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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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Han X, Zhao R, Zhang Q, Shen X, Sun K. Increased expression of keratin 17 in oral lichen planus and its correlation with disease severity. J Dent Sci 2024; 19:1525-1532. [PMID: 39035284 PMCID: PMC11259633 DOI: 10.1016/j.jds.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/21/2024] [Indexed: 07/23/2024] Open
Abstract
Background/purpose Oral lichen planus (OLP) is a chronic inflammatory disease with unknown mechanisms of pathogenesis. Keratin 17 (KRT17) is a protein that regulates numerous cellular processes. This study aimed to explore the expression of KRT17 in OLP and its correlation with the severity of OLP. Materials and methods RNA sequencing using epithelium from 5 OLP patients and 5 health control (HC) was performed, followed by functional analysis. The validation cohort of 20 OLP and 20 HC tissues were used to investigate positive area value of KRT17 by immunohistochemical analysis. Reticular, erosive and ulcerative (REU) scores were used for measuring the severity of OLP. Results A total of 15493 genes were detected, of which 1492 genes were significantly up-regulated in OLP and 622 were down-regulated. The mRNA expression of KRT17 was elevated by 13.09-fold in OLP compared to that in HC. Pathway analysis demonstrated high KRT17 expression was associated with multiple biological processes. The median of percentage of KRT17 positive area value was 19.30 % in OLP and 0.01 % in HC (P < 0.001). Percentage of KRT17 positive area value was higher in erosive OLP patients (27.25 %) compared to that in non-erosive patients (15.02 %, P = 0.006). REU scores were positively correlated with percentage of KRT17 positive area value (r = 0.628, P = 0.003). Conclusion The mRNA expression of KRT17 was elevated in OLP tissues compared to that in HC. KRT17 was positively correlated with the severity of OLP, indicating KRT17 might play a vital role in the pathogenesis of OLP.
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Affiliation(s)
| | | | - Qianqian Zhang
- Department of Oral Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xuemin Shen
- Department of Oral Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Kai Sun
- Department of Oral Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
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3
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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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4
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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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5
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Marin AM, Wosniaki DK, Sanchuki HBS, Munhoz EC, Nardin JM, Soares GS, Espinace DC, de Holanda Farias JS, Veroneze B, Becker LF, Costa GL, Beltrame OC, de Oliveira JC, Cambri G, Zanette DL, Aoki MN. Molecular BCR::ABL1 Quantification and ABL1 Mutation Detection as Essential Tools for the Clinical Management of Chronic Myeloid Leukemia Patients: Results from a Brazilian Single-Center Study. Int J Mol Sci 2023; 24:10118. [PMID: 37373266 DOI: 10.3390/ijms241210118] [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: 04/27/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a well-characterized oncological disease in which virtually all patients possess a translocation (9;22) that generates the tyrosine kinase BCR::ABL1 protein. This translocation represents one of the milestones in molecular oncology in terms of both diagnostic and prognostic evaluations. The molecular detection of the BCR::ABL1 transcription is a required factor for CML diagnosis, and its molecular quantification is essential for assessing treatment options and clinical approaches. In the CML molecular context, point mutations on the ABL1 gene are also a challenge for clinical guidelines because several mutations are responsible for tyrosine kinase inhibitor resistance, indicating that a change may be necessary in the treatment protocol. So far, the European LeukemiaNet and the National Comprehensive Cancer Network (NCCN) have presented international guidelines on CML molecular approaches, especially those related to BCR::ABL1 expression. In this study, we show almost three years' worth of data regarding the clinical treatment of CML patients at the Erasto Gaertner Hospital, Curitiba, Brazil. These data primarily comprise 155 patients and 532 clinical samples. BCR::ABL1 quantification by a duplex-one-step RT-qPCR and ABL1 mutations detection were conducted. Furthermore, digital PCR for both BCR::ABL1 expression and ABL1 mutations were conducted in a sub-cohort. This manuscript describes and discusses the clinical importance and relevance of molecular biology testing in Brazilian CML patients, demonstrating its cost-effectiveness.
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Affiliation(s)
- Anelis Maria Marin
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Denise Kusma Wosniaki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | | | | | - Gabriela Silva Soares
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Dhienifer Caroline Espinace
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | | | | | | | | | | | | | - Geison Cambri
- Instituto de Biologia Molecular do Paraná (IBMP), Curitiba 81350-010, Brazil
| | - Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba 81350-010, Brazil
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6
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Lee H, Seo J, Shin S, Lee ST, Choi JR. Development and validation of sensitive BCR::ABL1 fusion gene quantitation using next-generation sequencing. Cancer Cell Int 2023; 23:106. [PMID: 37248544 DOI: 10.1186/s12935-023-02938-2] [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: 11/30/2022] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND BCR::ABL1 fusion has significant prognostic value and is screened for chronic myeloid leukemia (CML) disease monitoring as a part of routine molecular testing. To overcome the limitations of the current standard real-time quantitative polymerase chain reaction (RQ-PCR), we designed and validated a next-generation sequencing (NGS)-based assay to quantify BCR::ABL1 and ABL1 transcript copy numbers. METHODS After PCR amplification of the target sequence, deep sequencing was performed using an Illumina Nextseq 550Dx sequencer and in-house-designed bioinformatics pipeline. The Next-generation Quantitative sequencing (NQ-seq) assay was validated for its analytical performance, including precision, linearity, and limit of detection, using serially diluted control materials. A comparison with conventional RQ-PCR was performed with 145 clinical samples from 77 patients. RESULTS The limit of detection of the NQ-seq was the molecular response (MR) 5.6 [BCR::ABL1 0.00028% international scale (IS)]. The NQ-seq exhibited excellent precision and linear range from MR 2.0 to 5.0. The IS value from the NQ-seq was highly correlated with conventional RQ-PCR. CONCLUSIONS We conclude that the NQ-seq is an effective tool for monitoring BCR::ABL1 transcripts in CML patients with high sensitivity and reliability. Prospective assessment of the unselected large series is required to validate the clinical impact of this NGS-based monitoring strategy.
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Affiliation(s)
- Hyeonah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jieun Seo
- Department of Genetics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome Co. Ltd, 8, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome Co. Ltd, 8, Seongnam-daero 331beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
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7
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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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8
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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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9
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Deng X, Zhang M, Zhou J, Xiao M. Next-generation sequencing for MRD monitoring in B-lineage malignancies: from bench to bedside. Exp Hematol Oncol 2022; 11:50. [PMID: 36057673 PMCID: PMC9440501 DOI: 10.1186/s40164-022-00300-2] [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] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/21/2022] [Indexed: 12/02/2022] Open
Abstract
Minimal residual disease (MRD) is considered the strongest relevant predictor of prognosis and an effective decision-making factor during the treatment of hematological malignancies. Remarkable breakthroughs brought about by new strategies, such as epigenetic therapy and chimeric antigen receptor-T (CAR-T) therapy, have led to considerably deeper responses in patients than ever, which presents difficulties with the widely applied gold-standard techniques of MRD monitoring. Urgent demands for novel approaches that are ultrasensitive and provide sufficient information have put a spotlight on high-throughput technologies. Recently, advances in methodology, represented by next-generation sequencing (NGS)-based clonality assays, have proven robust and suggestive in numerous high-quality studies and have been recommended by some international expert groups as disease-monitoring modalities. This review demonstrates the applicability of NGS-based clonality assessment for MRD monitoring of B-cell malignancies by summarizing the oncogenesis of neoplasms and the corresponding status of immunoglobulin (IG) rearrangements. Furthermore, we focused on the performance of NGS-based assays compared with conventional approaches and the interpretation of results, revealing directions for improvement and prospects in clinical practice.
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Affiliation(s)
- Xinyue Deng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, 430030, China
| | - Meilan Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, 430030, China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, 430030, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China. .,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, 430030, China.
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10
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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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11
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Revealing the Mysteries of Acute Myeloid Leukemia: From Quantitative PCR through Next-Generation Sequencing and Systemic Metabolomic Profiling. J Clin Med 2022; 11:jcm11030483. [PMID: 35159934 PMCID: PMC8836582 DOI: 10.3390/jcm11030483] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 12/13/2022] Open
Abstract
The efforts made in the last decade regarding the molecular landscape of acute myeloid leukemia (AML) have created the possibility of obtaining patients’ personalized treatment. Indeed, the improvement of accurate diagnosis and precise assessment of minimal residual disease (MRD) increased the number of new markers suitable for novel and targeted therapies. This progress was obtained thanks to the development of molecular techniques starting with real-time quantitative PCR (Rt-qPCR) passing through digital droplet PCR (ddPCR) and next-generation sequencing (NGS) up to the new attractive metabolomic approach. The objective of this surge in technological advances is a better delineation of AML clonal heterogeneity, monitoring patients without disease-specific mutation and designing customized post-remission strategies based on MRD assessment. In this context, metabolomics, which pertains to overall small molecules profiling, emerged as relevant access for risk stratification and targeted therapies improvement. In this review, we performed a detailed overview of the most popular modern methods used in hematological laboratories, pointing out their vital importance for MRD monitoring in order to improve overall survival, early detection of possible relapses and treatment efficacy.
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