1
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Li X, Huang Z, Zhu L, Lai W, Li Y, Chen H, Liu D, Huang J, Zhou D, Li Y, Weng W, Xu H, Xu L, Luo Z, Fang J. The potential role of RNA sequencing in diagnosing unexplained insensitivity to conventional chemotherapy in pediatric patients with B-cell acute lymphoblastic leukemia. BMC Med Genomics 2024; 17:149. [PMID: 38811988 PMCID: PMC11137891 DOI: 10.1186/s12920-024-01892-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is a highly heterogeneous disease. According to large-scale RNA sequencing (RNA-seq) data, B-ALL patients can be divided into more than 10 subgroups. However, many genomic defects associated with resistance mechanisms have not yet been identified. As an individual clinical tool for molecular diagnostic risk classification, RNA-seq and gene expression pattern-based therapy could be potential upcoming strategies. In this study, we retrospectively analyzed the RNA-seq gene expression profiles of 45 children whose molecular diagnostic classifications were inconsistent with the response to chemotherapy. The relationship between the transcriptome and chemotherapy response was analyzed. Fusion gene identification was conducted for the included patients who did not have known high-risk associated fusion genes or gene mutations. The most frequently detected fusion gene pair in the high-risk group was the DHRSX duplication, which is a novel finding. Fusions involving ABL1, LMNB2, NFATC1, PAX5, and TTYH3 at onset were more frequently detected in the high-risk group, while fusions involving LFNG, TTYH3, and NFATC1 were frequently detected in the relapse group. According to the pathways involved, the underlying drug resistance mechanism is related to DNA methylation, autophagy, and protein metabolism. Overall, the implementation of an RNA-seq diagnostic system will identify activated markers associated with chemotherapy response, and guide future treatment adjustments.
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Affiliation(s)
- Xinyu Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China
| | - Zaoli Huang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Liwen Zhu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Weixin Lai
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yunyao Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Han Chen
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Diandian Liu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Dunhua Zhou
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Yang Li
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Wenjun Weng
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Honggui Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China
| | - Luhong Xu
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
| | - Zhenhua Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China.
| | - Jianpei Fang
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, West Yan Jiang Road, 510120, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, China.
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2
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van Outersterp I, van der Velden VH, Hoogeveen PG, Vaitkevičienė GE, Sonneveld E, van Haaften G, Kuiper RP, zur Stadt U, Escherich G, Boer JM, den Boer ML. ABL-class Genomic Breakpoint Q-PCR: A Patient-specific Approach for MRD Monitoring in Acute Lymphoblastic Leukemia. Hemasphere 2023; 7:e967. [PMID: 37736661 PMCID: PMC10511034 DOI: 10.1097/hs9.0000000000000967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/03/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
| | - Vincent H.J. van der Velden
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Patricia G. Hoogeveen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Goda E. Vaitkevičienė
- Faculty of Medicine, Vilnius University, Lithuania
- Center for Pediatric Oncology and Hematology, Vilnius University Hospital Santaros Klinikos, Lithuania
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | - Roland P. Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, The Netherlands
| | - Udo zur Stadt
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg Eppendorf, Germany
| | - Gabriele Escherich
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg Eppendorf, Germany
| | - Judith M. Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Monique L. den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology and Hematology, Erasmus MC - Sophia Children’s Hospital, Rotterdam, The Netherlands
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3
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Burmeister T, Gröger D, Gökbuget N, Spriewald B, Starck M, Elmaagacli A, Hoelzer D, Keller U, Schwartz S. Molecular characterization of TCF3::PBX1 chromosomal breakpoints in acute lymphoblastic leukemia and their use for measurable residual disease assessment. Sci Rep 2023; 13:15167. [PMID: 37704696 PMCID: PMC10499895 DOI: 10.1038/s41598-023-42294-9] [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: 06/08/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
The translocation t(1;19)(q23;p13) with the resulting chimeric TCF3::PBX1 gene is the third most prevalent recurrent chromosomal translocation in acute lymphoblastic leukemia and accounts for 3-5% of cases. The molecular background of this translocation has been incompletely studied, especially in adult cases. We characterized the chromosomal breakpoints of 49 patients with TCF3::PBX1 and the corresponding reciprocal PBX1::TCF3 breakpoints in 15 cases at the molecular level, thus providing an extensive molecular overview of this translocation in a well-defined study patient population. Breakpoints were found to be remarkably clustered not only in TCF3 but also in PBX1. No association with DNA repeats or putative cryptic recombination signal sequence sites was observed. A simplified detection method for breakpoint identification was developed and the feasibility of patient-specific chromosomal break sites as molecular markers for detecting measurable residual disease (MRD) was explored. A highly sensitive generic real-time PCR for MRD assessment using these breakpoint sequences was established that could serve as a useful alternative to the classical method utilizing rearranged immune gene loci. This study provides the first extensive molecular data set on the chromosomal breakpoints of the t(1;19)/TCF3::PBX1 aberration in adult ALL. Based on the obtained data a generic MRD method was developed that has several theoretical advantages, including an on average higher sensitivity and a greater stability of the molecular marker in the course of disease.
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Affiliation(s)
- Thomas Burmeister
- Department of Hematology, Oncology and Tumor Immunology, CVK, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Daniela Gröger
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicola Gökbuget
- Medical Department 2, Goethe-Universität, Frankfurt, Germany
| | - Bernd Spriewald
- Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Michael Starck
- I. Medical Department, München Klinik Schwabing, Munich, Germany
| | - Ahmet Elmaagacli
- Department of Hematology, Oncology, Asklepios Klinik St. Georg, Hamburg, Germany
| | - Dieter Hoelzer
- Medical Department 2, Goethe-Universität, Frankfurt, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Schwartz
- Department of Hematology, Oncology and Tumor Immunology, CBF, Charité - Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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4
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Kipf E, Schlenker F, Borst N, Fillies M, Kirschner-Schwabe R, Zengerle R, Eckert C, von Stetten F, Lehnert M. Advanced Minimal Residual Disease Monitoring for Acute Lymphoblastic Leukemia with Multiplex Mediator Probe PCR. J Mol Diagn 2021; 24:57-68. [PMID: 34757015 DOI: 10.1016/j.jmoldx.2021.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/16/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most frequent malignancy in childhood. Minimal residual disease (MRD) monitoring is an important prognostic factor for treatment response and patient stratification. It uses personalized real-time PCR to measure the amount of cancer cells among normal cells. Due to clonal tumor evolution or secondary rearrangement processes, MRD markers can disappear during treatment, leading to false-negative MRD results and wrong decision-making in personalized treatments. Therefore, monitoring of multiple MRD markers per patient is required. For the first time, the authors present personalized multiplex mediator probe PCR (MP PCR) for MRD monitoring in ALL. These assays can precisely quantify more MRD markers in less sample material. Therefore, clinical outcomes will be less affected by clonal tumor evolution. Personalized duplex MP PCR assays were developed for different genomic MRD markers, including immunoglobulin/T-cell receptor gene rearrangements, gene fusions, and gene deletions. One duplex assay was successfully applied in a prospective patient case and compared with hydrolysis probes. Moreover, the authors increased the multiplex level from duplex to 4-plex and still met the EuroMRD requirements for reliable quantification. In addition, the authors' MRD-MP design guidelines and multiplex workflow facilitate and accelerate MP PCR assay development. This helps the standardization of personal diagnostics.
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Affiliation(s)
- Elena Kipf
- Hahn-Schickard, Freiburg, Germany; Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | | | - Nadine Borst
- Hahn-Schickard, Freiburg, Germany; Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Marion Fillies
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Renate Kirschner-Schwabe
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Freiburg, Germany; Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Cornelia Eckert
- Department of Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Freiburg, Germany; Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany.
| | - Michael Lehnert
- Hahn-Schickard, Freiburg, Germany; Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
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5
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Kuiper RP, Hoogeveen PG, Bladergroen R, van Dijk F, Sonneveld E, van Leeuwen FN, Boer J, Sergeeva I, Feitsma H, den Boer ML, van der Velden VHJ. Minimal residual disease (MRD) detection in acute lymphoblastic leukaemia based on fusion genes and genomic deletions: towards MRD for all. Br J Haematol 2021; 194:888-892. [PMID: 34337744 PMCID: PMC9291030 DOI: 10.1111/bjh.17744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/18/2021] [Indexed: 12/16/2022]
Abstract
Minimal residual disease (MRD) diagnostics are implemented in most clinical protocols for patients with acute lymphoblastic leukaemia (ALL) and are mostly performed using rearranged immunoglobulin (IG) and/or T-cell receptor (TR) gene rearrangements as molecular polymerase chain reaction targets. Unfortunately, in 5-10% of patients no or no sensitive IG/TR targets are available, and patients therefore cannot be stratified appropriately. In the present study, we used fusion genes and genomic deletions as alternative MRD targets in these patients, which retrospectively revealed appropriate MDR stratification in 79% of patients with no (sensitive) IG/TR target, and a different risk group stratification in more than half of the cases.
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Affiliation(s)
- Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patricia G Hoogeveen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Reno Bladergroen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Freerk van Dijk
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Judith Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | | | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands.,Department of Pediatric Oncology, Erasmus MC - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Vincent H J van der Velden
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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6
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Huang YJ, Kuo MC, Jaing TH, Liu HC, Yeh TC, Chen SH, Lin TL, Yang CP, Wang PN, Sheen JM, Chang TK, Chang CH, Hu SF, Huang TY, Wang SC, Wu KH, Chiou SS, Hsiao CC, Shih LY. Comparison of Two Quantitative PCR-Based Assays for Detection of Minimal Residual Disease in B-Precursor Acute Lymphoblastic Leukemia Harboring Three Major Fusion Transcripts. J Mol Diagn 2021; 23:1373-1379. [PMID: 34325057 DOI: 10.1016/j.jmoldx.2021.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/17/2021] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
Two quantitative PCR (qPCR)-based methods, for clonal Ig or T-cell receptor gene (Ig/TCR) rearrangements and for fusion transcripts, are widely used for the measurement of minimal residual disease (MRD) in patients with B-precursor acute lymphoblastic leukemia (ALL). MRD of bone marrow samples from 165 patients carrying the three major fusion transcripts, including 74 BCR-ABL1, 54 ETV6-RUNX1, and 37 TCF3-PBX1, was analyzed by using the two qPCR-based methods. The coefficient correlation of both methods was good for TCF3-PBX1 (R2 = 0.8088) and BCR-ABL1 (R2 = 0.8094) ALL and moderate for ETV6-RUNX1 (R2 = 0.5972). The concordance was perfect for TCF3-PBX1 ALL (97.2%), substantially concordant for ETV6-RUNX1 ALL (87.1%), and only moderate for BCR-ABL1 ALL (70.6%). The discordant MRD, positive for only one method with a difference greater than one log, was found in 4 of 93 samples (4.3%) with ETV6-RUNX1, 31 of 245 samples (12.7%) with BCR-ABL1, and 0 of TCF3-PBX1 ALL. None of the eight nontransplanted patients with BCR-ABL1-MRD (+)/Ig/TCR-MRD (-) with a median follow-up time of 73.5 months had hematologic relapses. Our study showed an excellent MRD concordance between the two qPCR-based methods in TCF3-PBX1 ALL, whereas qPCR for Ig/TCR is more reliable in BCR-ABL1 ALL.
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Affiliation(s)
- Ying-Jung Huang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Ming-Chung Kuo
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tang-Her Jaing
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Hematology-Oncology, Chang Gung Children's Hospital at Linkou, Taoyuan, Taiwan
| | - Hsi-Che Liu
- Department of Hematology-Oncology, Mackay Children's Hospital and Mackay Medical College, Taipei, Taiwan
| | - Ting-Chi Yeh
- Department of Hematology-Oncology, Mackay Children's Hospital and Mackay Medical College, Taipei, Taiwan
| | - Shih-Hsiang Chen
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Hematology-Oncology, Chang Gung Children's Hospital at Linkou, Taoyuan, Taiwan
| | - Tung-Liang Lin
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chao-Ping Yang
- Department of Hematology-Oncology, Chang Gung Children's Hospital at Linkou, Taoyuan, Taiwan
| | - Po-Nan Wang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Jiunn-Ming Sheen
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Kaohsiung, Kaohsiung, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Te-Kau Chang
- Division of Pediatric Hematology and Oncology, China Medical University Children's Hospital, Taichung, Taiwan
| | - Chia-Hui Chang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Shu-Fen Hu
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Ting-Yu Huang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Shih-Chung Wang
- Division of Pediatric Hematology-Oncology, Changhua Christian Children's Hospital, Changhua, Taiwan
| | - Kang-Hsi Wu
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shyh-Shin Chiou
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chih-Cheng Hsiao
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Kaohsiung, Kaohsiung, Taiwan
| | - Lee-Yung Shih
- Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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7
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Juelg P, Kipf E, Specht M, Fillies M, Eckert C, Paust N, Zengerle R, Lehnert M, Hutzenlaub T. The MRD disk: automated minimal residual disease monitoring by highly sensitive centrifugal microfluidic multiplex qPCR. LAB ON A CHIP 2021; 21:558-570. [PMID: 33319895 DOI: 10.1039/d0lc00945h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present a proof-of-principle study on automated, highly sensitive and multiplexed qPCR quantification by centrifugal microfluidics. The MRD disk can be used for standardisation of repetitive, longitudinal assays with high requirements on reproducibility and sensitivity, such as cancer monitoring. In contrast to high-throughput qPCR automation by bulky and expensive robotic workstations we employ a small centrifugal microfluidic instrument, addressing the need of low- to mid-throughput applications. As a potential application we demonstrate automated minimum residual disease (MRD) monitoring of prognostic markers in patients with acute lymphoblastic leukaemia (ALL). The disk-workflow covers all aspects of clinical gold standard MRD quantification: generation of standard curves, specificity controls, no template controls and quantification of the ALL patient sample. We integrated a highly sensitive, colorimetric 2-plex analysis of MRD targets, as well as a 2-plex analysis of reference genes, both in parallel and in a single LabDisk cartridge. For this purpose, a systematic procedure for crosstalk- and signal-to-noise-optimisation is introduced, providing a guideline for efficient multiplex readout inside microfluidic platforms. The qPCR standard curves (n = 12/12) generated on-disk reach clinically required linearity (R2 = 98.1% to R2 = 99.8%). In three consecutive MRD disk runs with an ALL patient sample containing the two representative MRD targets VH3D3D5JH3 and VkIkde, we observe high accordance between the on-disk quantifications (48 ± 6 copies/reaction and 69 ± 6 copies/reaction) and the expected concentrations (57 copies/reaction for both targets). In comparison to the clinical gold standard of manually pipetted, singleplex assays, the MRD disk yields comparable limit of quantification (1 × 10-4) in n = 6/6 analyses (vs. n = 4/4 in gold standard) and a limit of detection (1 × 10-5) in n = 6/6 analysis (vs. n = 2/4 in gold standard). The automation reduces the risk of manual liquid handling errors, making the MRD disk an attractive solution to assure reproducibility in moderate-throughput, longitudinal gene quantification applications.
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Affiliation(s)
- Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Elena Kipf
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Mara Specht
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Marion Fillies
- Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Cornelia Eckert
- Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nils Paust
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. and Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. and Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Michael Lehnert
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
| | - Tobias Hutzenlaub
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany. and Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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8
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Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy. Cancer Lett 2020; 499:24-38. [PMID: 33248210 DOI: 10.1016/j.canlet.2020.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
The incidence of pediatric cancers is rising steadily across the world, along with the challenges in understanding the molecular mechanisms and devising effective therapeutic strategies. Pediatric cancers are presented with diverse molecular characteristics and more distinct subtypes when compared to adult cancers. Recent studies on the genomic landscape of pediatric cancers using next-generation sequencing (NGS) approaches have redefined this field by providing better subtype characterization and novel actionable targets. Since early identification and personalized treatment strategies influence therapeutic outcomes, survival, and quality of life in pediatric cancer patients, the quest for actionable biomarkers is of great value in this field. Fusion genes that are prevalent and recurrent in several pediatric cancers are ideally suited in this context due to their disease-specific occurrence. In this review, we explore the current status of fusion genes in pediatric cancer subtypes and their use as biomarkers for diagnosis and personalized therapy. We discuss the technological advancements made in recent years in NGS sequencing and their impact on fusion detection algorithms that have revolutionized this field. Finally, we also discuss the advantages of pairing liquid biopsy protocols for fusion detection and their eventual use in diagnosis and treatment monitoring.
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9
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Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL. Blood Cancer J 2019; 9:96. [PMID: 31784504 PMCID: PMC6884523 DOI: 10.1038/s41408-019-0257-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/01/2019] [Accepted: 11/06/2019] [Indexed: 12/20/2022] Open
Abstract
B-cell precursor (BCP) ALL carry a variety of classical V(D)J rearrangements as well as genomic fusions and translocations. Here, we assessed the value of genomic capture high-throughput sequencing (gc-HTS) in BCP ALL (n = 183) for the identification and implementation of targets for minimal residual disease (MRD) testing. For TRδ, a total of 300 clonal rearrangements were detected in 158 of 183 samples (86%). Beside clonal Vδ2-Dδ3, Dδ2-Dδ3, and Vδ2-Jα we identified a novel group of recurrent Dδ-Jα rearrangements, comprising Dδ2 or Dδ3 segments fused predominantly to Jα29. For IGH-JH, 329 clonal rearrangements were identified in 172 of 183 samples (94%) including novel types of V(D)J joining. Oligoclonality was found in ~1/3 (n = 57/183) of ALL samples. Genomic breakpoints were identified in 71 BCP-ALL. A distinct MRD high-risk subgroup of IGH-V(D)J-germline ALL revealed frequent deletions of IKZF1 (n = 7/11) and the presence of genomic fusions (n = 10/11). Quantitative measurement using genomic fusion breakpoints achieved equivalent results compared to conventional V(D)J-based MRD testing and could be advantageous upon persistence of a leukemic clone. Taken together, selective gc-HTS expands the spectrum of suitable MRD targets and allows for the identification of genomic fusions relevant to risk and treatment stratification in childhood ALL.
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Juelg P, Specht M, Kipf E, Lehnert M, Eckert C, Keller M, Hutzenlaub T, von Stetten F, Zengerle R, Paust N. Automated serial dilutions for high-dynamic-range assays enabled by fill-level-coupled valving in centrifugal microfluidics. LAB ON A CHIP 2019; 19:2205-2219. [PMID: 31139783 DOI: 10.1039/c9lc00092e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We introduce a new concept for centrifugal microfluidics that enables fully automated serial dilution generation without any additional means besides temperature control. The key feature is time-independent, serial valving of mixing chambers by fill-level-coupled temperature change rate (FLC-TCR) actuated valving. The automated dilution is realized under continuous rotation which enables reliable control of wetting liquids without the need for any additional fabrication steps such as hydrophobic coating. All fluidic features are implemented in a monolithic fashion and disks are manufactured by foil thermoforming for scalable manufacturing. The new valving concept is demonstrated to reliably prevent valving if the diluted sample is not added to the mixing chamber (n = 30) and ensure valving if the dilution stage is completed (n = 15). The accuracy and precision of automated serial dilutions are verified by on-disk generation of qPCR standard curve dilutions and compared with manually generated reference dilutions. In a first step, the 5-log-stage standard curves are evaluated in a commercial qPCR thermocycler revealing a linearity of R2 ≥ 99.92% for the proposed LabDisk method vs. R2 ≥ 99.67% in manual reference dilutions. In a second step, the disk automated serial dilutions are combined with on-disk qPCR thermocycling and readout, both inside a LabDisk player. A 4-log-stage linearity of R2 ≥ 99.81% and a sensitivity of one leukemia associated ETV6-RUNX1 mutant DNA copy in a background of 100 000 wild-type DNA copies are achieved.
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Affiliation(s)
- Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
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