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Pagliaro L, Chen SJ, Herranz D, Mecucci C, Harrison CJ, Mullighan CG, Zhang M, Chen Z, Boissel N, Winter SS, Roti G. Acute lymphoblastic leukaemia. Nat Rev Dis Primers 2024; 10:41. [PMID: 38871740 DOI: 10.1038/s41572-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Acute lymphoblastic leukaemia (ALL) is a haematological malignancy characterized by the uncontrolled proliferation of immature lymphoid cells. Over past decades, significant progress has been made in understanding the biology of ALL, resulting in remarkable improvements in its diagnosis, treatment and monitoring. Since the advent of chemotherapy, ALL has been the platform to test for innovative approaches applicable to cancer in general. For example, the advent of omics medicine has led to a deeper understanding of the molecular and genetic features that underpin ALL. Innovations in genomic profiling techniques have identified specific genetic alterations and mutations that drive ALL, inspiring new therapies. Targeted agents, such as tyrosine kinase inhibitors and immunotherapies, have shown promising results in subgroups of patients while minimizing adverse effects. Furthermore, the development of chimeric antigen receptor T cell therapy represents a breakthrough in ALL treatment, resulting in remarkable responses and potential long-term remissions. Advances are not limited to treatment modalities alone. Measurable residual disease monitoring and ex vivo drug response profiling screening have provided earlier detection of disease relapse and identification of exceptional responders, enabling clinicians to adjust treatment strategies for individual patients. Decades of supportive and prophylactic care have improved the management of treatment-related complications, enhancing the quality of life for patients with ALL.
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Affiliation(s)
- Luca Pagliaro
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Daniel Herranz
- Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Cristina Mecucci
- Department of Medicine, Hematology and Clinical Immunology, University of Perugia, Perugia, Italy
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ming Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Nicolas Boissel
- Hôpital Saint-Louis, APHP, Institut de Recherche Saint-Louis, Université Paris Cité, Paris, France
| | - Stuart S Winter
- Children's Minnesota Cancer and Blood Disorders Program, Minneapolis, MN, USA
| | - Giovanni Roti
- Department of Medicine and Surgery, University of Parma, Parma, Italy.
- Translational Hematology and Chemogenomics (THEC), University of Parma, Parma, Italy.
- Hematology and BMT Unit, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy.
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2
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Del Giudice I, Della Starza I, De Falco F, Gaidano G, Sportoletti P. Monitoring Response and Resistance to Treatment in Chronic Lymphocytic Leukemia. Cancers (Basel) 2024; 16:2049. [PMID: 38893168 PMCID: PMC11171231 DOI: 10.3390/cancers16112049] [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: 03/30/2024] [Revised: 05/09/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
The recent evolution in chronic lymphocytic leukemia (CLL) targeted therapies led to a progressive change in the way clinicians manage the goals of treatment and evaluate the response to treatment in respect to the paradigm of the chemoimmunotherapy era. Continuous therapies with BTK inhibitors achieve prolonged and sustained control of the disease. On the other hand, venetoclax and anti-CD20 monoclonal antibodies or, more recently, ibrutinib plus venetoclax combinations, given for a fixed duration, achieve undetectable measurable residual disease (uMRD) in the vast majority of patients. On these grounds, a time-limited MRD-driven strategy, a previously unexplored scenario in CLL, is being attempted. On the other side of the spectrum, novel genetic and non-genetic mechanisms of resistance to targeted treatments are emerging. Here we review the response assessment criteria, the evolution and clinical application of MRD analysis and the mechanisms of resistance according to the novel treatment strategies within clinical trials. The extent to which this novel evidence will translate in the real-life management of CLL patients remains an open issue to be addressed.
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Affiliation(s)
- Ilaria Del Giudice
- Hematology, Department of Translational and Precision Medicine, Sapienza University, 00161 Rome, Italy;
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, Sapienza University, 00161 Rome, Italy;
- AIL Roma, ODV, 00161 Rome, Italy
| | - Filomena De Falco
- Department of Medicine and Surgery, Institute of Hematology and Center for Hemato-Oncological Research, University of Perugia, 06129 Perugia, Italy;
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy;
| | - Paolo Sportoletti
- Department of Medicine and Surgery, Institute of Hematology and Center for Hemato-Oncological Research, University of Perugia, 06129 Perugia, Italy;
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3
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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.
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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
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Feng Y, Qi S, Liu X, Zhang L, Hu Y, Shen Q, Gong X, Zhang W, Wang J, Yan W, Wang T, Wang H, Song Z, Zhu X, Gale RP, Chen J. Have we been qualifying measurable residual disease correctly? Leukemia 2023; 37:2168-2172. [PMID: 37704711 PMCID: PMC10624632 DOI: 10.1038/s41375-023-02026-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Affiliation(s)
- Yahui Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Saibing Qi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xueou Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Li Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Yu Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Qiujin Shen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaowen Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Wei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Junxia Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Wen Yan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Tiantian Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Huijun Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Zhen Song
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
- Tianjin Institutes of Health Science, Tianjin, China.
| | - Robert Peter Gale
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College of Science, Technology and Medicine, London, UK
| | - Junren Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
- Tianjin Institutes of Health Science, Tianjin, China.
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Fardoos R, Christensen C, Øbro NF, Overgaard UM, Als-Nielsen B, Madsen HO, Marquart HV. Flow Sorting, Whole Genome Amplification and Next-Generation Sequencing as Combined Tools to Study Heterogeneous Acute Lymphoblastic Leukemia. Diagnostics (Basel) 2023; 13:3306. [PMID: 37958202 PMCID: PMC10650172 DOI: 10.3390/diagnostics13213306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Next-generation sequencing (NGS) methods have been introduced for immunoglobulin (IG)/T-cell receptor (TR) gene rearrangement analysis in acute lymphoblastic leukemia (ALL) and lymphoma (LBL). These methods likely constitute faster and more sensitive approaches to analyze heterogenous cases of ALL/LBL, yet it is not known whether gene rearrangements constituting low percentages of the total sequence reads represent minor subpopulations of malignant cells or background IG/TR gene rearrangements in normal B-and T-cells. In a comparison of eight cases of B-cell precursor ALL (BCP-ALL) using both the EuroClonality NGS method and the IdentiClone multiplex-PCR/gene-scanning method, the NGS method identified between 29% and 139% more markers than the gene-scanning method, depending on whether the NGS data analysis used a threshold of 5% or 1%, respectively. As an alternative to using low thresholds, we show that IG/TR gene rearrangements in subpopulations of cancer cells can be discriminated from background IG/TR gene rearrangements in normal B-and T-cells through a combination of flow cytometry cell sorting and multiple displacement amplification (MDA)-based whole genome amplification (WGA) prior to the NGS. Using this approach to investigate the clonal evolution in a BCP-ALL patient with double relapse, clonal TR rearrangements were found in sorted leukemic cells at the time of second relapse that could be identified at the time of diagnosis, below 1% of the total sequence reads. These data emphasize that caution should be exerted when interpreting rare sequences in NGS experiments and show the advantage of employing the flow sorting of malignant cell populations in NGS clonality assessments.
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Affiliation(s)
- Rabiah Fardoos
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Claus Christensen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Nina Friesgaard Øbro
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Ulrik Malthe Overgaard
- Department of Hematology, The University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Bodil Als-Nielsen
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Hans Ole Madsen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
- Faculty of Health and Medical Sciences, Institute of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
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6
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Jia MZ, Li WJ, Wang CJ, Zhang Q, Gao C, Huang XT, Zhu T, Zhang RD, Cui L, Li ZG. Tracing back of relapse clones by Ig/TCR gene rearrangements reveals complex patterns of recurrence in pediatric acute lymphoblastic leukemia. Int J Lab Hematol 2023; 45:717-725. [PMID: 37194559 DOI: 10.1111/ijlh.14100] [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: 12/15/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Relapse remained the major obstacle to improving the prognosis of children with acute lymphoblastic leukemia (ALL). This study aimed to investigate the changing patterns of Ig/TCR gene rearrangements between diagnosis and relapse and the clinical relevance and to explore the mechanism of leukemic relapse. METHODS Clonal Ig/TCR gene rearrangements were screened by multiplex PCR amplification in 85 paired diagnostic and relapse bone marrow (BM) samples from children with ALL. The new rearrangements presented at relapse were quantitatively assessed by the RQ-PCR approach targeting the patient-specific junctional region sequence in 19 diagnostic samples. The relapse clones were further back-traced to diagnostic and follow-up BM samples from 12 patients. RESULTS Comparison of Ig/TCR gene rearrangements between diagnosis and relapse showed that 40 (57.1%) B-ALL and 5 (33.3%) T-ALL patients exhibited a change from diagnosis to relapse, and 25 (35.7%) B-ALL patients acquired new rearrangements at relapse. The new relapse rearrangements were present in 15 of the 19 (78.9%) diagnostic samples as shown by RQ-PCR, with a median level of 5.26 × 10-2 . The levels of minor rearrangements correlated with B immunophenotype, WBC counts, age at diagnosis, and recurrence time. Furthermore, back-tracing rearrangements in 12 patients identified three patterns of relapse clone dynamics, which suggested the recurrence mechanisms not only through clonal selection of pre-existing subclones but also through an ongoing clonal evolution during remission and relapse. CONCLUSION Backtracking Ig/TCR gene rearrangements in relapse clones of pediatric ALL revealed complex patterns of clonal selection and evolution for leukemic relapse.
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Affiliation(s)
- Ming-Zhu Jia
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Wei-Jing Li
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chan-Juan Wang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
| | - Qing Zhang
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Chao Gao
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xiao-Tong Huang
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Ting Zhu
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Rui-Dong Zhang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
| | - Lei Cui
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Zhi-Gang Li
- Hematologic Diseases Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology-Oncology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Hematology Center, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
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Vynck M, Chen Y, Gleerup D, Vandesompele J, Trypsteen W, Lievens A, Thas O, De Spiegelaere W. Digital PCR Partition Classification. Clin Chem 2023; 69:976-990. [PMID: 37401391 DOI: 10.1093/clinchem/hvad063] [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: 01/27/2023] [Accepted: 04/19/2023] [Indexed: 07/05/2023]
Abstract
BACKGROUND Partition classification is a critical step in the digital PCR data analysis pipeline. A range of partition classification methods have been developed, many motivated by specific experimental setups. An overview of these partition classification methods is lacking and their comparative properties are often unclear, likely impacting the proper application of these methods. CONTENT This review provides a summary of all available digital PCR partition classification approaches and the challenges they aim to overcome, serving as a guide for the digital PCR practitioner wishing to apply them. We additionally discuss strengths and weaknesses of these methods, which can further guide practitioners in vigilant application of these existing methods. This review provides method developers with ideas for improving methods or designing new ones. The latter is further stimulated by our identification and discussion of application gaps in the literature, for which there are currently no or few methods available. SUMMARY This review provides an overview of digital PCR partition classification methods, their properties, and potential applications. Ideas for further advances are presented and may bolster method development.
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Affiliation(s)
- Matthijs Vynck
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Yao Chen
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - David Gleerup
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- CellCarta, Zwijnaarde, Belgium
| | - Wim Trypsteen
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Antoon Lievens
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- BASF Innovation Center Ghent, Zwijnaarde, Belgium
| | - Olivier Thas
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium
- National Institute for Applied Statistics Research Australia, School of Mathematics and Applied Statistics, University of Wollongong, Wollongong, Australia
| | - Ward De Spiegelaere
- Digital PCR Consortium, Ghent University, Ghent, Belgium
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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Giusti GNN, Ribeiro AV, Jotta PY, Thonier F, Yunes JA, Meidanis J. Vidjil add-on for MRD quantification of samples processed using the EuroClonality-NGS protocol. EJHAEM 2023; 4:770-774. [PMID: 37601854 PMCID: PMC10435716 DOI: 10.1002/jha2.749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 08/22/2023]
Abstract
Assessment of minimal residual disease in acute lymphoblastic leukemia by immune repertoire NGS requires spiking CDR3 sequences at known quantities into the patient's sample. Recently, the EuroClonality-NGS group released one of the most comprehensive protocols for this purpose. ARResT/Interrogate is a closed-source software for processing these NGS libraries, developed by this same group. Vidjil, an open-source alternative, currently cannot handle libraries prepared using this protocol. Here, we present a Vidjil add-on to solve this issue. EuroClonality-NGS prepared samples analyzed with Vidjil and ARResT/Interrogate were highly concordant (r = 0.998) and presented low error (root-mean-square error, RMSE = 0.112).
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Affiliation(s)
- Guilherme Navarro Nilo Giusti
- Centro de Pesquisa BoldriniCentro Infantil BoldriniCampinasSão PauloBrazil
- Instituto de BiologiaUniversidade Estadual de CampinasCampinasSão PauloBrazil
| | - Antonio Vítor Ribeiro
- Instituto de MatemáticaEstatística e Computação CientíficaUniversidade Estadual de CampinasCampinasSão PauloBrazil
| | | | | | - José Andrés Yunes
- Centro de Pesquisa BoldriniCentro Infantil BoldriniCampinasSão PauloBrazil
- Faculdade de Ciências MédicasUniversidade Estadual de CampinasCampinasSão PauloBrazil
| | - João Meidanis
- Instituto de ComputaçãoUniversidade Estadual de CampinasCampinasSão PauloBrazil
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Medina-Herrera A, Sarasquete ME, Jiménez C, Puig N, García-Sanz R. Minimal Residual Disease in Multiple Myeloma: Past, Present, and Future. Cancers (Basel) 2023; 15:3687. [PMID: 37509348 PMCID: PMC10377959 DOI: 10.3390/cancers15143687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Responses to treatment have improved over the last decades for patients with multiple myeloma. This is a consequence of the introduction of new drugs that have been successfully combined in different clinical contexts: newly diagnosed, transplant-eligible or ineligible patients, as well as in the relapsed/refractory setting. However, a great proportion of patients continue to relapse, even those achieving complete response, which underlines the need for updated response criteria. In 2014, the international myeloma working group established new levels of response, prompting the evaluation of minimal residual disease (MRD) for those patients already in complete or stringent complete response as defined by conventional serological assessments: the absence of tumor plasma cells in 100,000 total cells or more define molecular and immunophenotypic responses by next-generation sequencing and flow cytometry, respectively. In this review, we describe all the potential methods that may be used for MRD detection based on the evidence found in the literature, paying special attention to their advantages and pitfalls from a critical perspective.
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Affiliation(s)
- Alejandro Medina-Herrera
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - María Eugenia Sarasquete
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Cristina Jiménez
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Noemí Puig
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Ramón García-Sanz
- Departament of Hematology, University Hospital of Salamanca (HUSA/IBSAL), CIBERONC, CIC-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
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10
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Yu Z, Xie L, Zhang J, Lin H, Niu T. The evolution of minimal residual disease: key insights based on a bibliometric visualization analysis from 2002 to 2022. Front Oncol 2023; 13:1186198. [PMID: 37534257 PMCID: PMC10391156 DOI: 10.3389/fonc.2023.1186198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/15/2023] [Indexed: 08/04/2023] Open
Abstract
Background The topic of minimal residual disease (MRD) has emerged as a crucial subject matter in the domain of oncology in recent years. The detection and monitoring of MRD have become essential for the diagnosis, treatment, and prognosis of various types of malignancy. Aims The purpose of this study is to explore the research trends, hotspots, and frontiers of MRD in the last two decades through bibliometric analysis. Methods We employed Web of Science databases to carry out a bibliometric visualization analysis of research on 8,913 academic papers about MRD research from 2002 to 2022. VOSviewer, CiteSpace, RStudio, and a bibliometric online analysis platform were mainly used to conduct co-occurrence analysis and cooperative relationship analysis of countries/regions, institutions, journals, and authors in the literature. Furthermore, co-occurrence, co-citation, and burst analyses of keyword and reference were also conducted to generate relevant knowledge maps. Results In the past 20 years, the number of MRD research papers has presented an overall rising trend, going through three stages: a plateau, development, and an explosion. The output of articles in the United States was notably superior and plays a dominant role in this field, and the Netherlands had the highest average citation per article. The most productive and influential institution was the University of Texas MD Anderson Cancer Center. Blood published the most papers and was the most cited journal. A collection of leading academics has come to the fore in the research field, the most prolific of which is Kantarjian HM. It was found that the application of MRD in "acute myeloid leukemia", "acute lymphoblastic leukemia", "multiple myeloma", as well as the detection technology of MRD, are the research hotspots and frontiers in this domain. Furthermore, we analyzed the co-citation network of references and found that the top 10 co-cited references were all associated with MRD in hematological malignancies. Conclusion This bibliometric visualization analysis conducted a thorough exploration into the research hotspots and trends in MRD from 2002 to 2022. Our findings can aid researchers in recognizing possible collaborations, guiding future research directions, and fostering the growth of MRD detection and monitoring technologies.
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Affiliation(s)
- Zhengyu Yu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
| | - Li Xie
- State Key Laboratory of Wildlife Quarantine and Surveillance (Sichuan), Technology Center of Chengdu Customs, Chengdu, China
| | - Jing Zhang
- State Key Laboratory of Wildlife Quarantine and Surveillance (Sichuan), Technology Center of Chengdu Customs, Chengdu, China
| | - Hua Lin
- State Key Laboratory of Wildlife Quarantine and Surveillance (Sichuan), Technology Center of Chengdu Customs, Chengdu, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
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11
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Jahromi FNA, Dowran R, Jafari R. Recent advances in the roles of exosomal microRNAs (exomiRs) in hematologic neoplasms: pathogenesis, diagnosis, and treatment. Cell Commun Signal 2023; 21:88. [PMID: 37127640 PMCID: PMC10152632 DOI: 10.1186/s12964-023-01102-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/15/2023] [Indexed: 05/03/2023] Open
Abstract
In clinical diagnosis, the capability of exosomes to serve as biomarkers is one of the most important biological functions of exosomes. The superior stability of exosome biomarkers makes them superior to those isolated from traditional samples such as serum and urine. Almost all body fluids contain exosomes, which contain proteins, nucleic acids, and lipids. Several molecular components of exosomes, including exosome proteins and microRNAs (miRNAs), are promising diagnostic biomarkers. These exosomes may carry genetic information by containing messenger RNA (mRNA) and miRNA. The miRNAs are small noncoding RNAs that regulate protein-coding genes by acting as translational repressors. It has been shown that miRNAs are mis-expressed in a range of conditions, including hematologic neoplasms. Additionally, miRNAs found within exosomes have been linked with specific diseases, including hematologic neoplasms. Numerous studies suggest that circulating exosomes contain miRNAs similar to those found in parental cancer cells. Exosomes contain miRNAs that are released by almost all kinds of cells. MiRNAs are packaged into exosomes and delivered to recipient cells, and manipulate its function. It has been recognized that exosomes are new therapeutic targets for immunotherapy and biomedicine of cancers. The current review discusses the current evidence around exosomal miRNAs involved in the pathogenesis, diagnosis, and treatment of hematologic neoplasms. Video Abstract.
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Affiliation(s)
- Faride Nam Avar Jahromi
- Department of Hematology, School of Paramedical, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Razieh Dowran
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Jafari
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, P.O. BoX: 1138, Shafa St., Ershad Blvd., 57147, Urmia, Iran.
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12
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Fisher A, Goradia H, Martinez-Calle N, Patten PEM, Munir T. The evolving use of measurable residual disease in chronic lymphocytic leukemia clinical trials. Front Oncol 2023; 13:1130617. [PMID: 36910619 PMCID: PMC9992794 DOI: 10.3389/fonc.2023.1130617] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Measurable residual disease (MRD) status in chronic lymphocytic leukemia (CLL), assessed on and after treatment, correlates with increased progression-free and overall survival benefit. More recently, MRD assessment has been included in large clinical trials as a primary outcome and is increasingly used in routine practice as a prognostic tool, a therapeutic goal, and potentially a trigger for early intervention. Modern therapy for CLL delivers prolonged remissions, causing readout of traditional trial outcomes such as progression-free and overall survival to be inherently delayed. This represents a barrier for the rapid incorporation of novel drugs to the overall therapeutic armamentarium. MRD offers a dynamic and robust platform for the assessment of treatment efficacy in CLL, complementing traditional outcome measures and accelerating access to novel drugs. Here, we provide a comprehensive review of recent major clinical trials of CLL therapy, focusing on small-molecule inhibitors and monoclonal antibody combinations that have recently emerged as the standard frontline and relapse treatment options. We explore the assessment and reporting of MRD (including novel techniques) and the challenges of standardization and provide a comprehensive review of the relevance and adequacy of MRD as a clinical trial endpoint. We further discuss the impact that MRD data have on clinical decision-making and how it can influence a patient's experience. Finally, we evaluate how upcoming trial design and clinical practice are evolving in the face of MRD-driven outcomes.
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Affiliation(s)
- A. Fisher
- Division of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
- Department of Haematology, Leeds Teaching Hospitals National Health Service (NHS) Trust, Leeds, United Kingdom
| | - H. Goradia
- Department of Haematology, Nottingham University Hospitals National Health Service (NHS) Trust, Nottingham, United Kingdom
| | - N. Martinez-Calle
- Department of Haematology, Nottingham University Hospitals National Health Service (NHS) Trust, Nottingham, United Kingdom
| | - PEM. Patten
- Department of Haematology, Kings College Hospital National Health Service (NHS) Foundation Trust, London, United Kingdom
- Comprehensive Cancer Centre, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - T. Munir
- Department of Haematology, Leeds Teaching Hospitals National Health Service (NHS) Trust, Leeds, United Kingdom
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13
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Detecting measurable residual disease beyond 10-4 by an IGHV leader-based NGS approach improves prognostic stratification in CLL. Blood 2023; 141:519-528. [PMID: 36084320 DOI: 10.1182/blood.2022017411] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023] Open
Abstract
The sensitivity of conventional techniques for reliable quantification of minimal/measurable residual disease (MRD) in chronic lymphocytic leukemia (CLL) is limited to MRD 10-4. Measuring MRD <10-4 could help to further distinguish between patients with CLL with durable remission and those at risk of early relapse. We herein present an academically developed immunoglobulin heavy-chain variable (IGHV) leader-based next-generation sequencing (NGS) assay for the quantification of MRD in CLL. We demonstrate, based on measurements in contrived MRD samples, that the linear range of detection and quantification of our assay reaches beyond MRD 10-5. If provided with sufficient DNA input, MRD can be detected down to MRD 10-6. There was high interassay concordance between measurements of the IGHV leader-based NGS assay and allele-specific oligonucleotide quantitative polymerase chain reaction (PCR) (r = 0.92 [95% confidence interval {CI}, 0.86-0.96]) and droplet digital PCR (r = 0.93 [95% CI, 0.88-0.96]) on contrived MRD samples. In a cohort of 67 patients from the CLL11 trial, using MRD 10-5 as a cutoff, undetectable MRD was associated with superior progression-free survival (PFS) and time to next treatment. More important, deeper MRD measurement allowed for additional stratification of patients with MRD <10-4 but ≥10-5. PFS of patients in this MRD range was significantly shorter, compared with patients with MRD <10-5 (hazard ratio [HR], 4.0 [95% CI, 1.6-10.3]; P = .004), but significantly longer, compared with patients with MRD ≥10-4 (HR, 0.44 [95% CI, 0.23-0.87]; P = .018). These results support the clinical utility of the IGHV leader-based NGS assay.
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14
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Schilhabel A, Szczepanowski M, van Gastel-Mol EJ, Schillalies J, Ray J, Kim D, Nováková M, Dombrink I, van der Velden VHJ, Boettcher S, Brüggemann M, Kneba M, van Dongen JJM, Langerak AW, Ritgen M. Patient specific real-time PCR in precision medicine - Validation of IG/TR based MRD assessment in lymphoid leukemia. Front Oncol 2023; 12:1111209. [PMID: 36727082 PMCID: PMC9885152 DOI: 10.3389/fonc.2022.1111209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Detection of patient- and tumor-specific clonally rearranged immune receptor genes using real-time quantitative (RQ)-PCR is an accepted method in the field of precision medicine for hematologic malignancies. As individual primers are needed for each patient and leukemic clone, establishing performance specifications for the method faces unique challenges. Results for series of diagnostic assays for CLL and ALL patients demonstrate that the analytic performance of the method is not dependent on patients' disease characteristics. The calibration range is linear between 10-1 and 10-5 for 90% of all assays. The detection limit of the current standardized approach is between 1.8 and 4.8 cells among 100,000 leukocytes. RQ-PCR has about 90% overall agreement to flow cytometry and next generation sequencing as orthogonal methods. Accuracy and precision across different labs, and above and below the clinically applied cutoffs for minimal/measurable residual disease (MRD) demonstrate the robustness of the technique. The here reported comprehensive, IVD-guided analytical validation provides evidence that the personalized diagnostic methodology generates robust, reproducible and specific MRD data when standardized protocols for data generation and evaluation are used. Our approach may also serve as a guiding example of how to accomplish analytical validation of personalized in-house diagnostics under the European IVD Regulation.
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Affiliation(s)
- Anke Schilhabel
- Hämatologie Labor Kiel, Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany,*Correspondence: Anke Schilhabel,
| | - Monika Szczepanowski
- Hämatologie Labor Kiel, Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ellen J. van Gastel-Mol
- Laboratory Medical Immunology, Department of Immunology, Erasmus Medical Center (MC), University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Janina Schillalies
- Hämatologie Labor Kiel, Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jill Ray
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, United States
| | - Doris Kim
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, United States
| | - Michaela Nováková
- Childhood Leukemia Investigation Prague (CLIP)-Department of Pediatric Hematology and Oncology, Second Medical Faculty, Charles University and University Hospital Motol, Prague, Czechia
| | - Isabel Dombrink
- Hämatologie Labor Kiel, Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Vincent H. J. van der Velden
- Laboratory Medical Immunology, Department of Immunology, Erasmus Medical Center (MC), University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sebastian Boettcher
- Department of Medicine III Hematology, Oncology and Palliative Care, University Hospital, Rostock, Germany
| | - Monika Brüggemann
- Hämatologie Labor Kiel, Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Michael Kneba
- Hämatologie Labor Kiel, Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jacques J. M. van Dongen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Anton W. Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus Medical Center (MC), University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Matthias Ritgen
- Hämatologie Labor Kiel, Medical Department II, Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
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15
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Antigen Receptors Gene Analysis for Minimal Residual Disease Detection in Acute Lymphoblastic Leukemia: The Role of High Throughput Sequencing. HEMATO 2023. [DOI: 10.3390/hemato4010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The prognosis of adult acute lymphoblastic leukemia (ALL) is variable but more often dismal. Indeed, its clinical management is challenging, current therapies inducing complete remission in 65–90% of cases, but only 30–40% of patients being cured. The major determinant of treatment failure is relapse; consequently, measurement of residual leukemic blast (minimal residual disease, MRD) has become a powerful independent prognostic indicator in adults. Numerous evidences have also supported the clinical relevance of MRD assessment for risk class assignment and treatment selection. MRD can be virtually evaluated in all ALL patients using different technologies, such as polymerase chain reaction amplification of fusion transcripts and clonal rearrangements of antigen receptor genes, flow cytometric study of leukemic immunophenotypes and, the most recent, high throughput sequencing (HTS). In this review, the authors focused on the latest developments on MRD monitoring with emphasis on the use of HTS, as well as on the clinical impact of MRD monitoring.
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16
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Optimizing Molecular Minimal Residual Disease Analysis in Adult Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:cancers15020374. [PMID: 36672325 PMCID: PMC9856386 DOI: 10.3390/cancers15020374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Minimal/measurable residual disease (MRD) evaluation has resulted in a fundamental instrument to guide patient management in acute lymphoblastic leukemia (ALL). From a methodological standpoint, MRD is defined as any approach aimed at detecting and possibly quantifying residual neoplastic cells beyond the sensitivity level of cytomorphology. The molecular methods to study MRD in ALL are polymerase chain reaction (PCR) amplification-based approaches and are the most standardized techniques. However, there are some limitations, and emerging technologies, such as digital droplet PCR (ddPCR) and next-generation sequencing (NGS), seem to have advantages that could improve MRD analysis in ALL patients. Furthermore, other blood components, namely cell-free DNA (cfDNA), appear promising and are also being investigated for their potential role in monitoring tumor burden and response to treatment in hematologic malignancies. Based on the review of the literature and on our own data, we hereby discuss how emerging molecular technologies are helping to refine the molecular monitoring of MRD in ALL and may help to overcome some of the limitations of standard approaches, providing a benefit for the care of patients.
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17
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Turner SA, Abou Shaar R, Yang Z. The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology. Diagn Cytopathol 2023; 51:83-94. [PMID: 36345929 PMCID: PMC10098847 DOI: 10.1002/dc.25067] [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: 08/09/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre-analytic considerations and limitations, and a description of common techniques that the modern cytopathologist should understand when ordering and interpreting molecular tests in practice.
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Affiliation(s)
- Scott A Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Rand Abou Shaar
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zhongbo Yang
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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18
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Karlsson L, Nyvold CG, Soboli A, Johansson P, Palmqvist L, Tierens A, Hasle H, Lausen B, Jónsson ÓG, Jürgensen GW, Ebbesen LH, Abrahamsson J, Fogelstrand L. Fusion transcript analysis reveals slower response kinetics than multiparameter flow cytometry in childhood acute myeloid leukaemia. Int J Lab Hematol 2022; 44:1094-1101. [PMID: 35918824 PMCID: PMC9804713 DOI: 10.1111/ijlh.13935] [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: 05/11/2022] [Accepted: 06/26/2022] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Analysis of measurable residual disease (MRD) is increasingly being implemented in the clinical care of children and adults with acute myeloid leukaemia (AML). However, MRD methodologies differ and discordances in results lead to difficulties in interpretation and clinical decision-making. The aim of this study was to compare results from reverse transcription quantitative polymerase chain reaction (RT-qPCR) and multiparameter flow cytometry (MFC) in childhood AML and describe the kinetics of residual leukaemic burden during induction treatment. METHODS In 15 children who were treated in the NOPHO-AML 2004 trial and had fusion transcripts quantified by RT-qPCR, we compared MFC with RT-qPCR for analysis of MRD during (day 15) and after induction therapy. Eight children had RUNX1::RUNX1T1, one CBFB::MYH11 and six KMT2A::MLLT3. RESULTS When ≥0.1% was used as cut-off for positivity, 10 of 22 samples were discordant. The majority (9/10) were MRD positive with RT-qPCR but MRD negative with MFC, and several such cases showed the presence of mature myeloid cells. Fusion transcript expression was verified in mature cells as well as in CD34 expressing cells sorted from diagnostic samples. CONCLUSIONS Measurement with RT-qPCR suggests slower response kinetics than indicated from MFC, presumably due to the presence of mature cells expressing fusion transcript. The prognostic impact of early measurements with RT-qPCR remains to be determined.
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Affiliation(s)
- Lene Karlsson
- Department of PediatricsInstitute of Clinical Sciences, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Charlotte Guldborg Nyvold
- Haemodiagnostic Laboratory, Department of HaematologyAarhus University HospitalAarhusDenmark,Haematolology‐Pathology Research LaboratoryResearch Unit for Haematology and Research Unit for Pathology, University of Southern Denmark and Odense University HospitalOdenseDenmark
| | - Anastasia Soboli
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden,Department of Laboratory MedicineInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Pegah Johansson
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden
| | - Lars Palmqvist
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden,Department of Laboratory MedicineInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Anne Tierens
- Laboratory Medicine ProgramUniversity Health Network, Toronto General HospitalTorontoOntarioCanada
| | - Henrik Hasle
- Department of PediatricsAarhus University HospitalAarhusDenmark
| | - Birgitte Lausen
- Department of Pediatrics and Adolescent MedicineRigshospitalet, University of CopenhagenCopenhagenDenmark
| | | | - Gitte Wulff Jürgensen
- Department of Clinical ImmunologyCopenhagen University Hospital RigshospitaletCopenhagenDenmark,Department of ImmunologyOslo University HosptialOsloNorway
| | - Lene Hyldahl Ebbesen
- Haemodiagnostic Laboratory, Department of HaematologyAarhus University HospitalAarhusDenmark
| | - Jonas Abrahamsson
- Department of PediatricsInstitute of Clinical Sciences, Sahlgrenska Academy at University of GothenburgGothenburgSweden
| | - Linda Fogelstrand
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden,Department of Laboratory MedicineInstitute of Biomedicine, Sahlgrenska Academy at University of GothenburgGothenburgSweden
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19
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Ferrero S, Grimaldi D, Genuardi E, Drandi D, Zaccaria GM, Alessandria B, Ghislieri M, Ferrante M, Evangelista A, Mantoan B, De Luca G, Stefani PM, Benedetti F, Casaroli I, Zanni M, Castellino C, Pavone V, Petrini M, Re F, Hohaus S, Musuraca G, Cascavilla N, Ghiggi C, Liberati AM, Cortelazzo S, Ladetto M. Punctual and kinetic MRD analysis from the Fondazione Italiana Linfomi MCL0208 phase 3 trial in mantle cell lymphoma. Blood 2022; 140:1378-1389. [PMID: 35737911 PMCID: PMC9507010 DOI: 10.1182/blood.2021014270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/27/2022] [Indexed: 11/20/2022] Open
Abstract
Minimal residual disease (MRD) analysis is a known predictive tool in mantle cell lymphoma (MCL). We describe MRD results from the Fondazione Italiana Linfomi phase 3 MCL0208 prospective clinical trial assessing lenalidomide (LEN) maintenance vs observation after autologous stem cell transplantation (ASCT) in the first prospective comprehensive analysis of different techniques, molecular markers, and tissues (peripheral blood [PB] and bone marrow [BM]), taken at well-defined time points. Among the 300 patients enrolled, a molecular marker was identified in 250 (83%), allowing us to analyze 234 patients and 4351 analytical findings from 10 time points. ASCT induced high rates of molecular remission (91% in PB and 83% in BM, by quantitative real-time polymerase chain reaction [RQ-PCR]). Nevertheless, the number of patients with persistent clinical and molecular remission decreased over time in both arms (up to 30% after 36 months). MRD predicted early progression and long-term outcome, particularly from 6 months after ASCT (6-month time to progression [TTP] hazard ratio [HR], 3.83; P < .001). In single-timepoint analysis, BM outperformed PB, and RQ-PCR was more reliable, while nested PCR appeared applicable to a larger number of patients (234 vs 176). To improve MRD performance, we developed a time-varying kinetic model based on regularly updated MRD results and the MIPI (Mantle Cell Lymphoma International Prognostic Index), showing an area under the ROC (Receiver Operating Characteristic) curve (AUROC) of up to 0.87 using BM. Most notably, PB reached an AUROC of up to 0.81; with kinetic analysis, it was comparable to BM in performance. MRD is a powerful predictor over the entire natural history of MCL and is suitable for models with a continuous adaptation of patient risk. The study can be found in EudraCT N. 2009-012807-25 (https://eudract.ema.europa.eu/).
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Affiliation(s)
- Simone Ferrero
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
- AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Daniele Grimaldi
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
- Hematology Division, AO S.Croce e Carle, Cuneo, Italy
| | - Elisa Genuardi
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | - Daniela Drandi
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | - Gian Maria Zaccaria
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
- Hematology and Cell Therapy Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Beatrice Alessandria
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | - Marco Ghislieri
- PoliToBIOMed Lab, Politecnico di Torino, Torino, Italy
- Department of Electronics and Telecommunications, Politecnico di Torino, Torino, Italy
| | - Martina Ferrante
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | - Andrea Evangelista
- Unit of Cancer Epidemiology, CPO, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Barbara Mantoan
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | - Gabriele De Luca
- Department of Molecular Biotechnologies and Health Sciences, University of Torino, Torino, Italy
| | | | - Fabio Benedetti
- Department of Medicine, Section of Hematology and Bone Marrow Transplant Unit, University of Verona, Verona, Italy
| | | | - Manuela Zanni
- Division of Hematology, Antonio e Biagio e Cesare Arrigo Hospital, Alessandria, Italy
| | | | | | | | - Francesca Re
- Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Stefan Hohaus
- Hematology Unit, Università Cattolica S.Cuore; Roma, Italy
| | - Gerardo Musuraca
- Department of Hematology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS
| | - Nicola Cascavilla
- Hematology, Casa Sollievo della Sofferenza IRCCS Hospital, San Giovanni Rotondo, Italy
| | - Chiara Ghiggi
- Department of Hematology, San Martino Hospital and University, Genova, Italy
| | - Anna Marina Liberati
- Department of Hematology, A.O. Santa Maria Terni, University of Perugia, Perugia, Italy; and
| | | | - Marco Ladetto
- Division of Hematology, Antonio e Biagio e Cesare Arrigo Hospital, Alessandria, Italy
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20
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Salvetti C, Vitale C, Griggio V, Drandi D, Jones R, Bonello L, Bomben R, Bragoni A, Bagnara D, Fais F, Gattei V, Cavallo F, Zamò A, Coscia M. Case Report: Sequential Development of Three Mature Lymphoid Neoplasms in a Single Patient: Clonal Relationship and Molecular Insights. Front Oncol 2022; 12:917115. [PMID: 35734588 PMCID: PMC9207196 DOI: 10.3389/fonc.2022.917115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/09/2022] [Indexed: 12/29/2022] Open
Abstract
Two main variants of Richter syndrome (RS) are recognized, namely, the diffuse large B-cell lymphoma (DLBCL) and the Hodgkin’s lymphoma (HL) variant. Clonal relationship, defined as an identity of the immunoglobulin heavy chain variable (IGHV) region sequence between chronic lymphocytic leukemia (CLL) and RS clones, characterizes patients with a poor prognosis. Due to method sensitivity, this categorization is performed without considering the possibility of small-size ancillary clones, sharing the same phenotype with the preexisting predominant CLL clone, but with different IGHV rearrangements. Here we describe and molecularly profile the peculiar case of a patient with a CLL-like monoclonal B-cell lymphocytosis (MBL), who sequentially developed a DLBCL, which occurred concomitantly to progression of MBL to CLL, and a subsequent HL. Based on standard IGHV clonality analysis, DLBCL was considered clonally unrelated to the concomitantly expanded CLL clone and treated as a de novo lymphoma, achieving a persistent response. Three years later, the patient further developed a clonally unrelated HL, refractory to bendamustine, which was successfully treated with brentuximab vedotin and radiotherapy, and later with pembrolizumab. We retrospectively performed additional molecular testing, by applying next-generation sequencing (NGS) of immunoglobulin repertoire (Ig-rep) techniques and a more sensitive allele-specific oligonucleotide-droplet digital PCR (ASO-ddPCR) strategy, in order to quantitatively investigate the presence of the rearranged IGHV genes in tumor specimens collected during the disease course. In this highly complex case, the application of modern and sensitive molecular technologies uncovered that DLBCL, initially considered as a de novo lymphoma, was instead the result of the transformation of a preexisting ancillary B-cell clone, which was already present at the time of first MBL diagnosis. A similar approach was also applied on the HL sample, showing its clonal unrelatedness to the previous MBL and DLBCL.
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Affiliation(s)
- Chiara Salvetti
- Division of Hematology, University of Torino, A.O.U. Città della Salute e della Scienza di Torino, Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Candida Vitale
- Division of Hematology, University of Torino, A.O.U. Città della Salute e della Scienza di Torino, Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Valentina Griggio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Daniela Drandi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Rebecca Jones
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Lisa Bonello
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Molecular Pathology Unit, A.O.U. Città della Salute e della Scienza di Torino, Torino, Italy
| | - Riccardo Bomben
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Alberto Bragoni
- Pathology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Davide Bagnara
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Franco Fais
- Department of Experimental Medicine, University of Genova, Genova, Italy.,U.O. Molecular Pathology, I.R.C.C.S. Policlinico San Martino, Genova, Italy
| | - Valter Gattei
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Federica Cavallo
- Division of Hematology, University of Torino, A.O.U. Città della Salute e della Scienza di Torino, Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Alberto Zamò
- Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Marta Coscia
- Division of Hematology, University of Torino, A.O.U. Città della Salute e della Scienza di Torino, Torino, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
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21
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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.
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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.
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22
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LymphoTrack Is Equally Sensitive as PCR GeneScan and Sanger Sequencing for Detection of Clonal Rearrangements in ALL Patients. Diagnostics (Basel) 2022; 12:diagnostics12061389. [PMID: 35741199 PMCID: PMC9222020 DOI: 10.3390/diagnostics12061389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/26/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Monoclonal rearrangements of immunoglobulin (Ig) genes and T-cell receptor (TCR) genes are used for minimal measurable disease in acute lymphoblastic leukemia (ALL). The golden standard for screening of gene rearrangements in ALL has been PCR GeneScan and Sanger sequencing, which are laborsome and time-consuming methods. More rapid next-generation sequencing methods, such as LymphoTrack could possibly replace PCR GeneScan and Sanger sequencing for clonality assessment. Our aim was to evaluate to what extent LymphoTrack can replace PCR GeneScan and Sanger sequencing concerning sensitivity and quantifiability in clonality assessment in 78 ALL samples. With LymphoTrack, clonality assessment was based on the %Total reads, where ≥10% was used as cut off for clonal rearrangements. The patients displayed 0 to 4 clonal rearrangements per assay. The detection rate (rearrangements detected with PCR GeneScan and/or Sanger sequencing, also detected with LymphoTrack) was 85/85 (100%) for IGH, 64/67 (96%) for IGK, 91/93 (98%) for TCRG and 34/35 (97%) for TCRB. Our findings demonstrate that LymphoTrack was equally sensitive in detecting clonal rearrangements as PCR GeneScan and Sanger Sequencing. The LymphoTrack assay is reliable and therefore applicable for clonal assessment in ALL patients in clinical laboratories.
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23
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Fronkova E, Svaton M, Trka J. Quality Control for IG /TR Marker Identification and MRD Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:91-99. [PMID: 35622322 DOI: 10.1007/978-1-0716-2115-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Selection of the proper target is crucial for clinically relevant monitoring of minimal residual disease (MRD) in patients with acute lymphoblastic leukemia using the quantitation of clonal-specific immunoreceptor (immunoglobulin/T cell receptor) gene rearrangements. Consequently, correct interpretation of the results of the entire analysis is of utmost importance. Here we present an overview of the quality control measures that need to be implemented into the process of marker identification, selection, and subsequent quantitation of the MRD level.
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Affiliation(s)
- 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
| | - 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
| | - 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.
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24
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Rozowsky JS, Meesters-Ensing JI, Lammers JAS, Belle ML, Nierkens S, Kranendonk MEG, Kester LA, Calkoen FG, van der Lugt J. A Toolkit for Profiling the Immune Landscape of Pediatric Central Nervous System Malignancies. Front Immunol 2022; 13:864423. [PMID: 35464481 PMCID: PMC9022116 DOI: 10.3389/fimmu.2022.864423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The prognosis of pediatric central nervous system (CNS) malignancies remains dismal due to limited treatment options, resulting in high mortality rates and long-term morbidities. Immunotherapies, including checkpoint inhibition, cancer vaccines, engineered T cell therapies, and oncolytic viruses, have promising results in some hematological and solid malignancies, and are being investigated in clinical trials for various high-grade CNS malignancies. However, the role of the tumor immune microenvironment (TIME) in CNS malignancies is mostly unknown for pediatric cases. In order to successfully implement immunotherapies and to eventually predict which patients would benefit from such treatments, in-depth characterization of the TIME at diagnosis and throughout treatment is essential. In this review, we provide an overview of techniques for immune profiling of CNS malignancies, and detail how they can be utilized for different tissue types and studies. These techniques include immunohistochemistry and flow cytometry for quantifying and phenotyping the infiltrating immune cells, bulk and single-cell transcriptomics for describing the implicated immunological pathways, as well as functional assays. Finally, we aim to describe the potential benefits of evaluating other compartments of the immune system implicated by cancer therapies, such as cerebrospinal fluid and blood, and how such liquid biopsies are informative when designing immune monitoring studies. Understanding and uniformly evaluating the TIME and immune landscape of pediatric CNS malignancies will be essential to eventually integrate immunotherapy into clinical practice.
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Affiliation(s)
| | | | | | - Muriël L. Belle
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | | | - Friso G. Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
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25
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Wu M, Shen H, Wang Z, Kanu N, Chen K. Research Progress on Postoperative Minimal/Molecular Residual Disease Detection in Lung Cancer. Chronic Dis Transl Med 2022; 8:83-90. [PMID: 35774426 PMCID: PMC9215711 DOI: 10.1002/cdt3.10] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/22/2021] [Indexed: 12/05/2022] Open
Abstract
Lung cancer is the leading cause of cancer‐related deaths worldwide. Approximately 10%–50% of patients experience relapse after radical surgery, which may be attributed to the persistence of minimal/molecular residual disease (MRD). Circulating tumor DNA (ctDNA), a common liquid biopsy approach, has been demonstrated to have significant clinical merit. In this study, we review the evidence supporting the use of ctDNA for MRD detection and discuss the potential clinical applications of postoperative MRD detection, including monitoring recurrence, guiding adjuvant treatment, and driving clinical trials in lung cancer. We will also discuss the problems that prevent the routine application of ctDNA MRD detection. Multi‐analyte methods and identification of specific genetic and molecular alterations, especially methylation, are effective detection strategies and show considerable prospects for future development. Interventional prospective studies based on ctDNA detection are needed to determine whether the application of postoperative MRD detection can improve the clinical outcomes of lung cancer patients, and the accuracy, sensitivity, specificity, and robustness of different detection methods still require optimization and refinement.
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Affiliation(s)
- Manqi Wu
- Department of Thoracic Surgery Peking University People's Hospital, Peking University Beijing 100044 China
| | - Haifeng Shen
- Department of Thoracic Surgery Peking University People's Hospital, Peking University Beijing 100044 China
| | - Ziyang Wang
- Department of Thoracic Surgery Peking University People's Hospital, Peking University Beijing 100044 China
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence University College London Cancer Institute, University College London 72 Huntley St London WC1E 6DD UK
| | - Kezhong Chen
- Department of Thoracic Surgery Peking University People's Hospital, Peking University Beijing 100044 China
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26
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Ozono S, Yano S, Oishi S, Mitsuo M, Nakagawa S, Toki T, Terui K, Ito E. A Case of Congenital Leukemia With MYB-GATA1 Fusion Gene in a Female Patient. J Pediatr Hematol Oncol 2022; 44:e250-e252. [PMID: 33661169 DOI: 10.1097/mph.0000000000002119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/11/2021] [Indexed: 11/26/2022]
Abstract
We report a female newborn with acute myelogenous leukemia (AML) associated with a MYB-GATA1 fusion gene. Morphologic findings of myeloid lineage were obtained using light microscopy. Cytogenetic analysis of peripheral blood showed a complex karyotype: 46,X,-X,add(3)(q21),der(6)add(6)(q21)del(6)(q?), +mar1[5]/46,XX[15]. Targeted RNA sequencing revealed a MYB-GATA1 fusion gene. Reduced-dose AML-type chemotherapy resulted in remission and survival for >3 years without relapse. The present case demonstrated the feasibility of carrying out targeted RNA sequencing for identifying MYB-GATA1 and supports the notion that neonatal AML with MYB-GATA1 with reduced chemotherapy may show better prognosis than other highly toxic therapies.
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MESH Headings
- Chromosome Aberrations
- Female
- GATA1 Transcription Factor/genetics
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/drug therapy
- Infant, Newborn, Diseases/genetics
- Leukemia, Myeloid, Acute/congenital
- Leukemia, Myeloid, Acute/drug therapy
- Oncogene Proteins, Fusion/genetics
- Proto-Oncogene Proteins c-myb/genetics
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Affiliation(s)
- Shuichi Ozono
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka
| | - Shoichiro Yano
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka
| | - Saori Oishi
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka
| | - Miho Mitsuo
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka
| | - Shinichiro Nakagawa
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Fukuoka
| | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Kiminori Terui
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Aomori, Japan
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27
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Harada T, Toyoda H, Tsuboya N, Hanaki R, Amano K, Hirayama M. Successful hematopoietic stem cell transplantation for two patients with relapse of intrachromosomal amplification of chromosome 21-positive B-cell precursor acute lymphoblastic leukemia. Front Pediatr 2022; 10:960126. [PMID: 36160794 PMCID: PMC9492991 DOI: 10.3389/fped.2022.960126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
In children with relapsed acute lymphoblastic leukemia (ALL), it is essential to identify patients in need of treatment intensification. Minimal residual disease (MRD)-based treatment stratification resulted in excellent survival in children with late relapsed B-cell precursor (BCP)-ALL. Chemotherapy alone produced a favorable outcome in patients with negative MRD after induction. The genetic abnormality also plays an important role in determining the prognosis and stratification for treatment. Intrachromosomal amplification of chromosome 21 (iAMP21) is associated with a poor outcome and a high risk for relapse, and there is no standard treatment after relapse. Herein, we present two patients with relapsed iAMP21-positive ALL who were successfully treated by cord blood transplantation (CBT). Although both patients had late bone marrow relapse and favorable MRD response, CBT was performed due to iAMP21 positive. Patients 1 and 2 have been in remission post-CBT for 15 and 45 months, respectively. Patients with relapsed iAMP21-positive ALL may be considered for stem cell transplantation even in late relapses and favorable MRD response.
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Affiliation(s)
- Tomoya Harada
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Hidemi Toyoda
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Naoki Tsuboya
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Ryo Hanaki
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Keishiro Amano
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
| | - Masahiro Hirayama
- Department of Pediatrics, Mie University Graduate School of Medicine, Tsu, Japan
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28
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Yang S, Kay NE, Shi M, Ossenkoppele G, Walter RB, Gale RP. Measurable residual disease testing in chronic lymphocytic leukaemia: hype, hope neither or both? Leukemia 2021; 35:3364-3370. [PMID: 34580401 DOI: 10.1038/s41375-021-01419-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023]
Affiliation(s)
- Shenmiao Yang
- Peking University Peoples Hospital, Peking University Institute of Hematology, Beijing, China
| | - Neil E Kay
- Mayo Clinic, Department of Medicine, Division of Hematology, Rochester, MN, USA
| | - Min Shi
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Gert Ossenkoppele
- Department of Hematology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Roland B Walter
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA
| | - Robert Peter Gale
- Haematology Research Centre, Department of Immunology and Inflammation, Imperial College London, London, UK.
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29
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Gjærde LK, Rank CU, Andersen MK, Jakobsen LH, Sengeløv H, Olesen G, Kornblit B, Marquart H, Friis LS, Petersen SL, Andersen NS, Nielsen OJ, Toft N, Schjødt I. Improved survival after allogeneic transplantation for acute lymphoblastic leukemia in adults: a Danish population-based study. Leuk Lymphoma 2021; 63:416-425. [PMID: 34672245 DOI: 10.1080/10428194.2021.1992620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We investigated trends of survival in a population-based cohort study of all 181 adults who received HCT for ALL in Denmark between 2000-2019. Patients had a median (min-max) age of 36 (18-74) years at HCT and were followed for a median of eight years. Overall survival (OS) improved over time with an estimated 2-year OS of 49% (CI 27-66%) in year 2000 versus 77% (CI 59-88%) in year 2019. More patients achieved cure over time (OR for cure per year 1.07, CI 1.00-1.15), while the rate of death in non-cured patients remained stable (HR of excess mortality per year 0.99, CI 0.93-1.06). Relapse decreased over time (HR 0.92 per year, CI 0.87-0.98), whereas non-relapse mortality did not change notably (HR 0.98 per year, CI 0.93-1.04). In conclusion, survival after HCT in adults with ALL has improved over the past two decades, primarily due to more patients achieving cure.
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Affiliation(s)
- Lars Klingen Gjærde
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie Utke Rank
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mette Klarskov Andersen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lasse Hjort Jakobsen
- Department of Hematology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Henrik Sengeløv
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Gitte Olesen
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Brian Kornblit
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hanne Marquart
- Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark
| | - Lone Smidstrup Friis
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Søren Lykke Petersen
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Ove Juul Nielsen
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Nina Toft
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ida Schjødt
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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30
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Chen D, Sutton R, Giles J, Venn NC, Huang L, Law T, Subhash VV, Trahair TN, Henderson MJ. Analytical Quality Controls for ddPCR Detection of Minimal Residual Disease in Acute Lymphoblastic Leukemia. Clin Chem 2021. [DOI: 10.1093/clinchem/hvab117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Background
Droplet digital PCR (ddPCR) is a promising technique for absolute quantification of minimal residual disease (MRD) in acute lymphoblastic leukemia (ALL), but there is no comprehensive quality assurance program to enable its application in clinical laboratories. Current guidelines for real-time quantitative PCR (qPCR) assays targeting immunoglobulin/T-cell receptor (Ig/TCR) gene rearrangements needed adaptation for ddPCR to cover droplet generation, intraassay variation, and interassay variation in the absence of standard curves.
Methods
Six qPCR MRD assays for Ig/TCR gene rearrangements and a standard albumin control gene assay were migrated to a ddPCR platform and used to test 82 remission samples from 6 patients with ALL. Three analytical quality controls (QC) were developed and evaluated for ddPCR MRD detection.
Results
Analytical QC for droplet number generation (DN-QC), for albumin ddPCR assay performance (Alb-QC) and for patient-specific marker assay performance (PS-QC) were established with pass/fail limits and corresponding QC rules. Compared to established qPCRs, the ddPCR assays had comparable sensitivity and quantitative range. Overall, there was close agreement (91%) of MRD results between qPCR and ddPCR (κ = 0.86, P < 0.0001) and stronger concordance in 32 quantifiable samples (R2 = 0.97, P < 0.0001).
Conclusions
The use of this newly developed quality control system for ddPCR MRD testing avoids the need to repeat standard curves and provides reliable results comparable to standardized qPCR methods for MRD detection in ALL.
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Affiliation(s)
- Dan Chen
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Rosemary Sutton
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Medicine, Randwick, Australia
| | - Jodie Giles
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Nicola C Venn
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Libby Huang
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Tamara Law
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Vinod Vijay Subhash
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Toby N Trahair
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Medicine, Randwick, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, Australia
| | - Michelle J Henderson
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Medicine, Randwick, Australia
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31
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Izumi A, Tachibana T, Ando T, Tanaka M, Kanamori H, Nakajima H. A case series of patients treated with inotuzumab ozogamicin for acute lymphoblastic leukemia relapsed after allogeneic hematopoietic cell transplantation. Int J Hematol 2021; 115:69-76. [PMID: 34490598 DOI: 10.1007/s12185-021-03217-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022]
Abstract
This single-center retrospective study was performed in consecutive patients with acute lymphoblastic leukemia who relapsed after allogeneic hematopoietic cell transplantation (HCT) and received salvage therapy using inotuzumab ozogamicin (InO). Ten patients (median age: 27 years) treated between June 2018 and July 2020 who met the eligibility criteria were included in this study. Nine patients received InO in one cycle and seven of these patients achieved complete hematological remission after salvage chemotherapy including InO. Negative minimal residual disease was confirmed in all four evaluable patients. Eight patients were successfully bridged to the subsequent HCT. After HCT, veno-occlusive disease (VOD) developed in three patients, and caused the death of one. No patient received maintenance therapy. At present, five patients are disease-free and alive, and the overall and progression-free survival rates at 1 year were 60% and 40%, respectively. High rates of disease remission and bridging to HCT with comprehensive treatments including InO may have contributed to favorable outcomes. However, further investigation is needed to reduce post-HCT complications including VOD.
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Affiliation(s)
- Akihiko Izumi
- Department of Hematology, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Takayoshi Tachibana
- Department of Hematology, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi-ku, Yokohama, 241-8515, Japan.
| | - Taiki Ando
- Department of Hematology, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Masatsugu Tanaka
- Department of Hematology, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Heiwa Kanamori
- Department of Hematology, Kanagawa Cancer Center, 2-3-2 Nakao, Asahi-ku, Yokohama, 241-8515, Japan
| | - Hideaki Nakajima
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Yokohama, Japan
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32
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Navrkalova V, Plevova K, Hynst J, Pal K, Mareckova A, Reigl T, Jelinkova H, Vrzalova Z, Stranska K, Pavlova S, Panovska A, Janikova A, Doubek M, Kotaskova J, Pospisilova S. LYmphoid NeXt-Generation Sequencing (LYNX) Panel: A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. J Mol Diagn 2021; 23:959-974. [PMID: 34082072 DOI: 10.1016/j.jmoldx.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (≥6 Mb) and recurrent chromosomal aberrations (≥300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel represents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine II - Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrea Mareckova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Tomas Reigl
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Zuzana Vrzalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Andrea Janikova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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Doucette K, Karp J, Lai C. Advances in therapeutic options for newly diagnosed, high-risk AML patients. Ther Adv Hematol 2021; 12:20406207211001138. [PMID: 33995985 PMCID: PMC8111550 DOI: 10.1177/20406207211001138] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive malignancy characterized by clonal proliferation of neoplastic immature precursor cells. AML impacts older adults and has a poor prognosis. Despite recent advances in treatment, AML is complex, with both genetic and epigenetic aberrations in the malignant clone and elaborate interactions with its microenvironment. We are now able to stratify patients on the basis of specific clinical and molecular features in order to optimize individual treatment strategies. However, our understanding of the complex nature of these molecular abnormalities continues to expand the defining characteristics of high-risk mutations. In this review, we focus on genetic and microenvironmental factors in adverse risk AML that play critical roles in leukemogenesis, including those not described in an European LeukemiaNet adverse risk group, and describe therapies that are currently in the clinical arena, either approved or under development.
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Affiliation(s)
- Kimberley Doucette
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - Judith Karp
- Johns Hopkins University Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Catherine Lai
- Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, 3800 Reservoir Road, NW, Washington, DC 20007, USA
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Pandzic Jaksic V, Grizelj D, Livun A, Ajduk M, Boscic D, Vlasic A, Marusic M, Gizdic B, Kusec R, Jaksic O. Inflammatory Gene Expression in Neck Perivascular and Subcutaneous Adipose Tissue in Men With Carotid Stenosis. Angiology 2021; 73:234-243. [PMID: 33906471 DOI: 10.1177/00033197211012539] [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: 12/22/2022]
Abstract
The inflammatory phenotype of neck adipose tissue (NAT) might reflect its involvement in the pathogenesis of carotid atherosclerosis. We investigated inflammatory gene expression in the subcutaneous and the perivascular (pericarotid) adipose tissue from patients with carotid stenosis (CS) undergoing endarterectomy and a control group of patients without significant carotid atherosclerosis undergoing thyroid surgery. Only male patients were included (n = 13 in each study group). Clinical and biochemical data along with serum leptin, adiponectin, and monocyte chemoattractant protein 1 (MCP-1) were collected. Adipose tissue samples were obtained from both the subcutaneous and pericarotid compartments. Real-time polymerase chain reaction was used to measure gene expression of macrophage markers and adipokines. The CS group had higher subcutaneous and pericarotid visfatin gene expression and higher pericarotid expression of MCP-1 and CD68 genes. The ratio between pericarotid CD206 and CD68 gene expression was similar between study groups. Adiponectin gene expression in both NAT compartments did not differ between groups, but it was negatively associated with body weight. These observations suggest that NAT, and especially the pericarotid compartment, express enhanced inflammatory properties in patients with CS, but the proportion of anti-inflammatory macrophages in advanced atherosclerosis seems to be maintained.
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Affiliation(s)
- Vlatka Pandzic Jaksic
- Department of Endocrinology, Diabetes and Clinical Pharmacology, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Danijela Grizelj
- Department of Cardiology, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Ana Livun
- Department of Laboratory Diagnostics, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Marko Ajduk
- Department of Vascular Surgery, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Drago Boscic
- Department of Otorhinolaryngology, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Ana Vlasic
- Department of Otorhinolaryngology, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Maruska Marusic
- Department of Laboratory Diagnostics, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Branimir Gizdic
- Department of Laboratory Diagnostics, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Rajko Kusec
- Department of Laboratory Diagnostics, Dubrava Clinical Hospital, Zagreb, Croatia.,Department of Hematology, Dubrava Clinical Hospital, Zagreb, Croatia
| | - Ozren Jaksic
- Department of Hematology, Dubrava Clinical Hospital, Zagreb, Croatia
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35
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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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Dreisig K, Brünner ED, Marquart HV, Helt LR, Nersting J, Frandsen TL, Jonsson OG, Taskinen M, Vaitkeviciene G, Lund B, Abrahamsson J, Lepik K, Schmiegelow K. TPMT polymorphisms and minimal residual disease after 6-mercaptopurine post-remission consolidation therapy of childhood acute lymphoblastic leukaemia. Pediatr Hematol Oncol 2021; 38:227-238. [PMID: 33205673 DOI: 10.1080/08880018.2020.1842570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bone marrow minimal residual disease (MRD) is the strongest predictor of relapse in children with acute lymphoblastic leukemia (ALL). 6-mercaptopurine (6MP) in ALL therapy has wide inter-individual variation in disposition and is strongly influenced by polymorphisms in the thiopurine methyltransferase (TPMT) gene. In 952 patients treated according to the NOPHO ALL2008 protocol, we explored the association between thiopurine disposition, TPMT genotypes and MRD levels after consolidation therapy with 6MP, high-dose methotrexate (HD-MTX), asparaginase, and vincristine. The levels of the cytotoxic DNA-incorporated thioguanine were significantly higher on day 70-79 in G460A/A719G TPMT heterozygous (TPMTHZ) compared to TPMT wild type (TPMTWT) patients (mean: 230.7 vs. 149.7 fmol/µg DNA, p = 0.002). In contrast, TPMT genotype did not associate with the end of consolidation MRD levels irrespective of randomization of the patients to fixed dose (25 mg/m2/day) or 6MP escalation (up to 50 or 75 mg/m2/day) during consolidation therapy.
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Affiliation(s)
- Karin Dreisig
- Pediatric Oncology research laboratory, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Emilie Damgaard Brünner
- Pediatric Oncology research laboratory, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Hanne V Marquart
- The Tissue Typing Laboratory, Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Louise Rold Helt
- Pediatric Oncology research laboratory, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Jacob Nersting
- Pediatric Oncology research laboratory, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Thomas Leth Frandsen
- Department of Pediatrics and adolescent medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark
| | | | - Mervi Taskinen
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Children and Adolescents, Helsinki University Hospital, Helsinki, Finland
| | - Goda Vaitkeviciene
- Children's Hospital, Vilnius University Hospital Santaros Klinikos and Vilnius University, Vilnius, Lithuania
| | - Bendik Lund
- Department of Pediatrics, St. Olavs Hospital, Trondheim; Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jonas Abrahamsson
- Department of Pediatrics, Institution for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Kjeld Schmiegelow
- Pediatric Oncology research laboratory, The University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Pediatrics and adolescent medicine, The University Hospital Rigshospitalet, Copenhagen, Denmark.,Institute of Clinical Medicine, Faculty of Medicine, University of Copenhagen, Denmark
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37
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Genuardi E, Klous P, Mantoan B, Drandi D, Ferrante M, Cavallo F, Alessandria B, Dogliotti I, Grimaldi D, Ragaini S, Clerico M, Lo Schirico M, Saraci E, Yilmaz M, Zaccaria GM, Cortelazzo S, Vitolo U, Luminari S, Federico M, Boccadoro M, van Min M, Splinter E, Ladetto M, Ferrero S. Targeted locus amplification to detect molecular markers in mantle cell and follicular lymphoma. Hematol Oncol 2021; 39:293-303. [PMID: 33742718 PMCID: PMC8451873 DOI: 10.1002/hon.2864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/22/2021] [Accepted: 03/06/2021] [Indexed: 11/16/2022]
Abstract
Minimal residual disease (MRD) monitoring by PCR methods is a strong and standardized predictor of clinical outcome in mantle cell lymphoma (MCL) and follicular lymphoma (FL). However, about 20% of MCL and 40% of FL patients lack a reliable molecular marker, being thus not eligible for MRD studies. Recently, targeted locus amplification (TLA), a next‐generation sequencing (NGS) method based on the physical proximity of DNA sequences for target selection, identified novel gene rearrangements in leukemia. The aim of this study was to test TLA in MCL and FL diagnostic samples lacking a classical, PCR‐detectable, t(11; 14) MTC (BCL1/IGH), or t(14; 18) major breakpoint region and minor cluster region (BCL2/IGH) rearrangements. Overall, TLA was performed on 20 MCL bone marrow (BM) or peripheral blood (PB) primary samples and on 20 FL BM, identifying a novel BCL1 or BCL2/IGH breakpoint in 16 MCL and 8 FL patients (80% and 40%, respectively). These new breakpoints (named BCL1‐TLA and BCL2‐TLA) were validated by ASO primers design and compared as MRD markers to classical IGH rearrangements in eight MCL: overall, MRD results by BCL1‐TLA were superimposable (R Pearson = 0.76) to the standardized IGH‐based approach. Moreover, MRD by BCL2‐TLA reached good sensitivity levels also in FL and was predictive of a primary refractory case. In conclusion, this study offers the proof of principle that TLA is a promising and reliable NGS‐based technology for the identification of novel molecular markers, suitable for further MRD analysis in previously not traceable MCL and FL patients.
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Affiliation(s)
- Elisa Genuardi
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | | | - Barbara Mantoan
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | - Daniela Drandi
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | - Martina Ferrante
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | - Federica Cavallo
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Beatrice Alessandria
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | - Irene Dogliotti
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Daniele Grimaldi
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Simone Ragaini
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Michele Clerico
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | - Mariella Lo Schirico
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | | | | | - Gian Maria Zaccaria
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy
| | | | - Umberto Vitolo
- Department of Oncology, Division of Hematology, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Stefano Luminari
- Hematology Unit, Azienda USL IRCCS di Reggio Emilia, Reggio Emilia, Modena, Italy.,Medical Oncology, CHIMOMO department, University of Modena and Reggio Emilia, Modena, Italy
| | - Massimo Federico
- Medical Oncology, CHIMOMO department, University of Modena and Reggio Emilia, Modena, Italy
| | - Mario Boccadoro
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
| | | | | | - Marco Ladetto
- Division of Hematology, Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Simone Ferrero
- Department of Molecular Biotechnology and Health Sciences, Division of Hematology, University of Torino, Torino, Italy.,Division of Hematology 1, AOU "Città della Salute e della Scienza di Torino", Torino, Italy
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38
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Droplet Digital PCR Improves IG-/TR-based MRD Risk Definition in Childhood B-cell Precursor Acute Lymphoblastic Leukemia. Hemasphere 2021; 5:e543. [PMID: 33655199 PMCID: PMC7909459 DOI: 10.1097/hs9.0000000000000543] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 02/04/2023] Open
Abstract
Minimal residual disease (MRD) is the most powerful prognostic factor in pediatric acute lymphoblastic leukemia (ALL). Real-time quantitative polymerase chain reaction (RQ-PCR) represents the gold standard for molecular MRD assessment and risk-based stratification of front-line treatment. In the protocols of the Italian Association of Pediatric Hematology and Oncology (AIEOP) and the Berlin-Frankfurth-Munschen (BFM) group AIEOP-BFM ALL2009 and ALL2017, B-lineage ALL patients with high RQ-PCR-MRD at day+33 and positive at day+78 are defined slow early responders (SERs). Based on results of the AIEOP-BFM ALL2000 study, these patients are treated as high-risk also when positive MRD signal at day +78 is below the lower limit of quantification of RQ-PCR (“positive not-quantifiable,” POS-NQ). To assess whether droplet digital polymerase chain reaction (ddPCR) could improve patients’ risk definition, we analyzed MRD in 209 pediatric B-lineage ALL cases classified by RQ-PCR as POS-NQ and/or negative (NEG) at days +33 and/or +78 in the AIEOP-BFM ALL2000 trial. ddPCR MRD analysis was performed on 45 samples collected at day +78 from SER patients, who had RQ-PCR MRD ≥ 5.0 × 10–4 at day+33 and POS-NQ at day+78 and were treated as medium risk (MR). The analysis identified 13 of 45 positive quantifiable cases. Most relapses occurred in this patients’ subgroup, while ddPCR NEG or ddPCR-POS-NQ patients had a significantly better outcome (P < 0.001). Overall, in 112 MR cases and 52 standard-risk patients, MRD negativity and POS-NQ were confirmed by the ddPCR analysis except for a minority of cases, for whom no differences in outcome were registered. These data indicate that ddPCR is more accurate than RQ-PCR in the measurement of MRD, particularly in late follow-up time points, and may thus allow improving patients’ stratification in ALL protocols.
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39
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Li MX, Chen Y, Chen ZP, Yu RQ. An assumption-free quantitative polymerase chain reaction method with internal standard. Talanta 2020; 220:121405. [PMID: 32928421 DOI: 10.1016/j.talanta.2020.121405] [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: 12/18/2019] [Revised: 05/05/2020] [Accepted: 07/09/2020] [Indexed: 10/23/2022]
Abstract
In real-time quantitative polymerase chain reaction (PCR), the standard curve between threshold cycle and logarithm of template concentration is currently the gold standard for template quantification. The efficacy of this approach is limited by the necessary assumption that all samples are amplified with the same efficiency. To overcome this limitation, a new method has been proposed in this contribution for quantitative PCR with internal standard. Unlike existing methods based upon analysis of amplification profile position, the new method tries to determine the initial quantity of the target template in a sample from the fluorescence spectrum measured at a certain point during its PCR reaction. There is no unrealistic prerequisite (e.g., constant amplification efficiency) for the successful application of the new method. The performance of the new method was evaluated by the quantification of KRAS gene in HepG2 samples. Quantitative results with recovery rates in the range of 91.2-118% were achieved by the new method. It is reasonable to expect that the new method would have a place in real-time quantitative PCR, thanks to its features of no unrealistic prerequisite, sound theoretical basis, good performance, and implementation simplicity.
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Affiliation(s)
- Min-Xi Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China
| | - Yao Chen
- Hunan Key Lab of Biomedical Materials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, 412008, PR China.
| | - Zeng-Ping Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China.
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China
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40
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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
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41
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Sacco A, Forgione L, Carotenuto M, De Luca A, Ascierto PA, Botti G, Normanno N. Circulating Tumor DNA Testing Opens New Perspectives in Melanoma Management. Cancers (Basel) 2020; 12:E2914. [PMID: 33050536 PMCID: PMC7601606 DOI: 10.3390/cancers12102914] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022] Open
Abstract
Malignant melanoma accounts for about 1% of all skin cancers, but it causes most of the skin cancer-related deaths. Circulating tumor DNA (ctDNA) testing is emerging as a relevant tool for the diagnosis and monitoring of cancer. The availability of highly sensitive techniques, including next generation sequencing (NGS)-based panels, has increased the fields of application of ctDNA testing. While ctDNA-based tests for the early detection of melanoma are not available yet, perioperative ctDNA analysis in patients with surgically resectable melanoma offers relevant prognostic information: i) the detection of ctDNA before surgery correlates with the extent and the aggressiveness of the disease; ii) ctDNA testing after surgery/adjuvant therapy identifies minimal residual disease; iii) testing ctDNA during the follow-up can detect a tumor recurrence, anticipating clinical/radiological progression. In patients with advanced melanoma, several studies have demonstrated that the analysis of ctDNA can better depict tumor heterogeneity and provides relevant prognostic information. In addition, ctDNA testing during treatment allows assessing the response to systemic therapy and identifying resistance mechanisms. Although validation in prospective clinical trials is needed for most of these approaches, ctDNA testing opens up new scenarios in the management of melanoma patients that could lead to improvements in the diagnosis and therapy of this disease.
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Affiliation(s)
- Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
| | - Laura Forgione
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
| | - Marianeve Carotenuto
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
| | - Paolo A. Ascierto
- Department of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Napoli, Italy;
| | - Gerardo Botti
- Scientific Direction, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Napoli, Italy;
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.S.); (L.F.); (M.C.); (A.D.L.)
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42
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Reading the B-cell receptor immunome in chronic lymphocytic leukemia: revelations and applications. Exp Hematol 2020; 93:14-24. [PMID: 32976948 DOI: 10.1016/j.exphem.2020.09.194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/25/2020] [Accepted: 09/19/2020] [Indexed: 12/19/2022]
Abstract
B-Cell receptor (BCR) sequencing has been the force driving many recent advances in chronic lymphocytic leukemia (CLL) research. Here, we discuss the general principles, revelations, and applications of reading the BCR immunome in the context of CLL. First, IGHV mutational status, obtained by measuring the mutational imprint on the IGHV gene of the CLL clonotype, is the cornerstone of CLL risk stratification. Furthermore, the discovery of "BCR-stereotyped" groups of unrelated patients that share not only a highly similar BCR on their leukemic clone, but also certain clinical characteristics has provided insights key to understanding disease ontogeny. Additionally, whereas the BCR repertoire of most CLL patients is characterized by a single dominant rearrangement, next-generation sequencing (NGS) has revealed a rich subclonal landscape in a larger than previously expected proportion of CLL patients. We review the mechanisms underlying these "multiple dominant" cases, including V(D)J-recombination errors, failure of allelic exclusion, intraclonal diversification, and "true" bi- or oligoclonality, and their implications, in detail. Finally, BCR repertoire sequencing can be used for sensitive quantification of minimal residual disease to potentially unprecedented depth. To surmount pitfalls inherent to this approach and develop internationally harmonized protocols, the EuroClonality-NGS Working Group has been established.
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43
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Miao P, Tang Y. Two-Dimensional Hybridization Chain Reaction Strategy for Highly Sensitive Analysis of Intracellular mRNA. Anal Chem 2020; 92:12700-12709. [DOI: 10.1021/acs.analchem.0c03181] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
- Department of Chemistry, New York University, New York 10003, United States
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P. R. China
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44
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Abstract
The evaluation of minimal residual disease (MRD) in chronic lymphocytic leukemia (CLL) has evolved in parallel with the enormous progresses in the therapeutic armamentarium and the application of cutting-edge diagnostic techniques the CLL community witnessed in the past few years. Minimal residual disease is considered an objective measure of disease status defined by the number of residual leukemic cells detected in a sample of peripheral blood and/or bone marrow as proportion of the total white blood cells and defined undetectable if fewer than 1 CLL cell among 10,000 white blood cells (10 or 0.01%) is detected. In this review, we aim at shedding light on how to evaluate MRD, what we already know about MRD from the experience with chemoimmunotherapy, and why MRD evaluation remains still relevant in the era of targeted agents.
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45
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Zuo Z, Li S, Xu J, You MJ, Khoury JD, Yin CC. Philadelphia-Negative Myeloproliferative Neoplasms: Laboratory Workup in the Era of Next-Generation Sequencing. Curr Hematol Malig Rep 2020; 14:376-385. [PMID: 31388824 DOI: 10.1007/s11899-019-00534-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE OF REVIEW To review the impact of next-generation sequencing (NGS) on laboratory approach of myeloproliferative neoplasms (MPNs). RECENT FINDINGS Next-generation sequencing has provided valuable information on the mutational landscape of MPNs and has been used for various applications, including diagnosis, risk stratification, monitoring of residual disease or disease progression, and target therapy. Most commonly, targeted sequencing of a panel of genes that have been shown to be recurrently mutated in myeloid neoplasms is used. Although numerous studies have shown the benefit of using NGS in the routine clinical care of MPN patients, the complexity of NGS data and how these data may contribute to the clinical outcome have limited the development of a standard clinical guideline. We review recent literature and discuss how to interpret and use NGS data in the clinical care of MPN patients.
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Affiliation(s)
- Zhuang Zuo
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoying Li
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie Xu
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M James You
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph D Khoury
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Cameron Yin
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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46
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Gökbuget N, Zugmaier G, Dombret H, Stein A, Bonifacio M, Graux C, Faul C, Brüggemann M, Taylor K, Mergen N, Reichle A, Horst HA, Havelange V, Topp MS, Bargou RC. Curative outcomes following blinatumomab in adults with minimal residual disease B-cell precursor acute lymphoblastic leukemia. Leuk Lymphoma 2020; 61:2665-2673. [PMID: 32619115 DOI: 10.1080/10428194.2020.1780583] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Minimal residual disease (MRD) is the strongest predictor of relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In BLAST study (NCT01207388), adults with BCP-ALL in remission with MRD after chemotherapy received blinatumomab, a CD19 BiTE® immuno-oncotherapy, 15 µg/m2/day for up to four 6-week cycles (4 weeks continuous infusion, 2 weeks off). Survival was evaluated for 110 patients, including 74 who received HSCT in continuous complete remission. With a median follow-up of 59·8 months, median survival (months) was 36·5 (95% CI: 22.0-not reached [NR]). Median survival was NR (29.5-NR) for complete MRD responders (n = 84) and 14.4 (3.8-32.3) for MRD non-responders (n = 23; p = 0.002); after blinatumomab and HSCT, median survival was NR (25.7-NR) (n = 61) and 16.5 (1.1-NR) (n = 10; p = 0.065), respectively. This final analysis suggests complete MRD response during blinatumomab treatment is curative. Post-hoc analysis of study data suggests while post blinatumomab HSCT may be beneficial in appropriate patients, long-term survival without HSCT is also possible.
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Affiliation(s)
| | | | - Hervé Dombret
- University Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Anthony Stein
- City of Hope National Medical Center, Duarte, CA, USA
| | | | - Carlos Graux
- CHU UCL Namur - Site Godinne, Université Catholique de Louvain, Yvoir, Belgium
| | - Christoph Faul
- University Hospital and Comprehensive Cancer Center Tübingen, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Monika Brüggemann
- Klinik für Innere Medizin II, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | | | | | - Albrecht Reichle
- Department of Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Heinz-August Horst
- Klinik für Innere Medizin II, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Violaine Havelange
- Department of Hematology, Cliniques Universitaires St. Luc, Brussels, Belgium
| | - Max S Topp
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany and
| | - Ralf C Bargou
- Comprehensive Cancer Center Mainfranken, Uniklinikum Würzburg, Würzburg, Germany
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47
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Hu EY, Blachly JS, Saygin C, Ozer HG, Workman SE, Lozanski A, Doong TJ, Chiang CL, Bhat S, Rogers KA, Woyach JA, Coombes KR, Jones D, Muthusamy N, Lozanski G, Byrd JC. LC-FACSeq is a method for detecting rare clones in leukemia. JCI Insight 2020; 5:134973. [PMID: 32554930 DOI: 10.1172/jci.insight.134973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 05/06/2020] [Indexed: 01/07/2023] Open
Abstract
Detecting, characterizing, and monitoring rare populations of cells can increase testing sensitivity, give insight into disease mechanism, and inform clinical decision making. One area that can benefit from increased resolution is management of cancers in clinical remission but with measurable residual disease (MRD) by multicolor FACS. Detecting and monitoring genomic clonal resistance to treatment in the setting of MRD is technically difficult and resource intensive due to the limited amounts of disease cells. Here, we describe limited-cell FACS sequencing (LC-FACSeq), a reproducible, highly sensitive method of characterizing clonal evolution in rare cells relevant to different types of acute and chronic leukemias. We demonstrate the utility of LC-FACSeq for broad multigene gene panels and its application for monitoring sequential acquisition of mutations conferring therapy resistance and clonal evolution in long-term ibrutinib treatment of patients with chronic lymphocytic leukemia. This technique is generalizable for monitoring of other blood and marrow infiltrating cancers.
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Affiliation(s)
- Eileen Y Hu
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center.,Medical Scientist Training Program
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center.,Department of Biomedical Informatics, and
| | - Caner Saygin
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | | | - Stephanie E Workman
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | - Arletta Lozanski
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | - Tzyy-Jye Doong
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | - Chi-Ling Chiang
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | - Seema Bhat
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | - Kerry A Rogers
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | - Jennifer A Woyach
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | | | - Daniel Jones
- Department of Pathology, Ohio State University, Columbus, Ohio, USA
| | - Natarajan Muthusamy
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
| | - Gerard Lozanski
- Department of Pathology, Ohio State University, Columbus, Ohio, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine and Comprehensive Cancer Center
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48
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Capture-based Next-Generation Sequencing Improves the Identification of Immunoglobulin/T-Cell Receptor Clonal Markers and Gene Mutations in Adult Acute Lymphoblastic Leukemia Patients Lacking Molecular Probes. Cancers (Basel) 2020; 12:cancers12061505. [PMID: 32526928 PMCID: PMC7352935 DOI: 10.3390/cancers12061505] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/23/2020] [Accepted: 06/05/2020] [Indexed: 01/08/2023] Open
Abstract
The monitoring of minimal residual disease (MRD) in Philadelphia-negative acute lymphoblastic leukemia (ALL) requires the identification at diagnosis of immunoglobulin/T-cell receptor (Ig/TCR) rearrangements as clonality markers. Aiming to simplify and possibly improve the patients' initial screening, we designed a capture-based next-generation sequencing (NGS) panel combining the Ig/TCR rearrangement detection with the profiling of relevant leukemia-related genes. The validation of the assay on well-characterized samples allowed us to identify all the known Ig/TCR rearrangements as well as additional clonalities, including rare rearrangements characterized by uncommon combinations of variable, diversity, and joining (V-D-J) gene segments, oligoclonal rearrangements, and low represented clones. Upon validation, the capture NGS approach allowed us to identify Ig/TCR clonal markers in 87% of a retrospective cohort (MRD-unknown within the Northern Italy Leukemia Group (NILG)-ALL 09/00 clinical trial) and in 83% of newly-diagnosed ALL cases in which conventional method failed, thus proving its prospective applicability. Finally, we identified gene variants in 94.7% of patients analyzed for mutational status with the same implemented capture assay. The prospective application of this technology could simplify clonality assessment and improve standard assay development for leukemia monitoring, as well as provide information about the mutational status of selected leukemia-related genes, potentially representing new prognostic elements, MRD markers, and targets for specific therapies.
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49
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Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors: Challenges, Advances, and Applications. J Mol Diagn 2020; 22:994-1007. [PMID: 32480002 DOI: 10.1016/j.jmoldx.2020.04.213] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/17/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridization methods, for routine molecular testing of tumors. However, one limitation of routinely used NGS technologies is the inability to detect low-level genomic variants with high accuracy. This can be attributed to the frequent occurrence of low-level sequencing errors and artifacts in NGS workflow that need specialized approaches to be identified and eliminated. This review focuses on the origins and nature of these artifacts and recent improvements in the NGS technologies to overcome them to facilitate accurate high-sensitive detection of low-level mutations. Potential applications of high-sensitive NGS in oncology and comparisons with non-NGS technologies of similar capabilities are also summarized.
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50
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Rathe M, Preiss B, Marquart HV, Schmiegelow K, Wehner PS. Minimal residual disease monitoring cannot fully replace bone marrow morphology in assessing disease status in pediatric acute lymphoblastic leukemia. APMIS 2020; 128:414-419. [PMID: 32108963 DOI: 10.1111/apm.13037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/24/2019] [Indexed: 01/24/2023]
Abstract
Minimal residual disease (MRD) monitoring has a strong prognostic value in childhood lymphoblastic leukemia (ALL) and is currently utilized in all major pediatric ALL protocols. MRD monitoring is done by multiparameter flow cytometry, IG/TCR quantitative PCR or reverse transcriptase quantitative PCR of leukemic fusion transcripts providing a reliable measurement of treatment response. However, occasionally bone marrow (BM) aspirates may not yield representative material or be misinterpreted due to treatment-induced changes in MRD marker profile, undetected subclones at diagnosis, contamination with peripheral blood or cell adhesion and stroma cell interactions posing a risk for underestimating MRD levels and misclassifying resistant disease that may be detected by traditional BM morphology methods, immunohistochemistry, karyotyping and FISH. We present four cases with high MRD levels where MRD monitoring failed to provide the correct stratification information. Through these cases, we discuss the continued need to consider all available information including BM smears, touch imprints and trephine biopsy preparations not only at diagnosis but throughout remission monitoring in pediatric ALL.
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Affiliation(s)
- Mathias Rathe
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Birgitte Preiss
- Department of Pathology, Research Unit of Pathology, Odense University Hospital, Odense, Denmark
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Institute of Clinical Medicine, Faculty of Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peder Skov Wehner
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
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