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Wang D, Rausch C, Buerger SA, Tschuri S, Rothenberg-Thurley M, Schulz M, Hasenauer J, Ziemann F, Metzeler KH, Marr C. Modeling early treatment response in AML from cell-free tumor DNA. iScience 2023; 26:108271. [PMID: 38047080 PMCID: PMC10690559 DOI: 10.1016/j.isci.2023.108271] [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: 06/16/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
Monitoring disease response after intensive chemotherapy for acute myeloid leukemia (AML) currently requires invasive bone marrow biopsies, imposing a significant burden on patients. In contrast, cell-free tumor DNA (ctDNA) in peripheral blood, carrying tumor-specific mutations, offers a less-invasive assessment of residual disease. However, the relationship between ctDNA levels and bone marrow blast kinetics remains unclear. We explored this in 10 AML patients with NPM1 and IDH2 mutations undergoing initial chemotherapy. Comparison of mathematical mixed-effect models showed that (1) inclusion of blast cell death in the bone marrow, (2) transition of ctDNA to peripheral blood, and (3) ctDNA decay in peripheral blood describes kinetics of blast cells and ctDNA best. The fitted model allows prediction of residual bone marrow blast content from ctDNA, and its scaling factor, representing clonal heterogeneity, correlates with relapse risk. Our study provides precise insights into blast and ctDNA kinetics, offering novel avenues for AML disease monitoring.
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Affiliation(s)
- Dantong Wang
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Christian Rausch
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
- German Cancer Consortium (DKTK), partner sites Munich/Dresden, Germany
| | - Simon A. Buerger
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Sebastian Tschuri
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
| | - Melanie Schulz
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Jan Hasenauer
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
- Computational Health Center, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Faculty of Mathematics and Natural Sciences, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Frank Ziemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital (LMU), Munich, Germany
- German Cancer Consortium (DKTK), partner sites Munich/Dresden, Germany
| | - Klaus H. Metzeler
- Department of Hematology and Cell Therapy, University Hospital Leipzig (UHL) 04103, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany
- Center for Mathematics, Technische Universität München, Garching 85748, Germany
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Markou AN, Bagratuni T, Tsakiri C, Tserpeli V, Skourti S, Mavrianou Koutsoukou N, Papadimou A, Terpos E, Kastritis E, Lianidou E, Dimopoulos MA. Highly Sensitive Detection Method of CXCR4 Tumor Hotspot Mutations by Drop-Off Droplet Digital PCR in Patients with IgM Monoclonal Gammopathies. J Mol Diagn 2023; 25:502-512. [PMID: 37088135 DOI: 10.1016/j.jmoldx.2023.03.010] [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: 01/30/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023] Open
Abstract
CXCR4 mutations impact disease presentation and treatment outcomes in Waldenström macroglobulinemia. Current techniques used for CXCR4 mutation detection have a number of limitations. The aim of the present study was to develop and analytically validate a novel droplet digital PCR (ddPCR) assay for the simultaneous detection of five of the most common CXCR4 mutations in bone marrow (BM). In silico novel primers and probes designed for simultaneous detection of five hotspot mutations of CXCR4 were first performed. Experimental conditions were optimized, and the assay was analytically validated. The developed assay was further applied in 95 BM samples from patients with IgM gammopathy, 7 BM samples from patients with non-IgM gammopathy and 12 PBMCs from healthy donors, whereas a direct comparison study of Sanger sequencing and allele-specific PCR was performed by using 95 and 39 identical patient tumor DNA samples, respectively. The drop-off ddPCR assay is a robust, cost-effective, highly sensitive, and highly specific screening tool for CXCR4 mutations. Of 95 patients with IgM gammopathy samples, 27 had at least one CXCR4 mutation in their BM samples. With Sanger sequencing, 12 of the 95 samples tested positive, whereas the direct comparison of the developed assay with allele-specific PCR revealed substantial agreement. The clinical performance of the developed assay will be prospectively evaluated in a large number of patients, and the applicability of this assay will be further evaluated.
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Affiliation(s)
- Athina N Markou
- Analysis of Circulating Tumor Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - Tina Bagratuni
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Christina Tsakiri
- Analysis of Circulating Tumor Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Victoria Tserpeli
- Analysis of Circulating Tumor Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Stamatia Skourti
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Nefeli Mavrianou Koutsoukou
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexandra Papadimou
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Laboratory, Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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Ning W, Zhang C, Tian Z, Wu M, Luo Z, Hu S, Pan H, Li Y. Ω-shaped fiber optic LSPR biosensor based on mismatched hybridization chain reaction and gold nanoparticles for detection of circulating cell-free DNA. Biosens Bioelectron 2023; 228:115175. [PMID: 36871422 DOI: 10.1016/j.bios.2023.115175] [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: 10/19/2022] [Revised: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Circulating cell-free DNA (cfDNA) is a promising biomarker of liquid biopsy, but it still faces some difficulties in achieving sensitive and convenient detection. Herein, an Ω-shaped fiber optic localized surface plasmon resonance (FO-LSPR) biosensor based on hybridization chain reaction (HCR) coupled with gold nanoparticles (AuNPs) was developed, and applied in simple and sensitive detection of cfDNA. Specifically, one-base mismatch was designed in HCR hairpins (H1 and H2) to obtain high reaction efficiency, and AuNPs was introduced onto H1 through poly-adenine to construct HCR coupled with AuNPs strategy. Meanwhile, target cfDNA was designed into two domains: one could trigger HCR to generate dsDNA concatemer carrying numerous AuNPs, and the other could hybridize with capture DNA on the surface of Ω-shaped fiber optic (FO) probes. Thus, the presence of target cfDNA would initiate HCR, and bring the formed dsDNA concatemer and AuNPs to approach the probe surface, resulting in dramatically amplified LSPR signal. Besides, HCR required simple isothermal and enzyme-free condition, and Ω-shaped FO probe with high refractive index sensitivity just needed to be immersed into HCR solution directly for signal monitoring. Benefiting from the synergetic amplification of mismatched HCR and AuNPs, the proposed biosensor exhibited high sensitivity with a limit of detection of 14.0 pM, and therefore could provide a potential strategy for biomedical analysis and disease diagnosis.
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Affiliation(s)
- Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuyan Zhang
- Medical Equipment Innovation Research Center, Precision Medicine Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongzhi Pan
- The Affiliated Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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Yu Q, Jiang H, Su X, Jiang Z, Liang X, Zhang C, Shang W, Zhang Y, Chen H, Yang Z, Shen M, Huang F, Chen X, Yang Y, Pan B, Wang B, Lu D, Guo W. Development of multiplex drop-off digital PCR assays for hotspot mutation detection of KRAS, NRAS, BRAF and PIK3CA in the plasma of colorectal cancer patients. J Mol Diagn 2023; 25:388-402. [PMID: 36963484 DOI: 10.1016/j.jmoldx.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/30/2022] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
The detection of mutations in KRAS, NRAS, BRAF and PIK3CA has become essential in treatment management of metastatic colorectal cancer (mCRC), with the approval of new targeted therapies. We developed novel multiplex drop-off digital PCR (MDO-dPCR) assays, by combining amplitude-/ratio-based multiplexing with drop-off/double drop-off strategies, which allow for detection of at least 69 most frequent hotspot mutations in all four genes with only three reactions. We assessed the analytical performance of the assays using synthetic oligonucleotides, further validated on plasma cfDNA samples from a large cohort of CRC patients and compared with next generation sequencing (NGS) data. The MDO-dPCR assays showed a high sensitivity with a limit of detection (LOD) ranging from 0.084 to 0.182% in mutant allelic frequency (MAF). The screening of plasma cfDNAs from 106 CRC patients identified mutations in 42.45% of them, with a sensitivity of 95.24%, a specificity of 98.53% and an accuracy of 96.98% for mutation detection and a strong correlation of measured MAFs as compared to NGS results. The high sensitivity and comprehensive mutation coverage of the MDO-dPCR assays make them suitable for rapid and cost-effective detection of KRAS, NRAS, BRAF and PIK3CA mutations in the plasma of CRC patients, and could be useful in early response assessment and longitudinal disease monitoring.
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Affiliation(s)
- Qian Yu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Huiqin Jiang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xi Su
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | | | - Xue Liang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chunyan Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Wu Shang
- Nanjing Pregene Biotechnology, Nanjing, China
| | | | - Hao Chen
- Nanjing Pregene Biotechnology, Nanjing, China
| | - Zhijie Yang
- Nanjing Pregene Biotechnology, Nanjing, China
| | - Minna Shen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinning Chen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yihui Yang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China.
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Allam S, Nasr K, Khalid F, Shah Z, Khan Suheb MZ, Mulla S, Vikash S, Bou Zerdan M, Anwer F, Chaulagain CP. Liquid biopsies and minimal residual disease in myeloid malignancies. Front Oncol 2023; 13:1164017. [PMID: 37213280 PMCID: PMC10196237 DOI: 10.3389/fonc.2023.1164017] [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: 02/11/2023] [Accepted: 04/25/2023] [Indexed: 05/23/2023] Open
Abstract
Minimal residual disease (MRD) assessment through blood component sampling by liquid biopsies (LBs) is increasingly being investigated in myeloid malignancies. Blood components then undergo molecular analysis by flow cytometry or sequencing techniques and can be used as a powerful tool for prognostic and predictive purposes in myeloid malignancies. There is evidence and more is evolving about the quantification and identification of cell-based and gene-based biomarkers in myeloid malignancies to monitor treatment response. MRD based acute myeloid leukemia protocol and clinical trials are currently incorporating LB testing and preliminary results are encouraging for potential widespread use in clinic in the near future. MRD monitoring using LBs are not standard in myelodysplastic syndrome (MDS) but this is an area of active investigation. In the future, LBs can replace more invasive techniques such as bone marrow biopsies. However, the routine clinical application of these markers continues to be an issue due to lack of standardization and limited number of studies investigating their specificities. Integrating artificial intelligence (AI) could help simplify the complex interpretation of molecular testing and reduce errors related to operator dependency. Though the field is rapidly evolving, the applicability of MRD testing using LB is mostly limited to research setting at this time due to the need for validation, regulatory approval, payer coverage, and cost issues. This review focuses on the types of biomarkers, most recent research exploring MRD and LB in myeloid malignancies, ongoing clinical trials, and the future of LB in the setting of AI.
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Affiliation(s)
- Sabine Allam
- Department of Medicine and Medical Sciences, University of Balamand, Dekwaneh, Lebanon
| | - Kristina Nasr
- Department of Medicine and Medical Sciences, University of Balamand, Dekwaneh, Lebanon
| | - Farhan Khalid
- Department of Internal Medicine, Monmouth Medical Center, Long Branch, NJ, United States
| | - Zunairah Shah
- Department of Internal Medicine, Weiss Memorial Hospital, Chicago, IL, United States
| | | | - Sana Mulla
- Department of Internal Medicine, St Mary’s Medical Center, Apple Valley, CA, United States
| | - Sindhu Vikash
- Department of Medicine, Jacobi Medical center/AECOM Bronx, Bronx, NY, United States
| | - Maroun Bou Zerdan
- Department of Internal Medicine, SUNY Upstate Medical University, New York, NY, United States
| | - Faiz Anwer
- Department of Hematology and Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, United States
| | - Chakra P. Chaulagain
- Department of Hematology and Oncology, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
- *Correspondence: Chakra P. Chaulagain,
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Stanojevic M, Grant M, Vesely SK, Knoblach S, Kanakry CG, Nazarian J, Panditharatna E, Panchapakesan K, Gress RE, Holter-Chakrabarty J, Williams KM. Peripheral blood marker of residual acute leukemia after hematopoietic cell transplantation using multi-plex digital droplet PCR. Front Immunol 2022; 13:999298. [PMID: 36248870 PMCID: PMC9556966 DOI: 10.3389/fimmu.2022.999298] [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: 07/20/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Background Relapse remains the primary cause of death after hematopoietic cell transplantation (HCT) for acute leukemia. The ability to identify minimal/measurable residual disease (MRD) via the blood could identify patients earlier when immunologic interventions may be more successful. We evaluated a new test that could quantify blood tumor mRNA as leukemia MRD surveillance using droplet digital PCR (ddPCR). Methods The multiplex ddPCR assay was developed using tumor cell lines positive for the tumor associated antigens (TAA: WT1, PRAME, BIRC5), with homeostatic ABL1. On IRB-approved protocols, RNA was isolated from mononuclear cells from acute leukemia patients after HCT (n = 31 subjects; n = 91 specimens) and healthy donors (n = 20). ddPCR simultaneously quantitated mRNA expression of WT1, PRAME, BIRC5, and ABL1 and the TAA/ABL1 blood ratio was measured in patients with and without active leukemia after HCT. Results Tumor cell lines confirmed quantitation of TAAs. In patients with active acute leukemia after HCT (MRD+ or relapse; n=19), the blood levels of WT1/ABL1, PRAME/ABL1, and BIRC5/ABL1 exceeded healthy donors (p<0.0001, p=0.0286, and p=0.0064 respectively). Active disease status was associated with TAA positivity (1+ TAA vs 0 TAA) with an odds ratio=10.67, (p=0.0070, 95% confidence interval 1.91 - 59.62). The area under the curve is 0.7544. Changes in ddPCR correlated with disease response captured on standard of care tests, accurately denoting positive or negative disease burden in 15/16 (95%). Of patients with MRD+ or relapsed leukemia after HCT, 84% were positive for at least one TAA/ABL1 in the peripheral blood. In summary, we have developed a new method for blood MRD monitoring of leukemia after HCT and present preliminary data that the TAA/ABL1 ratio may may serve as a novel surrogate biomarker for relapse of acute leukemia after HCT.
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Affiliation(s)
- M. Stanojevic
- Department of Pediatrics, MedStar Georgetown University Hospital, Washington, DC, United States
| | - M. Grant
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA, United States
| | - S. K. Vesely
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - S. Knoblach
- Children’s Research Institute, Research Center for Genetic Medicine, Children’s National Health System, Washington, DC, United States
| | - C. G. Kanakry
- Experimental Transplantation and Immunotherapy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - J. Nazarian
- Children’s Research Institute, Research Center for Genetic Medicine, Children’s National Health System, Washington, DC, United States,Department of Oncology, Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland
| | - E. Panditharatna
- Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, United States
| | - K. Panchapakesan
- Children’s Research Institute, Research Center for Genetic Medicine, Children’s National Health System, Washington, DC, United States
| | - R. E. Gress
- Experimental Transplantation and Immunotherapy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - J. Holter-Chakrabarty
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Kirsten M. Williams
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA, United States,*Correspondence: Kirsten M. Williams,
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Waterhouse M, Pennisi S, Pfeifer D, Scherer F, Zeiser R, Duyster J, Bertz H, Finke J, Duque-Afonso J. Monitoring of Measurable Residual Disease Using Circulating DNA after Allogeneic Hematopoietic Cell Transplantation. Cancers (Basel) 2022; 14:cancers14143307. [PMID: 35884368 PMCID: PMC9323743 DOI: 10.3390/cancers14143307] [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: 05/07/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary The major cause of treatment failure after allogeneic stem cell transplantation (allo-HSCT) is due to relapse of the underlying disease. Novel methods and strategies are needed to detect early relapse after allo-HSCT. The present study reports the clinical utility of monitoring measurable residual disease (MRD) and mixed chimerism (MC) by droplet-digital PCR in circulating cell-free DNA (cfDNA) in 62 patients with myeloid malignancies undergoing allo-HSCT. MC in circulating cfDNA at an optimal threshold of 18% discriminated patients with hematological relapse from patients in complete remission after allo-HSCT. Most of the mutations identified using a targeted next-generation sequencing (NGS) panel were detected in cfDNA at relapse and were suitable for the monitoring of MRD. In several cases, mutations were detected earlier in cfDNA than in peripheral blood mononuclear cells. In conclusion, longitudinal analysis of cfDNA for MRD and MC can be used as a complementary tool for early detection of relapse in patients after allo-HSCT and could be used to guide clinical interventions. Abstract Relapse of the underlying disease is a frequent complication after allogeneic hematopoietic stem cell transplantation (allo-HSCT). In this study, we describe the clinical utility of measurable residual disease (MRD) and mixed chimerism (MC) assessment in circulating cell-free DNA (cfDNA) analysis to detect earlier relapse in patients with hematological malignancies after allo-HSCT. A total of 326 plasma and peripheral blood mononuclear cell (PBMCs) samples obtained from 62 patients with myeloid malignancies were analyzed by droplet-digital PCR (median follow-up: 827 days). Comparison of MC in patients at relapse and in complete remission identified an optimal discriminating threshold of 18% of recipient-derived cfDNA. After performing a targeted next-generation sequencing (NGS) panel, 136 mutations in 58 patients were detected. In a total of 119 paired samples, the putative mutations were detected in both cfDNA and PBMCs in 73 samples (61.3%). In 45 samples (37.8%) they were detected only in cfDNA, and in only one patient (0.9%) were they detected solely in DNA from PBMCs. Hence, in 6 out of 23 patients (26%) with relapse after allo-HSCT, MRD positivity was detected earlier in cfDNA (mean 397 days) than in DNA derived from PBMCs (mean 451 days). In summary, monitoring of MRD and MC in cfDNA might be useful for earlier relapse detection in patients with myeloid malignancies after allo-HSCT.
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Affiliation(s)
- Miguel Waterhouse
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
- Correspondence: (M.W.); (J.D.-A.); Tel.: +49-761-270-36000 (M.W. & J.D.-A.)
| | - Sandra Pennisi
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
- Faculty of Biology, Albert Ludwigs University of Freiburg, 79104 Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
| | - Florian Scherer
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
| | - Robert Zeiser
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
| | - Justus Duyster
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
| | - Hartmut Bertz
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
| | - Jürgen Finke
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
| | - Jesús Duque-Afonso
- Department of Hematology Oncology and Stem Cell Transplantation, University of Freiburg Medical Center, 79106 Freiburg, Germany; (S.P.); (D.P.); (F.S.); (R.Z.); (J.D.); (H.B.); (J.F.)
- Correspondence: (M.W.); (J.D.-A.); Tel.: +49-761-270-36000 (M.W. & J.D.-A.)
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Colmenares R, Álvarez N, Barrio S, Martínez-López J, Ayala R. The Minimal Residual Disease Using Liquid Biopsies in Hematological Malignancies. Cancers (Basel) 2022; 14:1310. [PMID: 35267616 PMCID: PMC8909350 DOI: 10.3390/cancers14051310] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 12/02/2022] Open
Abstract
The study of cell-free DNA (cfDNA) and other peripheral blood components (known as "liquid biopsies") is promising, and has been investigated especially in solid tumors. Nevertheless, it is increasingly showing a greater utility in the diagnosis, prognosis, and response to treatment of hematological malignancies; in the future, it could prevent invasive techniques, such as bone marrow (BM) biopsies. Most of the studies about this topic have focused on B-cell lymphoid malignancies; some of them have shown that cfDNA can be used as a novel way for the diagnosis and minimal residual monitoring of B-cell lymphomas, using techniques such as next-generation sequencing (NGS). In myelodysplastic syndromes, multiple myeloma, or chronic lymphocytic leukemia, liquid biopsies may allow for an interesting genomic representation of the tumor clones affecting different lesions (spatial heterogeneity). In acute leukemias, it can be helpful in the monitoring of the early treatment response and the prediction of treatment failure. In chronic lymphocytic leukemia, the evaluation of cfDNA permits the definition of clonal evolution and drug resistance in real time. However, there are limitations, such as the difficulty in obtaining sufficient circulating tumor DNA for achieving a high sensitivity to assess the minimal residual disease, or the lack of standardization of the method, and clinical studies, to confirm its prognostic impact. This review focuses on the clinical applications of cfDNA on the minimal residual disease in hematological malignancies.
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Affiliation(s)
- Rafael Colmenares
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
| | - Noemí Álvarez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
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Revealing the Mysteries of Acute Myeloid Leukemia: From Quantitative PCR through Next-Generation Sequencing and Systemic Metabolomic Profiling. J Clin Med 2022; 11:jcm11030483. [PMID: 35159934 PMCID: PMC8836582 DOI: 10.3390/jcm11030483] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 12/13/2022] Open
Abstract
The efforts made in the last decade regarding the molecular landscape of acute myeloid leukemia (AML) have created the possibility of obtaining patients’ personalized treatment. Indeed, the improvement of accurate diagnosis and precise assessment of minimal residual disease (MRD) increased the number of new markers suitable for novel and targeted therapies. This progress was obtained thanks to the development of molecular techniques starting with real-time quantitative PCR (Rt-qPCR) passing through digital droplet PCR (ddPCR) and next-generation sequencing (NGS) up to the new attractive metabolomic approach. The objective of this surge in technological advances is a better delineation of AML clonal heterogeneity, monitoring patients without disease-specific mutation and designing customized post-remission strategies based on MRD assessment. In this context, metabolomics, which pertains to overall small molecules profiling, emerged as relevant access for risk stratification and targeted therapies improvement. In this review, we performed a detailed overview of the most popular modern methods used in hematological laboratories, pointing out their vital importance for MRD monitoring in order to improve overall survival, early detection of possible relapses and treatment efficacy.
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