant, with a median variant allele frequency of 0.198%. The detectable DTA mutations (DNMT3A, TET2, and ASXL1 mutations) after allo-HSCT were not associated with an increased risk of relapse. After excluding DTA mutations, patients with ddPCR-MRD positivity had a significantly higher cumulative incidence of relapse (CIR, 38.7% vs. 9.7%, P < 0.001) and lower rates of relapse-free survival (RFS, 55.5% vs. 83.7%, P < 0.001) and overall survival (OS, 60.5% vs. 90.5%, P < 0.001). In multivariate analysis, ddPCR-MRD positivity of non-DTA genes was an independent adverse predictor for CIR (hazard ratio [HR], 4.02; P < 0.001), RFS (HR, 2.92; P = 0.002) and OS (HR, 3.12; P = 0.007). Moreover, the combination of ddPCR with multiparameter flow cytometry (MFC) can further accurately identify patients at high risk of relapse (F+/M+, HR, 22.44; P < 0.001, F+/M-, HR, 12.46; P < 0.001 and F-/M+, HR, 4.51; P = 0.003). CONCLUSION ddPCR-MRD is a feasible approach to predict relapse after allo-HSCT in AML/MDS patients with non-DTA genes and is more accurate when combined with MFC. TRIAL REGISTRATION ClinicalTrials.gov identifier: NCT06000306. Registered 17 August 2023 -Retrospectively registered ( https://clinicaltrials.gov/study/NCT06000306?term=NCT06000306&rank=1 ).
Collapse
Affiliation(s)
- Weihao Chen
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
| | - Jingtao Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, No.197 Ruijiner Road, Shanghai, 200025, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yeqian Zhao
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Luo Huang
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zhiyang Yuan
- Shanghai Dishuo Beken Biotechnology Co., Ltd, Shanghai, China
| | - Miner Gu
- Division of Hematology-Oncology, Children's Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaojun Xu
- Division of Hematology-Oncology, Children's Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jimin Shi
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Yi Luo
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Jian Yu
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Xiaoyu Lai
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Lizhen Liu
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Huarui Fu
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Chenhui Bao
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | - Xin Huang
- Zhejiang Province Key Laboratory of Hematology Oncology Diagnosis and Treatment, Hangzhou, China
| | | | - He Huang
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China.
- Institute of Hematology, Zhejiang University, Hangzhou, China.
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
| | - Xiaoxia Hu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, No.197 Ruijiner Road, Shanghai, 200025, China.
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yanmin Zhao
- Bone Marrow Transplantation Center of The First Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, No.79 Qingchun Road, Hangzhou, China.
- Institute of Hematology, Zhejiang University, Hangzhou, China.
- Zhejiang Province Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
| |
Collapse
|
2
|
Ip BBK, Wong ATC, Law JHY, Au CH, Ma SY, Chim JCS, Liang RHS, Leung AYH, Wan TSK, Ma ESK. Application of droplet digital PCR in minimal residual disease monitoring of rare fusion transcripts and mutations in haematological malignancies. Sci Rep 2024; 14:6400. [PMID: 38493200 PMCID: PMC10944481 DOI: 10.1038/s41598-024-57016-y] [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: 12/13/2023] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
Leukaemia of various subtypes are driven by distinct chromosomal rearrangement or genetic abnormalities. The leukaemogenic fusion transcripts or genetic mutations serve as molecular markers for minimal residual disease (MRD) monitoring. The current study evaluated the applicability of several droplet digital PCR assays for the detection of these targets at RNA and DNA levels (atypical BCR::ABL1 e19a2, e23a2ins52, e13a2ins74, rare types of CBFB::MYH11 (G and I), PCM1::JAK2, KMT2A::ELL2, PICALM::MLLT10 fusion transcripts and CEBPA frame-shift and insertion/duplication mutations) with high sensitivity. The analytical performances were assessed by the limit of blanks, limit of detection, limit of quantification and linear regression. Our data demonstrated serial MRD monitoring for patients at molecular level could become "digitalized", which was deemed important to guide clinicians in treatment decision for better patient care.
Collapse
Affiliation(s)
- Beca B K Ip
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Anthony T C Wong
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Janet Hei Yin Law
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Chun Hang Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Shing Yan Ma
- Specialist in Haematology & Haematological Oncology, Causeway Bay, Hong Kong
| | - James C S Chim
- Department of Medicine and Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Raymond H S Liang
- Department of Medicine and Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Anskar Y H Leung
- Department of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Thomas S K Wan
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong
| | - Edmond S K Ma
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium & Hospital, Happy Valley, Hong Kong.
| |
Collapse
|
3
|
Chea M, Rigolot L, Canali A, Vergez F. Minimal Residual Disease in Acute Myeloid Leukemia: Old and New Concepts. Int J Mol Sci 2024; 25:2150. [PMID: 38396825 PMCID: PMC10889505 DOI: 10.3390/ijms25042150] [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: 12/31/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Minimal residual disease (MRD) is of major importance in onco-hematology, particularly in acute myeloid leukemia (AML). MRD measures the amount of leukemia cells remaining in a patient after treatment, and is an essential tool for disease monitoring, relapse prognosis, and guiding treatment decisions. Patients with a negative MRD tend to have superior disease-free and overall survival rates. Considerable effort has been made to standardize MRD practices. A variety of techniques, including flow cytometry and molecular methods, are used to assess MRD, each with distinct strengths and weaknesses. MRD is recognized not only as a predictive biomarker, but also as a prognostic tool and marker of treatment efficacy. Expected advances in MRD assessment encompass molecular techniques such as NGS and digital PCR, as well as optimization strategies such as unsupervised flow cytometry analysis and leukemic stem cell monitoring. At present, there is no perfect method for measuring MRD, and significant advances are expected in the future to fully integrate MRD assessment into the management of AML patients.
Collapse
Affiliation(s)
- Mathias Chea
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
| | - Lucie Rigolot
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Alban Canali
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Francois Vergez
- Laboratoire d’Hématologie Biologique, Institut Universitaire du Cancer de Toulouse Oncopole, Centre Hospitalier Universitaire de Toulouse, 31059 Toulouse, France; (M.C.); (L.R.); (A.C.)
- School of Medicine, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| |
Collapse
|
4
|
Kovach AE, Wood BL. Updates on lymphoblastic leukemia/lymphoma classification and minimal/measurable residual disease analysis. Semin Diagn Pathol 2023; 40:457-471. [PMID: 37953192 DOI: 10.1053/j.semdp.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Lymphoblastic leukemia/lymphoma (ALL/LBL), especially certain subtypes, continues to confer morbidity and mortality despite significant therapeutic advances. The pathologic classification of ALL/LBL, especially that of B-ALL, has recently substantially expanded with the identification of several distinct and prognostically important genetic drivers. These discoveries are reflected in both current classification systems, the World Health Organization (WHO) 5th edition and the new International Consensus Classification (ICC). In this article, novel subtypes of B-ALL are reviewed, including DUX4, MEF2D and ZNF384-rearranged B-ALL; the rare pediatric entity B-ALL with TLF3::HLF, now added to the classifications, is discussed; updates to the category of B-ALL with BCR::ABL1-like features (Ph-like B-ALL) are summarized; and emerging genetic subtypes of T-ALL are presented. The second half of the article details current approaches to minimal/measurable residual disease (MRD) detection in B-ALL and T-ALL and presents anticipated challenges to current approaches in the burgeoning era of antigen-directed immunotherapy.
Collapse
Affiliation(s)
- Alexandra E Kovach
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
| | - Brent L Wood
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
5
|
Teixeira A, Carreira L, Abalde-Cela S, Sampaio-Marques B, Areias AC, Ludovico P, Diéguez L. Current and Emerging Techniques for Diagnosis and MRD Detection in AML: A Comprehensive Narrative Review. Cancers (Basel) 2023; 15:cancers15051362. [PMID: 36900154 PMCID: PMC10000116 DOI: 10.3390/cancers15051362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/06/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Acute myeloid leukemia (AML) comprises a group of hematologic neoplasms characterized by abnormal differentiation and proliferation of myeloid progenitor cells. AML is associated with poor outcome due to the lack of efficient therapies and early diagnostic tools. The current gold standard diagnostic tools are based on bone marrow biopsy. These biopsies, apart from being very invasive, painful, and costly, have low sensitivity. Despite the progress uncovering the molecular pathogenesis of AML, the development of novel detection strategies is still poorly explored. This is particularly important for patients that check the criteria for complete remission after treatment, since they can relapse through the persistence of some leukemic stem cells. This condition, recently named as measurable residual disease (MRD), has severe consequences for disease progression. Hence, an early and accurate diagnosis of MRD would allow an appropriate therapy to be tailored, improving a patient's prognosis. Many novel techniques with high potential in disease prevention and early detection are being explored. Among them, microfluidics has flourished in recent years due to its ability at processing complex samples as well as its demonstrated capacity to isolate rare cells from biological fluids. In parallel, surface-enhanced Raman scattering (SERS) spectroscopy has shown outstanding sensitivity and capability for multiplex quantitative detection of disease biomarkers. Together, these technologies can allow early and cost-effective disease detection as well as contribute to monitoring the efficiency of treatments. In this review, we aim to provide a comprehensive overview of AML disease, the conventional techniques currently used for its diagnosis, classification (recently updated in September 2022), and treatment selection, and we also aim to present how novel technologies can be applied to improve the detection and monitoring of MRD.
Collapse
Affiliation(s)
- Alexandra Teixeira
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Luís Carreira
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Sara Abalde-Cela
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Anabela C. Areias
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s–PT Government Associate Laboratory, 4710-057 Braga, Portugal
- Correspondence: (P.L.); (L.D.)
| | - Lorena Diéguez
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
- Correspondence: (P.L.); (L.D.)
| |
Collapse
|
6
|
Luib L, Kreyenberg H, Michaelis S, Handgretinger R, Mezger M. Transferring measurable residual disease measurement in pediatric acute lymphoblastic leukemia from quantitative real-time PCR to digital droplet PCR. Pediatr Transplant 2023; 27:e14483. [PMID: 36750990 DOI: 10.1111/petr.14483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/02/2023] [Accepted: 01/23/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND Since the measurement of measurable residual disease (MRD) is part of clinical routine examination for children affected with acute lymphoblastic leukemia (ALL), continuous efforts are made to improve its method, applicability and accuracy. Whereas quantitative real-time polymerase chain reaction (qPCR) is considered as the gold standard for MRD detection and endowed with international guidelines for implementation and evaluation, these do not yet exist for digital droplet PCR (ddPCR). However, advantages are seen in droplet partitioning for MRD measurement to allow absolute quantification without depending on reference samples. METHODS In this study, 17 MRD targets of nine patients with childhood B-ALL were analyzed with qPCR and ddPCR, respectively. All patients were assigned to high risk group and had hematopoietic stem cell transplantation and CD19 antibody therapy for relapse prevention. Starting with the sequences and guidelines of qPCR and optimizing the protocol for ddPCR, the MRD targets could also be measured precisely with this novel method, using the same primer and probe sets as for qPCR. RESULTS The already established MRD protocol of qPCR could be transferred to ddPCR and all 17 MRD targets were measured in dilution series reaching comparable Limit of detection levels with both PCR methods. CONCLUSIONS With a given qPCR protocol and some experience in conventional MRD monitoring, it is conceivable to transfer the procedure of MRD measurement to ddPCR technology. Our data is in line with other studies which are summarized and discussed here as well to facilitate the transfer of MRD diagnostics to ddPCR.
Collapse
Affiliation(s)
- Luise Luib
- Department of General Paediatrics, Haematology/Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Hermann Kreyenberg
- Clinic for Children and Adolescents, Department for Stem Cell Transplantation and Immunology, University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Sebastian Michaelis
- Department of General Paediatrics, Haematology/Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Rupert Handgretinger
- Department of General Paediatrics, Haematology/Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Markus Mezger
- Department of General Paediatrics, Haematology/Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| |
Collapse
|
7
|
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: 0] [Impact Index Per Article: 0] [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
|
8
|
Lu Y, Li Z, Lim EH, Huan PT, Kham SKY, Yeoh AEJ. Digital PCR for Minimal Residual Disease Quantitation Using Immunoglobulin/T-Cell Receptor Gene Rearrangements in Acute Lymphoblastic Leukemia: A Proposed Analytic Algorithm. J Mol Diagn 2022; 24:655-665. [PMID: 35390515 DOI: 10.1016/j.jmoldx.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/11/2022] [Accepted: 03/04/2022] [Indexed: 10/18/2022] Open
Abstract
In minimal residual disease (MRD), where there are exceedingly low target copy numbers, digital PCR (dPCR) can improve MRD quantitation. However, standards for dPCR MRD interpretation in acute lymphoblastic leukemia are lacking. Here, for immunoglobulin/T-cell receptor-based MRD, we propose an objective, statistics-based analytic algorithm. In 161 postinduction samples from 79 children with acute lymphoblastic leukemia, MRD was performed by dPCR and real-time quantitative PCR (qPCR) using the same markers and primer-probe sets. The dPCR raw data were analyzed by using an automated algorithm. dPCR and qPCR results were highly concordant (P < 0.0001): 98% (50 of 51) of qPCR positive were positive by dPCR, whereas 95% (61 of 64) of qPCR negative results were also negative by dPCR. For MRD quantitation, both qPCR and dPCR were tightly correlated (R2 = 0.94). Using more DNA (1 μg × 7 versus 630 ng × 3), dPCR improved sensitivity of MRD quantitation by one log10 (median MRD positive cutoff 1.6 × 10-5). With dPCR, 83% (29 of 35) of positive-not-quantifiable results by qPCR could be assigned positive/negative MRD status. Seven replicates of tested samples and negative controls were optimal. Compared with qPCR, dPCR could improve MRD sensitivity by one log10. We proposed an automatable, statistics-based algorithm that minimized interoperator variance for dPCR MRD.
Collapse
Affiliation(s)
- Yi Lu
- VIVA-NUS Centre for Translational Research in Acute Leukemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zhenhua Li
- VIVA-NUS Centre for Translational Research in Acute Leukemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Evelyn Huizi Lim
- VIVA-NUS Centre for Translational Research in Acute Leukemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pei Tee Huan
- VIVA-NUS Centre for Translational Research in Acute Leukemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shirley Kow Yin Kham
- VIVA-NUS Centre for Translational Research in Acute Leukemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Allen Eng-Juh Yeoh
- VIVA-NUS Centre for Translational Research in Acute Leukemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; VIVA-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| |
Collapse
|
9
|
Shelton DN, Bhagavatula P, Sepulveda N, Beppu L, Gandhi S, Qin D, Hauenstein S, Radich J. Performance characteristics of the first Food and Drug Administration (FDA)-cleared digital droplet PCR (ddPCR) assay for BCR::ABL1 monitoring in chronic myelogenous leukemia. PLoS One 2022; 17:e0265278. [PMID: 35298544 PMCID: PMC8929598 DOI: 10.1371/journal.pone.0265278] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/27/2022] [Indexed: 11/19/2022] Open
Abstract
Chronic myelogenous leukemia (CML) is a hematopoietic stem cell malignancy that accounts for 15-20% of all cases of leukemia. CML is caused by a translocation between chromosomes 9 and 22 which creates an abnormal fusion gene, BCR::ABL1. The amount of BCR::ABL1 transcript RNA is a marker of disease progression and the effectiveness of tyrosine kinase inhibitor (TKI) treatment. This study determined the analytical and clinical performance of a droplet digital PCR based assay (QXDx BCR-ABL %IS Kit; Bio-Rad) for BCR::ABL1 quantification. The test has a limit of detection of MR4.7 (0.002%) and a linear range of MR0.3-4.7 (50-0.002%IS). Reproducibility of results across multiple sites, days, instruments, and users was evaluated using panels made from BCR::ABL1 positive patient samples. Clinical performance of the assay was evaluated on patient samples and compared to an existing FDA-cleared test. The reproducibility study noted negligible contributions to variance from site, instrument, day, and user for samples spanning from MR 0.7-4.2. The assay demonstrated excellent clinical correlation with the comparator test using a Deming regression with a Pearson R of 0.99, slope of 1.037 and intercept of 0.1084. This data establishes that the QXDx™ BCR-ABL %IS Kit is an accurate, precise, and sensitive system for the diagnosis and monitoring of CML.
Collapse
MESH Headings
- Fusion Proteins, bcr-abl/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Polymerase Chain Reaction/methods
- Protein Kinase Inhibitors/therapeutic use
- Reproducibility of Results
- United States
- United States Food and Drug Administration
Collapse
Affiliation(s)
- Dawne N. Shelton
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Prasanthi Bhagavatula
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Nathan Sepulveda
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Lan Beppu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Shital Gandhi
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Dahui Qin
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Scott Hauenstein
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Jerald Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| |
Collapse
|
10
|
Lobo J, van Zogchel LMJ, Nuru MG, Gillis AJM, van der Schoot CE, Tytgat GAM, Looijenga LHJ. Combining Hypermethylated RASSF1A Detection Using ddPCR with miR-371a-3p Testing: An Improved Panel of Liquid Biopsy Biomarkers for Testicular Germ Cell Tumor Patients. Cancers (Basel) 2021; 13:5228. [PMID: 34680375 PMCID: PMC8534014 DOI: 10.3390/cancers13205228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 10/13/2021] [Indexed: 12/22/2022] Open
Abstract
The classical serum tumor markers used routinely in the management of testicular germ cell tumor (TGCT) patients-alpha fetoprotein (AFP) and human chorionic gonadotropin (HCG)-show important limitations. miR-371a-3p is the most recent promising biomarker for TGCTs, but it is not sufficiently informative for detection of teratoma, which is therapeutically relevant. We aimed to test the feasibility of hypermethylated RASSF1A (RASSF1AM) detected in circulating cell-free DNA as a non-invasive diagnostic marker of testicular germ cell tumors, combined with miR-371a-3p. A total of 109 serum samples of patients and 29 sera of healthy young adult males were included, along with representative cell lines and tumor tissue samples. We describe a novel droplet digital polymerase chain reaction (ddPCR) method for quantitatively assessing RASSF1AM in liquid biopsies. Both miR-371a-3p (sensitivity = 85.7%) and RASSF1AM (sensitivity = 86.7%) outperformed the combination of AFP and HCG (sensitivity = 65.5%) for TGCT diagnosis. RASSF1AM detected 88% of teratomas. In this representative cohort, 14 cases were negative for miR-371a-3p, all of which were detected by RASSF1AM, resulting in a combined sensitivity of 100%. We have described a highly sensitive and specific panel of biomarkers for TGCT patients, to be validated in the context of patient follow-up and detection of minimal residual disease.
Collapse
Affiliation(s)
- João Lobo
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS—School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Lieke M. J. van Zogchel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
- Department of Experimental Immunohematology, Sanquin Research Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands; (M.G.N.); (C.E.v.d.S.)
| | - Mohammed G. Nuru
- Department of Experimental Immunohematology, Sanquin Research Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands; (M.G.N.); (C.E.v.d.S.)
| | - Ad J. M. Gillis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
| | - C. Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands; (M.G.N.); (C.E.v.d.S.)
| | - Godelieve A. M. Tytgat
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
| | - Leendert H. J. Looijenga
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
- Lab. for Exp. Patho-Oncology (LEPO), Department of Pathology, Erasmus MC-University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| |
Collapse
|
11
|
Abstract
The detection of gene rearrangements in pediatric leukemia is an essential component of the work-up, with implications for accurate diagnosis, proper risk stratification, and therapeutic decisions, including the use of targeted therapies. The traditional methods of karyotype and fluorescence in situ hybridization are still valuable, but many new assays are also available, with different strengths and weaknesses. These assays include next-generation sequencing-based assays that have the potential for highly multiplexed and/or unbiased detection of rearrangements.
Collapse
Affiliation(s)
- Marian H Harris
- Department of Pathology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA.
| |
Collapse
|
12
|
Bai Y, Chen C, Guo X, Ding T, Yang X, Yu J, Yang J, Ruan J, Zheng X, Chen Z. miR-638 in circulating leukaemia cells as a non-invasive biomarker in diagnosis, treatment response and MRD surveillance of acute promyelocytic leukaemia. Cancer Biomark 2021; 29:125-137. [PMID: 32568176 DOI: 10.3233/cbm-190899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND MicroRNA (miRNA) expression has been implicated in leukaemia. In recent years, miRNAs have been under investigation for their potential as non-invasive biomarkers in acute promyelocytic leukaemia (APL). We investigated whether miR-638 in circulating leukaemia cells is a non-invasive biomarker in diagnosis, assessment of the treatment response and minimal residual disease (MRD) surveillance of APL. METHODS Sixty cases of acute myeloid leukaemia (AML), including 30 cases of APL and 30 cases of non-APL AML, were selected. Thirty healthy controls were also selected. Bone marrow (BM) and peripheral blood (PB) samples were collected from APL patients at diagnosis and post-induction. Microarray analysis and quantitative real-time PCR (qRT-PCR) were performed for miRNA profiling and miR-638 expression analysis, respectively. For statistical analysis, Mann-Whitney U test, Wilcoxon Signed Rank test, receiver operating characteristic (ROC) curve analysis and Spearman's rho correlation test were used. RESULTS Both microarray and qRT-PCR data showed that miR-638 was significantly upregulated in BM after APL patients received induction therapy. Moreover, miR-638, which is specifically downregulated in APL cell lines, was upregulated after all-trans retinoic acid (ATRA)-induced myeloid differentiation. Receiver operating characteristic (ROC) curve analyses revealed that miR-638 could serve as a valuable biomarker for differentiating APL from controls or non-APL AML. Furthermore, miR-638 expression was sharply increased after induction therapy and complete remission (CR). An inverse correlation was observed between miR-638 and PML-RARα transcripts levels in BM samples, while a positive correlation was revealed between PB miR-638 and BM miR-638 levels in APL patients after induction therapy. CONCLUSIONS Our study suggested that miR-638 may serve as a potential APL biomarker for diagnosis and assessment of the response to targeted therapy, and PB miR-638 could be used for non-invasive MRD surveillance in APL.
Collapse
Affiliation(s)
- Yuanyuan Bai
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Cheng Chen
- Department of Hematology, Wenzhou Key Laboratory of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoling Guo
- Center of Scientific Research, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ting Ding
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xinyun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junjun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jichen Ruan
- Department of Pediatric Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoqun Zheng
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhanguo Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| |
Collapse
|
13
|
Yang F, Anekpuritanang T, Press RD. Clinical Utility of Next-Generation Sequencing in Acute Myeloid Leukemia. Mol Diagn Ther 2021; 24:1-13. [PMID: 31848884 DOI: 10.1007/s40291-019-00443-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous disease that, even with current advancements in therapy, continues to have a poor prognosis. Recurrent somatic mutations have been identified in a core set of pathogenic genes including FLT3 (25-30% prevalence), NPM1 (25-30%), DNMT3A (25-30%), IDH1/2 (5-15%), and TET2 (5-15%), with direct diagnostic, prognostic, and targeted therapeutic implications. Advances in the understanding of the complex mechanisms of AML leukemogenesis have led to the development and recent US Food and Drug Administration (FDA) approval of several targeted therapies: midostaurin and gilteritinib targeting activated FLT3, and ivosidenib and enasidenib targeting mutated IDH1/2. Several additional drug candidates targeting other recurrently mutated gene pathways in AML are also being actively developed. Furthermore, outside of the realm of predicting responses to targeted therapies, many other mutated genes, which comprise the so-called long tail of oncogenic drivers in AML, have been shown to provide clinically useful diagnostic and prognostic information for AML patients. Many of these recurrently mutated genes have also been shown to be excellent biomarkers for post-treatment minimal residual disease (MRD) monitoring for assessing treatment response and predicting future relapse. In addition, the identification of germline mutations in a set of genes predisposing to myeloid malignancies may directly inform treatment decisions (particularly stem cell transplantation) and impact other family members. Recent advances in sequencing technology have made it practically and economically feasible to evaluate many genes simultaneously using next-generation sequencing (NGS). Mutation screening with NGS panels has been recommended by national and international professional guidelines as the standard of care for AML patients. NGS-based detection of the heterogeneous genes commonly mutated in AML has practical clinical utility for disease diagnosis, prognosis, prediction of targeted therapy response, and MRD monitoring.
Collapse
Affiliation(s)
- Fei Yang
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Tauangtham Anekpuritanang
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA.,Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Richard D Press
- Department of Pathology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, L113, Portland, OR, 97239, USA. .,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
| |
Collapse
|
14
|
Kim M, Park CJ. Minimal Residual Disease Detection in Pediatric Acute Lymphoblastic Leukemia. CLINICAL PEDIATRIC HEMATOLOGY-ONCOLOGY 2020. [DOI: 10.15264/cpho.2020.27.2.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Miyoung Kim
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Hallym University Medical Center, Hallym University College of Medicine, Anyang, Korea
| | - Chan-Jeoung Park
- Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| |
Collapse
|
15
|
Jiang XW, Chen SZ, Zhu XY, Xu XX, Liu Y. Development and validation of a droplet digital PCR assay for the evaluation of PML-RARα fusion transcripts in acute promyelocytic leukemia. Mol Cell Probes 2020; 53:101617. [PMID: 32585184 DOI: 10.1016/j.mcp.2020.101617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/25/2020] [Accepted: 06/03/2020] [Indexed: 11/11/2022]
Abstract
Acute promyelocytic leukemia (APL) is an aggressive disease that requires prompt treatment. Promyelocytic leukemia protein-retinoic acid receptor α (PML-RARα) fusion genes resulting from reciprocal translocation are considered a molecular basis for diagnosing APL. Moreover, PML-RARα fusion gene testing is an essential tool for monitoring the response to therapy via minimal residual disease and providing a diagnosis before rapid disease progression in APL. The present study developed a novel droplet digital PCR (ddPCR) assay to rapidly detect two PML-RARα variants (bcr1 and bcr3) and compared its limit of detection (LOD) with quantitative PCR (qPCR). It was demonstrated that the LOD of ddPCR for PML-RARα reached 0.001%, and the evaluation of high copy number samples of PML-RARα by ddPCR correlated well with qPCR. Furthermore, clinical sample testing with ddPCR found that 34 and 24% samples were bcr-1-positive and bcr3-positive, respectively. However, according to qPCR, 30% of the samples were bcr1-positive and 20% were bcr3-positive. In addition, the concordance rate between ddPCR and qPCR reaction was 86%. While monitoring minimal residual disease, the PML-RARα mutation rate of three patients who recovered well decreased to 0.34%. However, one patient who was bcr3-positive and relapsed had a mutation rate of 13% while in remission, indicating that the bcr3 isoform may be an adverse prognostic factor affecting recovery. Therefore, the present results suggested that this novel ddPCR assay may be useful for monitoring and evaluating the treatment effects and prognosis of APL.
Collapse
Affiliation(s)
- Xi-Wen Jiang
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China.
| | - Si-Ze Chen
- Central Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, China; The Precise Therapy Engineering Technology Research Cente of Guangdong Province for Esophageal Cancer, Guangzhou, 510080, China
| | - Xiao-Ya Zhu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
| | - Xiao-Xie Xu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
| | - Yue Liu
- DAAN Gene Co., Ltd. of Sun Yat-sen University, 19 Xiangshan Road, Science Park, High & New Technology Development District, Guangzhou, 510080, China; The Medicine and Biological Engineering Technology Research Center of the Ministry of Health, Guangzhou, 510080, China
| |
Collapse
|
16
|
Liang M, Wang L, Xiao M, Xiong J, Wang J, Wang Z, Huang W, Zhou J. Clinical significance of increased PML-RARa transcripts after induction therapy for acute promyelocytic leukaemia. Ann Med 2020; 52:233-238. [PMID: 32323584 PMCID: PMC7877940 DOI: 10.1080/07853890.2020.1753886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Objective: To analyze the clinical and biological significance of the acute promyelocytic leukemia (APL) whose PML-RARa transcripts increased after induction therapy.Methods: We analyzed 9 cases of APL whose PML-RARa transcripts increased after induction treatment and compare them with APL whose PML-RARa transcripts decreased.Results: The only factor affecting increased PML-RARa transcripts was the induction protocol. The cases of increased PML-RARa transcripts received induction treatment mainly based on ATRA and ATO. The evaluation of bone marrow aspirate cytology showed that the cell percentage from myelocyte to segmented neutrophil of the patients with increased PML-RARa transcripts was significantly higher than that of the patients with decreased PML-RARa transcripts. In the follow-up, MRD in 9 cases was consistently negative.Conclusions: Our studies showed the increased PML-RARa transcripts after induction treatment had different clinical significance from the decreased PML-RARa transcripts.
Collapse
Affiliation(s)
- Mi Liang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Lei Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jie Xiong
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jin Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Zhiqiong Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Wei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Hua Zhong University of Science and Technology, Wu Han, Hubei, China
| |
Collapse
|
17
|
Detection and management of acute myeloid leukemia measurable residual disease: is it standard of care? Curr Opin Hematol 2020; 27:81-87. [PMID: 31895104 DOI: 10.1097/moh.0000000000000566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW In the present manuscript, we will review the current approaches to investigate measurable residual disease (MRD) and its clinical applications in AML management. RECENT FINDINGS Over the last decades, several methods have been developed to trace MRD, with flow cytometry and polymerase chain reaction (PCR) being the most reliable. However, new technologies, such as digital PCR and Next-Generation Sequencing are emerging as particularly useful in AML. The 2017 European LeukemiaNet (ELN) recommendations have incorporated MRD assessment to define the response criteria to therapy, and more recently, the ELN MRD Working Party has published guidelines for the use of MRD in clinical practice. SUMMARY Morphologic complete remission (mCR) after induction therapy, has been consistently shown not only to have a critical prognostic role but also to fail in predicting relapse on an individual basis. Major attempts to improve our prediction capability have been made by measuring the residual levels of leukemic cells that persist in the bone marrow after chemotherapy. This number of cells, also called MRD, harbors in the bone marrow below the threshold of morphology and is responsible for leukemia recurrence. Therefore, the detection of MRD promises to help predict the risk of relapse, allowing a more proper patients' risk-stratification and the use of risk-tailored therapeutic strategy.
Collapse
|
18
|
Yoest JM, Shirai CL, Duncavage EJ. Sequencing-Based Measurable Residual Disease Testing in Acute Myeloid Leukemia. Front Cell Dev Biol 2020; 8:249. [PMID: 32457898 PMCID: PMC7225302 DOI: 10.3389/fcell.2020.00249] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/24/2020] [Indexed: 12/31/2022] Open
Abstract
Next generation sequencing (NGS) methods have allowed for unprecedented genomic characterization of acute myeloid leukemia (AML) over the last several years. Further advances in NGS-based methods including error correction using unique molecular identifiers (UMIs) have more recently enabled the use of NGS-based measurable residual disease (MRD) detection. This review focuses on the use of NGS-based MRD detection in AML, including basic methodologies and clinical applications.
Collapse
Affiliation(s)
- Jennifer M Yoest
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Cara Lunn Shirai
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, United States
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, United States
| |
Collapse
|
19
|
Cumbo C, Anelli L, Specchia G, Albano F. Monitoring of Minimal Residual Disease (MRD) in Chronic Myeloid Leukemia: Recent Advances. Cancer Manag Res 2020; 12:3175-3189. [PMID: 32440215 PMCID: PMC7211966 DOI: 10.2147/cmar.s232752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm caused by the BCR-ABL1 fusion gene generation as a consequence of the t(9;22)(q34;q11) rearrangement. The identification of the BCR-ABL1 transcript was of critical importance for both CML diagnosis and minimal residual disease (MRD) monitoring. In this review, we report the recent advances in the CML MRD monitoring based on RNA, DNA and protein analysis. The detection of the BCR-ABL1 transcript by the quantitative reverse-transcriptase polymerase chain reaction is the gold standard method, but other systems based on digital PCR or on GeneXpert technology have been developed. In the last years, DNA-based assays showed high sensitivity and specificity, and flow cytometric approaches for the detection of the BCR-ABL1 fusion protein have also been tested. Recently, new MRD monitoring systems based on the detection of molecular markers other than the BCR-ABL1 fusion were proposed. These approaches, such as the identification of CD26+ leukemic stem cells, microRNAs and mitochondrial DNA mutations, just remain preliminary and need to be implemented. In the precision medicine era, the constant improvement of the CML MRD monitoring practice could allow clinicians to choose the best therapeutic algorithm and a more accurate selection of CML patients eligible for the tyrosine kinase inhibitors discontinuation.
Collapse
Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| |
Collapse
|
20
|
Coccaro N, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies. Int J Mol Sci 2020; 21:ijms21093141. [PMID: 32365599 PMCID: PMC7247671 DOI: 10.3390/ijms21093141] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The digital polymerase chain reaction (dPCR) is considered to be the third-generation polymerase chain reaction (PCR), as it yields direct, absolute and precise measures of target sequences. dPCR has proven particularly useful for the accurate detection and quantification of low-abundance nucleic acids, highlighting its advantages in cancer diagnosis and in predicting recurrence and monitoring minimal residual disease, mostly coupled with next generation sequencing. In the last few years, a series of studies have employed dPCR for the analysis of hematologic malignancies. In this review, we will summarize these findings, attempting to focus on the potential future perspectives of the application of this promising technology.
Collapse
Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Correspondence: ; Tel.: +39-(0)80-5478031; Fax: +39-(0)80-5508369
| |
Collapse
|
21
|
van Zogchel LMJ, van Wezel EM, van Wijk J, Stutterheim J, Bruins WSC, Zappeij-Kannegieter L, Slager TJE, Schumacher-Kuckelkorn R, Verly IRN, van der Schoot CE, Tytgat GAM. Hypermethylated RASSF1A as Circulating Tumor DNA Marker for Disease Monitoring in Neuroblastoma. JCO Precis Oncol 2020; 4:1900261. [PMID: 32923888 PMCID: PMC7446415 DOI: 10.1200/po.19.00261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Circulating tumor DNA (ctDNA) has been used for disease monitoring in several types of cancer. The aim of our study was to investigate whether ctDNA can be used for response monitoring in neuroblastoma. METHODS One hundred forty-nine plasma samples from 56 patients were analyzed by quantitative polymerase chain reaction (qPCR) for total cell free DNA (cfDNA; albumin and β-actin) and ctDNA (hypermethylated RASSF1A). ctDNA results were compared with mRNA-based minimal residual disease (qPCR) in bone marrow (BM) and blood and clinical patient characteristics. RESULTS ctDNA was detected at diagnosis in all patients with high-risk and stage M neuroblastoma and in 3 of 7 patients with localized disease. The levels of ctDNA were highest at diagnosis, decreased during induction therapy, and not detected before or after autologous stem-cell transplantation. At relapse, the amount of ctDNA was comparable to levels at diagnosis. There was an association between ctDNA and blood or BM mRNA, with concordant results when tumor burden was high or no tumor was detected. The discrepancies indicated either low-level BM infiltration (ctDNA negative/mRNA positive) or primary tumor/soft tissue lesions with no BM involvement (ctDNA positive/mRNA negative). CONCLUSION ctDNA can be used for monitoring disease in patients with neuroblastoma. In high-risk patients and all patients with stage M at diagnosis, ctDNA is present. Our data indicate that at low tumor load, testing of both ctDNA and mRNA increases the sensitivity of molecular disease monitoring. It is likely that ctDNA can originate from both primary tumor and metastases and may be of special interest for disease monitoring in patients who experience relapse in other organs than BM.
Collapse
Affiliation(s)
- Lieke M J van Zogchel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Sanquin Research, Department of Experimental Immunohematology, and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Esther M van Wezel
- Sanquin Research, Department of Experimental Immunohematology, and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands.,Department of Pediatric Oncology, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jalenka van Wijk
- Sanquin Research, Department of Experimental Immunohematology, and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands.,Department of Pediatric Oncology, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | | | - Wassilis S C Bruins
- Sanquin Research, Department of Experimental Immunohematology, and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Lily Zappeij-Kannegieter
- Sanquin Research, Department of Experimental Immunohematology, and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Tirza J E Slager
- Department of Pediatric Oncology, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | | | - Iedan R N Verly
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pediatric Oncology, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - C Ellen van der Schoot
- Sanquin Research, Department of Experimental Immunohematology, and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | | |
Collapse
|
22
|
Liquori A, Ibañez M, Sargas C, Sanz MÁ, Barragán E, Cervera J. Acute Promyelocytic Leukemia: A Constellation of Molecular Events around a Single PML-RARA Fusion Gene. Cancers (Basel) 2020; 12:cancers12030624. [PMID: 32182684 PMCID: PMC7139833 DOI: 10.3390/cancers12030624] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/27/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022] Open
Abstract
Although acute promyelocytic leukemia (APL) is one of the most characterized forms of acute myeloid leukemia (AML), the molecular mechanisms involved in the development and progression of this disease are still a matter of study. APL is defined by the PML-RARA rearrangement as a consequence of the translocation t(15;17)(q24;q21). However, this abnormality alone is not able to trigger the whole leukemic phenotype and secondary cooperating events might contribute to APL pathogenesis. Additional somatic mutations are known to occur recurrently in several genes, such as FLT3, WT1, NRAS and KRAS, whereas mutations in other common AML genes are rarely detected, resulting in a different molecular profile compared to other AML subtypes. How this mutational spectrum, including point mutations in the PML-RARA fusion gene, could contribute to the 10%–15% of relapsed or resistant APL patients is still unknown. Moreover, due to the uncertain impact of additional mutations on prognosis, the identification of the APL-specific genetic lesion is still the only method recommended in the routine evaluation/screening at diagnosis and for minimal residual disease (MRD) assessment. However, the gene expression profile of genes, such as ID1, BAALC, ERG, and KMT2E, once combined with the molecular events, might improve future prognostic models, allowing us to predict clinical outcomes and to categorize APL patients in different risk subsets, as recently reported. In this review, we will focus on the molecular characterization of APL patients at diagnosis, relapse and resistance, in both children and adults. We will also describe different standardized molecular approaches to study MRD, including those recently developed. Finally, we will discuss how novel molecular findings can improve the management of this disease.
Collapse
Affiliation(s)
- Alessandro Liquori
- Accredited Research Group in Hematology and Hemotherapy, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.L.); (C.S.)
| | - Mariam Ibañez
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Claudia Sargas
- Accredited Research Group in Hematology and Hemotherapy, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (A.L.); (C.S.)
| | - Miguel Ángel Sanz
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Eva Barragán
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - José Cervera
- Department of Hematology, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (M.I.); (M.Á.S.); (E.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence:
| |
Collapse
|
23
|
Izzo B, Gottardi EM, Errichiello S, Daraio F, Baratè C, Galimberti S. Monitoring Chronic Myeloid Leukemia: How Molecular Tools May Drive Therapeutic Approaches. Front Oncol 2019; 9:833. [PMID: 31555590 PMCID: PMC6742705 DOI: 10.3389/fonc.2019.00833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/13/2019] [Indexed: 12/25/2022] Open
Abstract
More than 15 years ago, imatinib entered into the clinical practice as a "magic bullet"; from that point on, the prognosis of patients affected by chronic myeloid leukemia (CML) became comparable to that of aged-matched healthy subjects. The aims of treatment with tyrosine kinase inhibitors (TKIs) are for complete hematological response after 3 months of treatment, complete cytogenetic response after 6 months, and a reduction of the molecular disease of at least 3 logs after 12 months. Patients who do not reach their goal can switch to another TKI. Thus, the molecular monitoring of response is the main consideration of management of CML patients. Moreover, cases in deep and persistent molecular response can tempt the physician to interrupt treatment, and this "dream" is possible due to the quantitative PCR. After great international effort, today the BCR-ABL1 expression obtained in each laboratory is standardized and expressed as "international scale." This aim has been reached after the establishment of the EUTOS program (in Europe) and the LabNet network (in Italy), the platforms where biologists meet clinicians. In the field of quantitative PCR, the digital PCR is now a new and promising, sensitive and accurate tool. Some authors reported that digital PCR is able to better classify patients in precise "molecular classes," which could lead to a better identification of those cases that will benefit from the interruption of therapy. In addition, digital PCR can be used to identify a point mutation in the ABL1 domain, mutations that are often responsible for the TKI resistance. In the field of resistance, a prominent role is played by the NGS that enables identification of any mutation in ABL1 domain, even at sub-clonal levels. This manuscript reviews how the molecular tools can lead the management of CML patients, focusing on the more recent technical advances.
Collapse
Affiliation(s)
- Barbara Izzo
- Department of Clinical Medicine and Surgery, Molecular Biology, University Federico II, Naples, Italy
| | | | - Santa Errichiello
- Department of Clinical Medicine and Surgery, Molecular Biology, University Federico II, Naples, Italy
| | - Filomena Daraio
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Claudia Baratè
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| |
Collapse
|
24
|
Voso MT, Ottone T, Lavorgna S, Venditti A, Maurillo L, Lo-Coco F, Buccisano F. MRD in AML: The Role of New Techniques. Front Oncol 2019; 9:655. [PMID: 31396481 PMCID: PMC6664148 DOI: 10.3389/fonc.2019.00655] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/04/2019] [Indexed: 11/17/2022] Open
Abstract
In the context of precision medicine, assessment of minimal residual disease (MRD) has been used in acute myeloid leukemia (AML) to direct individual treatment programs, including allogeneic stem cell transplantation in patients at high-risk of relapse. One of the limits of this approach has been in the past the paucity of AML markers suitable for MRD assessment. Recently, the number of biomarkers has increased, due to the identification of highly specific leukemia-associated immunophenotypes by multicolor flow-cytometry, and of rare mutated gene sequences by digital droplet PCR, or next-generation sequencing (NGS). In addition, NGS allowed unraveling of clonal heterogeneity, present in AML at initial diagnosis or developing during treatment, which influences reliability of specific biomarkers, that may be unstable during the disease course. The technological advances have increased the application of MRD-based strategies to a significantly higher number of AML patients, and the information deriving from MRD assessment has been used to design individual post-remission protocols and pre-emptive treatments in patients with sub-clinical relapse. This led to the definition of MRD-negative complete remission as outcome definition in the recently published European Leukemianet MRD guidelines. In this review, we summarized the principles of modern technologies and their clinical applications for MRD detection in AML patients, according to the specific leukemic markers.
Collapse
Affiliation(s)
- Maria Teresa Voso
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
- Santa Lucia Foundation, IRCCS, Neuro-Oncohematology, Rome, Italy
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
- Santa Lucia Foundation, IRCCS, Neuro-Oncohematology, Rome, Italy
| | - Serena Lavorgna
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Adriano Venditti
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Luca Maurillo
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Francesco Lo-Coco
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Francesco Buccisano
- Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| |
Collapse
|
25
|
Galimberti S, Genuardi E, Mazziotta F, Iovino L, Morabito F, Grassi S, Ciabatti E, Guerrini F, Petrini M. The Minimal Residual Disease in Non-Hodgkin's Lymphomas: From the Laboratory to the Clinical Practice. Front Oncol 2019; 9:528. [PMID: 31293969 PMCID: PMC6606710 DOI: 10.3389/fonc.2019.00528] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/31/2019] [Indexed: 01/05/2023] Open
Abstract
Minimal residual disease (MRD) in non-Hodgkin's lymphomas (NHLs) still represents matter of interest and debate: indeed, the new available treatments offer higher rates of complete responses and MRD negativity than in the past, with a positive impact on the long-term survival. Furthermore, the introduction of more sensitive and accurate molecular techniques, such as digital PCR (ddPCR) and the next generation sequencing techniques (NGS), increased the possibility of identifying molecular targets to be followed after therapy (such as rearrangement of immunoglobulins, fusion genes, or mutations). This review focused on how molecular biology can help to detect MRD in different types of NHLs and how MRD can change the clinical practice in 2019. In follicular lymphoma (FL), contamination of the grafts and molecular disease persistence after transplantation represent a negative prognostic factors. The combination of Rituximab or Obinutuzumab with Bendamustine seems to be the most effective way to clear MRD in FL patients receiving chemo-immunotherapy (further studies are in progress), and also 90Yttrium-Ibritumomab-Tiuxetan offers a deep clearance of molecular disease. Finally, molecular MRD can further stratify PET-negative cases, with subjects both PET- and MRD-negative presenting the best outcome. In aggressive lymphomas, MRD has a relevant prognostic power and can represent the platform for immunotherapy (such as CAR-T). In diffuse large B-cell lymphoma (DLBCL), the assessment of MRD in the plasma (where cell-free DNA and exosomes circulate) seems to be more predictive than the bone marrow analysis or peripheral blood mononuclear cells. Finally, NGS technologies could be more useful than the classical "patient allele-specific PCR" because they can identify any possible clone emerging during the treatment or follow-up, even if different from that identified at diagnosis, thus predicting relapse. After all, the present available molecular approaches can move MRD from the bench side to the clinical practice.
Collapse
Affiliation(s)
- Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Turin, Italy
| | - Francesco Mazziotta
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Lorenzo Iovino
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Clinical and Translational Sciences School of Doctorate, University of Pisa, Pisa, Italy
| | - Fortunato Morabito
- Hematology Oncology Department, Augusta Victoria Hospital, East Jerusalem, Israel.,Biotechnology Research Unit, Cosenza, Italy
| | - Susanna Grassi
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,GeNOMEC School of Doctorate, University of Siena, Siena, Italy
| | - Elena Ciabatti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Guerrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mario Petrini
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| |
Collapse
|
26
|
Abstract
Increasing evidence supports the prognostic significance of measurable residual disease (MRD) in acute myeloid leukemia (AML). Dynamic MRD assessment for patients with AML complements baseline patient risk assessment factors in determining patient prognosis. MRD status may also be helpful in informing therapeutic decisions. The European Leukemia Net MRD working party recently issued consensus recommendations for the use of MRD in AML. The Food and Drug Administration also issued advice for using MRD in trials of hematologic malignancies. This article discusses MRD testing, highlights the challenges in adopting MRD testing in clinical practice, and provides insights into the future of the field.
Collapse
|
27
|
Digital PCR in Myeloid Malignancies: Ready to Replace Quantitative PCR? Int J Mol Sci 2019; 20:ijms20092249. [PMID: 31067725 PMCID: PMC6540058 DOI: 10.3390/ijms20092249] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
New techniques are on the horizon for the detection of small leukemic clones in both, acute leukemias and myeloproliferative disorders. A promising approach is based on digital polymerase chain reaction (PCR). Digital PCR (dPCR) is a breakthrough technology designed to provide absolute nucleic acid quantification. It is particularly useful to detect a low amount of target and therefore it represents an alternative method for detecting measurable residual disease (MRD). The main advantages are the high precision, the very reliable quantification, the absolute quantification without the need for a standard curve, and the excellent reproducibility. Nowadays the main disadvantages of this strategy are the costs that are still higher than standard qPCR, the lack of standardized methods, and the limited number of laboratories that are equipped with instruments for dPCR. Several studies describing the possibility and advantages of using digital PCR for the detection of specific leukemic transcripts or mutations have already been published. In this review we summarize the available data on the use of dPCR in acute myeloid leukemia and myeloproliferative disorders.
Collapse
|
28
|
Yuan D, Cui M, Yu S, Wang H, Jing R. Droplet digital PCR for quantification of PML-RARα in acute promyelocytic leukemia: a comprehensive comparison with real-time PCR. Anal Bioanal Chem 2019; 411:895-903. [PMID: 30617397 DOI: 10.1007/s00216-018-1508-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/09/2018] [Accepted: 11/21/2018] [Indexed: 11/26/2022]
Abstract
Real-time quantitative PCR (qPCR) has been widely implemented for molecular testing, but there are still some inherent limitations that hamper its usefulness. Droplet digital PCR (ddPCR), which can provide direct, standards-free quantification, has recently received increasing attention. In our study, a comprehensive comparison of ddPCR with qPCR in relation to the quantification of PML-RARα was performed to evaluate the diagnostic potential of ddPCR. Results showed that ddPCR displayed significant concordance with qPCR in the detection of PML-RARα in clinical samples, but showed advantages over qPCR in terms of precision, limit of detection (LOD), and other basic performance parameters. A study of the feasibility of duplexing also indicated that ddPCR could simultaneously quantify the target PML-RARα and the clinical common reference gene ABL in a reaction, in contrast to qPCR. Moreover, ddPCR was more tolerant than qPCR of inhibition, and was shown to be able to quantify inhibition-prone samples. Another advantage of using ddPCR in clinical applications is that it will yield accurate results for patients with PML-RARα levels that fluctuate around the LOD of qPCR. Therefore, ddPCR is considered to have the potential to become a reliable alternative technique for quantifying PML-RARα. Graphical abstract ᅟ.
Collapse
Affiliation(s)
- Dandan Yuan
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Shuping Yu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Huimin Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China.
| |
Collapse
|
29
|
Onecha E, Linares M, Rapado I, Ruiz-Heredia Y, Martinez-Sanchez P, Cedena T, Pratcorona M, Oteyza JP, Herrera P, Barragan E, Montesinos P, Vela JAG, Magro E, Anguita E, Figuera A, Riaza R, Martinez-Barranco P, Sanchez-Vega B, Nomdedeu J, Gallardo M, Martinez-Lopez J, Ayala R. A novel deep targeted sequencing method for minimal residual disease monitoring in acute myeloid leukemia. Haematologica 2018; 104:288-296. [PMID: 30093399 PMCID: PMC6355493 DOI: 10.3324/haematol.2018.194712] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/08/2018] [Indexed: 12/11/2022] Open
Abstract
A high proportion of patients with acute myeloid leukemia who achieve minimal residual disease negative status ultimately relapse because a fraction of pathological clones remains undetected by standard methods. We designed and validated a high-throughput sequencing method for minimal residual disease assessment of cell clonotypes with mutations of NPM1, IDH1/2 and/or FLT3-single nucleotide variants. For clinical validation, 106 follow-up samples from 63 patients in complete remission were studied by sequencing, evaluating the level of mutations detected at diagnosis. The predictive value of minimal residual disease status by sequencing, multiparameter flow cytometry, or quantitative polymerase chain reaction analysis was determined by survival analysis. The sequencing method achieved a sensitivity of 10−4 for single nucleotide variants and 10−5 for insertions/deletions and could be used in acute myeloid leukemia patients who carry any mutation (86% in our diagnostic data set). Sequencing–determined minimal residual disease positive status was associated with lower disease-free survival (hazard ratio 3.4, P=0.005) and lower overall survival (hazard ratio 4.2, P<0.001). Multivariate analysis showed that minimal residual disease positive status determined by sequencing was an independent factor associated with risk of death (hazard ratio 4.54, P=0.005) and the only independent factor conferring risk of relapse (hazard ratio 3.76, P=0.012). This sequencing-based method simplifies and standardizes minimal residual disease evaluation, with high applicability in acute myeloid leukemia. It is also an improvement upon flow cytometry- and quantitative polymerase chain reaction-based prediction of outcomes of patients with acute myeloid leukemia and could be incorporated in clinical settings and clinical trials.
Collapse
Affiliation(s)
- Esther Onecha
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Maria Linares
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Inmaculada Rapado
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid
| | - Yanira Ruiz-Heredia
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | | | - Teresa Cedena
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
| | - Marta Pratcorona
- Hematology Department, Hospital Santa Creu i Sant Pau, Barcelona
| | | | - Pilar Herrera
- Hematology Department, Hospital Universitario Ramon y Cajal, Madrid
| | - Eva Barragan
- Complutense University, Madrid.,Hematology Department, Hospital Universitario La Fe, Valencia
| | - Pau Montesinos
- Complutense University, Madrid.,Hematology Department, Hospital Universitario La Fe, Valencia
| | | | - Elena Magro
- Hematology Department, Hospital Universitario Principe de Asturias, Madrid
| | - Eduardo Anguita
- Hematology Department, Hospital Clínico San Carlos, IdISSC, UCM, Madrid
| | - Angela Figuera
- Hematology Department, Hospital Universitario de la Princesa, Madrid
| | - Rosalia Riaza
- Hematology Department, Hospital Universitario Severo Ochoa, Madrid
| | | | - Beatriz Sanchez-Vega
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Josep Nomdedeu
- Hematology Department, Hospital Santa Creu i Sant Pau, Barcelona
| | - Miguel Gallardo
- Hematological Malignancies Clinical Research Unit, CNIO, Madrid
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid.,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Madrid .,Hematological Malignancies Clinical Research Unit, CNIO, Madrid.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid.,Complutense University, Madrid
| |
Collapse
|
30
|
Molecular Minimal Residual Disease Testing in Acute Myeloid Leukemia: A Review for the Practicing Clinician. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2018; 18:636-647. [PMID: 30006258 DOI: 10.1016/j.clml.2018.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 11/21/2022]
Abstract
Minimal residual disease (MRD) testing in acute myeloid leukemia is increasingly being used to assess treatment response and stratify the risk of relapse for individual patients. Molecular methods for MRD testing began with PCR-based assays for individual recurrent mutations. To date, there is robust evidence for testing NPM1, CBFB-MYH11, and RUNX1/RUNXT1 mutations using this approach, though the best timing and threshold level for each mutation varies. More recent approaches have been with PCR-based multigene panels, occasionally combined with flow cytometric techniques, and next-generation sequencing techniques. This review outlines the various techniques used in molecular approaches to MRD, the evidence behind individual mutation testing, and the novel approaches for evaluating multigene MRD so that clinicians can understand and incorporate these evaluations into their practice.
Collapse
|
31
|
Selim AG, Moore AS. Molecular Minimal Residual Disease Monitoring in Acute Myeloid Leukemia. J Mol Diagn 2018; 20:389-397. [DOI: 10.1016/j.jmoldx.2018.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 02/22/2018] [Accepted: 03/27/2018] [Indexed: 01/22/2023] Open
|
32
|
Coccaro N, Anelli L, Zagaria A, Casieri P, Tota G, Orsini P, Impera L, Minervini A, Minervini CF, Cumbo C, Parciante E, Carluccio P, Brunetti C, Specchia G, Albano F. Droplet Digital PCR Is a Robust Tool for Monitoring Minimal Residual Disease in Adult Philadelphia-Positive Acute Lymphoblastic Leukemia. J Mol Diagn 2018; 20:474-482. [DOI: 10.1016/j.jmoldx.2018.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/13/2018] [Accepted: 03/09/2018] [Indexed: 12/16/2022] Open
|
33
|
Cumbo C, Impera L, Minervini CF, Orsini P, Anelli L, Zagaria A, Coccaro N, Tota G, Minervini A, Casieri P, Brunetti C, Rossi AR, Parciante E, Specchia G, Albano F. Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for "personalized monitoring" of residual disease in chronic myeloid leukemia patients. Oncotarget 2018. [PMID: 29541390 PMCID: PMC5834283 DOI: 10.18632/oncotarget.23971] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology. Finally, after defining the BCR-ABL1 genomic junction, we performed the target CML patient–specific quantification, using droplet digital PCR (ddPCR). FISH and MinION steps, respectively, together with ddPCR analysis, greatly reduce the complexity that has impeded the use of “personalized monitoring” of CML in clinical practice. Our report suggests a feasible pipeline, in terms of costs and reproducibility, aimed at characterizing and quantifying the genomic BCR-ABL1 rearrangement during MRD monitoring in CML patients.
Collapse
Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Luciana Impera
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | | | - Paola Orsini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Nicoletta Coccaro
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Giuseppina Tota
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Angela Minervini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Paola Casieri
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Claudia Brunetti
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Antonella Russo Rossi
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Elisa Parciante
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| |
Collapse
|