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Verbeek MWC, van der Velden VHJ. The Evolving Landscape of Flowcytometric Minimal Residual Disease Monitoring in B-Cell Precursor Acute Lymphoblastic Leukemia. Int J Mol Sci 2024; 25:4881. [PMID: 38732101 PMCID: PMC11084622 DOI: 10.3390/ijms25094881] [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: 03/29/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Detection of minimal residual disease (MRD) is a major independent prognostic marker in the clinical management of pediatric and adult B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL), and risk stratification nowadays heavily relies on MRD diagnostics. MRD can be detected using flow cytometry based on aberrant expression of markers (antigens) during malignant B-cell maturation. Recent advances highlight the significance of novel markers (e.g., CD58, CD81, CD304, CD73, CD66c, and CD123), improving MRD identification. Second and next-generation flow cytometry, such as the EuroFlow consortium's eight-color protocol, can achieve sensitivities down to 10-5 (comparable with the PCR-based method) if sufficient cells are acquired. The introduction of targeted therapies (especially those targeting CD19, such as blinatumomab or CAR-T19) introduces several challenges for flow cytometric MRD analysis, such as the occurrence of CD19-negative relapses. Therefore, innovative flow cytometry panels, including alternative B-cell markers (e.g., CD22 and CD24), have been designed. (Semi-)automated MRD assessment, employing machine learning algorithms and clustering tools, shows promise but does not yet allow robust and sensitive automated analysis of MRD. Future directions involve integrating artificial intelligence, further automation, and exploring multicolor spectral flow cytometry to standardize MRD assessment and enhance diagnostic and prognostic robustness of MRD diagnostics in BCP-ALL.
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Affiliation(s)
| | - Vincent H. J. van der Velden
- Laboratory for Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
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Lin M, Zhao X, Chang Y, Zhao X. Current assessment and management of measurable residual disease in patients with acute lymphoblastic leukemia in the setting of CAR-T-cell therapy. Chin Med J (Engl) 2024; 137:140-151. [PMID: 38148315 PMCID: PMC10798764 DOI: 10.1097/cm9.0000000000002945] [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: 06/18/2023] [Indexed: 12/28/2023] Open
Abstract
ABSTRACT Chimeric antigen receptor (CAR)-modified T-cell therapy has achieved remarkable success in the treatment of acute lymphoblastic leukemia (ALL). Measurable/minimal residual disease (MRD) monitoring plays a significant role in the prognostication and management of patients undergoing CAR-T-cell therapy. Common MRD detection methods include flow cytometry (FCM), polymerase chain reaction (PCR), and next-generation sequencing (NGS), and each method has advantages and limitations. It has been well documented that MRD positivity predicts a poor prognosis and even disease relapse. Thus, how to perform prognostic evaluations, stratify risk based on MRD status, and apply MRD monitoring to guide individual therapeutic decisions have important implications in clinical practice. This review assesses the common and novel MRD assessment methods. In addition, we emphasize the critical role of MRD as a prognostic biomarker and summarize the latest studies regarding MRD-directed combination therapy with CAR-T-cell therapy and allogeneic hematopoietic stem cell transplantation (allo-HSCT), as well as other therapeutic strategies to improve treatment effect. Furthermore, this review discusses current challenges and strategies for MRD detection in the setting of disease relapse after targeted therapy.
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Affiliation(s)
- Minghao Lin
- Peking University People’s Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - Xiaosu Zhao
- Peking University People’s Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - Yingjun Chang
- Peking University People’s Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
| | - Xiangyu Zhao
- Peking University People’s Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing 100044, China
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3
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Chen H, Gu M, Liang J, Song H, Zhang J, Xu W, Zhao F, Shen D, Shen H, Liao C, Tang Y, Xu X. Minimal residual disease detection by next-generation sequencing of different immunoglobulin gene rearrangements in pediatric B-ALL. Nat Commun 2023; 14:7468. [PMID: 37978187 PMCID: PMC10656538 DOI: 10.1038/s41467-023-43171-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
While the prognostic role of immunoglobulin heavy chain locus (IGH) rearrangement in minimal residual disease (MRD) in pediatric B-acute lymphoblastic leukemia (B-ALL) has been reported, the contribution of light chain loci (IGK/IGL) remains elusive. This study is to evaluate the prognosis of IGH and IGK/IGL rearrangement-based MRD detected by next-generation sequencing in B-ALL at the end of induction (EOI) and end of consolidation (EOC). IGK/IGL rearrangements identify 5.5% of patients without trackable IGH clones. Concordance rates for IGH and IGK/IGL are 79.9% (cutoff 0.01%) at EOI and 81.0% (cutoff 0.0001%) at EOC, respectively. Patients with NGS-MRD < 0.01% at EOI or <0.0001% at EOC present excellent outcome, with 3-year event-free survival rates higher than 95%. IGH-MRD is prognostic at EOI/EOC, while IGK-MRD at EOI/EOC and IGL-MRD at EOI are not. At EOI, NGS identifies 26.2% of higher risk patients whose MRD < 0.01% by flow cytometry. However, analyzing IGK/IGL along with IGH fails to identify additional higher risk patients both at EOI and at EOC. In conclusion, IGH is crucial for MRD monitoring while IGK and IGL have relatively limited value.
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Affiliation(s)
- Haipin Chen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Miner Gu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Juan Liang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Hua Song
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Jingying Zhang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Weiqun Xu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Fenying Zhao
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Diying Shen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Heping Shen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Chan Liao
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China
| | - Yongmin Tang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China.
| | - Xiaojun Xu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, No. 57 Zhugan Lane, Yan'an Street, 310003, Hangzhou, People's Republic of China.
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Svaton M, Skotnicova A, Reznickova L, Rennerova A, Valova T, Kotrova M, van der Velden VHJ, Brüggemann M, Darzentas N, Langerak AW, Zuna J, Stary J, Trka J, Fronkova E. NGS better discriminates true MRD positivity for the risk stratification of childhood ALL treated on an MRD-based protocol. Blood 2023; 141:529-533. [PMID: 36240445 PMCID: PMC10651772 DOI: 10.1182/blood.2022017003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/02/2022] [Accepted: 10/06/2022] [Indexed: 02/07/2023] Open
Abstract
We compared minimal/measurable residual disease (MRD) levels evaluated by routinely used real-time quantitative polymerase chain reaction (qPCR) patient-specific assays and by next-generation sequencing (NGS) approach in 780 immunoglobulin (IG) and T-cell receptor (TR) markers in 432 children with B-cell precursor acute lymphoblastic leukemia treated on the AIEOP-BFM ALL 2009 protocol. Our aim was to compare the MRD-based risk stratification at the end of induction. The results were concordant in 639 of 780 (81.9%) of these markers; 37 of 780 (4.7%) markers were detected only by NGS. In 104 of 780 (13.3%) markers positive only by qPCR, a large fraction (23/104; 22.1%) was detected also by NGS, however, owing to the presence of identical IG/TR rearrangements in unrelated samples, we classified those as nonspecific/false-positive. Risk group stratification based on the MRD results by qPCR and NGS at the end of induction was concordant in 76% of the patients; 19% of the patients would be assigned to a lower risk group by NGS, largely owing to the elimination of false-positive qPCR results, and 5% of patients would be assigned to a higher risk group by NGS. NGS MRD is highly concordant with qPCR while providing more specific results and can be an alternative in the front line of MRD evaluation in forthcoming MRD-based protocols.
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Affiliation(s)
- Michael Svaton
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Aneta Skotnicova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Leona Reznickova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Andrea Rennerova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Tatana Valova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michaela Kotrova
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Vincent H. J. van der Velden
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Monika Brüggemann
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nikos Darzentas
- Department of Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anton W. Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jan Zuna
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Trka
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Eva Fronkova
- CLIP–Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
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5
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Yasuda T, Sanada M, Tsuzuki S, Hayakawa F. Oncogenic lesions and molecular subtypes in adults with B-cell acute lymphoblastic leukemia. Cancer Sci 2022; 114:8-15. [PMID: 36106363 PMCID: PMC9807527 DOI: 10.1111/cas.15583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/12/2022] [Accepted: 09/04/2022] [Indexed: 01/07/2023] Open
Abstract
B-cell acute lymphoblastic leukemia (B-ALL), a genetically heterogeneous disease, is classified into different molecular subtypes that are defined by recurrent gene rearrangements, gross chromosomal abnormalities, or specific gene mutations. Cells with these genetic alterations acquire a leukemia-initiating ability and show unique expression profiles. The distribution of B-ALL molecular subtypes is greatly dependent on age, which also affects treatment responsiveness and long-term survival, partly accounting for the inferior outcome in adolescents and young adults (AYA) and (older) adults with B-ALL. Recent advances in sequencing technology, especially RNA sequencing and the application of these technologies in large B-ALL cohorts have uncovered B-ALL molecular subtypes prevalent in AYA and adults. These new insights supply more precise estimations of prognoses and targeted therapies informed by sequencing results, as well as a deeper understanding of the genetic basis of AYA/adult B-ALL. This article provides an account of these technological advances and an overview of the recent major findings of B-ALL molecular subtypes in adults.
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Affiliation(s)
- Takahiko Yasuda
- Clinical Research CenterNational Hospital Organization Nagoya Medical CenterNagoyaJapan
| | - Masashi Sanada
- Clinical Research CenterNational Hospital Organization Nagoya Medical CenterNagoyaJapan
| | - Shinobu Tsuzuki
- Department of BiochemistryAichi Medical University School of MedicineNagakuteJapan
| | - Fumihiko Hayakawa
- Division of Cellular and Genetic Sciences, Department of Integrated Health SciencesNagoya University Graduate School of MedicineNagoyaJapan
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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.
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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.
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Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:61-77. [PMID: 35622320 DOI: 10.1007/978-1-0716-2115-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Identification of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements in acute lymphoblastic leukemia (ALL) patients at initial presentation are crucial for monitoring of minimal residual disease (MRD) during subsequent follow-up and thereby for appropriate risk-group stratification. Here we describe how RNA-Seq data can be generated and subsequently analyzed with ARResT/Interrogate to identify possible MRD markers. In addition to the procedures, possible pitfalls will be discussed. Similar strategies can be employed for other lymphoid malignancies, such as lymphoma and myeloma.
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Elucidating minimal residual disease of paediatric B-cell acute lymphoblastic leukaemia by single-cell analysis. Nat Cell Biol 2022; 24:242-252. [PMID: 35145224 DOI: 10.1038/s41556-021-00814-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 11/12/2021] [Indexed: 12/31/2022]
Abstract
Minimal residual disease that persists after chemotherapy is the most valuable prognostic marker for haematological malignancies and solid cancers. Unfortunately, our understanding of the resistance elicited in minimal residual disease is limited due to the rarity and heterogeneity of the residual cells. Here we generated 161,986 single-cell transcriptomes to analyse the dynamic changes of B-cell acute lymphoblastic leukaemia (B-ALL) at diagnosis, residual and relapse by combining single-cell RNA sequencing and B-cell-receptor sequencing. In contrast to those at diagnosis, the leukaemic cells at relapse tended to shift to poorly differentiated states, whereas the changes in the residual cells were more complicated. Differential analyses highlighted the activation of the hypoxia pathway in residual cells, resistant clones and B-ALL with MLL rearrangement. Both in vitro and in vivo models demonstrated that inhibition of the hypoxia pathway sensitized leukaemic cells to chemotherapy. This single-cell analysis of minimal residual disease opens up an avenue for the identification of potent treatment opportunities for B-ALL.
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Distinct clinical characteristics of DUX4- and PAX5-altered childhood B-lymphoblastic leukemia. Blood Adv 2021; 5:5226-5238. [PMID: 34547766 PMCID: PMC9152998 DOI: 10.1182/bloodadvances.2021004895] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/11/2021] [Indexed: 12/05/2022] Open
Abstract
Despite poor end-of-induction MRD, DUX4 B-ALL has excellent outcome. PAX5alt B-ALL with IKZF1 codeletion is associated with poor outcome, which can be improved by treatment intensification.
Among the recently described subtypes in childhood B-lymphoblastic leukemia (B-ALL) were DUX4- and PAX5-altered (PAX5alt). By using whole transcriptome RNA sequencing in 377 children with B-ALL from the Malaysia-Singapore ALL 2003 (MS2003) and Malaysia-Singapore ALL 2010 (MS2010) studies, we found that, after hyperdiploid and ETV6-RUNX1, the third and fourth most common subtypes were DUX4 (n = 51; 14%) and PAX5alt (n = 36; 10%). DUX4 also formed the largest genetic subtype among patients with poor day-33 minimal residual disease (MRD; n = 12 of 44). But despite the poor MRD, outcome of DUX4 B-ALL was excellent (5-year cumulative risk of relapse [CIR], 8.9%; 95% confidence interval [CI], 2.8%-19.5% and 5-year overall survival, 97.8%; 95% CI, 85.3%-99.7%). In MS2003, 21% of patients with DUX4 B-ALL had poor peripheral blood response to prednisolone at day 8, higher than other subtypes (8%; P = .03). In MS2010, with vincristine at day 1, no day-8 poor peripheral blood response was observed in the DUX4 subtype (P = .03). The PAX5alt group had an intermediate risk of relapse (5-year CIR, 18.1%) but when IKZF1 was not deleted, outcome was excellent with no relapse among 23 patients. Compared with MS2003, outcome of PAX5alt B-ALL with IKZF1 codeletion was improved by treatment intensification in MS2010 (5-year CIR, 80.0% vs 0%; P = .05). In conclusion, despite its poor initial response, DUX4 B-ALL had a favorable overall outcome, and the prognosis of PAX5alt was strongly dependent on IKZF1 codeletion.
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Ni Chin WH, Li Z, Jiang N, Lim EH, Suang Lim JY, Lu Y, Chiew KH, Yin Kham SK, Zhi Oh BL, Tan AM, Ariffin H, Yang JJ, Eng-Juh Yeoh A. Practical Considerations for Using RNA Sequencing in Management of B-Cell Acute Lymphoblastic Leukemia: Malaysia-Singapore Acute Lymphoblastic Leukemia-Sequencing 2020 Implementation Strategy. J Mol Diagn 2021; 23:1359-1372. [PMID: 34365011 DOI: 10.1016/j.jmoldx.2021.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 12/31/2022] Open
Abstract
Despite the immense genetic heterogeneity of B-cell acute lymphoblastic leukemia (ALL), RNA sequencing (RNA-Seq) could comprehensively interrogate its genetic drivers, assigning a specific molecular subtype in >90% of patients. However, study groups have only started to use RNA-Seq. For broader clinical use, technical, quality control, and appropriate performance validation are needed. We describe the development and validation of an RNA-Seq workflow for subtype classification, TPMT/NUDT15/TP53 variant discovery, and IGH disease clone identification for Malaysia-Singapore ALL sequencing (ALL-Seq) 2020. We validated this workflow in 377 patients in our preceding Malaysia-Singapore ALL-Seq 2003/Malaysia-Singapore ALL-Seq 2010 studies and proposed the quality control measures for RNA quality, library size, sequencing, and data analysis using the International Organization for Standardization 15189 quality and competence standard for medical laboratories. Compared with conventional methods, we achieved >95% accuracy in oncogene fusion identification, digital karyotyping, and TPMT and NUDT15 variant discovery. We found seven pathogenic TP53 mutations, confirmed with Sanger sequencing, which conferred a poorer outcome. Applying this workflow prospectively to the first 21 patients in Malaysia-Singapore ALL-Seq 2020, we identified the genetic drivers and IGH disease clones in >90% of patients with concordant TPMT, NUDT15, and TP53 variants using PCR-based methods. The median turnaround time was 12 days, which was clinically actionable. In conclusion, RNA-Seq workflow could be used clinically in management of B-cell ALL patients.
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Affiliation(s)
- Winnie H Ni Chin
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zhenhua Li
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Nan Jiang
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Evelyn H Lim
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joshua Y Suang Lim
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yi Lu
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kean H Chiew
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shirley K Yin Kham
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bernice L Zhi Oh
- Viva-University Children's Cancer Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
| | - Ah M Tan
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Hany Ariffin
- University of Malaya Cancer Research Institute, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Allen Eng-Juh Yeoh
- VIVA-NUS Centre for Translational Research in Acute Leukaemia, 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.
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Huang YJ, Kuo MC, Jaing TH, Liu HC, Yeh TC, Chen SH, Lin TL, Yang CP, Wang PN, Sheen JM, Chang TK, Chang CH, Hu SF, Huang TY, Wang SC, Wu KH, Chiou SS, Hsiao CC, Shih LY. Comparison of Two Quantitative PCR-Based Assays for Detection of Minimal Residual Disease in B-Precursor Acute Lymphoblastic Leukemia Harboring Three Major Fusion Transcripts. J Mol Diagn 2021; 23:1373-1379. [PMID: 34325057 DOI: 10.1016/j.jmoldx.2021.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/17/2021] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
Two quantitative PCR (qPCR)-based methods, for clonal Ig or T-cell receptor gene (Ig/TCR) rearrangements and for fusion transcripts, are widely used for the measurement of minimal residual disease (MRD) in patients with B-precursor acute lymphoblastic leukemia (ALL). MRD of bone marrow samples from 165 patients carrying the three major fusion transcripts, including 74 BCR-ABL1, 54 ETV6-RUNX1, and 37 TCF3-PBX1, was analyzed by using the two qPCR-based methods. The coefficient correlation of both methods was good for TCF3-PBX1 (R2 = 0.8088) and BCR-ABL1 (R2 = 0.8094) ALL and moderate for ETV6-RUNX1 (R2 = 0.5972). The concordance was perfect for TCF3-PBX1 ALL (97.2%), substantially concordant for ETV6-RUNX1 ALL (87.1%), and only moderate for BCR-ABL1 ALL (70.6%). The discordant MRD, positive for only one method with a difference greater than one log, was found in 4 of 93 samples (4.3%) with ETV6-RUNX1, 31 of 245 samples (12.7%) with BCR-ABL1, and 0 of TCF3-PBX1 ALL. None of the eight nontransplanted patients with BCR-ABL1-MRD (+)/Ig/TCR-MRD (-) with a median follow-up time of 73.5 months had hematologic relapses. Our study showed an excellent MRD concordance between the two qPCR-based methods in TCF3-PBX1 ALL, whereas qPCR for Ig/TCR is more reliable in BCR-ABL1 ALL.
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Affiliation(s)
- Ying-Jung Huang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Ming-Chung Kuo
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tang-Her Jaing
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Hematology-Oncology, Chang Gung Children's Hospital at Linkou, Taoyuan, Taiwan
| | - Hsi-Che Liu
- Department of Hematology-Oncology, Mackay Children's Hospital and Mackay Medical College, Taipei, Taiwan
| | - Ting-Chi Yeh
- Department of Hematology-Oncology, Mackay Children's Hospital and Mackay Medical College, Taipei, Taiwan
| | - Shih-Hsiang Chen
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Hematology-Oncology, Chang Gung Children's Hospital at Linkou, Taoyuan, Taiwan
| | - Tung-Liang Lin
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chao-Ping Yang
- Department of Hematology-Oncology, Chang Gung Children's Hospital at Linkou, Taoyuan, Taiwan
| | - Po-Nan Wang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Jiunn-Ming Sheen
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Kaohsiung, Kaohsiung, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Te-Kau Chang
- Division of Pediatric Hematology and Oncology, China Medical University Children's Hospital, Taichung, Taiwan
| | - Chia-Hui Chang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Shu-Fen Hu
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Ting-Yu Huang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Shih-Chung Wang
- Division of Pediatric Hematology-Oncology, Changhua Christian Children's Hospital, Changhua, Taiwan
| | - Kang-Hsi Wu
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shyh-Shin Chiou
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chih-Cheng Hsiao
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Kaohsiung, Kaohsiung, Taiwan
| | - Lee-Yung Shih
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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12
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Role of transcriptome sequencing in clinical diagnosis of B-cell acute lymphoblastic leukemia. Leukemia 2021; 35:2135-2137. [PMID: 34112955 DOI: 10.1038/s41375-021-01185-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/14/2021] [Accepted: 02/02/2021] [Indexed: 12/15/2022]
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13
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Minimal Residual Disease in Acute Lymphoblastic Leukemia: Current Practice and Future Directions. Cancers (Basel) 2021; 13:cancers13081847. [PMID: 33924381 PMCID: PMC8069391 DOI: 10.3390/cancers13081847] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/31/2021] [Accepted: 04/11/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Acute lymphoblastic leukemia minimal residual disease (MRD) refers to the presence of residual leukemia cells following the achievement of complete remission, but below the limit of detection using conventional morphologic assessment. Up to two thirds of children may have MRD detectable after induction therapy depending on the biological subtype and method of detection. Patients with detectable MRD have an increased likelihood of relapse. A rapid reduction of MRD reveals leukemia sensitivity to therapy and under this premise, MRD has emerged as the strongest independent predictor of individual patient outcome and is crucial for risk stratification. However, it is a poor surrogate for treatment effect on long term outcome at the trial level, with impending need of randomized trials to prove efficacy of MRD-adapted interventions. Abstract Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer and advances in its clinical and laboratory biology have grown exponentially over the last few decades. Treatment outcome has improved steadily with over 90% of patients surviving 5 years from initial diagnosis. This success can be attributed in part to the development of a risk stratification approach to identify those subsets of patients with an outstanding outcome that might qualify for a reduction in therapy associated with fewer short and long term side effects. Likewise, recognition of patients with an inferior prognosis allows for augmentation of therapy, which has been shown to improve outcome. Among the clinical and biological variables known to impact prognosis, the kinetics of the reduction in tumor burden during initial therapy has emerged as the most important prognostic variable. Specifically, various methods have been used to detect minimal residual disease (MRD) with flow cytometric and molecular detection of antigen receptor gene rearrangements being the most common. However, many questions remain as to the optimal timing of these assays, their sensitivity, integration with other variables and role in treatment allocation of various ALL subgroups. Importantly, the emergence of next generation sequencing assays is likely to broaden the use of these assays to track disease evolution. This review will discuss the biological basis for utilizing MRD in risk assessment, the technical approaches and limitations of MRD detection and its emerging applications.
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Hansen MH, Cédile O, Larsen TS, Abildgaard N, Nyvold CG. Perspective: sensitive detection of residual lymphoproliferative disease by NGS and clonal rearrangements-how low can you go? Exp Hematol 2021; 98:14-24. [PMID: 33823225 DOI: 10.1016/j.exphem.2021.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/12/2023]
Abstract
Malignant lymphoproliferative disorders collectively constitute a large fraction of the hematological cancers, ranging from indolent to highly aggressive neoplasms. Being a diagnostically important hallmark, clonal gene rearrangements of the immunoglobulins enable the detection of residual disease in the clinical course of patients down to a minute fraction of malignant cells. The introduction of next-generation sequencing (NGS) has provided unprecedented assay specificity, with a sensitivity matching that of polymerase chain reaction-based measurable residual disease (MRD) detection down to the 10-6 level. Although reaching 10-6 to 10-7 is theoretically feasible, employing a sufficient amount of DNA and sequencing coverage is placed in the perspective of the practical challenges when relying on clinical samples in contrast to controlled serial dilutions. As we discuss, the randomness of subsampling must be taken into account to accommodate the sensitivity threshold-in terms of both the required number of cells and sequencing coverage. As a substantial part of the reviewed studies do not state the depth of coverage or even amount of DNA in some cases, we call for increased transparency to enable critical assessment of the MRD assays for clinical implementation and feasibility.
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Affiliation(s)
- Marcus H Hansen
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark.
| | - Oriane Cédile
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Thomas S Larsen
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Niels Abildgaard
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Charlotte G Nyvold
- Hematology-Pathology Research Laboratory, Research Unit for Hematology and Research Unit for Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
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15
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Potential and pitfalls of whole transcriptome-based immunogenetic marker identification in acute lymphoblastic leukemia; a EuroMRD and EuroClonality-NGS Working Group study. Leukemia 2021; 35:924-928. [PMID: 33608635 PMCID: PMC7932924 DOI: 10.1038/s41375-021-01154-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/15/2020] [Accepted: 01/22/2021] [Indexed: 11/08/2022]
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16
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Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblastic leukemia. Front Med 2021; 15:347-371. [PMID: 33400146 DOI: 10.1007/s11684-020-0821-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by genetic alterations with high heterogeneity. Precise subtypes with distinct genomic and/or gene expression patterns have been recently revealed using high-throughput sequencing technology. Most of these profiles are associated with recurrent non-overlapping rearrangements or hotspot point mutations that are analogous to the established subtypes, such as DUX4 rearrangements, MEF2D rearrangements, ZNF384/ZNF362 rearrangements, NUTM1 rearrangements, BCL2/MYC and/or BCL6 rearrangements, ETV6-RUNX1-like gene expression, PAX5alt (diverse PAX5 alterations, including rearrangements, intragenic amplifications, or mutations), and hotspot mutations PAX5 (p.Pro80Arg) with biallelic PAX5 alterations, IKZF1 (p.Asn159Tyr), and ZEB2 (p.His1038Arg). These molecular subtypes could be classified by gene expression patterns with RNA-seq technology. Refined molecular classification greatly improved the treatment strategy. Multiagent therapy regimens, including target inhibitors (e.g., imatinib), immunomodulators, monoclonal antibodies, and chimeric antigen receptor T-cell (CAR-T) therapy, are transforming the clinical practice from chemotherapy drugs to personalized medicine in the field of risk-directed disease management. We provide an update on our knowledge of emerging molecular subtypes and therapeutic targets in BCP-ALL.
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Sun YQ, Li SQ, Zhao XS, Chang YJ. Measurable residual disease of acute lymphoblastic leukemia in allograft settings: how to evaluate and intervene. Expert Rev Anticancer Ther 2020; 20:453-464. [PMID: 32459519 DOI: 10.1080/14737140.2020.1766973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains a curable strategy for acute lymphoblastic leukemia (ALL), especially for adult cases. However, leukemia relapse after allograft restricts the improvement of transplant outcomes. Measurable residual disease (MRD) has been the strongest predictor for relapse after allo-HSCT, allowing MRD-directed preemptive therapy. AREAS COVERED This manuscript summarizes the detection of MRD in patients with ALL who undergo allo-HSCT, focusing the effects of positive pre-HSCT MRD and post-HSCT MRD on outcomes as well as MRD-directed interventions. EXPERT OPINION Except for MFC and RQ-PCR, other strategies, such as next-generation sequencing and RNAseq, have been developed for MRD determination. Negative effects of positive MRD peri-transplantation on outcomes of ALL patients were observed both in human leukocyte antigen (HLA)-matched sibling donor transplantation and in alternative donor transplantation. Advances have been made in determining the need for transplant according to MRD evaluation after induction or consolidation therapy. A number of approaches, including CAR-T-cell therapy, antibodies (blinatumomab, etc), targeted therapy (imatinib, etc), transplant donor selection, as well as donor lymphocyte infusion and interferon-α, have been successfully used or are promising for peri-transplantation MRD interventions. This progress could lead to the significant improvement of transplant outcomes for ALL patients.
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Affiliation(s)
- Yu-Qian Sun
- National Clinical Research Center for Hematologic Disease, Peking University People's Hospital & Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation , Beijing, P.R.C
| | - Si-Qi Li
- National Clinical Research Center for Hematologic Disease, Peking University People's Hospital & Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation , Beijing, P.R.C
| | - Xiao-Su Zhao
- National Clinical Research Center for Hematologic Disease, Peking University People's Hospital & Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation , Beijing, P.R.C
| | - Ying-Jun Chang
- National Clinical Research Center for Hematologic Disease, Peking University People's Hospital & Peking University Institute of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation , Beijing, P.R.C
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