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Saisaard W, Owattanapanich W. Comparative analysis of BCR::ABL1 p210 mRNA transcript quantification and ratio to ABL1 control gene converted to the International Scale by chip digital PCR and droplet digital PCR for monitoring patients with chronic myeloid leukemia. Clin Chem Lab Med 2024; 0:cclm-2024-0456. [PMID: 39167824 DOI: 10.1515/cclm-2024-0456] [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: 04/13/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024]
Abstract
OBJECTIVES Chronic myeloid leukemia (CML) is characterized by the Philadelphia chromosome, leading to the BCR::ABL1 fusion gene and hyper-proliferation of granulocytes. Tyrosine kinase inhibitors (TKIs) are effective, and minimal residual disease (MRD) monitoring is crucial. Digital PCR platforms offer increased precision compared to quantitative PCR but lack comparative studies. METHODS Eighty CML patient samples were analyzed in parallel using digital droplet PCR (ddPCR) (QXDx™ BCR-ABL %IS Kit) and chip digital PCR (cdPCR) (Dr. PCR™ BCR-ABL1 Major IS Detection Kit). RESULTS Overall, qualitative and quantitative agreement was good. Sensitivity analysis showed positive percentage agreement and negative percentage agreement were both ≥90 %, and the quadratic weighted kappa index for molecular response (MR) level categorization was 0.94 (95 %CI 0.89, 0.98). MR levels subgroup analysis showed perfect categorical agreement on MR level at MR3 or above, while 35.4 % (17/48) of patient samples with MR4 or below showed discordant categorizations. Overall, Lin's concordance correlation coefficient (CCC) for the ratio of %BCR::ABL1/ABL1 converted to the International Scale (BCR::ABL1 IS) was almost perfect quantitative agreement (Lin's CCC=0.99). By subgroups of MR levels, Lin's CCC showed a quantitative agreement of BCR::ABL1 IS decreased as MR deepened. CONCLUSIONS Both cdPCR and ddPCR demonstrated comparable performance in detecting BCR::ABL1 transcripts with high concordance in MR3 level or above. Choosing between platforms may depend on cost, workflow, and sensitivity requirements.
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Affiliation(s)
- Wannachai Saisaard
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Weerapat Owattanapanich
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Center of Excellence of Siriraj Adult Acute Myeloid/Lymphoblastic Leukemia (SiAML), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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2
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Jabbour E, Kantarjian H. Chronic myeloid leukemia: 2025 update on diagnosis, therapy, and monitoring. Am J Hematol 2024. [PMID: 39093014 DOI: 10.1002/ajh.27443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024]
Abstract
DISEASE OVERVIEW Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm with an annual incidence of two cases/100 000. It accounts for approximately 15% of newly diagnosed cases of leukemia in adults. DIAGNOSIS CML is characterized by a balanced genetic translocation, t(9;22) (q34;q11.2), involving a fusion of the Abelson murine leukemia (ABL1) gene from chromosome 9q34 with the breakpoint cluster region (BCR) gene on chromosome 22q11.2. This rearrangement is known as the Philadelphia chromosome. The molecular consequence of this translocation is the generation of a BCR::ABL1 fusion oncogene, which in turn translates into a BCR::ABL1 oncoprotein. FRONTLINE THERAPY Four tyrosine kinase inhibitors (TKIs), imatinib, dasatinib, bosutinib, and nilotinib, are approved by the United States Food and Drug Administration (FDA) for first-line treatment of newly diagnosed CML in the chronic phase (CML-CP). Clinical trials with second and third-generation TKIs in frontline CML-CP therapy reported significantly deeper and faster responses but had no impact on survival prolongation, likely because of their potent efficacy and the availability of effective TKIs salvage therapies for patients who have a cytogenetic relapse with frontline TKI therapy. All four TKIs are equivalent if the aim of therapy is to improve survival. In younger patients with high-risk disease and in whom the aim of therapy is to induce a treatment-free remission status, second-generation TKIs may be favored. SALVAGE THERAPY For CML post-failure on frontline therapy, second-line options include second and third-generation TKIs. Although potent and selective, these TKIs exhibit unique pharmacological profiles and response patterns relative to different patient and disease characteristics, such as patients' comorbidities and financial status, disease stage, and BCR::ABL1 mutational status. Patients who develop the T315I "gatekeeper" mutation display resistance to all currently available TKIs except ponatinib, asciminib, and olverembatinib. Allogeneic stem cell transplantation remains an important therapeutic option for patients with CML-CP and failure (due to resistance) of at least two TKIs and for all patients in advanced-phase disease. Older patients who have a cytogenetic relapse post-failure on all TKIs can maintain long-term survival if they continue a daily most effective/least toxic TKI, with or without the addition of non-TKI anti-CML agents (hydroxyurea, omacetaxine, azacitidine, decitabine, cytarabine, and others).
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Affiliation(s)
- Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hagop Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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3
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Franke GN, Loewe G, Reiser M, Linde H, Josting A, von der Heyde E, Platzbecker U, Weide R, Tesch H, Nusch A, Dengler J, Jentsch-Ullrich K. Spotlight on the real-world treatment of CML pts in Germany: a retrospective survey in private oncology practices. Ann Hematol 2024; 103:1569-1575. [PMID: 38472361 PMCID: PMC11009736 DOI: 10.1007/s00277-024-05702-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Clinical trials in chronic myeloid leukemia (CML) are usually carried out in specialized centers whereas primary care for patients (pts) with CML is mainly provided by local oncology practices. The aim of this study was to assess treatment practices in pts with CML in the setting of private oncology practices in Germany. We collected data of 819 pts with a confirmed diagnosis (dx) of CML in 2013 or later from 43 practices. At dx, 84.2% (n=690) and 9.4% (n=77) of pts were in chronic or accelerated phase, 0.7% (n=6) had a blast crisis. Molecular monitoring was provided by EUTOS certified laboratories in 87.7% of pts. Typical BCR::ABL1 transcripts were detected in 86.6% (n=709). Molecular response was assessed after 2.8, 6.0, 9.4 and 12.9 m (mean) after start of treatment. Of the pts with available data, 11.1% did not achieve early molecular response and at 18 m, 83.7% had at least a major molecular response. 288 (35.2%) of pts switched to 2nd line (2L) treatment after a mean of 21.0 months. Reasons for 2L treatment were side effects in 43.4% and suboptimal response or failure in 31.4% of pts. 106 pts went on to third line (3L) treatment. 36.8 % of pts switched to and 92.8 % of pts still on 3L treatment achieved BCR::ABL1IS ≤1% at 12 m. In conclusion, in Germany pts with CML are routinely monitored by qPCR and good responses are achieved in the majority. Treatment changes are mainly due to adverse events rather than suboptimal responses.
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Affiliation(s)
- Georg-Nikolaus Franke
- Department for Hematology, Cellular Therapies, Hemostaseology and Infectious Diseases, University of Leipzig Medical Center, Leipzig, Germany.
| | | | - Marcel Reiser
- PIOH-Zentrum Praxis Internistischer Onkologie und Hämatologie, Cologne, Germany
| | - Hartmut Linde
- MVZ für Blut- und Krebserkrankungen, Potsdam, Germany
| | - Andreas Josting
- Schwerpunktpraxis für Onkologie, Gastroenterologie, Hämatologie und Palliativmedizin, Berlin, Germany
| | | | - Uwe Platzbecker
- Department for Hematology, Cellular Therapies, Hemostaseology and Infectious Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Rudolf Weide
- Praxis für Hämatologie und Onkologie, Koblenz, Germany
| | - Hans Tesch
- Centrum für Hämatologie und Onkologie Bethanien, Frankfurt, Germany
| | - Arndt Nusch
- MVZ-Onkologie Velbert/Ratingen GbR, Velbert, Germany
| | - Jolanta Dengler
- Onkologische Schwerpunktpraxis Heilbronn, Heilbronn, Germany
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Kwaśnik P, Zaleska J, Link-Lenczowska D, Zawada M, Wysogląd H, Ochrem B, Bober G, Wasilewska E, Hus I, Szarejko M, Prejzner W, Grzybowska-Izydorczyk O, Klonowska-Szymczyk A, Mędraś E, Kiełbus M, Sacha T, Giannopoulos K. High Level of CD8 +PD-1 + Cells in Patients with Chronic Myeloid Leukemia Who Experienced Loss of MMR after Imatinib Discontinuation. Cells 2024; 13:723. [PMID: 38667336 PMCID: PMC11048908 DOI: 10.3390/cells13080723] [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: 03/29/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Treatment-free remission (TFR) is achieved in approximately half of chronic myeloid leukemia (CML) patients treated with tyrosine kinase inhibitors. The mechanisms responsible for TFR maintenance remain elusive. This study aimed to identify immune markers responsible for the control of residual CML cells early in the TFR (at 3 months), which may be the key to achieving long-term TFR and relapse-free survival (RFS) after discontinuation of imatinib. Our study included 63 CML patients after imatinib discontinuation, in whom comprehensive analysis of changes in the immune system was performed by flow cytometry, and changes in the BCR::ABL1 transcript levels were assessed by RQ-PCR and ddPCR. We demonstrated a significant increase in the percentage of CD8+PD-1+ cells in patients losing TFR. The level of CD8+PD-1+ cells is inversely related to the duration of treatment and incidence of deep molecular response (DMR) before discontinuation. Analysis of the ROC curve showed that the percentage of CD8+PD-1+ cells may be a significant factor in early molecular recurrence. Interestingly, at 3 months of TFR, patients with the e13a2 transcript had a significantly higher proportion of the PD-1-expressing immune cells compared to patients with the e14a2. Our results suggest the important involvement of CD8+PD-1+ cells in the success of TFR and may help in identifying a group of patients who could successfully discontinue imatinib.
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MESH Headings
- Humans
- Imatinib Mesylate/therapeutic use
- Imatinib Mesylate/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/drug effects
- Female
- Male
- Middle Aged
- Adult
- Programmed Cell Death 1 Receptor/metabolism
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Aged
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Young Adult
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Affiliation(s)
- Paulina Kwaśnik
- Department of Experimental Hematooncology, Medical University of Lublin, 20-093 Lublin, Poland; (P.K.)
| | - Joanna Zaleska
- Department of Experimental Hematooncology, Medical University of Lublin, 20-093 Lublin, Poland; (P.K.)
| | - Dorota Link-Lenczowska
- Department of Hematology Diagnostics, Jagiellonian University Hospital in Kraków, 30-688 Kraków, Poland
| | - Magdalena Zawada
- Department of Hematology Diagnostics, Jagiellonian University Hospital in Kraków, 30-688 Kraków, Poland
| | - Hubert Wysogląd
- Department of Hematology, Jagiellonian University Hospital in Kraków, 30-688 Kraków, Poland
| | - Bogdan Ochrem
- Department of Hematology, Jagiellonian University Hospital in Kraków, 30-688 Kraków, Poland
| | - Grażyna Bober
- Department of Hematooncology and Bone Marrow Transplantation, School of Medicine in Katowice, Medical University of Silesia, 40-032 Katowice, Poland
| | - Ewa Wasilewska
- Department of Hematology, Medical University of Białystok, 15-276 Białystok, Poland
| | - Iwona Hus
- Department of Hematology, Institute of Hematology and Transfusion Medicine, 02-776 Warsaw, Poland
- Department of Clinical Transplantology, Medical University of Lublin, 20-093 Lublin, Poland
| | - Monika Szarejko
- Department of Hematology and Transplantology, Medical University of Gdańsk, 80-214 Gdańsk, Poland
| | - Witold Prejzner
- Department of Hematology and Transplantology, Medical University of Gdańsk, 80-214 Gdańsk, Poland
| | | | | | - Ewa Mędraś
- Department of Hematology, Neoplastic Blood Disorders and Bone Marrow Transplantation in Wrocław, 50-367 Wrocław, Poland
| | - Michał Kiełbus
- Department of Experimental Hematooncology, Medical University of Lublin, 20-093 Lublin, Poland; (P.K.)
| | - Tomasz Sacha
- Chair of Hematology, Jagiellonian University Medical College in Kraków, 31-501 Kraków, Poland
| | - Krzysztof Giannopoulos
- Department of Experimental Hematooncology, Medical University of Lublin, 20-093 Lublin, Poland; (P.K.)
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Lee SJ, Lee J, Ahn A, Lee S, Hong Y, Lee GD, Song H, Song M, Shin S, Kim M, Kim Y. Analytical Performance Evaluation of a Digital Real-Time PCR for Quantifying Major BCR::ABL1 Transcripts. J Clin Lab Anal 2024; 38:e25034. [PMID: 38525919 PMCID: PMC11033343 DOI: 10.1002/jcla.25034] [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: 09/27/2023] [Revised: 02/09/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Accurate quantification of the BCR::ABL1 transcripts is essential for measurable residual disease (MRD) monitoring in chronic myeloid leukemia (CML) after tyrosine kinase inhibitor (TKI) treatment. This study evaluated the newly developed digital real-time PCR method, Dr. PCR, as an alternative reverse transcription-PCR (qRT-PCR) for MRD detection. METHODS The performance of Dr. PCR was assessed using reference and clinical materials. Precision, linearity, and correlation with qRT-PCR were evaluated. MRD levels detected by Dr. PCR were compared with qRT-PCR, and practical advantages were investigated. RESULTS Dr. PCR detected MRD up to 0.0032%IS (MR4.5) with excellent precision and linearity and showed a strong correlation with qRT-PCR results. Notably, Dr. PCR identified higher levels of MRD in 12.7% (29/229) of patients than qRT-PCR, including six cases of MR4, which is a critical level for TKI discontinuation. Dr. PCR also allowed for sufficient ABL1 copies in all cases, while qRT-PCR necessitated multiple repeat tests in 3.5% (8/229) of cases. CONCLUSION Our study provides a body of evidence supporting the clinical application of Dr. PCR as a rapid and efficient method for assessing MRD in patients with CML under the current treatment regimen.
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Affiliation(s)
- Soo Jung Lee
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
| | - Jong‐Mi Lee
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
| | - Ari Ahn
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Sung‐Eun Lee
- Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Yuna Hong
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
- Department of Biomedicine & Health Sciences, Graduate SchoolThe Catholic University of KoreaSeoulKorea
| | - Gun Dong Lee
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
| | - Hyun‐Woo Song
- Bio Institute, Optolane Technologies Inc.PangyoSeong‐Nam‐SiKorea
| | - Min‐Sik Song
- Bio Institute, Optolane Technologies Inc.PangyoSeong‐Nam‐SiKorea
| | - Seung‐Shick Shin
- Bio Institute, Optolane Technologies Inc.PangyoSeong‐Nam‐SiKorea
| | - Myungshin Kim
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
| | - Yonggoo Kim
- Department of Laboratory MedicineSeoul St. Mary's Hospital, College of Medicine, The Catholic University of KoreaSeoulKorea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of MedicineThe Catholic University of KoreaSeoulKorea
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6
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Galli E, Viscovo M, Fosso F, Pansini I, Di Cesare G, Iacovelli C, Maiolo E, Sorà F, Hohaus S, Sica S, Bellesi S, Chiusolo P. Unlocking Predictive Power: Quantitative Assessment of CAR-T Expansion with Digital Droplet Polymerase Chain Reaction (ddPCR). Int J Mol Sci 2024; 25:2673. [PMID: 38473919 DOI: 10.3390/ijms25052673] [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: 01/15/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Flow cytometry (FCM) and quantitative PCR (qPCR) are conventional methods for assessing CAR-T expansion, while digital droplet PCR (ddPCR) is emerging as a promising alternative. We monitored CAR-T transcript expansion in 40 B-NHL patients post-infusion of CAR-T products (axi-cel; tisa-cel; and brexu-cel) with both His-Tag FCM and ddPCR techniques. Sensitivity and predictive capacity for efficacy and safety outcomes of ddPCR were analyzed and compared with FCM. A significant correlation between CAR-T counts determined by FCM and CAR transcripts assessed by ddPCR (p < 0.001) was observed. FCM revealed median CD3+CAR+ cell counts at 7, 14, and 30 days post-infusion with no significant differences. In contrast, ddPCR-measured median copies of CAR-T transcripts demonstrated significant lower copy numbers in tisa-cel recipients compared to the other products at day 7 and day 14. Patients with a peak of CAR transcripts at day 7 exceeding 5000 copies/microg gDNA, termed "good CAR-T expanders", were more likely to achieve a favorable response at 3 months (HR 10.79, 95% CI 1.16-100.42, p = 0.036). Good CAR-T expanders showed superior progression-free survival at 3, 6, and 12 months compared to poor CAR-T expanders (p = 0.088). Those reaching a peak higher than 5000 copies/microg gDNA were more likely to experience severe CRS and ICANS. DdPCR proves to be a practical method for monitoring CAR-T expansion, providing quantitative information that better predicts both treatment outcomes and toxicity.
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Affiliation(s)
- Eugenio Galli
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Marcello Viscovo
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Federica Fosso
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Ilaria Pansini
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Giacomo Di Cesare
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Camilla Iacovelli
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Elena Maiolo
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Federica Sorà
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Stefan Hohaus
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Simona Sica
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Silvia Bellesi
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Patrizia Chiusolo
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
- Sezione di Ematologia, Dipartimento di Scienze Radiologiche ed Ematologiche, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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7
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Zaninelli S, Meli C, Borleri G, Quaroni M, Pavoni C, Gaipa G, Biondi A, Introna M, Golay J, Rambaldi A, Rambaldi B. Optimization and validation of in vivo flow cytometry chimeric antigen receptor T cell detection method using CD19his indirect staining. Cytometry A 2024; 105:112-123. [PMID: 37707318 DOI: 10.1002/cyto.a.24796] [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: 06/27/2023] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/15/2023]
Abstract
CD19-targeted chimeric antigen receptor T (CAR-T) cell therapy has shown unprecedented results in patients with B cell relapsed/refractory acute lymphoblastic leukemia (R/R-ALL) and B cell non-Hodgkin lymphomas where no other curative options are available. In vivo monitoring of CAR-T cell kinetics is fundamental to understand the correlation between CAR-T cells expansion and persistence with treatment response and toxicity development. The aim of this study was to define a robust, sensitive, and universal method for CAR-T cell detection using flow cytometry. We set up and compared with each other three assays for CD19 CAR-T cell detection, all based on commercially available reagents. All methods used a recombinant human CD19 protein fragment recognized by the single-chain variable fragment of the CAR construct. The two indirect staining assays (CD19his + APC-conjugated antihistidine antibody and CD19bio + APC-conjugated antibiotin antibody) showed better sensitivity and specificity compared with the direct staining with CD19-FITC, and CD19his had a better cost-effective profile. We validated CAR detection with CD19his with parallel quantitative real-time polymerase chain reaction data and we could demonstrate a strong positive correlation. We also showed that CD19his staining can be easily included in a multicolor flow cytometry panel to achieve additional information about the cell phenotype of CAR-T cell positive subpopulations. Finally, this method can be used for different anti-CD19 CAR-T cell products and for different sample sources. These data demonstrate that detection of CAR-T cells by CD19his flow cytometry staining is a reliable, robust, and broadly applicable tool for in vivo monitoring of CAR-T cells.
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Affiliation(s)
- Silvia Zaninelli
- Division of Hematology, Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Cristian Meli
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
- Master of Science Programme in Biology Applied to Research in Biomedicine, Facoltà di Scienze e Tecnologie, Università degli Studi di Milano, Milan, Italy
| | - Gianmaria Borleri
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Michele Quaroni
- Laboratory of Cell and Gene Therapy Stefano Verri, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- M. Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Chiara Pavoni
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Giuseppe Gaipa
- Laboratory of Cell and Gene Therapy Stefano Verri, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- M. Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Andrea Biondi
- Laboratory of Cell and Gene Therapy Stefano Verri, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- M. Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Department of Pediatrics, University of Milano - Bicocca, Monza, Italy
| | - Martino Introna
- Division of Hematology, Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Josée Golay
- Division of Hematology, Center of Cellular Therapy "G. Lanzani", ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
- Department of Oncology and Hematology, Università degli Studi di Milano, Milan, Italy
| | - Benedetta Rambaldi
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII Hospital, Bergamo, Italy
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8
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Zhang Z, Zhou X, Zhou X, Cheng Z, Hu Y. Exploration of treatment-free remission in CML, based on molecular monitoring. Cancer Med 2024; 13:e6849. [PMID: 38133525 PMCID: PMC10807643 DOI: 10.1002/cam4.6849] [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: 09/26/2023] [Revised: 11/28/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Typical chronic myelogenous leukemia (CML) is a myeloproliferative neoplasm caused by t(9; 22)(q34; q11) translocation. This chromosomal translocation forms the BCR::ABL1 fusion gene. The tyrosine kinase encoded by the BCR::ABL1 is considered to be the main pathogenic diver. BCR::ABL1 is not only a therapeutic target, but also a monitoring target. Monitoring of BCR::ABL1 reveals the progression of the disease and guides the next treatment. Now for CML, the target of treatment has been focused on treatment-free remission (TFR). METHODS We conducted a literature review of current developments of treatment-free remission and molecular monitoring methods. RESULTS More effective and sensitive CML monitoring methods such as digital droplet PCR (ddPCR) and next generation sequencing (NGS) have further studied the measurable residual disease (MRD) and clonal heterogeneity, which provides strong support for the exploration of TFR. We discussed some of the factors that may be related to TFR outcomes at the molecular level, along with some monitoring strategies. CONCLUSION Currently, predictive indicators for treatment-free remission outcomes and recurrence are lacking in clinical practice. In future, treatment-free remission research should focus on combining the clinical indicators with molecular monitoring and biological markers to personalize patient conditions and guide clinicians to develop individualized treatment plans, so that more patients with CML can achieve safer and stabler treatment-free remission.
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MESH Headings
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Remission Induction
- Fusion Proteins, bcr-abl/genetics
- Neoplasm, Residual/genetics
- High-Throughput Nucleotide Sequencing
- Biomarkers, Tumor/genetics
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Affiliation(s)
| | | | - Xin Zhou
- Wuhan Union HospitalWuhanHubeiChina
| | | | - Yu Hu
- Wuhan Union HospitalWuhanHubeiChina
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9
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Kongruang A, Limsuwanachot N, Magmuang S, Areesirisuk P, Niparuck P, Siriboonpiputtana T, Rerkamnuaychoke B. Committed change of real-time quantitative PCR to droplet digital PCR for monitoring BCR:: ABL1 transcripts in tyrosine kinase inhibitor treated CML. Hematology 2023; 28:2256199. [PMID: 37695125 DOI: 10.1080/16078454.2023.2256199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/02/2023] [Indexed: 09/12/2023] Open
Abstract
OBJECTIVES We performed a feasibility study of an FDA-approved commercial ddPCR assay to measure BCR::ABL1 in CML patients treated using TKI therapy. METHODS Assay performance of standard RQ-PCR and commercially available FDA-approved ddPCR were compared to measure BCR::ABL1 p210 transcripts in RNA samples from 100 CML patients who received TKI therapy. RESULTS %BCR::ABL1/ABL1IS levels obtained from both methods were not statistically significant difference after normalization with batch-specific conversion factor (p = 0.0651). The correlation and agreement of %BCR::ABL1/ABL1IS between the two assays were high. Molecular response stratification data showed 56% concordance between RQ-PCR and ddPCR, and 37% higher residual disease detection using ddPCR. Furthermore, 21.21% (7/33) of RQ-PCR undetectable samples were detected by ddPCR, representing high sensitivity to quantify the low abundance of BCR::ABL1 transcripts. CONCLUSION ddPCR was proven to be a highly sensitive method with the potential to overcome some limitations of traditional RQ-PCR, and has the potential of being a valuable tool for monitoring BCR::ABL1 transcripts in CML during TKI therapy. (163 words).
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Affiliation(s)
- Adcharee Kongruang
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nittaya Limsuwanachot
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sutada Magmuang
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prapatsorn Areesirisuk
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pimjai Niparuck
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Teerapong Siriboonpiputtana
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Budsaba Rerkamnuaychoke
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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10
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Gao HL, Hao Y, Chen WM, Li LD, Wang X, Qin YZ, Jiang Q. [Comparison of BCR::ABL (P210) mRNA levels detected by dPCR and qPCR methods in patients with chronic myeloid leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:906-910. [PMID: 38185519 PMCID: PMC10753264 DOI: 10.3760/cma.j.issn.0253-2727.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 01/09/2024]
Abstract
Objective: To compare digital polymerase chain reaction (dPCR) and real-time quantitative PCR (qPCR) measurements of BCR::ABL (P210) mRNA expression in patients with chronic myeloid leukemia (CML) . Methods: In this non-interventional, cross-sectional study, BCR::ABL (P210) mRNA was simultaneously measured by dPCR and qPCR in peripheral blood samples collected from patients with CML who underwent tyrosine kinase inhibitor therapy and who achieved at least a complete cytogenetic response from September 2021 to February 2023 at Peking University People's Hospital. The difference, correlation, and agreement between the two methods were evaluated using the Wilcoxon signed-rank test, Spearman's correlation, and Bland-Altman analysis, respectively. Results: In total, 459 data pairs for BCR::ABL mRNA expression measured by dPCR and qPCR from 356 patients with CML were analyzed. There was a significant difference in BCR::ABL mRNA expression between the two methods (P<0.001). When analyzed by the depth of the molecular response (MR), a significant difference only existed for patients with ≥MR4.5 (P<0.001). No significant difference was observed for those who did not achieve a major MR (no MMR; P=0.922) or for those who achieved a major MR (MMR; P=0.723) or MR4 (P=0.099). There was a moderate correlation between the BCR::ABL mRNA expression between the two methods (r=0.761, P<0.001). However, the correlation gradually weakened or disappeared as the depth of the MR increased (no MMR: r=0.929, P<0.001; MMR: r=0.815, P<0.001; MR4: r=0.408, P<0.001; MR4.5: r=0.176, P=0.176). In addition, the agreement in BCR::ABL mRNA expression between the two methods in those with MR4.5 was weaker than other groups (no MMR: ▉= 0.042, P=0.846; MMR:▉=0.054, P=0.229; MR4:▉=-0.020, P=0.399; MR4.5:▉=-0.219, P<0.001) . Conclusions: dPCR is more accurate than qPCR for measuring BCR::ABL (P210) mRNA expression in patients with CML who achieve a stable deep MR.
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Affiliation(s)
- H L Gao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Y Hao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - W M Chen
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - L D Li
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - X Wang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Y Z Qin
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Q Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
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11
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Tembrock LR, Zink FA, Gilligan TM. Viral Prevalence and Genomic Xenology in the Coevolution of HzNV-2 (Nudiviridae) with Host Helicoverpa zea (Lepidoptera: Noctuidae). INSECTS 2023; 14:797. [PMID: 37887809 PMCID: PMC10607169 DOI: 10.3390/insects14100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/16/2023] [Accepted: 09/24/2023] [Indexed: 10/28/2023]
Abstract
Insect viruses have been described from numerous lineages, yet patterns of genetic exchange and viral prevalence, which are essential to understanding host-virus coevolution, are rarely studied. In Helicoverpa zea, the virus HzNV-2 can cause deformity of male and female genitalia, resulting in sterility. Using ddPCR, we found that male H. zea with malformed genitalia (agonadal) contained high levels of HzNV-2 DNA, confirming previous work. HzNV-2 was found to be prevalent throughout the United States, at more than twice the rate of the baculovirus HaSNPV, and that it contained several host-acquired DNA sequences. HzNV-2 possesses four recently endogenized lepidopteran genes and several more distantly related genes, including one gene with a bacteria-like sequence found in both host and virus. Among the recently acquired genes is cytosolic serine hydroxymethyltransferase (cSHMT). In nearly all tested H. zea, cSHMT contained a 200 bp transposable element (TE) that was not found in cSHMT of the sister species H. armigera. No other virus has been found with host cSHMT, and the study of this shared copy, including possible interactions, may yield new insights into the function of this gene with possible applications to insect biological control, and gene editing.
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Affiliation(s)
- Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Frida A. Zink
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Todd M. Gilligan
- USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, Fort Collins, CO 80526, USA
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12
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Arcila ME, Patel U, Momeni-Boroujeni A, Yao J, Chan R, Chan J, Rijo I, Yu W, Chaves N, Patel H, Kakadiya S, Lachhander S, Senechal B, Riviere IC, Wang X, Sadelain M, Nafa K, Salazar P, Palomba L, Curran KJ, Park JH, Daniyan A, Borsu L. Validation of a High-Sensitivity Assay for Detection of Chimeric Antigen Receptor T-Cell Vectors Using Low-Partition Digital PCR Technology. J Mol Diagn 2023; 25:634-645. [PMID: 37330049 PMCID: PMC10488325 DOI: 10.1016/j.jmoldx.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 05/18/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023] Open
Abstract
Although in vivo engraftment, expansion, and persistence of chimeric antigen receptor (CAR) T cells are pivotal components of treatment efficacy, quantitative monitoring has not been implemented in routine clinical practice. We describe the development and analytical validation of a digital PCR assay for ultrasensitive detection of CAR constructs after treatment, circumventing known technical limitations of low-partitioning platforms. Primers and probes, designed for detection of axicabtagene, brexucabtagene, and Memorial Sloan Kettering CAR constructs, were employed to validate testing on the Bio-Rad digital PCR low-partitioning platform; results were compared with Raindrop, a high-partitioning system, as reference method. Bio-Rad protocols were modified to enable testing of DNA inputs as high as 500 ng. Using dual-input reactions (20 and 500 ng) and a combined analysis approach, the assay demonstrated consistent target detection around 1 × 10-5 (0.001%) with excellent specificity and reproducibility and 100% accuracy compared with the reference method. Dedicated analysis of 53 clinical samples received during validation/implementation phases showed the assay effectively enabled monitoring across multiple time points of early expansion (day 6 to 28) and long-term persistence (up to 479 days). CAR vectors were detected at levels ranging from 0.005% to 74% (vector versus reference gene copies). The highest levels observed in our cohort correlated strongly with the temporal diagnosis of grade 2 and 3 cytokine release syndrome diagnosis (P < 0.005). Only three patients with undetectable constructs had disease progression at the time of sampling.
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Affiliation(s)
- Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Utsav Patel
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amir Momeni-Boroujeni
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinJuan Yao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger Chan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joe Chan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wayne Yu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nelio Chaves
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hina Patel
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Srushti Kakadiya
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sean Lachhander
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brigitte Senechal
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isabelle C Riviere
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xiuyan Wang
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michel Sadelain
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lia Palomba
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kevin J Curran
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jae H Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthony Daniyan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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13
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Kojabad AA, Chegeni R, Rostami S, Zaker F, Safa M. Ultrasensitive quantitation of FLT3-ITD mutation in patients with acute myeloid leukemia using ddPCR. Mol Biol Rep 2023:10.1007/s11033-023-08534-x. [PMID: 37300744 DOI: 10.1007/s11033-023-08534-x] [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: 10/28/2022] [Accepted: 05/17/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND FLT3-ITD mutations occur in 45-50% of cytogenetically normal AML patients. Conventional fragment analysis using capillary electrophoresis is routinely used to quantitate FLT3-ITD mutations. Fragment analysis however has limited sensitivity. METHODS AND RESULTS Here, FLT3-ITD was quantified in AML patients using an in-house developed ultra-sensitive droplet digital polymerase chain reaction assay (ddPCR). The allelic ratio of FLT3-ITD was also absolutely measured by both Fragment analysis and ddPCR. The sensitivity of ddPCR in quantitation of FLT3-ITD mutation was superior to Fragment analysis. CONCLUSION This study demonstrates the feasibility of using the described in-house ddPCR method to quantify the FLT3-ITD mutation and measure FLT3-ITD AR in AML patients.
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Affiliation(s)
- Amir Asri Kojabad
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rouzbeh Chegeni
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Shaharbano Rostami
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad Zaker
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Hailu S, Kinde S, Cross M, Tsegaye A, Kelemu T, Seifu D, Alemayehu D, Tarekegn A, Jabessa G, Abeje D, Abebe M, Sherif A, Tadesse F, Platzbecker U, Howe R, Gebremedhin A. Estimating prognostic relevant cutoff values for a multiplex PCR detecting BCR::ABL1 in chronic myeloid leukemia patients on tyrosine kinase inhibitor therapy in resource-limited settings. Ann Hematol 2023:10.1007/s00277-023-05254-x. [PMID: 37212909 DOI: 10.1007/s00277-023-05254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/23/2023] [Indexed: 05/23/2023]
Abstract
The prognosis of chronic myeloid leukemia (CML) on tyrosine kinase inhibitor (TKI) treatment is based on the quantification of BCR::ABL1 fusion gene transcript copy number, harmonized by an international scale (IS) based on TaqMan-based real-time quantitative PCR (qRT-PCR). In Ethiopia, as in most low- and middle-income countries (LMICs), access to standard diagnostic, follow-up, and prognostic tools is very limited, and it has been challenging to strictly follow international guidelines. This seriously compromises clinical outcome, despite the availability of TKIs through the Glivec International Patient Assistance Program (GIPAP). Multiplex PCR (mpx-PCR), conventionally regarded as a "screening tool," offers a potential solution to this problem. A total of 219 samples from confirmed CML patients were assayed. In reference to qRT-PCR, the AUC of ROC curve for mpx-PCR was 0.983 (95% CI: 0.957 to 0.997). At the optimum cut-off value, equivalent to BCR::ABL1 (IS) transcript copy number of 0.6%, the specificity and sensitivity were 93% and 95%, respectively, with 94% accuracy. Albeit the sensitivity and accuracy of mpx-PCR decrease below the optimum cutoff of 0.6% (IS), the specificity at 0.1% (IS) was 100%, making it an attractive means to rule-out relapse and drug non-adherence at later stages of treatment, which is particularly an issue in a low income setting. We conclude that the relative simplicity and low cost of mpx-PCR and prognostic relevant cutoff values (0.1-0.6% IS) should allow its use in peripheral clinics and thus maximize the positive impact of TKIs made available through GIPAP in most LMICs.
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Affiliation(s)
- Saifu Hailu
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Madda Walabu University, Bale Robe, Ethiopia
| | - Samuel Kinde
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
- Leipzig University Hospital, Leipzig, Germany.
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
| | | | - Aster Tsegaye
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Seifu
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Azeb Tarekegn
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Gutema Jabessa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Desalegn Abeje
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Abdulaziz Sherif
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Rawleigh Howe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Amha Gebremedhin
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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15
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Luib L, Kreyenberg H, Michaelis S, Handgretinger R, Mezger M. Transferring measurable residual disease measurement in pediatric acute lymphoblastic leukemia from quantitative real-time PCR to digital droplet PCR. Pediatr Transplant 2023; 27:e14483. [PMID: 36750990 DOI: 10.1111/petr.14483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/02/2023] [Accepted: 01/23/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND Since the measurement of measurable residual disease (MRD) is part of clinical routine examination for children affected with acute lymphoblastic leukemia (ALL), continuous efforts are made to improve its method, applicability and accuracy. Whereas quantitative real-time polymerase chain reaction (qPCR) is considered as the gold standard for MRD detection and endowed with international guidelines for implementation and evaluation, these do not yet exist for digital droplet PCR (ddPCR). However, advantages are seen in droplet partitioning for MRD measurement to allow absolute quantification without depending on reference samples. METHODS In this study, 17 MRD targets of nine patients with childhood B-ALL were analyzed with qPCR and ddPCR, respectively. All patients were assigned to high risk group and had hematopoietic stem cell transplantation and CD19 antibody therapy for relapse prevention. Starting with the sequences and guidelines of qPCR and optimizing the protocol for ddPCR, the MRD targets could also be measured precisely with this novel method, using the same primer and probe sets as for qPCR. RESULTS The already established MRD protocol of qPCR could be transferred to ddPCR and all 17 MRD targets were measured in dilution series reaching comparable Limit of detection levels with both PCR methods. CONCLUSIONS With a given qPCR protocol and some experience in conventional MRD monitoring, it is conceivable to transfer the procedure of MRD measurement to ddPCR technology. Our data is in line with other studies which are summarized and discussed here as well to facilitate the transfer of MRD diagnostics to ddPCR.
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Affiliation(s)
- Luise Luib
- Department of General Paediatrics, Haematology/Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Hermann Kreyenberg
- Clinic for Children and Adolescents, Department for Stem Cell Transplantation and Immunology, University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Sebastian Michaelis
- Department of General Paediatrics, Haematology/Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Rupert Handgretinger
- Department of General Paediatrics, Haematology/Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Markus Mezger
- Department of General Paediatrics, Haematology/Oncology, University Children's Hospital Tübingen, Tübingen, Germany
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16
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Cheng J, Mao X, Chen C, Long X, Chen L, Zhou J, Zhu L. Monitoring anti-CD19 chimeric antigen receptor T cell population by flow cytometry and its consistency with digital droplet polymerase chain reaction. Cytometry A 2023; 103:16-26. [PMID: 35875964 PMCID: PMC10087589 DOI: 10.1002/cyto.a.24676] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/31/2022] [Accepted: 07/21/2022] [Indexed: 01/21/2023]
Abstract
Anti-CD19 chimeric antigen receptor (CAR19) T cell therapy has produced impressive clinical efficacy in patients with relapsed or refractory B-cell malignancies. As a living drug, monitoring the pharmacokinetics of CAR T cells in vivo is an important part of clinical work, which provides valuable information for assessing therapeutic response and related side effects. However, no guidelines are available regarding the detection and quantification of CAR T cells. Flow cytometry is a convenient and commonly used method in monitoring CAR T cell kinetics, but its performance remains to be validated. By using a commercial anti-idiotype antibody that detects unique epitopes on the most popular CAR19 construct, we evaluated important performance parameters, including specificity, lower limit of detection, lower limit of quantification, and precision of flow cytometry in the detection and quantification of CAR19 T cells. Consistency between the results generated by flow cytometry and droplet digital PCR was then investigated in 188 pairs of clinical data and in cell line experiments. Rabbit anti-mouse FMC63 monoclonal antibody possesses high specificity in the detection of CAR19 positive cells by FCM with a cut-off value of 0.05%. The results produced by flow cytometry and ddPCR were well correlated in the clinical samples and in cell lines, but the correlation deteriorated as the abundance of CAR19 positive cells decreased. This was especially evident with less than 0.5% of lymphocytes in clinical data, possibly due to reduced precision (indicated by intra- and inter-assay coefficients of variability) of both droplet digital PCR and flow cytometry. We demonstrated that flow cytometry using anti-idiotype antibody is a reliable and robust approach in the detection and quantification of CAR19 T cells in vivo and has good consistency with droplet digital PCR in monitoring CAR19 T cell kinetics.
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Affiliation(s)
- Jiali Cheng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xia Mao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Caixia Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaolu Long
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liting Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zhu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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17
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Digital PCR as a New Method for Minimal Residual Disease Monitoring and Treatment Free Remission Management in Chronic Myeloid Leukemia Patients: Is It Reliable? HEMATO 2022. [DOI: 10.3390/hemato4010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The effective and sensitive monitoring of Minimal Residual Disease or Measurable Residual Disease (MRD) is a very important aspect in the management of patients affected by hematologic malignancies. The recent availability of new technologies has opened to the improvement of MRD monitoring. It is particularly relevant in patients affected by Chronic Myeloid Leukemia (CML). MRD monitoring is key in the management of CML patients thanks to the efficacy of TKIs therapy. Moreover, the policies of TKIs discontinuation aimed at treatment free remission are strongly based on the good selection of patients eligible for stopping TKIs therapy. The recently described application of digital PCR in CML patients monitoring seems to improve the accuracy and precision in the identification of optimal responders. The present review reports an overview on the application of digital PCR in the monitoring of MRD in CML and its impact on TKIs discontinuation trials and, consequently, on TFR success.
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Pang L, Pi X, Yang X, Song D, Qin X, Wang L, Man C, Zhang Y, Jiang Y. Nucleic acid amplification-based strategy to detect foodborne pathogens in milk: a review. Crit Rev Food Sci Nutr 2022; 64:5398-5413. [PMID: 36476145 DOI: 10.1080/10408398.2022.2154073] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Milk contaminated with trace amounts of foodborne pathogens can considerably threaten food safety and public health. Therefore, rapid and accurate detection techniques for foodborne pathogens in milk are essential. Nucleic acid amplification (NAA)-based strategies are widely used to detect foodborne pathogens in milk. This review article covers the mechanisms of the NAA-based detection of foodborne pathogens in milk, including polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), rolling circle amplification (RCA), and enzyme-free amplification, among others. Key factors affecting detection efficiency and the advantages and disadvantages of the above techniques are analyzed. Potential on-site detection tools based on NAA are outlined. We found that NAA-based strategies were effective in detecting foodborne pathogens in milk. Among them, PCR was the most reliable. LAMP showed high specificity, whereas RPA and RCA were most suitable for on-site and in-situ detection, respectively, and enzyme-free amplification was more economical. However, factors such as sample separation, nucleic acid target conversion, and signal transduction affected efficiency of NAA-based strategies. The lack of simple and effective sample separation methods to reduce the effect of milk matrices on detection efficiency was noteworthy. Further research should focus on simplifying, integrating, and miniaturizing microfluidic on-site detection platforms.
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Affiliation(s)
- Lidong Pang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xiaowen Pi
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Danliangmin Song
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xue Qin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Lihan Wang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yu Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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19
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Branford S, Apperley JF. Measurable residual disease in chronic myeloid leukemia. Haematologica 2022; 107:2794-2809. [PMID: 36453517 PMCID: PMC9713565 DOI: 10.3324/haematol.2022.281493] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Chronic myeloid leukemia is characterized by a single genetic abnormality resulting in a fusion gene whose mRNA product is easily detected and quantified by reverse-transcriptase polymerase chain reaction analysis. Measuring residual disease was originally introduced to identify patients relapsing after allogeneic stem cell transplantation but rapidly adopted to quantify responses to tyrosine kinase inhibitors. Real-time quantitative polymerase chain reaction is now an essential tool for the management of patients and is used to influence treatment decisions. In this review we track this development including the international collaboration to standardize results, discuss the integration of molecular monitoring with other factors that affect patients' management, and describe emerging technology. Four case histories describe varying scenarios in which the accurate measurement of residual disease identified patients at risk of disease progression and allowed appropriate investigations and timely clinical intervention.
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Affiliation(s)
- Susan Branford
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, Australia,School of Medicine, University of Adelaide, Adelaide, Australia,Clinical and Health Sciences, University of South Australia, Adelaide, Australia,S. Branford
| | - Jane F. Apperley
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK,Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK
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20
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Salmon M, White HE, Zizkova H, Gottschalk A, Motlova E, Cerveira N, Colomer D, Coriu D, Franke GN, Gottardi E, Izzo B, Jurcek T, Lion T, Schäfer V, Venturi C, Vigneri P, Zawada M, Zuna J, Hovorkova L, Koblihova J, Klamova H, Markova MS, Srbova D, Benesova A, Polivkova V, Zackova D, Mayer J, Roeder I, Glauche I, Ernst T, Hochhaus A, Polakova KM, Cross NCP. Impact of BCR::ABL1 transcript type on RT-qPCR amplification performance and molecular response to therapy. Leukemia 2022; 36:1879-1886. [PMID: 35676453 PMCID: PMC9252903 DOI: 10.1038/s41375-022-01612-2] [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: 03/28/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 12/03/2022]
Abstract
Several studies have reported that chronic myeloid leukaemia (CML) patients expressing e14a2 BCR::ABL1 have a faster molecular response to therapy compared to patients expressing e13a2. To explore the reason for this difference we undertook a detailed technical comparison of the commonly used Europe Against Cancer (EAC) BCR::ABL1 reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assay in European Treatment and Outcome Study (EUTOS) reference laboratories (n = 10). We found the amplification ratio of the e13a2 amplicon was 38% greater than e14a2 (p = 0.015), and the amplification efficiency was 2% greater (P = 0.17). This subtle difference led to measurable transcript-type dependent variation in estimates of residual disease which could be corrected by (i) taking the qPCR amplification efficiency into account, (ii) using alternative RT-qPCR approaches or (iii) droplet digital PCR (ddPCR), a technique which is relatively insensitive to differences in amplification kinetics. In CML patients, higher levels of BCR::ABL1/GUSB were identified at diagnosis for patients expressing e13a2 (n = 67) compared to e14a2 (n = 78) when analysed by RT-qPCR (P = 0.0005) but not ddPCR (P = 0.5). These data indicate that widely used RT-qPCR assays result in subtly different estimates of disease depending on BCR::ABL1 transcript type; these differences are small but may need to be considered for optimal patient management.
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Affiliation(s)
- Matthew Salmon
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Helen E White
- Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Hana Zizkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Andrea Gottschalk
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Eliska Motlova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Nuno Cerveira
- Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Dolors Colomer
- Pathology Department, Hospital Clinic, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), CIBERONC, Barcelona, Spain
| | - Daniel Coriu
- Fundeni Clinical Institute, Hematology Department, Bucharest, Romania.,Hematology Department, Faculty of Medicine, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Georg N Franke
- University of Leipzig Medical Center, Department for Hematology, Cellular Therapies and Hemostaseology, Leipzig, Germany
| | - Enrico Gottardi
- Laboratory of Chemical and Clinical Analysis "Area 3" A.O.U San Luigi Gonzaga-Orbassano, Turin, Italy
| | - Barbara Izzo
- Department of Molecular Medicine and Medical Biotechnology University 'Federico II' and CEINGE - Advanced Biotechnologies, Naples, Italy
| | - Tomas Jurcek
- Center of Molecular Biology and Gene Therapy, Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Thomas Lion
- Labdia Labordiagnostik / St. Anna Children´s Cancer Research Institute (CCRI), Vienna, Austria
| | - Vivien Schäfer
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | - Claudia Venturi
- IRCSS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Paolo Vigneri
- University of Catania, Department of Clinical and Experimental Medicine, Center of Experimental Oncology and Hematology, Catania, Italy
| | | | - Jan Zuna
- CLIP, Dept. of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Lenka Hovorkova
- CLIP, Dept. of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jitka Koblihova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Hana Klamova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | | | - Dana Srbova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Adela Benesova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Vaclava Polivkova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Daniela Zackova
- Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Internal Hematology and Oncology Clinic, Faculty Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany. Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Ingmar Glauche
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Thomas Ernst
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | - Andreas Hochhaus
- Abteilung Hämatologie/Onkologie, Klinik für Innere Medizin II, University of Jena, Jena, Germany
| | | | - Nicholas C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK. .,Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK.
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21
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Lu L, Kok CH, Dang P, Branford S, Saunders VA, Shanmuganathan N, Ross DM, Hughes TP, Yeung DTO. Highly sensitive droplet digital polymerase chain reaction for BCR::ABL1 messenger RNA identifies patients with chronic myeloid leukaemia with a low probability of achieving treatment-free remission. Br J Haematol 2022; 198:600-603. [PMID: 35620965 DOI: 10.1111/bjh.18277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/02/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Liu Lu
- South Australian Health and Medical Research Institute (SAHMRI), Precision Medicine Cancer Theme, Adelaide, South Australia, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Chung Hoow Kok
- South Australian Health and Medical Research Institute (SAHMRI), Precision Medicine Cancer Theme, Adelaide, South Australia, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Phuong Dang
- South Australian Health and Medical Research Institute (SAHMRI), Precision Medicine Cancer Theme, Adelaide, South Australia, Australia
| | - Susan Branford
- School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Genetics and Molecular Pathology & Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia
| | - Verity A Saunders
- South Australian Health and Medical Research Institute (SAHMRI), Precision Medicine Cancer Theme, Adelaide, South Australia, Australia
| | - Naranie Shanmuganathan
- South Australian Health and Medical Research Institute (SAHMRI), Precision Medicine Cancer Theme, Adelaide, South Australia, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Genetics and Molecular Pathology & Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Science, University of South Australia, Adelaide, Australia.,Department of Haematology, SA Pathology, Adelaide, South Australia, Australia
| | - David M Ross
- South Australian Health and Medical Research Institute (SAHMRI), Precision Medicine Cancer Theme, Adelaide, South Australia, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Genetics and Molecular Pathology & Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,Department of Haematology, SA Pathology, Adelaide, South Australia, Australia
| | - Timothy P Hughes
- South Australian Health and Medical Research Institute (SAHMRI), Precision Medicine Cancer Theme, Adelaide, South Australia, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Haematology, SA Pathology, Adelaide, South Australia, Australia
| | - David T O Yeung
- South Australian Health and Medical Research Institute (SAHMRI), Precision Medicine Cancer Theme, Adelaide, South Australia, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Genetics and Molecular Pathology & Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,Department of Haematology, SA Pathology, Adelaide, South Australia, Australia
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22
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Galimberti S, Balducci S, Guerrini F, Del Re M, Cacciola R. Digital Droplet PCR in Hematologic Malignancies: A New Useful Molecular Tool. Diagnostics (Basel) 2022; 12:1305. [PMID: 35741115 PMCID: PMC9221914 DOI: 10.3390/diagnostics12061305] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023] Open
Abstract
Digital droplet PCR (ddPCR) is a recent version of quantitative PCR (QT-PCR), useful for measuring gene expression, doing clonality assays and detecting hot spot mutations. In respect of QT-PCR, ddPCR is more sensitive, does not need any reference curve and can quantify one quarter of samples already defined as "positive but not quantifiable". In the IgH and TCR clonality assessment, ddPCR recapitulates the allele-specific oligonucleotide PCR (ASO-PCR), being not adapt for detecting clonal evolution, that, on the contrary, does not represent a pitfall for the next generation sequencing (NGS) technique. Differently from NGS, ddPCR is not able to sequence the whole gene, but it is useful, cheaper, and less time-consuming when hot spot mutations are the targets, such as occurs with IDH1, IDH2, NPM1 in acute leukemias or T315I mutation in Philadelphia-positive leukemias or JAK2 in chronic myeloproliferative neoplasms. Further versions of ddPCR, that combine different primers/probes fluorescences and concentrations, allow measuring up to four targets in the same PCR reaction, sparing material, time, and money. ddPCR is also useful for quantitating BCR-ABL1 fusion gene, WT1 expression, donor chimerism, and minimal residual disease, so helping physicians to realize that "patient-tailored therapy" that is the aim of the modern hematology.
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Affiliation(s)
- Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Serena Balducci
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Francesca Guerrini
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Marzia Del Re
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Rossella Cacciola
- Department of Clinical and Experimental Medicine, Section of Hemostasis, University of Catania, 95123 Catania, Italy
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23
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Shelton DN, Bhagavatula P, Sepulveda N, Beppu L, Gandhi S, Qin D, Hauenstein S, Radich J. Performance characteristics of the first Food and Drug Administration (FDA)-cleared digital droplet PCR (ddPCR) assay for BCR::ABL1 monitoring in chronic myelogenous leukemia. PLoS One 2022; 17:e0265278. [PMID: 35298544 PMCID: PMC8929598 DOI: 10.1371/journal.pone.0265278] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/27/2022] [Indexed: 11/19/2022] Open
Abstract
Chronic myelogenous leukemia (CML) is a hematopoietic stem cell malignancy that accounts for 15-20% of all cases of leukemia. CML is caused by a translocation between chromosomes 9 and 22 which creates an abnormal fusion gene, BCR::ABL1. The amount of BCR::ABL1 transcript RNA is a marker of disease progression and the effectiveness of tyrosine kinase inhibitor (TKI) treatment. This study determined the analytical and clinical performance of a droplet digital PCR based assay (QXDx BCR-ABL %IS Kit; Bio-Rad) for BCR::ABL1 quantification. The test has a limit of detection of MR4.7 (0.002%) and a linear range of MR0.3-4.7 (50-0.002%IS). Reproducibility of results across multiple sites, days, instruments, and users was evaluated using panels made from BCR::ABL1 positive patient samples. Clinical performance of the assay was evaluated on patient samples and compared to an existing FDA-cleared test. The reproducibility study noted negligible contributions to variance from site, instrument, day, and user for samples spanning from MR 0.7-4.2. The assay demonstrated excellent clinical correlation with the comparator test using a Deming regression with a Pearson R of 0.99, slope of 1.037 and intercept of 0.1084. This data establishes that the QXDx™ BCR-ABL %IS Kit is an accurate, precise, and sensitive system for the diagnosis and monitoring of CML.
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MESH Headings
- Fusion Proteins, bcr-abl/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Polymerase Chain Reaction/methods
- Protein Kinase Inhibitors/therapeutic use
- Reproducibility of Results
- United States
- United States Food and Drug Administration
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Affiliation(s)
- Dawne N. Shelton
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Prasanthi Bhagavatula
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Nathan Sepulveda
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Lan Beppu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Shital Gandhi
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Dahui Qin
- Department of Pathology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Scott Hauenstein
- Digital Biology Group, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Jerald Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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24
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Kim Y, Kim S, Lee JM, Ahn A, Yoo JW, Lee JW, Cho B, Chung NG, Kim Y, Kim M. Discontinuation of tyrosine kinase inhibitors based on BCR-ABL1 monitoring by digital droplet PCR in pediatric chronic myeloid leukemia. Front Pediatr 2022; 10:928136. [PMID: 35967571 PMCID: PMC9363655 DOI: 10.3389/fped.2022.928136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Lifelong treatment of pediatric chronic myeloid leukemia (CML) patients with tyrosine kinase inhibitors (TKIs) can affect their growth and development. For these reasons, clinical trials have explored the feasibility of TKI discontinuation in children with a sufficient TKI response. We evaluated the analytical performance of digital droplet PCR (ddPCR) to quantify BCR-ABL1 and compared the results with reverse transcription quantitative polymerase chain reaction (RT-qPCR). We further investigated whether ddPCR could be used to determine TKI discontinuation in a clinical setting. Performance of ddPCR was evaluated using standard materials for BCR-ABL1, and a total of 197 clinical samples from 45 pediatric CML patients was included for comparison with RT-qPCR. ddPCR showed excellent analytical sensitivity with 0.001% international scale (IS) and linearity with R 2 > 0.99 in log scale. BCR-ABL1 % IS results correlated well with those of RT-qPCR (R 2 = 0.9435), however, they showed a moderate strength for agreement with a Cohen's kappa of 0.41 due to higher sensitivity of ddPCR. Among 45 pediatric CML patients, 42 were treated with first-line TKIs including imatinib (n = 27, 64%) and dasatinib (n = 12, 29%), and three patients that were started with imatinib were switched to dasatinib. When we evaluated whether follow-up samples fulfilled ABL1 copies ≥ 10,000 required for deep molecular response (DMR), all samples were acceptable by ddPCR, whereas 18% by RT-qPCR did not reached acceptable ABL1 copies. Moreover, 52 and 13% reached ABL1 copies ≥ 32,000 required for MR4.5 by ddPCR and RT-qPCR, respectively. Seven patients discontinued TKI and the median TKI treatment duration was 73 months prior to discontinuation. Prior to discontinuation, the median duration of sustained undetected BCR-ABL1 was 60 months. Two patients experienced loss of major MR (MMR) during follow-up and restarted dasatinib 5 months after discontinuation. They achieved MMR again and maintained better than DMR afterward. Results from those patients demonstrated that RT-qPCR did not match the need for adequate ABL1 copies for MR4.5 while majority of ddPCR could. Therefore, ddPCR was technically more acceptable to decide and monitor pediatric CML patients before and after TKI discontinuation.
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Affiliation(s)
- Yeojae Kim
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul, South Korea
| | - Seongkoo Kim
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Jong Mi Lee
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Ari Ahn
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jae Won Yoo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Jae Wook Lee
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Bin Cho
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Nack-Gyun Chung
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, The Catholic University of Korea, Seoul, South Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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25
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Jacky L, Yurk D, Alvarado J, Leatham B, Schwartz J, Annaloro J, MacDonald C, Rajagopal A. Virtual-Partition Digital PCR for High-Precision Chromosomal Counting Applications. Anal Chem 2021; 93:17020-17029. [PMID: 34905685 DOI: 10.1021/acs.analchem.1c03527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Digital PCR (dPCR) is the gold-standard analytical platform for rapid high-precision quantification of genomic fragments. However, current dPCR assays are generally limited to monitoring 1-2 analytes per sample, thereby limiting the platform's ability to address some clinical applications that require the simultaneous monitoring of 20-50 analytes per sample. Here, we present virtual-partition dPCR (VPdPCR), a novel analysis methodology enabling the detection of 10 or more target regions per color channel using conventional dPCR hardware and workflow. Furthermore, VPdPCR enables dPCR instruments to overcome upper quantitation limits caused by partitioning error. While traditional dPCR analysis establishes a single threshold to separate negative and positive partitions, VPdPCR establishes multiple thresholds to identify the number of unique targets present in each positive droplet based on fluorescence intensity. Each physical partition is then divided into a series of virtual partitions, and the resulting increase in partition count substantially decreases partitioning error. We present both a theoretical analysis of the advantages of VPdPCR and an experimental demonstration in the form of a 20-plex assay for noninvasive fetal aneuploidy testing. This demonstration assay─tested on 432 samples contrived from sheared cell-line DNA at multiple input concentrations and simulated fractions of euploid or trisomy-21 "fetal" DNA─is analyzed using both traditional dPCR thresholding and VPdPCR. VPdPCR analysis significantly lowers the variance of the chromosomal ratio across replicates and increases the accuracy of trisomy identification when compared to traditional dPCR, yielding > 98% single-well sensitivity and specificity. VPdPCR has substantial promise for increasing the utility of dPCR in applications requiring ultrahigh-precision quantitation.
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Affiliation(s)
- Lucien Jacky
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Dominic Yurk
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States.,Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - John Alvarado
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Bryan Leatham
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Jerrod Schwartz
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - John Annaloro
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Chris MacDonald
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Aditya Rajagopal
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States.,Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, United States.,Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, United States
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26
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Mika T, Thomson J, Nilius-Eliliwi V, Vangala D, Baraniskin A, Wulf G, Klein-Scory S, Schroers R. Quantification of cell-free DNA for the analysis of CD19-CAR-T cells during lymphoma treatment. Mol Ther Methods Clin Dev 2021; 23:539-550. [PMID: 34853800 PMCID: PMC8606297 DOI: 10.1016/j.omtm.2021.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/21/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022]
Abstract
Chimeric antigen receptor (CAR)-T cells are increasingly used for the treatment of hematologic malignancies. Treatment success relies highly upon sufficient expansion of CAR-T effector cells. Accordingly, longitudinal quantification of CAR-T cells during therapy is clinically important. Techniques to quantify CAR-T cells in patient blood samples are based on flow cytometry and PCR. However, cellular kinetics of CAR-T cells are very complex and under current investigation. In this study, feasibility of CAR-T cell quantification by cell-free DNA (cfDNA) was analyzed. cfDNA isolated from 74 blood samples of 12 patients during lymphoma treatment with the anti-CD19 CAR-T cell product axicabtagene ciloleucel (axi-cel) were analyzed. Concentrations of cfDNA specific for the CAR-T gene construct (cfCAR-DNA) and a reference gene were quantified by a newly designed digital-droplet PCR (ddPCR) assay. Detection and quantification of cfCAR-DNA was feasible and reliable for all patients included. Relative quantification of cfCAR-DNA compared to a reference gene, suitable for genomic DNA analysis, was heterogeneous in treatment responders and non-responders. In contrast, parallel analyses of cfCAR-DNA and reference cfDNA in a patient-specific approach gave insight into active lymphoma killing and treatment responses. In summary, plasma cfDNA determination in lymphoma patients is a promising tool for future clinical decision making.
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Olmedillas-López S, Olivera-Salazar R, García-Arranz M, García-Olmo D. Current and Emerging Applications of Droplet Digital PCR in Oncology: An Updated Review. Mol Diagn Ther 2021; 26:61-87. [PMID: 34773243 DOI: 10.1007/s40291-021-00562-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 12/14/2022]
Abstract
In the era of personalized medicine and targeted therapies for the management of patients with cancer, ultrasensitive detection methods for tumor genotyping, such as next-generation sequencing or droplet digital polymerase chain reaction (ddPCR), play a significant role. In the search for less invasive strategies for diagnosis, prognosis and disease monitoring, the number of publications regarding liquid biopsy approaches using ddPCR has increased substantially in recent years. There is a long list of malignancies in which ddPCR provides a reliable and accurate tool for detection of nucleic acid-based markers derived from cell-free DNA, cell-free RNA, circulating tumor cells, extracellular vesicles or exosomes when isolated from whole blood, plasma and serum, helping to anticipate tumor relapse or unveil intratumor heterogeneity and clonal evolution in response to treatment. This updated review describes recent developments in ddPCR platforms and provides a general overview about the major applications of liquid biopsy in blood, including its utility for molecular response and minimal residual disease monitoring in hematological malignancies or the therapeutic management of patients with colorectal or lung cancer, particularly for the selection and monitoring of treatment with tyrosine kinase inhibitors. Although plasma is the main source of genetic material for tumor genomic profiling, liquid biopsy by ddPCR is being investigated in a wide variety of biologic fluids, such as cerebrospinal fluid, urine, stool, ocular fluids, sputum, saliva, bronchoalveolar lavage, pleural effusion, mucin, peritoneal fluid, fine needle aspirate, bile or pancreatic juice. The present review focuses on these "alternative" sources of genetic material and their analysis by ddPCR in different kinds of cancers.
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Affiliation(s)
- Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Rocío Olivera-Salazar
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Damián García-Olmo
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.,Department of Surgery, Fundación Jiménez Díaz University Hospital (FJD), 28040, Madrid, Spain
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28
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Droplet Digital PCR for BCR-ABL1 Monitoring in Diagnostic Routine: Ready to Start? Cancers (Basel) 2021; 13:cancers13215470. [PMID: 34771634 PMCID: PMC8582412 DOI: 10.3390/cancers13215470] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The introduction to clinical practice of a treatment-free remission approach in chronic myeloid leukemia patients with a stable deep molecular response highlighted how crucial it is to monitor the molecular levels of BCR–ABL1 as accurately and precisely as possible. In this context, the droplet digital PCR (ddPCR) presents an alternative methodology for such quantification. To hypothesize the introduction of this technology in routine practice, we performed a multicentric study that compares ddPCR with the standard methodology currently used. Our results demonstrate that the use of ddPCR in clinical practice is feasible and could be beneficial. Abstract BCR–ABL1 mRNA levels represent the key molecular marker for the evaluation of minimal residual disease (MRD) in chronic myeloid leukemia (CML) patients and real-time quantitative PCR (RT-qPCR) is currently the standard method to monitor it. In the era of tyrosine kinase inhibitors (TKIs) discontinuation, droplet digital PCR (ddPCR) has emerged to provide a more precise detection of MRD. To hypothesize the use of ddPCR in clinical practice, we designed a multicentric study to evaluate the potential value of ddPCR in the diagnostic routine. Thirty-seven RNA samples from CML patients and five from healthy donors were analyzed using both ddPCR QXDxTMBCR-ABL %IS Kit and LabNet-approved RT-qPCR methodologies in three different Italian laboratories. Our results show that ddPCR has a good agreement with RT-qPCR, but it is more precise to quantify BCR–ABL1 transcript levels. Furthermore, we did not find differences between duplicate or quadruplicate analysis in terms of BCR–ABL1% IS values. Droplet digital PCR could be confidently introduced into the diagnostic routine as a complement to the RT-qPCR.
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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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30
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Scott S, Cartwright A, Francis S, Whitby L, Sanzone AP, Mulder A, Galimberti S, Dulucq S, Mauté C, Lauricella C, Salmon M, Rose S, Willoughby J, Boeckx N, Pallisgaard N, Maier J, Leibundgut EO, Zizkova H, Ling Goh L, Duong C, Tang WF, Ma E, Shivakumar Y, Beppu L, Bhagavatula P, Chantry A. Assessment of droplet digital polymerase chain reaction for measuring BCR-ABL1 in chronic myeloid leukaemia in an international interlaboratory study. Br J Haematol 2021; 194:53-60. [PMID: 34114218 DOI: 10.1111/bjh.17521] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/21/2021] [Indexed: 01/24/2023]
Abstract
Measurement of BCR activator of RhoGEF and GTPase -ABL proto-oncogene 1, non-receptor tyrosine kinase (BCR-ABL1) mRNA levels by reverse transcription quantitative polymerase chain reaction (RTqPCR) has been critical to treatment protocols and clinical trials in chronic myeloid leukaemia; however, interlaboratory variation remains a significant issue. Reverse transcriptase droplet digital PCR (RTddPCR) has shown potential to improve testing but a large-scale interlaboratory study is required to definitively establish this. In the present study, 10 BCR-ABL1-positive samples with levels ranging from molecular response (MR)1·0 -MR5·0 were tested by 23 laboratories using RTddPCR with the QXDX BCR-ABL %IS kit. A subset of participants tested the samples using RTqPCR. All 23 participants using RTddPCR detected BCR-ABL1 in all samples to MR4·0 . Detection rates for deep-response samples were 95·7% at MR4·5 , 78·3% at MR4·7 and 87·0% at MR5·0 . Interlaboratory coefficient of variation was indirectly proportional to BCR-ABL1 level ranging from 29·3% to 69·0%. Linearity ranged from 0·9330 to 1·000 (average 0·9936). When results were compared for the 11 participants who performed both RTddPCR and RTqPCR, RTddPCR showed a similar limit of detection to RTqPCR with reduced interlaboratory variation and better assay linearity. The ability to detect deep responses with RTddPCR, matched with an improved linearity and reduced interlaboratory variation will allow improved patient management, and is of particular importance for future clinical trials focussed on achieving and maintaining treatment-free remission.
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Affiliation(s)
- Stuart Scott
- Sheffield Teaching Hospital NHS Foundation Trust, UK National External Quality Assessment Services (NEQAS) for Leucocyte Immunophenotyping, Sheffield, UK.,Faculty of Medicine Dentistry and Health, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Ashley Cartwright
- Sheffield Teaching Hospital NHS Foundation Trust, UK National External Quality Assessment Services (NEQAS) for Leucocyte Immunophenotyping, Sheffield, UK
| | - Sebastian Francis
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Liam Whitby
- Sheffield Teaching Hospital NHS Foundation Trust, UK National External Quality Assessment Services (NEQAS) for Leucocyte Immunophenotyping, Sheffield, UK
| | - A Pia Sanzone
- Advanced Therapies, National Institute for Biological Standards and Control, Potters Bar, UK
| | - André Mulder
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sara Galimberti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Stephanie Dulucq
- Laboratory of Hematology, University Hospital Centre Bordeaux, Pessac, France.,University of Bordeaux, INSERM, U1218, Bordeaux, France
| | - Carole Mauté
- Haematology Laboratory, Hôpital Saint-Louis, Paris, France
| | - Calogero Lauricella
- Department of Laboratory Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Matthew Salmon
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.,University of Southampton, School of Medicine, Southampton, UK
| | - Susan Rose
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Josh Willoughby
- Sheffield Diagnostic Genetics Service, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Nancy Boeckx
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Niels Pallisgaard
- Department of Surgical Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Jacqueline Maier
- Department of Transfusion Medicine, University Hospital Leipzig, Leipzig, Germany
| | | | - Hana Zizkova
- Department of Molecular Genetics, Institute of Hematology and Blood Transfusion, Praha, Czech Republic
| | - Liuh Ling Goh
- Personalized Medicine Service, Tan Tock Seng Hospital, Singapore, Singapore
| | - Chinh Duong
- Genetics and Molecular Biology, National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam.,Department of Hematology and Blood Transfusion, University of Medicine and Pharmacy, Vietnam National University, Hanoi, Vietnam
| | - Wing F Tang
- Department of Pathology, Division of Haematology, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Edmond Ma
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong.,Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, Hong Kong
| | | | - Lan Beppu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Andrew Chantry
- Faculty of Medicine Dentistry and Health, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK.,Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
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31
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Radich J. Building a better mousetrap for accurate and sensitive polymerase chain reaction. Br J Haematol 2021; 194:11-13. [PMID: 34114207 DOI: 10.1111/bjh.17520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Jerry Radich
- Clinical Research Division, Departments of Oncology and Haematology, University of Washingon, Seattle, WA, USA
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32
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Moncada A, Pancrazzi A. Lab tests for MPN. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 366:187-220. [PMID: 35153004 DOI: 10.1016/bs.ircmb.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular laboratory investigations for myeloproliferative neoplasm (MPN) can ideally be divided into two distincts groups, those for the detection of the BCR-ABL rearrangement (suspect of chronic myeloid leukemia) and those for the variants determination of the driver genes of the negative Philadelphia forms (MPN Ph neg). The BCR-ABL detection is based on RT-Polymerase Chain Reaction techniques and more recently on droplet digital PCR (ddPCR). For this type of analysis, combined with chromosome banding analysis (CBA) and Fluorescent in situ hybridization (FISH), it is essential to quantify BCR-ABL mutated copies by standard curve method. The investigation on driver genes for MPN Ph neg forms includes activity for erythroid forms such as Polycythemia Vera (test JAK2V617F and JAK2 exon 12), for non-erythroid forms such as essential thrombocythemia and myelofibrosis (test JAK2V617F, CALR exon 9, MPL exon 10), for "atypical" ones such as mastocytosis (cKIT D816V test) and for hypereosinophilic syndrome (FIP1L1-PDGFRalpha test). It's crucial to assign prognosis value through calculating allelic burden of JAK2 V617F variant and determining CALR esone 9 variants (type1/1like, type2/2like and atypical ones). A fundamental innovation for investigating triple negative cases for JAK2, CALR, MPL and for providing prognostic score is the use of Next Generation Sequencing panels containing high molecular risk genes as ASXL1, EZH2, TET2, IDH1/IDH2, SRSF2. This technique allows to detect additional or subclonal mutations which are usually acquired in varying sized sub-clones of hematopoietic progenitors. These additional variants have a prognostic significance and should be indagated to exclude false negative cases.
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Affiliation(s)
- Alice Moncada
- Laboratory Medicine Department, Molecular and Clinical Pathology Sector, Azienda USL Toscana Sudest, Ospedale San Donato, Arezzo, Italy
| | - Alessandro Pancrazzi
- Laboratory Medicine Department, Molecular and Clinical Pathology Sector, Azienda USL Toscana Sudest, Ospedale San Donato, Arezzo, Italy.
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33
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Kao YF, Peake B, Madden R, Cowan SR, Scimeca RC, Thomas JE, Reichard MV, Ramachandran A, Miller CA. A probe-based droplet digital polymerase chain reaction assay for early detection of feline acute cytauxzoonosis. Vet Parasitol 2021; 292:109413. [PMID: 33765571 DOI: 10.1016/j.vetpar.2021.109413] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/14/2022]
Abstract
Cytauxzoonosis is a tick-borne disease of domestic cats with high mortality and narrow therapeutic window, particularly in the southcentral and southeastern United States. The causative agent is the apicomplexan protozoal parasite Cytauxzoon felis and is primarily transmitted by Amblyomma americanum, the lone star tick. Currently there is no vaccine available to prevent cytauxzoonosis and treatment is often ineffective if not initiated early enough in the course of disease. Early diagnosis and therapeutic intervention are therefore crucial for the survival of infected cats. Several methods are available for diagnosis of cytauxzoonosis, with PCR being the most sensitive. However, current PCR assays, which employ double-stranded DNA intercalating dyes to detect C. felis infection, have inherent limitations such as the potential for false positive detection of non-specific amplification products and inability to provide absolute quantification of parasite load. The objective of this study was to develop a probe-based droplet digital PCR (ddPCR) assay capable of detection and quantification of C. felis load over time and during treatment. The C. felis ddPCR assay was able to (i) reliably detect and quantify C. felis DNA in clinical blood samples from cats with acute cytauxzoonosis and (ii) monitor clinical parasite load in response to anti-protozoal treatment through absolute quantification of C. felis DNA over time. When tested on blood samples from cats with experimental C. felis infection, the assay was able to detect infection in cats as early as 24 h prior to the development of clinical signs. In addition, we demonstrate that this probe-based design can be utilized in traditional real-time PCR systems, with similar detection capabilities as compared to ddPCR. The C. felis probe-based ddPCR was also able to detect infection in samples with lower parasite loads when compared to existing nested PCR assays, although these results were not significant due to small sample size. To the author's knowledge, this is the first reported probe-based ddPCR assay to detect Cytauxzoon felis infection in domestic cats.
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Affiliation(s)
- Yun-Fan Kao
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA
| | - Brittanie Peake
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, 1950 W Farm Rd, Stillwater, OK, 74078, USA
| | - Robin Madden
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, 1950 W Farm Rd, Stillwater, OK, 74078, USA
| | - Shannon R Cowan
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA
| | - Ruth C Scimeca
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, 1950 W Farm Rd, Stillwater, OK, 74078, USA
| | - Jennifer E Thomas
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA
| | - Mason V Reichard
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, 1950 W Farm Rd, Stillwater, OK, 74078, USA
| | - Craig A Miller
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, 250 McElroy Hall, Stillwater, OK, 74078, USA.
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Branford S. Why is it critical to achieve a deep molecular response in chronic myeloid leukemia? Haematologica 2020; 105:2730-2737. [PMID: 33054104 PMCID: PMC7716360 DOI: 10.3324/haematol.2019.240739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The primary goal of tyrosine kinase inhibitor (TKI) therapy for patients with chronic myeloid leukemia is survival, which is achieved by the vast majority of patients. The initial response to therapy provides a sensitive measure of future clinical outcome. Measurement of BCR-ABL1 transcript levels using real-time quantitative polymerase chain reaction standardized to the international reporting scale is now the principal recommended monitoring strategy. The method is used to assess early milestone responses and provides a guide for therapeutic intervention. When patients successfully traverse the critical first 12 months of TKI therapy, most will head towards another milestone response, deep molecular response (DMR, BCR-ABL1 ≤0.01%). DMR is essential for patients aiming to achieve treatment-free remission and a prerequisite for a trial of TKI discontinuation. The success of discontinuation trials has led to new treatment strategies in order for more patients to reach this milestone response. DMR has been incorporated into endpoints of clinical trials and is considered by some expert groups as the optimal treatment response. But is DMR a stable response and does it provide the ultimate protection against TKI resistance and death? Do we need to increase the sensitivity of detection of BCR-ABL1 to better identify the patients who would likely remain in treatment-free remission after TKI discontinuation? Is it necessary to switch current TKI therapy to a more potent inhibitor if the goal is to achieve DMR? These are issues that I will explore in this review.
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Affiliation(s)
- Susan Branford
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology; School of Pharmacy and Medical Science, Division of Health Sciences, University of South Australia; School of Medicine, Faculty of Health and Medical Sciences, University of Adelaide and School of Biological Sciences, University of Adelaide, Adelaide.
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35
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Kockerols CC, Valk PJ, Levin MD, Pallisgaard N, Cornelissen JJ, Westerweel PE. Digital PCR for BCR-ABL1 Quantification in CML: Current Applications in Clinical Practice. Hemasphere 2020; 4:e496. [PMID: 33283168 PMCID: PMC7710259 DOI: 10.1097/hs9.0000000000000496] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular monitoring of the BCR-ABL1 transcript for patients with chronic phase chronic myeloid leukemia (CML) has become increasingly demanding. Real-time quantitative PCR (qPCR) is the routinely used method, but has limitations in quantification accuracy due to its inherent technical variation. Treatment recommendations rely on specific BCR-ABL1 values set at timed response milestones, making precise measurement of BCR-ABL1 a requisite. Furthermore, the sensitivity of qPCR may be insufficient to reliably quantify low levels of residual BCR-ABL1 in patients in deep molecular response (DMR) who could qualify for an attempt to discontinue Tyrosine Kinase Inhibitor (TKI) therapy. We reviewed the current use of digital PCR (dPCR) as a promising alternative for response monitoring in CML. dPCR offers an absolute BCR-ABL1 quantification at various disease levels with remarkable precision and a clinical sensitivity reaching down to at least MR5.0. Moreover, dPCR has been validated in multiple studies as prognostic marker for successful TKI treatment discontinuation, while this could not be achieved using classical qPCR. dPCR may thus prospectively be the preferred method to reliably identify patients achieving treatment milestones after initiation of TKI therapy as well as for the selection and timing for TKI discontinuation.
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Affiliation(s)
| | - Peter J.M. Valk
- Department of Molecular Biology and Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark-David Levin
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | | | - Jan J. Cornelissen
- Department of Molecular Biology and Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter E. Westerweel
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
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36
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Soverini S, Bernardi S, Galimberti S. Molecular Testing in CML between Old and New Methods: Are We at a Turning Point? J Clin Med 2020; 9:E3865. [PMID: 33261150 PMCID: PMC7760306 DOI: 10.3390/jcm9123865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular monitoring of minimal residual disease (MRD) and BCR-ABL1 kinase domain (KD) mutation testing have a well consolidated role in the routine management of chronic myeloid leukemia (CML) patients, as they provide precious information for therapeutic decision-making. Molecular response levels are used to define whether a patient has an "optimal", "warning", or "failure" response to tyrosine kinase inhibitor (TKI) therapy. Mutation status may be useful to decide whether TKI therapy should be changed and which alternative TKI (or TKIs) are most likely to be effective. Real-time quantitative polymerase chain reaction (RQ-qPCR) and Sanger sequencing are currently the gold standard for molecular response monitoring and mutation testing, respectively. However, in recent years, novel technologies such as digital PCR (dPCR) and next-generation sequencing (NGS) have been evaluated. Here, we critically describe the main features of these old and novel technologies, provide an overview of the recently published studies assessing the potential clinical value of dPCR and NGS, and discuss how the state of the art might evolve in the next years.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Hematology/Oncology “Lorenzo e Ariosto Seràgnoli”, University of Bologna, 40138 Bologna, Italy;
| | - Simona Bernardi
- Department of Clinical and Experimental Sciences, University of Brescia, Bone Marrow Transplant Unit, ASST Spedali Civili, 25123 Brescia, Italy
- Centro di Ricerca Emato-Oncologica AIL (CREA), ASST Spedali Civili, 25123 Brescia, Italy
| | - Sara Galimberti
- Department of Clinical and Experimental Medicine, Hematology Unit, University of Pisa, 56126 Pisa, Italy;
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Jovanovski A, Petiti J, Giugliano E, Gottardi EM, Saglio G, Cilloni D, Fava C. Standardization of BCR-ABL1 p210 Monitoring: From Nested to Digital PCR. Cancers (Basel) 2020; 12:cancers12113287. [PMID: 33172063 PMCID: PMC7694607 DOI: 10.3390/cancers12113287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022] Open
Abstract
The introduction of tyrosine kinase inhibitors in 2001 as a targeted anticancer therapy has significantly improved the quality of life and survival of patients with chronic myeloid leukemia. At the same time, with the introduction of tyrosine kinase inhibitors, the need for precise monitoring of the molecular response to therapy has emerged. Starting with a qualitative polymerase chain reaction, followed by the introduction of a quantitative polymerase chain reaction to determine the exact quantity of the transcript of interest-p210 BCR-ABL1, molecular monitoring in patients with chronic myeloid leukemia was internationally standardized. This enabled precise monitoring of the therapeutic response, unification of therapeutic protocols, and comparison of results between different laboratories. This review aims to summarize the steps in the diagnosis and molecular monitoring of p210 BCR-ABL1, as well as to consider the possible future application of a more sophisticated method such as digital polymerase chain reaction.
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Affiliation(s)
- Aleksandar Jovanovski
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
- Correspondence: (A.J.); (J.P.); Tel.: +39-0119026800 (A.J. & J.P.)
| | - Jessica Petiti
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
- Correspondence: (A.J.); (J.P.); Tel.: +39-0119026800 (A.J. & J.P.)
| | - Emilia Giugliano
- Division of Internal Medicine and Hematology, San Luigi Gonzaga Hospital, Orbassano, 10043 Turin, Italy; (E.G.); (E.M.G.)
| | - Enrico Marco Gottardi
- Division of Internal Medicine and Hematology, San Luigi Gonzaga Hospital, Orbassano, 10043 Turin, Italy; (E.G.); (E.M.G.)
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
| | - Carmen Fava
- Department of Clinical and Biological Sciences, University of Turin, 10043 Turin, Italy; (G.S.); (D.C.); (C.F.)
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Treatment-Free Remission in Chronic Myeloid Leukemia Harboring Atypical BCR-ABL1 Transcripts. Mediterr J Hematol Infect Dis 2020; 12:e2020066. [PMID: 32952977 PMCID: PMC7485467 DOI: 10.4084/mjhid.2020.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/14/2020] [Indexed: 11/08/2022] Open
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Comparison of Droplet Digital PCR versus qPCR Measurements on the International Scale for the Molecular Monitoring of Chronic Myeloid Leukemia Patients. Mol Diagn Ther 2020; 24:593-600. [PMID: 32875515 DOI: 10.1007/s40291-020-00485-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND BCR-ABL1/ABL1 p210 measurement by quantitative polymerase chain reaction (qPCR) is used worldwide to monitor the molecular response in chronic myeloid leukemia (CML) patients. Droplet digital polymerase chain reaction (ddPCR) seems to show a greater sensitivity than qPCR, probably due to the high number of replicates analyzed in ddPCR for the comparison. Additionally, in a recently published comparison, ddPCR measurements were not adequately transformed into International Scale (IS). METHOD We have analyzed 50 CML patients and ten non-CML donors in parallel by qPCR and ddPCR. To the best of our knowledge, this is the first study comparing both techniques under similar conditions, with BCR-ABL1/ABL1 measurements performed via both techniques transformed into IS. RESULTS Qualitative and quantitative comparisons showed excellent results. The qualitative correlation showed a Kappa index of 0.94 (95% confidence interval [CI] 0.90-0.98) (P < 0.001). In the quantitative comparison, the absolute intra-class correlation coefficient was 0.868 (95% CI 0.734-0.937; P < 0.001), and Lin's concordance correlation coefficient was 0.863. The Passing-Bablock test indicated a slight proportional difference between qPCR and ddPCR. A quantitative and qualitative subanalysis including 40 patients with a molecular response of 3.0 or deeper showed similar results in every test. In addition, the proportional difference in the Passing-Bablock test disappeared. There were no differences in the sensitivity for BCR-ABL1 detection between qPCR and ddPCR (McNemar test, P = 0.5). CONCLUSIONS In conclusion, our results show very good quantitative and qualitative correlations between BCR-ABL1/ABL1 p210 results obtained by qPCR and by ddPCR and confirm previous scarce data regarding the lack of an increase in sensitivity of ddPCR over qPCR in this setting.
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Mika T, Maghnouj A, Klein-Scory S, Ladigan-Badura S, Baraniskin A, Thomson J, Hasenkamp J, Hahn SA, Wulf G, Schroers R. Digital-Droplet PCR for Quantification of CD19-Directed CAR T-Cells. Front Mol Biosci 2020; 7:84. [PMID: 32500079 PMCID: PMC7243121 DOI: 10.3389/fmolb.2020.00084] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/16/2020] [Indexed: 01/01/2023] Open
Abstract
CD19-directed CAR-T-cells (CD19-CAR) have demonstrated remarkable clinical results in patients suffering from refractory or relapsed lymphoma and acute lymphoblastic leukemia. In order to further optimize follow-up, to explain treatment failure, and to control adverse events biomarkers for monitoring of response are urgently needed. Peak expansion and persistence are correlated with response rates and severity of side effects. However, no standardized method or commercially assay for CD19-CAR measurement is established yet. In this study, two primer-probe assays for digital-droplet PCR (ddPCR) were designed and subsequently explored on 54 samples collected from seven patients after CD19-CAR treatment with axi-cel over time. Detection and quantification of CAR-T-cells were feasible and reliable for all patients included. Peak expansion measured with our assay significantly correlated with the grade of neurologic adverse events but not with cytokine release syndrome. All patients with loss of CAR-signal eventually had disease progression. In summary, our novel assay allows monitoring of CAR-T-cells in vivo and may add to safety and efficacy of CAR-T treatment.
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Affiliation(s)
- Thomas Mika
- Department of Medicine, Hematology and Oncology, Ruhr University Bochum, Bochum, Germany.,Department of Molecular Gastroenterologic Oncology, Ruhr University Bochum, Bochum, Germany
| | - Abdelouahid Maghnouj
- Department of Molecular Gastroenterologic Oncology, Ruhr University Bochum, Bochum, Germany
| | | | - Swetlana Ladigan-Badura
- Department of Medicine, Hematology and Oncology, Ruhr University Bochum, Bochum, Germany.,Department of Molecular Gastroenterologic Oncology, Ruhr University Bochum, Bochum, Germany
| | - Alexander Baraniskin
- Department of Medicine, Hematology and Oncology, Ruhr University Bochum, Bochum, Germany
| | - Julia Thomson
- Clinic for Hematology and Medical Oncology, Georg-August University, Göttingen, Germany
| | - Justin Hasenkamp
- Clinic for Hematology and Medical Oncology, Georg-August University, Göttingen, Germany
| | - Stephan A Hahn
- Department of Molecular Gastroenterologic Oncology, Ruhr University Bochum, Bochum, Germany
| | - Gerald Wulf
- Clinic for Hematology and Medical Oncology, Georg-August University, Göttingen, Germany
| | - Roland Schroers
- Department of Medicine, Hematology and Oncology, Ruhr University Bochum, Bochum, Germany
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Cumbo C, Anelli L, Specchia G, Albano F. Monitoring of Minimal Residual Disease (MRD) in Chronic Myeloid Leukemia: Recent Advances. Cancer Manag Res 2020; 12:3175-3189. [PMID: 32440215 PMCID: PMC7211966 DOI: 10.2147/cmar.s232752] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm caused by the BCR-ABL1 fusion gene generation as a consequence of the t(9;22)(q34;q11) rearrangement. The identification of the BCR-ABL1 transcript was of critical importance for both CML diagnosis and minimal residual disease (MRD) monitoring. In this review, we report the recent advances in the CML MRD monitoring based on RNA, DNA and protein analysis. The detection of the BCR-ABL1 transcript by the quantitative reverse-transcriptase polymerase chain reaction is the gold standard method, but other systems based on digital PCR or on GeneXpert technology have been developed. In the last years, DNA-based assays showed high sensitivity and specificity, and flow cytometric approaches for the detection of the BCR-ABL1 fusion protein have also been tested. Recently, new MRD monitoring systems based on the detection of molecular markers other than the BCR-ABL1 fusion were proposed. These approaches, such as the identification of CD26+ leukemic stem cells, microRNAs and mitochondrial DNA mutations, just remain preliminary and need to be implemented. In the precision medicine era, the constant improvement of the CML MRD monitoring practice could allow clinicians to choose the best therapeutic algorithm and a more accurate selection of CML patients eligible for the tyrosine kinase inhibitors discontinuation.
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Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari 70124, Italy
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Coccaro N, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies. Int J Mol Sci 2020; 21:ijms21093141. [PMID: 32365599 PMCID: PMC7247671 DOI: 10.3390/ijms21093141] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The digital polymerase chain reaction (dPCR) is considered to be the third-generation polymerase chain reaction (PCR), as it yields direct, absolute and precise measures of target sequences. dPCR has proven particularly useful for the accurate detection and quantification of low-abundance nucleic acids, highlighting its advantages in cancer diagnosis and in predicting recurrence and monitoring minimal residual disease, mostly coupled with next generation sequencing. In the last few years, a series of studies have employed dPCR for the analysis of hematologic malignancies. In this review, we will summarize these findings, attempting to focus on the potential future perspectives of the application of this promising technology.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Correspondence: ; Tel.: +39-(0)80-5478031; Fax: +39-(0)80-5508369
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