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Sala-Torra O, Reddy S, Hung LH, Beppu L, Wu D, Radich J, Yeung KY, Yeung CCS. Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002267. [PMID: 37699001 PMCID: PMC10497132 DOI: 10.1371/journal.pgph.0002267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/17/2023] [Indexed: 09/14/2023]
Abstract
Recurrent gene fusions are common drivers of disease pathophysiology in leukemias. Identifying these structural variants helps stratify disease by risk and assists with therapy choice. Precise molecular diagnosis in low-and-middle-income countries (LMIC) is challenging given the complexity of assays, trained technical support, and the availability of reliable electricity. Current fusion detection methods require a long turnaround time (7-10 days) or advance knowledge of the genes involved in the fusions. Recent technology developments have made sequencing possible without a sophisticated molecular laboratory, potentially making molecular diagnosis accessible to remote areas and low-income settings. We describe a long-read sequencing DNA assay designed with CRISPR guides to select and enrich for recurrent leukemia fusion genes, that does not need a priori knowledge of the abnormality present. By applying rapid sequencing technology based on nanopores, we sequenced long pieces of genomic DNA and successfully detected fusion genes in cell lines and primary specimens (e.g., BCR::ABL1, PML::RARA, CBFB::MYH11, KMT2A::AFF1) using cloud-based bioinformatics workflows with novel custom fusion finder software. We detected fusion genes in 100% of cell lines with the expected breakpoints and confirmed the presence or absence of a recurrent fusion gene in 12 of 14 patient cases. With our optimized assay and cloud-based bioinformatics workflow, these assays and analyses could be performed in under 8 hours. The platform's portability, potential for adaptation to lower-cost devices, and integrated cloud analysis make this assay a candidate to be placed in settings like LMIC to bridge the need of bedside rapid molecular diagnostics.
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Affiliation(s)
- Olga Sala-Torra
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- University of Washington, Seattle, Washington, United States of America
| | - Shishir Reddy
- University of Washington, Seattle, Washington, United States of America
| | - Ling-Hong Hung
- University of Washington, Seattle, Washington, United States of America
| | - Lan Beppu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - David Wu
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
| | - Jerald Radich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
| | - Ka Yee Yeung
- University of Washington, Seattle, Washington, United States of America
| | - Cecilia C. S. Yeung
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- School of Engineering and Technology, University of Washington Tacoma, Tacoma, Washington, United States of America
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2
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L'Abbate A, Moretti V, Pungolino E, Micheloni G, Valli R, Frattini A, Barcella M, Acquati F, Reinbold RA, Costantino L, Ferrara F, Trojani A, Ventura M, Porta G, Cairoli R. Occurrence of L1M Elements in Chromosomal Rearrangements Associated to Chronic Myeloid Leukemia (CML): Insights from Patient-Specific Breakpoints Characterization. Genes (Basel) 2023; 14:1351. [PMID: 37510256 PMCID: PMC10379433 DOI: 10.3390/genes14071351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a rare myeloproliferative disorder caused by the reciprocal translocation t(9;22)(q34;q11) in hematopoietic stem cells (HSCs). This chromosomal translocation results in the formation of an extra-short chromosome 22, called a Philadelphia chromosome (Ph), containing the BCR-ABL1 fusion gene responsible for the expression of a constitutively active tyrosine kinase that causes uncontrolled growth and replication of leukemic cells. Mechanisms behind the formation of this chromosomal rearrangement are not well known, even if, as observed in tumors, repetitive DNA may be involved as core elements in chromosomal rearrangements. We have participated in the explorative investigations of the PhilosoPhi34 study to evaluate residual Ph+ cells in patients with negative FISH analysis on CD34+/lin- cells with gDNA qPCR. Using targeted next-generation deep sequencing strategies, we analyzed the genomic region around the t(9;22) translocations of 82 CML patients and one CML cell line and assessed the relevance of interspersed repeat elements at breakpoints (BP). We found a statistically higher presence of LINE elements, in particular belonging to the subfamily L1M, in BP cluster regions of both chromosome 22 and 9 compared to the whole human genome. These data suggest that L1M elements could be potential drivers of t(9;22) translocation leading to the generation of the BCR-ABL1 chimeric gene and the expression of the active BCR-ABL1-controlled tyrosine kinase chimeric protein responsible for CML.
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Affiliation(s)
- Alberto L'Abbate
- Institute of Biomembranes, Bioenergetics, and Molecular Biotechnologies, National Research Council (IBIOM-CNR), 70125 Bari, Italy
| | - Vittoria Moretti
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5 Varese, 21100 Varese, Italy
| | - Ester Pungolino
- Division of Hematology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milano, Italy
| | - Giovanni Micheloni
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5 Varese, 21100 Varese, Italy
| | - Roberto Valli
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5 Varese, 21100 Varese, Italy
| | - Annalisa Frattini
- Genetics and Biomedical Research Institute, National Research Council (IRGB-CNR), 20090 Milano, Italy
| | - Matteo Barcella
- Department of Health Science, University degli Studi of Milan, Via Rudini 8, 20142 Milan, Italy
| | - Francesco Acquati
- Department of Biotechnology and Life Science, University of Insubria, Via JH Dunant 3, 21100 Varese, Italy
- Genomic Medicine Research Center, Department of Biotechnology and Life Science, University of Insubria, Via JH Dunant 3, 21100 Varese, Italy
| | - Rolland A Reinbold
- Institute of Biomedical Technologies, National Research Council of Italy, 20054 Segrate, Milano, Italy
| | - Lucy Costantino
- Department of Molecular Genetics, Centro Diagnostico Italiano, 20147 Milano, Italy
| | - Fulvio Ferrara
- Department of Molecular Genetics, Centro Diagnostico Italiano, 20147 Milano, Italy
| | - Alessandra Trojani
- Division of Hematology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milano, Italy
| | - Mario Ventura
- Department of Biology, University of Bari 'Aldo Moro', Via Edoardo Orabona 4, 70124 Bari, Italy
| | - Giovanni Porta
- Genomic Medicine Research Center, Department of Medicine and Surgery, University of Insubria, Via JH Dunant 5 Varese, 21100 Varese, Italy
| | - Roberto Cairoli
- Division of Hematology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milano, Italy
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3
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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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4
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Krumbholz M, Goerlitz K, Albert C, Lawlor J, Suttorp M, Metzler M. Large amplicon droplet digital PCR for DNA-based monitoring of pediatric chronic myeloid leukaemia. J Cell Mol Med 2019; 23:4955-4961. [PMID: 31199062 PMCID: PMC6653534 DOI: 10.1111/jcmm.14321] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/27/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Quantification of tumour‐specific molecular markers at the RNA and DNA level for treatment response monitoring is crucial for risk‐adapted stratification and guidance of individualized therapy in leukaemia and other malignancies. Most pediatric leukaemias and solid tumours of mesenchymal origin are characterized by a relatively low mutation burden at the single nucleotide level and the presence of recurrent chromosomal translocations. The genomic fusion sites resulting from translocations are stable molecular tumour markers; however, repeat‐rich DNA sequences flanking intronic breakpoints limit the design of high sensitivity PCR assays for minimal residual disease (MRD) monitoring. Here, we quantitatively evaluated the impact of repeat elements on assay selection and the feasibility of using extended amplicons (≤1330 bp) amplified by droplet digital PCR to monitor pediatric chronic myeloid leukaemia (CML). Molecular characterization of 178 genomic BCR‐ABL1 fusion sites showed that 64% were located within sequence repeat elements, impeding optimal primer/probe design. Comparative quantification of DNA and RNA BCR‐ABL1 copy numbers in 687 specimens from 55 pediatric patients revealed that their levels were highly correlated. The combination of droplet digital PCR, double quenched probes and extended amplicons represents a valuable tool for sensitive MRD assessment in CML and may be adapted to other translocation‐positive tumours.
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Affiliation(s)
- Manuela Krumbholz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Katharina Goerlitz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Christian Albert
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Jennifer Lawlor
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany.,Department of Biology, Division of Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Meinolf Suttorp
- Medical Faculty, Pediatric Hemato-Oncology, Technical University, Dresden, Germany
| | - Markus Metzler
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
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5
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Tomuleasa C, Selicean C, Cismas S, Jurj A, Marian M, Dima D, Pasca S, Petrushev B, Moisoiu V, Micu WT, Vischer A, Arifeen K, Selicean S, Zdrenghea M, Bumbea H, Tanase A, Grewal R, Pop L, Aanei C, Berindan-Neagoe I. Minimal residual disease in chronic lymphocytic leukemia: A consensus paper that presents the clinical impact of the presently available laboratory approaches. Crit Rev Clin Lab Sci 2018; 55:329-345. [PMID: 29801428 DOI: 10.1080/10408363.2018.1463508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is a malignancy defined by the accumulation of mature lymphocytes in the lymphoid tissues, bone marrow, and blood. Therapy for CLL is guided according to the Rai and Binet staging systems. Nevertheless, state-of-the-art protocols in disease monitoring, diagnostics, and prognostics for CLL are based on the assessment of minimal residual disease (MRD). MRD is internationally considered to be the level of disease that can be detected by sensitive techniques and represents incomplete treatment and a probability of disease relapse. MRD detection has been continuously improved by the quick development of both flow cytometry and molecular biology technology, as well as by next-generation sequencing. Considering that MRD detection is moving more and more from research to clinical practice, where it can be an independent prognostic marker, in this paper, we present the methodologies by which MRD is evaluated, from translational research to clinical practice.
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Affiliation(s)
- Ciprian Tomuleasa
- a Department of Hematology , Ion Chiricuta Clinical Cancer Center , Cluj Napoca , Romania.,b Research Center for Functional Genomics and Translational Medicine/Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Cristina Selicean
- a Department of Hematology , Ion Chiricuta Clinical Cancer Center , Cluj Napoca , Romania
| | - Sonia Cismas
- c Department of Genetics , Victor Babes University of Medicine and Pharmacy , Timisoara , Romania.,d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Anca Jurj
- e Research Center for Functional Genomics and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Mirela Marian
- a Department of Hematology , Ion Chiricuta Clinical Cancer Center , Cluj Napoca , Romania
| | - Delia Dima
- a Department of Hematology , Ion Chiricuta Clinical Cancer Center , Cluj Napoca , Romania
| | - Sergiu Pasca
- e Research Center for Functional Genomics and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Bobe Petrushev
- e Research Center for Functional Genomics and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Vlad Moisoiu
- e Research Center for Functional Genomics and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Wilhelm-Thomas Micu
- e Research Center for Functional Genomics and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Anna Vischer
- d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Kanza Arifeen
- d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Sonia Selicean
- d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Mihnea Zdrenghea
- a Department of Hematology , Ion Chiricuta Clinical Cancer Center , Cluj Napoca , Romania.,d Department of Hematology , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Horia Bumbea
- f Department of Hematology , Carol Davila University of Medicine and Pharmacy , Bucharest , Romania.,g Department of Hematology , University Clinical Hospital , Bucharest , Romania
| | - Alina Tanase
- h Department of Stem Cell Transplantation , Fundeni Clinical Institute , Bucharest , Romania
| | - Ravnit Grewal
- i South African Medical Research Council Bioinformatics Unit , The South African National Bioinformatics Institute (SANBI), University of the Western Cape , Bellville , South Africa
| | - Laura Pop
- e Research Center for Functional Genomics and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
| | - Carmen Aanei
- j Hematology Laboratory, Pole de Biologie-Pathologie , University Hospital of St. Etienne , St. Etienne , France
| | - Ioana Berindan-Neagoe
- e Research Center for Functional Genomics and Translational Medicine , Iuliu Hatieganu University of Medicine and Pharmacy , Cluj Napoca , Romania
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6
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Rainero A, Angaroni F, D'Avila F, Conti A, Pirrone C, Micheloni G, Tararà L, Millefanti G, Maserati E, Valli R, Spinelli O, Buklijas K, Michelato A, Casalone R, Barlassina C, Barcella M, Sirchia S, Piscitelli E, Caccia M, Porta G. gDNA qPCR is statistically more reliable than mRNA analysis in detecting leukemic cells to monitor CML. Cell Death Dis 2018; 9:349. [PMID: 29500381 PMCID: PMC5834620 DOI: 10.1038/s41419-018-0387-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023]
Abstract
Chronic Myeloid Leukemia (CML) is a stem cell cancer that arises when t(9;22) translocation occurs in a hematopoietic stem cells. This event results in the expression of the BCR-ABL1 fusion gene, which codes for a constitutively active tyrosine kinase that is responsible for the transformation of a HSC into a CML stem cell, which then gives rise to a clonal myeloproliferative disease. The introduction of Tyrosine Kinase Inhibitors (TKIs) has revolutionized the management of the disease. However, these drugs do not seem to be able to eradicate the malignancy. Indeed, discontinuation trials (STIM; TWISER; DADI) for those patients who achieved a profound molecular response showed 50% relapsing within 12 months. We performed a comparative analysis on 15 CML patients and one B-ALL patient, between the standard quantitative reverse-transcriptase PCR (qRT-PCR) and our genomic DNA patient-specific quantitative PCR assay (gDNA qPCR). Here we demonstrate that gDNA qPCR is better than standard qRT-PCR in disease monitoring after an average follow-up period of 200 days. Specifically, we statistically demonstrated that DNA negativity is more reliable than RNA negativity in indicating when TKIs therapy can be safely stopped.
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Affiliation(s)
- Alessia Rainero
- Department of Medicine and Surgery, University of Insubria, Varese, Italy.
| | - Fabrizio Angaroni
- Department of Science and High Technology, University of Insubria, Como, Italy
- IFN (National Institute of Nuclear Physics), Como, Italy
| | - Francesca D'Avila
- Immunology and Functional Genomics Unit, Centro Cardiologico Monzino IRCCS, via Parea 4, 20138, Milan, Italy
| | - Andrea Conti
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Cristina Pirrone
- Department of Biology and Life Sciences, University of Insubria, Varese, Italy
| | - Giovanni Micheloni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Lucia Tararà
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Giorgia Millefanti
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Emanuela Maserati
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Roberto Valli
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Orietta Spinelli
- Department of Hematology, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Ksenija Buklijas
- Department of Hematology, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Michelato
- Department of Hematology, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Rosario Casalone
- Department of Genetics and Cytogenetics, ASST Sette Laghi, Ospedale di Circolo Fondazione Macchi, Varese, Italy
| | | | - Matteo Barcella
- Department of Health Sciences, University of Milan, Milan, Italy
| | - Silvia Sirchia
- Department of Health Sciences, University of Milan, Milan, Italy
| | | | - Massimo Caccia
- Department of Science and High Technology, University of Insubria, Como, Italy
| | - Giovanni Porta
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
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Cumbo C, Impera L, Minervini CF, Orsini P, Anelli L, Zagaria A, Coccaro N, Tota G, Minervini A, Casieri P, Brunetti C, Rossi AR, Parciante E, Specchia G, Albano F. Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for "personalized monitoring" of residual disease in chronic myeloid leukemia patients. Oncotarget 2018. [PMID: 29541390 PMCID: PMC5834283 DOI: 10.18632/oncotarget.23971] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology. Finally, after defining the BCR-ABL1 genomic junction, we performed the target CML patient–specific quantification, using droplet digital PCR (ddPCR). FISH and MinION steps, respectively, together with ddPCR analysis, greatly reduce the complexity that has impeded the use of “personalized monitoring” of CML in clinical practice. Our report suggests a feasible pipeline, in terms of costs and reproducibility, aimed at characterizing and quantifying the genomic BCR-ABL1 rearrangement during MRD monitoring in CML patients.
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Affiliation(s)
- Cosimo Cumbo
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Luciana Impera
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | | | - Paola Orsini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Nicoletta Coccaro
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Giuseppina Tota
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Angela Minervini
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Paola Casieri
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Claudia Brunetti
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Antonella Russo Rossi
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Elisa Parciante
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
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8
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Alikian M, Gale RP, Apperley JF, Foroni L. Molecular techniques for the personalised management of patients with chronic myeloid leukaemia. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 11:4-20. [PMID: 28331814 PMCID: PMC5348117 DOI: 10.1016/j.bdq.2017.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 12/28/2016] [Accepted: 01/18/2017] [Indexed: 12/25/2022]
Abstract
Chronic myeloid leukemia (CML) is the paradigm for targeted cancer therapy. RT-qPCR is the gold standard for monitoring response to tyrosine kinase-inhibitor (TKI) therapy based on the reduction of blood or bone marrow BCR-ABL1. Some patients with CML and very low or undetectable levels of BCR-ABL1 transcripts can stop TKI-therapy without CML recurrence. However, about 60 percent of patients discontinuing TKI-therapy have rapid leukaemia recurrence. This has increased the need for more sensitive and specific techniques to measure residual CML cells. The clinical challenge is to determine when it is safe to stop TKI-therapy. In this review we describe and critically evaluate the current state of CML clinical management, different technologies used to monitor measurable residual disease (MRD) focus on comparingRT-qPCR and new methods entering clinical practice. We discuss advantages and disadvantages of new methods.
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Key Words
- ABL1, Abelson murine leukaemia virus
- ALL, acute lymphoblastic leukaemia
- AP, accelerated phase
- ARQ, armored RNA Quant
- ATP, adenosine triphosphate
- BC, blast crisis
- BCR, breakpoint cluster region
- BM, bone marrow
- BMT, bone marrow transplantation
- Bp, base pair
- CAP, College of American Pathology
- CES, capillary electrophoresis sequencing
- CML
- CML, chronic myeloid leukaemia
- CMR, complete molecular response/remission
- CP, chronic phase
- DESTINY, De-Escalation and Stopping Treatment of Imatinib, Nilotinib or sprYcel in Chronic Myeloid Leukaemia
- DNA, deoxyribonucleic acid
- EAC, Europe Against Cancer
- ELN, European Leukaemia Net
- EURO-SKI, European Stop Tyrosine Kinase Inhibitor Study
- GUSB, glucuronidase beta gene
- IC, inhibotory concentration
- IRIS, interferon and cytarabine versus STI571
- IS, International Scale
- InDels, insertions and deletions
- KDa, Kilo Dalton
- Kbp, Kilo Base Pairs
- LPC, leukemic progenitor cells
- LSC, leukemic stem cell
- LoD, limit of detection
- LoQ, limit of quantification
- M-bcr, major-breakpoint cluster region
- MMR, major molecular response/remission
- MR, deep molecular response/remission
- MRD
- MRD, minimal residual disease
- Mbp, mega base pair
- Molecular monitoring
- NCCN, National Comprehensive Cancer Network
- NEQAS, National External Quality Assessement Service
- NGS
- NGS, next generation sequencing
- NTC, No Template Control
- PB, Peripheral Blood
- PCR, Polymerase Chain Reaction
- PFS, Progression Free Survival
- Ph, Philadelpia
- Q-PCR, quantitative polymerase chain reaction
- QC, Quality Control
- RT, reverse transcription
- RT-dPCR, reverse transcription-digital polymerase chain reaction
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- SCT, stem cell transplant
- SMRT, single-molecule real-time sequencing
- STIM, stop imatinib
- TKD, tyrosine kinase domain
- TKI, tyrosine kinase inhibitor
- WHO, World Health Organisation
- ZMW, zero-mode wave-guided
- allo-SCT, Allogeneic Stem Cell Transplantation
- cDNA, coding or complimentary DNA
- dMIQE, Minimum Information for Publication of Quantitative Digital PCR Experiments
- dPCR
- dPCR, digital polymerase chain reaction
- emPCR, emulsion PCR
- gDNA, genomic deoxyribonucleic acid
- m-bcr, minor-breakpoint cluster region
- mRNA, messenger RNA
- nM, manomolar
- μ-bcr, micro-breakpoint cluster region
- μg, microgram
- μl, microliter
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Affiliation(s)
- Mary Alikian
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK; Imperial Molecular Pathology, Imperial College Healthcare Trust, Hammersmith Hospital, London, UK
| | - Robert Peter Gale
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
| | - Jane F Apperley
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
| | - Letizia Foroni
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
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9
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Vinhas R, Cordeiro M, Pedrosa P, Fernandes AR, Baptista PV. Current trends in molecular diagnostics of chronic myeloid leukemia. Leuk Lymphoma 2016; 58:1791-1804. [PMID: 27919203 DOI: 10.1080/10428194.2016.1265116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nearly 1.5 million people worldwide suffer from chronic myeloid leukemia (CML), characterized by the genetic translocation t(9;22)(q34;q11.2), involving the fusion of the Abelson oncogene (ABL1) with the breakpoint cluster region (BCR) gene. Early onset diagnosis coupled to current therapeutics allow for a treatment success rate of 90, which has focused research on the development of novel diagnostics approaches. In this review, we present a critical perspective on current strategies for CML diagnostics, comparing to gold standard methodologies and with an eye on the future trends on nanotheranostics.
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Affiliation(s)
- Raquel Vinhas
- a Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, UCIBIO , Universidade Nova de Lisboa , Caparica , Portugal
| | - Milton Cordeiro
- a Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, UCIBIO , Universidade Nova de Lisboa , Caparica , Portugal
| | - Pedro Pedrosa
- a Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, UCIBIO , Universidade Nova de Lisboa , Caparica , Portugal
| | - Alexandra R Fernandes
- a Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, UCIBIO , Universidade Nova de Lisboa , Caparica , Portugal
| | - Pedro V Baptista
- a Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, UCIBIO , Universidade Nova de Lisboa , Caparica , Portugal
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10
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Affiliation(s)
- Giovanni Porta
- a Department of Clinical and Experimental Medicine ; University of Insubria ; Varese , Italy
| | - Ilaria Stefania Pagani
- a Department of Clinical and Experimental Medicine ; University of Insubria ; Varese , Italy.,b Department of Experimental Medicine and Surgery ; Tor Vergata University ; Rome , Italy
| | - Cristina Pirrone
- a Department of Clinical and Experimental Medicine ; University of Insubria ; Varese , Italy
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11
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Soverini S, De Benedittis C, Mancini M, Martinelli G. Present and future of molecular monitoring in chronic myeloid leukaemia. Br J Haematol 2016; 173:337-49. [PMID: 26947577 DOI: 10.1111/bjh.13966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Currently, physicians treating chronic myeloid leukaemia (CML) patients can rely on a wide spectrum of therapeutic options: the best use of such options is essential to achieve excellent clinical outcomes and, possibly, treatment-free remission (TFR). To accomplish this, proper integration of expert clinical and laboratory monitoring of CML patients is fundamental. Molecular response (MR) monitoring of patients at defined time points has emerged as an important success factor for optimal disease management and BCR-ABL1 kinase domain mutation screening is useful to guide therapeutic reassessment in patients who do not achieve optimal responses to tyrosine kinase inhibitor therapy. Deeper MRs might be associated with improved long-term survival outcomes. More importantly, they are considered a gateway to TFR. In molecular biology, novel procedures and technologies are continually being developed. More sophisticated molecular tools and automated analytical solutions are emerging as CML treatment endpoints and expectations become more and more ambitious. Here we provide a critical overview of current and novel methodologies, present their strengths and pitfalls and discuss what their present and future role might be.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Caterina De Benedittis
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Manuela Mancini
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
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12
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Alikian M, Ellery P, Forbes M, Gerrard G, Kasperaviciute D, Sosinsky A, Mueller M, Whale AS, Milojkovic D, Apperley J, Huggett JF, Foroni L, Reid AG. Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients. J Mol Diagn 2016; 18:176-89. [PMID: 26857065 DOI: 10.1016/j.jmoldx.2015.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 08/31/2015] [Accepted: 09/17/2015] [Indexed: 01/06/2023] Open
Abstract
Recent studies indicate that 40% of chronic myeloid leukemia patients who achieve sustained undetectable BCR-ABL1 transcripts on tyrosine kinase inhibitor therapy remain disease-free after drug discontinuation. In contrast, 60% experience return of detectable disease and have to restart treatment, thus highlighting the need for an improved method of identifying patients with the lowest likelihood of relapse. Here we describe the validation of a personalized DNA-based digital PCR (dPCR) approach for quantifying very low levels of residual disease, which involves the rapid identification of t(9;22) fusion junctions using targeted next-generation sequencing coupled with the use of a dPCR platform. t(9;22) genomic breakpoints were successfully mapped in samples from 32 of 32 patients with early stage disease. Disease quantification by DNA-based dPCR was performed using the Fluidigm BioMark platform on 46 follow-up samples from 6 of the 32 patients, including 36 samples that were in deep molecular remission. dPCR detected persistent disease in 81% of molecular-remission samples, outperforming both RT-dPCR (25%) and DNA-based quantitative PCR (19%). We conclude that dPCR for BCR-ABL1 DNA is the most sensitive available method of residual-disease detection in chronic myeloid leukemia and may prove useful in the management of tyrosine kinase inhibitor withdrawal.
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Affiliation(s)
- Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom.
| | - Peter Ellery
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom
| | - Martin Forbes
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Gareth Gerrard
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dalia Kasperaviciute
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alona Sosinsky
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Michael Mueller
- Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alexandra S Whale
- Molecular & Cell Biology, LGC Limited, Queens Road, Teddington, United Kingdom
| | - Dragana Milojkovic
- Clinical Haematology, Imperial College Healthcare National Health Institute Trust, London, United Kingdom
| | - Jane Apperley
- Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jim F Huggett
- Molecular & Cell Biology, LGC Limited, Queens Road, Teddington, United Kingdom
| | - Letizia Foroni
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alistair G Reid
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
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13
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Mattarucchi E, Pallotti F, Casalone R. Authors' Reply to Crampe and Langabeer: Technical Issues Behind Molecular Monitoring in Chronic Myeloid Leukemia. Mol Diagn Ther 2015. [PMID: 26224626 DOI: 10.1007/s40291-015-0152-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elia Mattarucchi
- Department of Experimental and Clinical Medicine, Università dell'Insubria, via Dunant 5, 21100, Varese, Italy,
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14
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Kobayashi K, Miyagawa N, Mitsui K, Matsuoka M, Kojima Y, Takahashi H, Ootsubo K, Nagai J, Ueno H, Ishibashi T, Sultana S, Okada Y, Akimoto S, Okita H, Matsumoto K, Goto H, Kiyokawa N, Ohara A. TKI dasatinib monotherapy for a patient with Ph-like ALL bearing ATF7IP/PDGFRB translocation. Pediatr Blood Cancer 2015; 62:1058-60. [PMID: 25400122 DOI: 10.1002/pbc.25327] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/01/2014] [Indexed: 11/06/2022]
Abstract
We report a 10-year-old male with relapsing Ph-like acute lymphoblastic leukemia (ALL) bearing ATF7IP/PDGFRB translocation. He was refractory to conventional therapy, and was finally treated with single-agent second-generation TKI dasatinib. The therapeutic response was prompt, with the disappearance of minimum residual disease (MRD) based on genomic PCR analysis within 3 months, and he has maintained complete molecular remission for 12 months. This case report describes an early-phase response to TKI monotherapy on Ph-like ALL, and technical tips for MRD monitoring on long-term follow-up.
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Affiliation(s)
- Kenichiro Kobayashi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health Development, Tokyo, Japan
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15
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Azzato EM, Bagg A. Molecular genetic evaluation of myeloproliferative neoplasms. Int J Lab Hematol 2015; 37 Suppl 1:61-71. [DOI: 10.1111/ijlh.12353] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/16/2015] [Indexed: 01/06/2023]
Affiliation(s)
- E. M. Azzato
- Department of Pathology and Laboratory Medicine; Hospital of the University of Pennsylvania; Philadelphia PA USA
| | - A. Bagg
- Department of Pathology and Laboratory Medicine; Hospital of the University of Pennsylvania; Philadelphia PA USA
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16
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Linhartova J, Hovorkova L, Soverini S, Benesova A, Jaruskova M, Klamova H, Zuna J, Machova Polakova K. Characterization of 46 patient-specific BCR-ABL1 fusions and detection of SNPs upstream and downstream the breakpoints in chronic myeloid leukemia using next generation sequencing. Mol Cancer 2015; 14:89. [PMID: 25928096 PMCID: PMC4409993 DOI: 10.1186/s12943-015-0363-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/08/2015] [Indexed: 11/22/2022] Open
Abstract
In chronic myeloid leukemia, the identification of individual BCR-ABL1 fusions is required for the development of personalized medicine approach for minimal residual disease monitoring at the DNA level. Next generation sequencing (NGS) of amplicons larger than 1000 bp simplified and accelerated a process of characterization of patient-specific BCR-ABL1 genomic fusions. NGS of large regions upstream and downstream the individual breakpoints in BCR and ABL1 genes, respectively, also provided information about the sequence variants such are single nucleotide polymorphisms.
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Affiliation(s)
- Jana Linhartova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.
| | - Lenka Hovorkova
- CLIP, Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic.
| | - Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology "L. e A. Seragnoli", University of Bologna, Bologna, Italy.
| | - Adela Benesova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic.
| | - Monika Jaruskova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic. .,Institute of Clinical and Experimental Hematology of First Faculty of Medicine and Institute of Hematology and Blood Transfusion, Charles University, Prague, Czech Republic.
| | - Hana Klamova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic. .,Institute of Clinical and Experimental Hematology of First Faculty of Medicine and Institute of Hematology and Blood Transfusion, Charles University, Prague, Czech Republic.
| | - Jan Zuna
- CLIP, Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic.
| | - Katerina Machova Polakova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic. .,Institute of Clinical and Experimental Hematology of First Faculty of Medicine and Institute of Hematology and Blood Transfusion, Charles University, Prague, Czech Republic.
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17
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Mattarucchi E, Pallotti F, Casalone R. Technical Issues Behind Molecular Monitoring in Chronic Myeloid Leukemia. Mol Diagn Ther 2015; 19:139-40. [DOI: 10.1007/s40291-015-0139-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Pagani IS, Spinelli O, Mattarucchi E, Pirrone C, Pigni D, Amelotti E, Lilliu S, Boroni C, Intermesoli T, Giussani U, Caimi L, Bolda F, Baffelli R, Candi E, Pasquali F, Lo Curto F, Lanfranchi A, Porta F, Rambaldi A, Porta G. Genomic quantitative real-time PCR proves residual disease positivity in more than 30% samples with negative mRNA-based qRT-PCR in Chronic Myeloid Leukemia. Oncoscience 2014; 1:510-21. [PMID: 25594053 PMCID: PMC4278316 DOI: 10.18632/oncoscience.65] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 07/23/2014] [Indexed: 12/20/2022] Open
Abstract
Imatinib mesylate (IM) is the first line therapy against Chronic Myeloid Leukemia, effectively prolonging overall survival. Because discontinuation of treatment is associated with relapse, IM is required indefinitely to maintain operational cure. To assess minimal residual disease, cytogenetic analysis is insensitive in a high background of normal lymphocytes. The qRT-PCR provides highly sensitive detection of BCR-ABL1 transcripts, but mRNA levels are not directly related to the number of leukemic cells, and undetectable results are difficult to interpret. We developed a sensitive approach to detect the number of leukemic cells by a genomic DNA (gDNA) Q-PCR assay based on the break-point sequence, with a formula to calculate the number of Ph-positive cells. We monitored 8 CML patients treated with IM for more than 8 years. We tested each samples by patient specific gDNA Q-PCR in parallel by the conventional techniques. In all samples positive for chimeric transcripts we showed corresponding chimeric gDNA by Q-PCR, and in 32.8% (42/128) of samples with undetectable levels of mRNA we detected the persistence of leukemic cells. The gDNA Q-PCR assay could be a new diagnostic tool used in parallel to conventional techniques to support the clinician's decision to vary or to STOP IM therapy.
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Affiliation(s)
- Ilaria S Pagani
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy ; Department of Experimental Medicine and Surgery, Tor Vergata University, Rome, Italy
| | - Orietta Spinelli
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Elia Mattarucchi
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Cristina Pirrone
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Diana Pigni
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Elisabetta Amelotti
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Silvia Lilliu
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Chiara Boroni
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Tamara Intermesoli
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Ursula Giussani
- Laboratory of Medical Genetics, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Luigi Caimi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Federica Bolda
- Laboratory of chemical-clinical analysis, Section of Hematology and blood coagulation, Stem Cells laboratory, Spedali Civili of Brescia, Brescia, Italy
| | - Renata Baffelli
- Laboratory of chemical-clinical analysis, Section of Hematology and blood coagulation, Stem Cells laboratory, Spedali Civili of Brescia, Brescia, Italy
| | - Eleonora Candi
- Department of Experimental Medicine and Surgery, Tor Vergata University, Rome, Italy
| | - Francesco Pasquali
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Francesco Lo Curto
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
| | - Arnalda Lanfranchi
- Laboratory of chemical-clinical analysis, Section of Hematology and blood coagulation, Stem Cells laboratory, Spedali Civili of Brescia, Brescia, Italy
| | - Fulvio Porta
- Laboratory of chemical-clinical analysis, Section of Hematology and blood coagulation, Stem Cells laboratory, Spedali Civili of Brescia, Brescia, Italy
| | - Alessandro Rambaldi
- Hematology laboratory, USC Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Giovanni Porta
- Department of Experimental and Clinical Medicine, Insubria University, Varese, Italy
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19
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Menon H. Issues in current management of chronic myeloid leukemia: Importance of molecular monitoring on long term outcome. South Asian J Cancer 2014; 2:38-43. [PMID: 24455544 PMCID: PMC3876638 DOI: 10.4103/2278-330x.105893] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Monitoring of CML patients while on therapy is vitally important and ENL has come up with specific guidelines for the same. Since we are currently talking about operational cure, this review shall focus on evaluating the emerging data to optimize response. This requires attention to all outstanding controversial issues. Only careful, accurate and regular monitoring with specific attention to grey areas will help us select first line therapy, decide when to discontinue TKIs and also move to second line TKIs in a timely manner.
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Affiliation(s)
- Hari Menon
- Department of Medical Oncology, Tata Memorial Hospital, Mumbai, India
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20
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Jennings LJ, George D, Czech J, Yu M, Joseph L. Detection and Quantification of BCR-ABL1 Fusion Transcripts by Droplet Digital PCR. J Mol Diagn 2014; 16:174-9. [DOI: 10.1016/j.jmoldx.2013.10.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/04/2013] [Accepted: 10/24/2013] [Indexed: 12/20/2022] Open
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21
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Ross DM, Branford S. Minimal residual disease: the advantages of digital over analog polymerase chain reaction. Leuk Lymphoma 2011; 52:1161-3. [DOI: 10.3109/10428194.2011.580481] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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22
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Shibata Y, Malhotra A, Dutta A. Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET. Genome Med 2010; 2:70. [PMID: 20860819 PMCID: PMC3092121 DOI: 10.1186/gm191] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/09/2010] [Accepted: 09/22/2010] [Indexed: 12/13/2022] Open
Abstract
Anchored ChromPET, a technique to capture and interrogate targeted sequences in the genome, has been developed to identify chromosomal aberrations and define breakpoints. Using this method, we could define the BCR-ABL1 translocation DNA breakpoint to a base-pair resolution in Philadelphia chromosome-positive samples. This DNA-based method is highly sensitive and can detect the fusion junction using samples from which it is hard to obtain RNA or cells where the RNA expression has been silenced.
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Affiliation(s)
- Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1300 Jefferson Pk Ave, Charlottesville, VA 22908-0733, USA.
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23
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Abstract
Previous experience in the treatment of chronic myeloid leukaemia (CML) has shown that the achievement of clinical, morphological and cytogenetic remission does not indicate eradication of the disease. A complete molecular response (CMR; no detectable BCR-ABL mRNA) represents a deeper level of response, but even CMR is not a guarantee of elimination of the leukaemia, because the significance of CMR is determined by the detection limit of the assay that is used. Two studies of imatinib cessation in CMR are underway, cumulatively involving over 100 patients. The current estimated rate of stable CMR after stopping imatinib is approximately 40%, but the duration of follow-up is relatively short. The factors that determine relapse risk are yet to be identified. The intrinsic capacity of any residual leukaemia [corrected] cells to proliferate following the withdrawal of treatment may be important, but there may also be a role for immunological suppression of the leukaemia [corrected] clone. No currently available test can formally prove that the leukaemic clone is eradicated. Here we discuss the sensitive measurement of minimal residual disease, and speculate on the biology of BCR-ABL-positive cells that may persist after effective therapy of CML.
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Affiliation(s)
- D M Ross
- Department of Haematology, SA Pathology Centre for Cancer Biology, University of Adelaide, Adelaide, Australia
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24
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In search of the original leukemic clone in chronic myeloid leukemia patients in complete molecular remission after stem cell transplantation or imatinib. Blood 2010; 116:1329-35. [PMID: 20462961 DOI: 10.1182/blood-2009-11-255109] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
It is not clear if absence of BCR-ABL transcripts--complete molecular response (CMR)--is synonymous with, or required for, cure of chronic myeloid leukemia (CML). Some patients achieve CMR with imatinib (IM), but most relapse shortly after treatment discontinuation. Furthermore, most patients in long-term remission (LTR) post-stem cell transplantation (SCT) are considered functionally cured, although some remain occasionally positive for low-level BCR-ABL mRNA. Interpretation of the latter is complicated because it has been observed in healthy subjects. We designed a patient-specific, highly sensitive, DNA quantitative polymerase chain reaction to test follow-up samples for the original leukemic clone, identified by its unique genomic BCR-ABL fusion (gBCR-ABL). In 5 IM-treated patients in CMR, gBCR-ABL was detected in transcript-negative samples; 4 patients became gBCR-ABL-negative with continuing IM therapy. In contrast, of 9 patients in LTR (13-27 years) post-SCT, gBCR-ABL was detected in only 1, despite occasional transcript-positive samples in 8 of them. In conclusion, in IM-treated patients, absence of transcripts should not be interpreted as absence of the leukemic clone, although continuing IM after achievement of CMR may lead to further reduction of residual disease. Post-SCT, we found little evidence that the transcripts occasionally detected originate from the leukemic clone.
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