1
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Antigen Receptors Gene Analysis for Minimal Residual Disease Detection in Acute Lymphoblastic Leukemia: The Role of High Throughput Sequencing. HEMATO 2023. [DOI: 10.3390/hemato4010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The prognosis of adult acute lymphoblastic leukemia (ALL) is variable but more often dismal. Indeed, its clinical management is challenging, current therapies inducing complete remission in 65–90% of cases, but only 30–40% of patients being cured. The major determinant of treatment failure is relapse; consequently, measurement of residual leukemic blast (minimal residual disease, MRD) has become a powerful independent prognostic indicator in adults. Numerous evidences have also supported the clinical relevance of MRD assessment for risk class assignment and treatment selection. MRD can be virtually evaluated in all ALL patients using different technologies, such as polymerase chain reaction amplification of fusion transcripts and clonal rearrangements of antigen receptor genes, flow cytometric study of leukemic immunophenotypes and, the most recent, high throughput sequencing (HTS). In this review, the authors focused on the latest developments on MRD monitoring with emphasis on the use of HTS, as well as on the clinical impact of MRD monitoring.
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2
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Application of Fluorescence In Situ Hybridization (FISH) in Oral Microbial Detection. Pathogens 2022; 11:pathogens11121450. [PMID: 36558784 PMCID: PMC9788346 DOI: 10.3390/pathogens11121450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Varieties of microorganisms reside in the oral cavity contributing to the occurrence and development of microbes associated with oral diseases; however, the distribution and in situ abundance in the biofilm are still unclear. In order to promote the understanding of the ecosystem of oral microbiota and the diagnosis of oral diseases, it is necessary to monitor and compare the oral microorganisms from different niches of the oral cavity in situ. The fluorescence in situ hybridization (FISH) has proven to be a powerful tool for representing the status of oral microorganisms in the oral cavity. FISH is one of the most routinely used cytochemical techniques for genetic detection, identification, and localization by a fluorescently labeled nucleic acid probe, which can hybridize with targeted nucleic acid sequences. It has the advantages of rapidity, safety, high sensitivity, and specificity. FISH allows the identification and quantification of different oral microorganisms simultaneously. It can also visualize microorganisms by combining with other molecular biology technologies to represent the distribution of each microbial community in the oral biofilm. In this review, we summarized and discussed the development of FISH technology and the application of FISH in oral disease diagnosis and oral ecosystem research, highlighted its advantages in oral microbiology, listed the existing problems, and provided suggestions for future development..
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3
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Boni C, Bonifacio M, Vezzalini M, Scaffidi L, Tomasello L, Parker LL, Boscarino D, Paladin D, Krampera M, Sorio C. Successful Preservation of Native BCR::ABL1 in Chronic Myeloid Leukemia Primary Leukocytes Reveals a Reduced Kinase Activity. Front Oncol 2022; 12:904510. [PMID: 35756686 PMCID: PMC9216732 DOI: 10.3389/fonc.2022.904510] [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: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 11/25/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disease caused by the acquisition of t(9;22) generating the fusion tyrosine kinase BCR::ABL1. However, despite the crucial role of this protein in the dysregulation of numerous signal transduction pathways, a direct measure of BCR::ABL1 kinase activity in chronic phase (CP) CML was never accomplished due to intense degradative activity present in mature leukocytes. Therefore, we developed a procedure suitable to preserve BCR::ABL1 protein under non-denaturing, neutral pH conditions in primary, chronic phase (CP)-CML samples. As a result, specific kinase activity was detected utilizing a biotinylated peptide substrate highly selective for c-ABL1. Furthermore, through this approach, BCR::ABL1 kinase activity was barely detectable in CP-CML compared to Ph+ acute lymphoblastic leukemia primary samples, where kinase activity is comparable to those measured in Ph+ cell lines. These in vitro findings provide the first direct measure of BCR::ABL1 kinase activity in primary CP-CML and reveal the presence of a still uncharacterized inhibitory mechanism that maintains BCR::ABL1 in a low activity state in CP-CML despite its overexpression.
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Affiliation(s)
- Christian Boni
- Department of Medicine, General Pathology Section, University of Verona, Verona, Italy
| | | | - Marzia Vezzalini
- Department of Medicine, General Pathology Section, University of Verona, Verona, Italy
| | - Luigi Scaffidi
- Department of Medicine, Hematology Section, University of Verona, Verona, Italy
| | - Luisa Tomasello
- Department of Medicine, General Pathology Section, University of Verona, Verona, Italy
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota, Minneapolis, United States
| | | | | | - Mauro Krampera
- Department of Medicine, Hematology Section, University of Verona, Verona, Italy
| | - Claudio Sorio
- Department of Medicine, General Pathology Section, University of Verona, Verona, Italy
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4
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Miyashita N, Onozawa M, Suto K, Fujisawa S, Okazaki N, Hidaka D, Ohigashi H, Yasumoto A, Sugita J, Hashimoto D, Matsuno Y, Teshima T. Aleukemic Extramedullary Blast Crisis as an Initial Presentation of Chronic Myeloid Leukemia with E1A3 BCR-ABL1 Fusion Transcript. Intern Med 2022; 61:1049-1054. [PMID: 34511573 PMCID: PMC9038454 DOI: 10.2169/internalmedicine.8319-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Right neck swelling and pain occurred in a 49-year-old man. A Blood count showed a slight increase in platelet count without leukemoid reaction. After a biopsy of the cervical mass and bone marrow aspiration, a diagnosis of extramedullary blast crisis (EBC) of chronic myeloid leukemia (CML) was made. Fluorescence in situ hybridization (FISH) analysis showed a BCR-ABL1 fusion signal, but results of real-time polymerase chain reaction (RT-PCR) for major and minor BCR-ABL1 transcripts were negative. We identified a rare e1a3 BCR-ABL1 fusion transcript. Administration of dasatinib resulted in disappearance of the extramedullary tumor. This is the first reported case of CML-EBC with e1a3 transcript. An aleukemic extramedullary tumor can be the initial presentation of CML.
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MESH Headings
- Blast Crisis/genetics
- Blast Crisis/pathology
- Dasatinib/therapeutic use
- Fusion Proteins, bcr-abl/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Male
- Middle Aged
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Affiliation(s)
- Naoki Miyashita
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
| | - Masahiro Onozawa
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
| | - Keito Suto
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
| | - Shinichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Japan
| | - Nanase Okazaki
- Department of Surgical Pathology, Hokkaido University Hospital, Japan
| | - Daisuke Hidaka
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
| | - Hiroyuki Ohigashi
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
| | - Atsushi Yasumoto
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
| | - Junichi Sugita
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
| | - Daigo Hashimoto
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
| | - Yoshihiro Matsuno
- Department of Surgical Pathology, Hokkaido University Hospital, Japan
| | - Takanori Teshima
- Department of Hematology, Faculty of Medicine, Hokkaido University, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Japan
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5
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Multiparametric Flow Cytometry for MRD Monitoring in Hematologic Malignancies: Clinical Applications and New Challenges. Cancers (Basel) 2021; 13:cancers13184582. [PMID: 34572809 PMCID: PMC8470441 DOI: 10.3390/cancers13184582] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary In hematologic cancers, Minimal Residual Disease (MRD) monitoring, using either molecular (PCR) or immunophenotypic (MFC) diagnostics, allows the identification of rare cancer cells, readily detectable either in the bone marrow or in the peripheral blood at very low levels, far below the limit of classic microscopy. In this paper, we outlined the state-of-the-art of MFC-based MRD detection in different hematologic settings, highlighting main recommendations and new challenges for using such method in patients with acute leukemias or chronic hematologic neoplasms. The combination of new molecular technologies with advanced flow cytometry is progressively allowing clinicians to design a personalized therapeutic path, proportionate to the biological aggressiveness of the disease, in particular by using novel immunotherapies, in view of a modern decision-making process, based on precision medicine. Abstract Along with the evolution of immunophenotypic and molecular diagnostics, the assessment of Minimal Residual Disease (MRD) has progressively become a keystone in the clinical management of hematologic malignancies, enabling valuable post-therapy risk stratifications and guiding risk-adapted therapeutic approaches. However, specific prognostic values of MRD in different hematological settings, as well as its appropriate clinical uses (basically, when to measure it and how to deal with different MRD levels), still need further investigations, aiming to improve standardization and harmonization of MRD monitoring protocols and MRD-driven therapeutic strategies. Currently, MRD measurement in hematological neoplasms with bone marrow involvement is based on advanced highly sensitive methods, able to detect either specific genetic abnormalities (by PCR-based techniques and next-generation sequencing) or tumor-associated immunophenotypic profiles (by multiparametric flow cytometry, MFC). In this review, we focus on the growing clinical role for MFC-MRD diagnostics in hematological malignancies—from acute myeloid and lymphoblastic leukemias (AML, B-ALL and T-ALL) to chronic lymphocytic leukemia (CLL) and multiple myeloma (MM)—providing a comparative overview on technical aspects, clinical implications, advantages and pitfalls of MFC-MRD monitoring in different clinical settings.
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6
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Emde B, Kreher H, Bäumer N, Bäumer S, Bouwes D, Tickenbrock L. Microfluidic-Based Detection of AML-Specific Biomarkers Using the Example of Promyelocyte Leukemia. Int J Mol Sci 2020; 21:ijms21238942. [PMID: 33255664 PMCID: PMC7728129 DOI: 10.3390/ijms21238942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 01/22/2023] Open
Abstract
A microfluidic assay for the detection of promyelocytic leukemia (PML)-retinoic acid receptor α (RARα) fusion protein was developed. This microfluidic-based system can be used for rapid personalized differential diagnosis of acute promyelocyte leukemia (APL) with the aim of early initiation of individualized therapy. The fusion protein PML-RARα occurs in 95% of acute promyelocytic leukemia cases and is considered as diagnostically relevant. The fusion protein is formed as a result of translocation t(15,17) and is detected in the laboratory by fluorescence in situ hybridization (FISH) or reverse transcriptase polymerase chain reaction (RT-PCR). Diagnostic methods require many laboratory steps with specialized staff. The developed microfluidic assay includes a sandwich enzyme-linked immunosorbent assay (ELISA) system for PML-RARα on surface of magnetic microparticles in a microfluidic chip. A rapid detection of PML-RARα in cell lysates is achieved in less than one hour. A biotinylated PML-antibody on the surface of magnetic streptavidin coated microparticles is used as capture antibody. The bound translocation product is detected by a RARα antibody conjugated with horseradish peroxidase and the substrate QuantaRed. The analysis is performed in microfluidic channels which involves automated liquid processing with stringent washing and short incubation times. The results of the developed assay show that cell lysates of PML-RARα-positive cells (NB-4) can be clearly distinguished from PML-RARα-negative cells (HL-60, MV4-11).
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/isolation & purification
- Granulocyte Precursor Cells/metabolism
- Granulocyte Precursor Cells/pathology
- Humans
- In Situ Hybridization, Fluorescence/methods
- Leukemia, Promyelocytic, Acute/diagnosis
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/pathology
- Microfluidics/methods
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/isolation & purification
- Precision Medicine
- Promyelocytic Leukemia Protein/genetics
- Retinoic Acid Receptor alpha/genetics
- Translocation, Genetic/genetics
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Affiliation(s)
- Benedikt Emde
- Department Hamm 1, Hamm-Lippstadt University of Applied Science, 59063 Hamm, Germany;
- Correspondence: ; Tel.: +49-(0)2381-8789-443
| | - Heike Kreher
- Micronit GmbH, 44263 Dortmund, Germany; (H.K.); (D.B.)
| | - Nicole Bäumer
- Department of Medicine A, Hematology and Oncology, University of Muenster, 48149 Muenster, Germany; (N.B.); (S.B.)
| | - Sebastian Bäumer
- Department of Medicine A, Hematology and Oncology, University of Muenster, 48149 Muenster, Germany; (N.B.); (S.B.)
| | | | - Lara Tickenbrock
- Department Hamm 1, Hamm-Lippstadt University of Applied Science, 59063 Hamm, Germany;
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7
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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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8
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Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Angelov A, Werner T, Bantscheff M, Wilhelm M, Klingenspor M, Lemeer S, Liebl W, Hahne H, Savitski MM, Kuster B. Meltome atlas-thermal proteome stability across the tree of life. Nat Methods 2020; 17:495-503. [PMID: 32284610 DOI: 10.1038/s41592-020-0801-4] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic proteins show a nonlinear relationship between the degree of disordered protein structure and thermal stability. The data indicate that evolutionary conservation of protein complexes is reflected by similar thermal stability of their proteins, and we show examples in which genomic alterations can affect thermal stability. Proteins of the respiratory chain were found to be very stable in many organisms, and human mitochondria showed close to normal respiration at 46 °C. We also noted cell-type-specific effects that can affect protein stability or the efficacy of drugs. This meltome atlas broadly defines the proteome amenable to thermal profiling in biology and drug discovery and can be explored online at http://meltomeatlas.proteomics.wzw.tum.de:5003/ and http://www.proteomicsdb.org.
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Affiliation(s)
- Anna Jarzab
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Nils Kurzawa
- Genome Biology Unit, EMBL, Heidelberg, Germany.,Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | | | - Matthias Moerch
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Niels Leijten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Yangyang Bian
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Eva Musiol
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | | | | | | | - Charlotte Daly
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Britta Spanier
- Chair of Nutritional Physiology, Technical University of Munich, Freising, Germany
| | - Angel Angelov
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Molecular Nutrition Unit, Technical University of Munich, Freising, Germany
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Wolfgang Liebl
- Department of Microbiology, Technical University of Munich, Freising, Germany
| | | | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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9
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van Dongen JJM, O'Gorman MRG, Orfao A. EuroFlow and its activities: Introduction to the special EuroFlow issue of The Journal of Immunological Methods. J Immunol Methods 2019; 475:112704. [PMID: 31758969 DOI: 10.1016/j.jim.2019.112704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Jacques J M van Dongen
- Department of Immunohematology and Blood Transfusion (IHB), Leiden University Medical Center (LUMC), Leiden, the Netherlands.
| | - Maurice R G O'Gorman
- Departments of Pathology and Pediatrics, The Keck School of Medicine, U. of Southern California, Children's Hospital of Los Angeles Los Angeles, CA, USA
| | - Alberto Orfao
- Cancer Research Centre (IBMCC-CASIC/USAL), Department of Medicine, Cytometry Service (NUCLEUS) and Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca (Spain) and CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
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10
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Izzo B, Gottardi EM, Errichiello S, Daraio F, Baratè C, Galimberti S. Monitoring Chronic Myeloid Leukemia: How Molecular Tools May Drive Therapeutic Approaches. Front Oncol 2019; 9:833. [PMID: 31555590 PMCID: PMC6742705 DOI: 10.3389/fonc.2019.00833] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/13/2019] [Indexed: 12/25/2022] Open
Abstract
More than 15 years ago, imatinib entered into the clinical practice as a "magic bullet"; from that point on, the prognosis of patients affected by chronic myeloid leukemia (CML) became comparable to that of aged-matched healthy subjects. The aims of treatment with tyrosine kinase inhibitors (TKIs) are for complete hematological response after 3 months of treatment, complete cytogenetic response after 6 months, and a reduction of the molecular disease of at least 3 logs after 12 months. Patients who do not reach their goal can switch to another TKI. Thus, the molecular monitoring of response is the main consideration of management of CML patients. Moreover, cases in deep and persistent molecular response can tempt the physician to interrupt treatment, and this "dream" is possible due to the quantitative PCR. After great international effort, today the BCR-ABL1 expression obtained in each laboratory is standardized and expressed as "international scale." This aim has been reached after the establishment of the EUTOS program (in Europe) and the LabNet network (in Italy), the platforms where biologists meet clinicians. In the field of quantitative PCR, the digital PCR is now a new and promising, sensitive and accurate tool. Some authors reported that digital PCR is able to better classify patients in precise "molecular classes," which could lead to a better identification of those cases that will benefit from the interruption of therapy. In addition, digital PCR can be used to identify a point mutation in the ABL1 domain, mutations that are often responsible for the TKI resistance. In the field of resistance, a prominent role is played by the NGS that enables identification of any mutation in ABL1 domain, even at sub-clonal levels. This manuscript reviews how the molecular tools can lead the management of CML patients, focusing on the more recent technical advances.
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Affiliation(s)
- Barbara Izzo
- Department of Clinical Medicine and Surgery, Molecular Biology, University Federico II, Naples, Italy
| | | | - Santa Errichiello
- Department of Clinical Medicine and Surgery, Molecular Biology, University Federico II, Naples, Italy
| | - Filomena Daraio
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Claudia Baratè
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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11
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Neckles C, Sundara Rajan S, Caplen NJ. Fusion transcripts: Unexploited vulnerabilities in cancer? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1562. [PMID: 31407506 PMCID: PMC6916338 DOI: 10.1002/wrna.1562] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/05/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Gene fusions are an important class of mutations in several cancer types and include genomic rearrangements that fuse regulatory or coding elements from two different genes. Analysis of the genetics of cancers harboring fusion oncogenes and the proteins they encode have enhanced cancer diagnosis and in some cases patient treatment. However, the effect of the complex structure of fusion genes on the biogenesis of the resulting chimeric transcripts they express is not well studied. There are two potential RNA‐related vulnerabilities inherent to fusion‐driven cancers: (a) the processing of the fusion precursor messenger RNA (pre‐mRNA) to the mature mRNA and (b) the mature mRNA. In this study, we discuss the effects that the genetic organization of fusion oncogenes has on the generation of translatable mature RNAs and the diversity of fusion transcripts expressed in different cancer subtypes, which can fundamentally influence both tumorigenesis and treatment. We also discuss functional genomic approaches that can be utilized to identify proteins that mediate the processing of fusion pre‐mRNAs. Furthermore, we assert that an enhanced understanding of fusion transcript biogenesis and the diversity of the chimeric RNAs present in fusion‐driven cancers will increase the likelihood of successful application of RNA‐based therapies in this class of tumors. This article is categorized under:RNA Processing > RNA Editing and Modification RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland
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12
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Alves PU, Vinhas R, Fernandes AR, Birol SZ, Trabzon L, Bernacka-Wojcik I, Igreja R, Lopes P, Baptista PV, Águas H, Fortunato E, Martins R. Multifunctional microfluidic chip for optical nanoprobe based RNA detection - application to Chronic Myeloid Leukemia. Sci Rep 2018; 8:381. [PMID: 29321602 PMCID: PMC5762653 DOI: 10.1038/s41598-017-18725-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/13/2017] [Indexed: 11/24/2022] Open
Abstract
Many diseases have their treatment options narrowed and end up being fatal if detected during later stages. As a consequence, point-of-care devices have an increasing importance for routine screening applications in the health sector due to their portability, fast analyses and decreased cost. For that purpose, a multifunctional chip was developed and tested using gold nanoprobes to perform RNA optical detection inside a microfluidic chip without the need of molecular amplification steps. As a proof-of-concept, this device was used for the rapid detection of chronic myeloid leukemia, a hemato-oncological disease that would benefit from early stage diagnostics and screening tests. The chip passively mixed target RNA from samples, gold nanoprobes and saline solution to infer a result from their final colorimetric properties. An optical fiber network was used to evaluate its transmitted spectra inside the chip. Trials provided accurate output results within 3 min, yielding signal-to-noise ratios up to 9 dB. When compared to actual state-of-art screening techniques of chronic myeloid leukemia, these results were, at microscale, at least 10 times faster than the reported detection methods for chronic myeloid leukemia. Concerning point-of-care applications, this work paves the way for other new and more complex versions of optical based genosensors.
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Affiliation(s)
- Pedro Urbano Alves
- CENIMAT/I3N, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa and CEMOP/UNINOVA, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Raquel Vinhas
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Semra Zuhal Birol
- MEMS, Department of Nanoscience and Nanoengineering, Istanbul Technical University, Ayazaga Campus, 34469, Maslak, Turkey
| | - Levent Trabzon
- MEMS, Department of Nanoscience and Nanoengineering, Istanbul Technical University, Ayazaga Campus, 34469, Maslak, Turkey
| | - Iwona Bernacka-Wojcik
- CENIMAT/I3N, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa and CEMOP/UNINOVA, Campus de Caparica, 2829-516, Caparica, Portugal
- Laboratory of Organic Electronics, Department of Science and Technology, Linköping University, SE-601 74, Norrköping, Sweden
| | - Rui Igreja
- CENIMAT/I3N, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa and CEMOP/UNINOVA, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Paulo Lopes
- Department of Physics and IEETA (Institute of Electronics and Informatics Engineering of Aveiro), Campus Santiago, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal.
| | - Hugo Águas
- CENIMAT/I3N, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa and CEMOP/UNINOVA, Campus de Caparica, 2829-516, Caparica, Portugal.
| | - Elvira Fortunato
- CENIMAT/I3N, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa and CEMOP/UNINOVA, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Rodrigo Martins
- CENIMAT/I3N, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa and CEMOP/UNINOVA, Campus de Caparica, 2829-516, Caparica, Portugal
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13
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Dasgupta S, Ray UK, Mitra AG, Bhattacharyya DM, Mukhopadhyay A, Das P, Gangopadhyay S, Roy S, Mukhopadhyay S. Evaluation of a new flow cytometry based method for detection of BCR-ABL1 fusion protein in chronic myeloid leukemia. Blood Res 2017; 52:112-118. [PMID: 28698847 PMCID: PMC5503888 DOI: 10.5045/br.2017.52.2.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/17/2016] [Accepted: 01/06/2017] [Indexed: 11/29/2022] Open
Abstract
Background Philadelphia chromosome, a hallmark of chronic myeloid leukemia (CML), plays a key role in disease pathogenesis. It reflects a balanced reciprocal translocation between long arms of chromosomes 9 and 22 involving BCR and ABL1 genes, respectively. An accurate and reliable detection of BCR-ABL fusion gene is necessary for the diagnosis and monitoring of CML. Previously, many technologies, most of which are laborious and time consuming, have been developed to detect BCR-ABL chimeric gene or chromosome. Methods A new flow cytometric immunobead assay was used for detection of BCR-ABL fusion proteins and applicability, sensitivity, reliability, efficacy and rapidity of this method was evaluated. Results From February 2009 to January 2014, a total 648 CML patients were investigated for the status of BCR-ABL1 protein. Among them, 83 patients were enrolled for comparative study of BCR-ABL1 positivity by three routinely used procedures like karyotyping, and quantitative real time PCR (RT-PCR) as well as immunobead flow cytometry assay. BCR-ABL protein analysis was found consistent, more sensitive (17% greater sensitivity) and reliable than the conventional cytogenetics, as flow cytometry showed 95% concordance rate to RT-PCR. Conclusion BCR-ABL fusion protein assay using a new flow cytometric immunobead might be useful in the diagnosis and monitoring CML patients.
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Affiliation(s)
- Swati Dasgupta
- Department of Molecular Biology and Hematology, Netaji Subhas Chandra Bose Cancer Research Institute, West Bengal, India
| | - Ujjal K Ray
- Department of Pathology, Netaji Subhas Chandra Bose Cancer Research Institute, West Bengal, India
| | - Arpita Ghosh Mitra
- Department of HLA & Molecular Lab, Medica Superspeciality Hospital, West Bengal, India
| | - Deboshree M Bhattacharyya
- Department of Molecular Biology and Hematology, Netaji Subhas Chandra Bose Cancer Research Institute, West Bengal, India
| | - Ashis Mukhopadhyay
- Department of Hemato-Oncology, Netaji Subhas Chandra Bose Cancer Research Institute, West Bengal, India
| | - Priyabrata Das
- Department of Molecular Biology and Hematology, Netaji Subhas Chandra Bose Cancer Research Institute, West Bengal, India
| | - Sudeshna Gangopadhyay
- Department of Molecular Biology and Hematology, Netaji Subhas Chandra Bose Cancer Research Institute, West Bengal, India
| | - Sudip Roy
- Department of HLA & Molecular Lab, Medica Superspeciality Hospital, West Bengal, India
| | - Soma Mukhopadhyay
- Department of Molecular Biology and Hematology, Netaji Subhas Chandra Bose Cancer Research Institute, West Bengal, India
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14
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Keramatinia A, Ahadi A, Akbari ME, Mohseny M, Jarahi AM, Mehrvar N, Mansouri N, Tabatabaei SAM, Movafagh A. Genomic Profiling of Chronic Myelogenous Leukemia: Basic and Clinical Approach. J Cancer Prev 2017; 22:74-81. [PMID: 28698860 PMCID: PMC5503218 DOI: 10.15430/jcp.2017.22.2.74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/10/2017] [Accepted: 06/12/2017] [Indexed: 01/11/2023] Open
Abstract
Chronic myeloid leukemia (CML) is a hematological stem cell cancer driven by BCR-ABL1 fusion protein. We review the previous and recent evidence on the significance of CML in diagnostic and clinic management. The technical monitoring of BCR-ABL1 with quantitative real time-PCR has been used in assessing patient outcome. The cytogenetic mark of CML is Philadelphia chromosome, that is formed by reciprocal chromosomal translocations between human chromosome 9 and 22, t(9:22) (q34:q11). It makes a BCR-ABL1 fusion protein with an anomaly tyrosine kinase activity that promotes the characteristic proliferation of progenitor cells in CML and acute lymphoblastic lymphoma. The targeting of BCR-ABL1 fusion kinase is the first novel paradigm of molecularly targeted curing.
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Affiliation(s)
- Aliasghar Keramatinia
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahadi
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Maryam Mohseny
- Department of Social Medicine, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Mosavi Jarahi
- Department of Social Medicine, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Narjes Mehrvar
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Mansouri
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S A Mortazavi Tabatabaei
- Proteomics Research Center, School of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abolfazl Movafagh
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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15
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Yu S, Cui M, He X, Jing R, Wang H. A review of the challenge in measuring and standardizing BCR-ABL1. ACTA ACUST UNITED AC 2017; 55:1465-1473. [DOI: 10.1515/cclm-2016-0927] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/02/2017] [Indexed: 01/28/2023]
Abstract
AbstractBreakpoint cluster region-Abelson (
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16
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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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17
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Proctor A, Zigoneanu IG, Wang Q, Sims CE, Lawrence DS, Allbritton NL. Development of a protease-resistant reporter to quantify BCR-ABL activity in intact cells. Analyst 2016; 141:6008-6017. [PMID: 27704073 PMCID: PMC5111365 DOI: 10.1039/c6an01378c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A peptidase-resistant ABL kinase substrate was developed by identifying protease-susceptible bonds on an ABL substrate peptide and replacing flanking amino acids with non-native amino acids. After an iterative design process, the lead, or designed, peptide X-A possesses a six-fold longer life in a cytosolic lysate than that of the starting peptide. The catalytic efficiency (kcat/KM) of purified ABL kinase for the lead peptide (125 s-1 μM-1) is similar to that of the starting peptide (103 s-1 μM-1) demonstrating preservation of the peptide's ability to serve as a kinase substrate. When incubated in cytosolic lysates, the lead peptide is slowly degraded into 4 fragments over time. In contrast, when loaded into intact cells, the peptide is metabolized into 5 fragments, with only 2 of the fragments corresponding to those in the lysate. Thus the two environments possess differing peptidase activities, which must be accounted for when designing peptidase-resistant peptides. In both settings, the substrate is phosphorylated by BCR-ABL providing a readout of BCR-ABL activity. A small panel of tyrosine kinase inhibitors verified the substrate's specificity for BCR-ABL/ABL kinase activity in both lysates and cells in spite of the multitude of other kinases present. The designed peptide X-A acts as a long-lived BCR-ABL kinase reporter in the leukemic cells possessing the BCR-ABL mutation.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Imola G Zigoneanu
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA, and North Carolina State University, Raleigh, NC, 27695, USA
| | - Qunzhao Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christopher E Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David S Lawrence
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599, USA
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA, and North Carolina State University, Raleigh, NC, 27695, USA
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18
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Aberrant Wnt Signaling in Leukemia. Cancers (Basel) 2016; 8:cancers8090078. [PMID: 27571104 PMCID: PMC5040980 DOI: 10.3390/cancers8090078] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/25/2016] [Accepted: 08/22/2016] [Indexed: 12/21/2022] Open
Abstract
The Wnt signaling pathway is essential in the development and homeostasis of blood and immune cells, but its exact role is still controversial and is the subject of intense research. The malignant counterpart of normal hematopoietic cells, leukemic (stem) cells, have hijacked the Wnt pathway for their self-renewal and proliferation. Here we review the multiple ways dysregulated Wnt signaling can contribute to leukemogenesis, both cell autonomously as well as by changes in the microenvironment.
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19
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Chakraborty SN, Leng X, Perazzona B, Sun X, Lin YH, Arlinghaus RB. Combination of JAK2 and HSP90 inhibitors: an effective therapeutic option in drug-resistant chronic myelogenous leukemia. Genes Cancer 2016; 7:201-208. [PMID: 27551334 PMCID: PMC4979592 DOI: 10.18632/genesandcancer.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Recent studies suggest that JAK2 serves as a novel therapeutic target in Bcr-Abl+ chronic myelogenous leukemia (CML). We have reported the existence of an HSP90- associated high molecular weight network complex (HMWNC) that is composed of HSP90 client proteins BCR-ABL, JAK2, and STAT3 in wild type Bcr-Abl+ leukemic cells. Here we showed that the HSP90-HMWNC is present in leukemia cells from CML patients in blast stage, and in Imatinib (IM)-resistant 32Dp210 (T315I) leukemia cells. We found that the HSP90-HMWNC could be disassembled by depleting JAK2 with either Jak2-specific shRNA or treatment with JAK2 inhibitors (TG101209 or Ruxolitinib) and HSP90 inhibitor (AUY922). Combinational treatment with JAK2 and HSP90 inhibitors diminished the activation of BCR-ABL, JAK2 and its downstream targets. As a result, the IM-resistant 32Dp210 T315I cells underwent apoptosis. When administered in mice bearing 32Dp210 T315I leukemia, combinational therapy using Ruxolitinib and AUY922 prolonged the survival significantly. Thus, a combination of JAK2 and HSP90 inhibitors could be a powerful strategy for the treatment of CML, especially in IM-resistant patients.
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Affiliation(s)
- Sandip N Chakraborty
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Xiaohong Leng
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Bastianella Perazzona
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Xiaoping Sun
- Department of Laboratory Medicine, M.D. Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Yu-Hsi Lin
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Ralph B Arlinghaus
- Department of Translational Molecular Pathology, M.D. Anderson Cancer Center, University of Texas, Houston, TX, USA
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20
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Vinhas R, Correia C, Ribeiro P, Lourenço A, Botelho de Sousa A, Fernandes AR, Baptista PV. Colorimetric assessment of BCR-ABL1 transcripts in clinical samples via gold nanoprobes. Anal Bioanal Chem 2016; 408:5277-84. [PMID: 27225178 DOI: 10.1007/s00216-016-9622-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/29/2016] [Accepted: 05/09/2016] [Indexed: 11/28/2022]
Abstract
Gold nanoparticles functionalized with thiolated oligonucleotides (Au-nanoprobes) have been used in a range of applications for the detection of bioanalytes of interest, from ions to proteins and DNA targets. These detection strategies are based on the unique optical properties of gold nanoparticles, in particular, the intense color that is subject to modulation by modification of the medium dieletric. Au-nanoprobes have been applied for the detection and characterization of specific DNA sequences of interest, namely pathogens and disease biomarkers. Nevertheless, despite its relevance, only a few reports exist on the detection of RNA targets. Among these strategies, the colorimetric detection of DNA has been proven to work for several different targets in controlled samples but demonstration in real clinical bioanalysis has been elusive. Here, we used a colorimetric method based on Au-nanoprobes for the direct detection of the e14a2 BCR-ABL fusion transcript in myeloid leukemia patient samples without the need for retro-transcription. Au-nanoprobes directly assessed total RNA from 38 clinical samples, and results were validated against reverse transcription-nested polymerase chain reaction (RT-nested PCR) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The colorimetric Au-nanoprobe assay is a simple yet reliable strategy to scrutinize myeloid leukemia patients at diagnosis and evaluate progression, with obvious advantages in terms of time and cost, particularly in low- to medium-income countries where molecular screening is not routinely feasible. Graphical abstract Gold nanoprobe for colorimetric detection of BCR-ABL1 fusion transcripts originating from the Philadelphia chromosome.
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Affiliation(s)
- Raquel Vinhas
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Cláudia Correia
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Patricia Ribeiro
- Serviço de Hematologia, Hospital dos Capuchos (CHLC), 1169-050, Lisbon, Portugal
| | - Alexandra Lourenço
- Serviço de Hematologia, Hospital dos Capuchos (CHLC), 1169-050, Lisbon, Portugal
| | | | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal
| | - Pedro V Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516, Caparica, Portugal.
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21
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Saleem M, Yusoff NM. Fusion genes in malignant neoplastic disorders of haematopoietic system. ACTA ACUST UNITED AC 2016; 21:501-12. [PMID: 26871368 DOI: 10.1080/10245332.2015.1106816] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVES The new World Health Organization's (WHO) classification of haematopoietic and lymphoid tissue neoplasms incorporating the recurrent fusion genes as the defining criteria for different haematopoietic malignant phenotypes is reviewed. The recurrent fusion genes incorporated in the new WHO's classification and other chromosomal rearrangements of haematopoietic and lymphoid tissue neoplasms are reviewed. METHODOLOGY Cytokines and transcription factors in haematopoiesis and leukaemic mechanisms are described. Genetic features and clinical implications due to the encoded chimeric neoproteins causing malignant haematopoietic disorders are reviewed. RESULTS AND DISCUSSION Multiple translocation partner genes are well known for leukaemia such as MYC, MLL, RARA, ALK, and RUNX1. With the advent of more sophisticated diagnostic tools and bioinformatics algorithms, an exponential growth in fusion genes discoveries is likely to increase. CONCLUSION Demonstration of fusion genes and their specific translocation breakpoints in malignant haematological disorders are crucial for understanding the molecular pathogenesis and clinical phenotype of cancer, determining prognostic indexes and therapeutic responses, and monitoring residual disease and relapse status.
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Affiliation(s)
- Mohamed Saleem
- a Advanced Medical and Dental Institute , Universiti Sains Malaysia , Kepala Batas , Penang , Malaysia
| | - Narazah Mohd Yusoff
- a Advanced Medical and Dental Institute , Universiti Sains Malaysia , Kepala Batas , Penang , Malaysia
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22
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Subbannayya Y, Pinto SM, Gowda H, Prasad TSK. Proteogenomics for understanding oncology: recent advances and future prospects. Expert Rev Proteomics 2016; 13:297-308. [PMID: 26697917 DOI: 10.1586/14789450.2016.1136217] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The concept of proteogenomics has emerged rapidly as a valuable approach to integrate mass spectrometry-derived proteomic data with genomic and transcriptomic data. It is used to harness the full potential of the former dataset in the discovery of potential biomarkers, therapeutic targets and novel proteins associated with various biological processes including diseases. Proteogenomic strategies have been successfully utilized to identify novel genes and redefine annotation of existing gene models in various genomes. In recent years, this approach has been extended to the field of cancer biology to unravel complexities in the tumor genomes and proteomes. Standard proteomics workflows employing translated cancer genomes and transcriptomes can potentially identify peptides from mutant proteins, splice variants and fusion proteins in the tumor proteome, which in addition to the currently available biomarker panels can serve as potential diagnostic and prognostic biomarkers, besides having therapeutic utility. This review focuses on the role of proteogenomics to understand cancer biology.
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Affiliation(s)
- Yashwanth Subbannayya
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - Sneha M Pinto
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - Harsha Gowda
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - T S Keshava Prasad
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India.,c NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre , National Institute of Mental Health and Neurosciences , Bangalore , India
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23
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Kanderova V, Kuzilkova D, Stuchly J, Vaskova M, Brdicka T, Fiser K, Hrusak O, Lund-Johansen F, Kalina T. High-resolution Antibody Array Analysis of Childhood Acute Leukemia Cells. Mol Cell Proteomics 2016; 15:1246-61. [PMID: 26785729 DOI: 10.1074/mcp.m115.054593] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 11/06/2022] Open
Abstract
Acute leukemia is a disease pathologically manifested at both genomic and proteomic levels. Molecular genetic technologies are currently widely used in clinical research. In contrast, sensitive and high-throughput proteomic techniques for performing protein analyses in patient samples are still lacking. Here, we used a technology based on size exclusion chromatography followed by immunoprecipitation of target proteins with an antibody bead array (Size Exclusion Chromatography-Microsphere-based Affinity Proteomics, SEC-MAP) to detect hundreds of proteins from a single sample. In addition, we developed semi-automatic bioinformatics tools to adapt this technology for high-content proteomic screening of pediatric acute leukemia patients.To confirm the utility of SEC-MAP in leukemia immunophenotyping, we tested 31 leukemia diagnostic markers in parallel by SEC-MAP and flow cytometry. We identified 28 antibodies suitable for both techniques. Eighteen of them provided excellent quantitative correlation between SEC-MAP and flow cytometry (p< 0.05). Next, SEC-MAP was applied to examine 57 diagnostic samples from patients with acute leukemia. In this assay, we used 632 different antibodies and detected 501 targets. Of those, 47 targets were differentially expressed between at least two of the three acute leukemia subgroups. The CD markers correlated with immunophenotypic categories as expected. From non-CD markers, we found DBN1, PAX5, or PTK2 overexpressed in B-cell precursor acute lymphoblastic leukemias, LAT, SH2D1A, or STAT5A overexpressed in T-cell acute lymphoblastic leukemias, and HCK, GLUD1, or SYK overexpressed in acute myeloid leukemias. In addition, OPAL1 overexpression corresponded to ETV6-RUNX1 chromosomal translocation.In summary, we demonstrated that SEC-MAP technology is a powerful tool for detecting hundreds of proteins in clinical samples obtained from pediatric acute leukemia patients. It provides information about protein size and reveals differences in protein expression between particular leukemia subgroups. Forty-seven of SEC-MAP identified targets were validated by other conventional method in this study.
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Affiliation(s)
- Veronika Kanderova
- From the ‡CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, 2 Faculty of Medicine, Charles University in Prague, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Daniela Kuzilkova
- From the ‡CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, 2 Faculty of Medicine, Charles University in Prague, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Jan Stuchly
- From the ‡CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, 2 Faculty of Medicine, Charles University in Prague, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Martina Vaskova
- From the ‡CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, 2 Faculty of Medicine, Charles University in Prague, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Tomas Brdicka
- §Institute of Molecular Genetics, Academy of Sciences of the Czech Republic; Videnska 1083, 14220 Prague, Czech Republic
| | - Karel Fiser
- From the ‡CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, 2 Faculty of Medicine, Charles University in Prague, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Ondrej Hrusak
- From the ‡CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, 2 Faculty of Medicine, Charles University in Prague, V Uvalu 84, 15006 Prague 5, Czech Republic
| | - Fridtjof Lund-Johansen
- ¶Department of Immunology, Oslo University Hospital, Rikshospitalet; Sognsvannsveien 20, 0372 Oslo, Norway
| | - Tomas Kalina
- From the ‡CLIP - Childhood Leukaemia Investigation Prague, Department of Paediatric Haematology and Oncology, 2 Faculty of Medicine, Charles University in Prague, V Uvalu 84, 15006 Prague 5, Czech Republic;
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Du Pisani LA, Shires K. Development of a flow cytometric method to detect the presence of mutated nucleophosmin 1 in acute myeloid leukemia. Hematol Oncol Stem Cell Ther 2015; 8:106-14. [DOI: 10.1016/j.hemonc.2015.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 01/09/2023] Open
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Recchia AG, Caruso N, Bossio S, Pellicanò M, De Stefano L, Franzese S, Palummo A, Abbadessa V, Lucia E, Gentile M, Vigna E, Caracciolo C, Agostino A, Galimberti S, Levato L, Stagno F, Molica S, Martino B, Vigneri P, Di Raimondo F, Morabito F. Flow Cytometric Immunobead Assay for Detection of BCR-ABL1 Fusion Proteins in Chronic Myleoid Leukemia: Comparison with FISH and PCR Techniques. PLoS One 2015; 10:e0130360. [PMID: 26111048 PMCID: PMC4482505 DOI: 10.1371/journal.pone.0130360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/18/2015] [Indexed: 11/19/2022] Open
Abstract
Chronic Myeloid Leukemia (CML) is characterized by a balanced translocation juxtaposing the Abelson (ABL) and breakpoint cluster region (BCR) genes. The resulting BCR-ABL1 oncogene leads to increased proliferation and survival of leukemic cells. Successful treatment of CML has been accompanied by steady improvements in our capacity to accurately and sensitively monitor therapy response. Currently, measurement of BCR-ABL1 mRNA transcript levels by real-time quantitative PCR (RQ-PCR) defines critical response endpoints. An antibody-based technique for BCR-ABL1 protein recognition could be an attractive alternative to RQ-PCR. To date, there have been no studies evaluating whether flow-cytometry based assays could be of clinical utility in evaluating residual disease in CML patients. Here we describe a flow-cytometry assay that detects the presence of BCR-ABL1 fusion proteins in CML lysates to determine the applicability, reliability, and specificity of this method for both diagnosis and monitoring of CML patients for initial response to therapy. We show that: i) CML can be properly diagnosed at onset, (ii) follow-up assessments show detectable fusion protein (i.e. relative mean fluorescent intensity, rMFI%>1) when BCR-ABL1IS transcripts are between 1-10%, and (iii) rMFI% levels predict CCyR as defined by FISH analysis. Overall, the FCBA assay is a rapid technique, fully translatable to the routine management of CML patients.
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Affiliation(s)
| | - Nadia Caruso
- Hematology Unit, Azienda Ospedaliera Annunziata di Cosenza, Cosenza, Italy
| | - Sabrina Bossio
- Biotechnology Research Unit, ASP Cosenza, Aprigliano, Italy
| | | | | | - Stefania Franzese
- Hematology Unit, Azienda Ospedaliera Annunziata di Cosenza, Cosenza, Italy
| | - Angela Palummo
- Biotechnology Research Unit, ASP Cosenza, Aprigliano, Italy
| | - Vincenzo Abbadessa
- Department of Oncology, Hematology and Bone Marrow Transplantation Unit, University of Palermo, Policlinico P. Giaccone, Palermo, Italy
| | - Eugenio Lucia
- Hematology Unit, Azienda Ospedaliera Annunziata di Cosenza, Cosenza, Italy
| | - Massimo Gentile
- Hematology Unit, Azienda Ospedaliera Annunziata di Cosenza, Cosenza, Italy
| | - Ernesto Vigna
- Hematology Unit, Azienda Ospedaliera Annunziata di Cosenza, Cosenza, Italy
| | - Clementina Caracciolo
- Department of Oncology, Hematology and Bone Marrow Transplantation Unit, University of Palermo, Policlinico P. Giaccone, Palermo, Italy
| | - Antolino Agostino
- Centro Trasfusionale Ospedale, Azienda Sanitaria Provinciale 7, Ragusa, Italy
| | - Sara Galimberti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Luciano Levato
- Medical Oncology Unit, Hematology-Oncology Department, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| | - Fabio Stagno
- Divisione di Ematologia, Ospedale Ferrarotto, Università degli Studi di Catania, Catania, Italy
| | - Stefano Molica
- Medical Oncology Unit, Hematology-Oncology Department, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| | - Bruno Martino
- U.O.C. di Ematologia dell'Azienda"Bianchi-Melacrino-Morelli" di Reggio Calabria, Reggio Calabria, Italy
| | - Paolo Vigneri
- Dipartimento di Scienze Mediche e Pediatriche, Università degli Studi di Catania, Catania, Italy
| | - Francesco Di Raimondo
- Divisione di Ematologia, Ospedale Ferrarotto, Università degli Studi di Catania, Catania, Italy
| | - Fortunato Morabito
- Biotechnology Research Unit, ASP Cosenza, Aprigliano, Italy
- Hematology Unit, Azienda Ospedaliera Annunziata di Cosenza, Cosenza, Italy
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Kelani R, Monem F. Reconsideration of BCR-ABL protein flow cytometric immunobead assay: how potent to diagnose and monitor chronic myeloid leukemia? Int J Lab Hematol 2015; 37:723-8. [PMID: 26059167 DOI: 10.1111/ijlh.12394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/17/2015] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Chronic myeloid leukemia (CML) is typically associated with the Philadelphia chromosome, resulting in the production of BCR-ABL fusion oncoprotein with upregulated tyrosine kinase activity. We aimed to evaluate a new flow cytometric immunobead assay to detect BCR-ABL protein in a group of patients with CML. METHODS We enrolled 49 patients with CML, whose qRT-PCR and/or cytogenetic analysis of Philadelphia chromosome aberration was available, including tyrosine kinase inhibitors (TKIs)-naïve and (TKIs)-treated patients with various levels of response. Twenty Philadelphia-negative healthy individuals were also enrolled to obtain analytical negative controls. Peripheral blood samples were analyzed for BCR-ABL fusion protein by flow cytometry. RESULTS The BCR-ABL fusion protein flow cytometric assay seemed efficacious to both diagnose the presence (P-value <0.0001) and distinguish the levels (P-value = 0) of the Philadelphia chromosome aberration. Groups of TKI-naïve and TKI-treated patients as well as levels of molecular/cytogenetic response to TKI-therapy were effectively discriminated (P-value <0.01). The receiver operating characteristic (ROC) curve analysis indicated the diagnostic value of the assay as excellent (AUC = 0.95, P-value = 0). CONCLUSIONS The evaluated BCR-ABL fusion protein assay might be useful for diagnosing and monitoring Philadelphia chromosome aberration.
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Affiliation(s)
- R Kelani
- Department of Biochemistry and Microbiology, Faculty of Pharmacy, Damascus University, Damascus, Syria
| | - F Monem
- Department of Biochemistry and Microbiology, Faculty of Pharmacy, Damascus University, Damascus, Syria.,Clinical Laboratories Department, AL-Assad Hospital, Damascus University, Damascus, Syria
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An on-bacterium flow cytometric immunoassay for protein quantification. J Pharm Biomed Anal 2013; 83:129-34. [DOI: 10.1016/j.jpba.2013.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 01/27/2023]
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van Dongen JJM, Orfao A. EuroFlow: Resetting leukemia and lymphoma immunophenotyping. Basis for companion diagnostics and personalized medicine. Leukemia 2012; 26:1899-907. [PMID: 22948488 PMCID: PMC3437406 DOI: 10.1038/leu.2012.121] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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29
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He Y, Zhao YX, Zhu MQ, Wu Q, Ruan CG. Detection of autoantibodies against platelet glycoproteins in patients with immune thrombocytopenic purpura by flow cytometric immunobead array. Clin Chim Acta 2012; 415:176-80. [PMID: 23103637 DOI: 10.1016/j.cca.2012.10.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/08/2012] [Accepted: 10/18/2012] [Indexed: 11/24/2022]
Abstract
BACKGROUND The goal of this study is to develop a flow cytometric immunobead array (FCIA) assay to detect platelet autoantibodies commonly present in bleeding patients with immune thrombocytopenic purpura (ITP). METHODS Polystyrene microbeads coated with antibodies against human platelet glycoproteins (GPs) IX (SZ1), Ib (SZ2), IIIa (SZ21), IIb (SZ22), and P-selectin (SZ51) were incubated with platelet lysate from 50 ITP patients and 86 controls. The platelet antigen-autoantibody complexes were detected by flow cytometry using an FITC-labeled antibody. The results were compared with that of a monoclonal antibody immobilization of platelet antigen (MAIPA) assay. RESULTS By FCIA, platelet autoantibodies against GPIb, GPIIb, GPIIIa, GPIX and P-selectin were detected in ITP patients. Mean fluorescent intensity values with antibodies SZ1, SZ2, SZ21, SZ22 and SZ51 were all higher in ITP patients than controls (p values<0.01). In ROC analysis, values of the area under the curve were 0.89, 0.82, 0.93, 0.94 and 0.95, respectively. In ITP diagnosis, the FCIA assay with these five antibodies had better sensitivity and accuracy than the MAIPA assay (96% vs. 44% in sensitivity; 80.9% vs. 64.7% in accuracy, p<0.01). CONCLUSION FCIA assays with multiple antibodies against platelet GPs may be used to improve the diagnosis of ITP in hospitals.
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Affiliation(s)
- Yang He
- Key Lab of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
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30
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Le diagnostic de la leucémie myéloïde chronique (LMC) en 2012. ONCOLOGIE 2012. [DOI: 10.1007/s10269-012-2211-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Flow cytometric immunobead assay for fast and easy detection of PML-RARA fusion proteins for the diagnosis of acute promyelocytic leukemia. Leukemia 2012; 26:1976-85. [PMID: 22948489 PMCID: PMC3437408 DOI: 10.1038/leu.2012.125] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The PML–RARA fusion protein is found in approximately 97% of patients with acute promyelocytic leukemia (APL). APL can be associated with life-threatening bleeding complications when undiagnosed and not treated expeditiously. The PML–RARA fusion protein arrests maturation of myeloid cells at the promyelocytic stage, leading to the accumulation of neoplastic promyelocytes. Complete remission can be obtained by treatment with all-trans-retinoic acid (ATRA) in combination with chemotherapy. Diagnosis of APL is based on the detection of t(15;17) by karyotyping, fluorescence in situ hybridization or PCR. These techniques are laborious and demand specialized laboratories. We developed a fast (performed within 4–5 h) and sensitive (detection of at least 10% malignant cells in normal background) flow cytometric immunobead assay for the detection of PML–RARA fusion proteins in cell lysates using a bead-bound anti-RARA capture antibody and a phycoerythrin-conjugated anti-PML detection antibody. Testing of 163 newly diagnosed patients (including 46 APL cases) with the PML–RARA immunobead assay showed full concordance with the PML–RARA PCR results. As the applied antibodies recognize outer domains of the fusion protein, the assay appeared to work independently of the PML gene break point region. Importantly, the assay can be used in parallel with routine immunophenotyping for fast and easy diagnosis of APL.
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Brüggemann M, Gökbuget N, Kneba M. Acute Lymphoblastic Leukemia: Monitoring Minimal Residual Disease as a Therapeutic Principle. Semin Oncol 2012; 39:47-57. [DOI: 10.1053/j.seminoncol.2011.11.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Comparative proteomics in acute myeloid leukemia. Contemp Oncol (Pozn) 2012; 16:95-103. [PMID: 23788862 PMCID: PMC3687393 DOI: 10.5114/wo.2012.28787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 07/25/2011] [Accepted: 02/13/2012] [Indexed: 01/22/2023] Open
Abstract
The term proteomics was used for the first time in 1995 to describe large-scale protein analyses. At the same time proteomics was distinguished as a new domain of the life sciences. The major object of proteomic studies is the proteome, i.e. the set of all proteins accumulating in a given cell, tissue or organ. During the last years several new methods and techniques have been developed to increase the fidelity and efficacy of proteomic analyses. The most widely used are two-dimensional electrophoresis (2DE) and mass spectrometry (MS). In the past decade proteomic analyses have also been successfully applied in biomedical research. They allow one to determine how various diseases affect the pattern of protein accumulation. In this paper, we attempt to summarize the results of the proteomic analyses of acute myeloid leukemia (AML) cells. They have increased our knowledge on the mechanisms underlying AML development and contributed to progress in AML diagnostics and treatment.
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Yujie W, Yu Z, Sixuan Q, Li W, Peng L, Zeng G, Sujiang Z, Jianyong L. Detection of BCR-ABL fusion proteins in patients with leukemia using a cytometric bead array. Leuk Lymphoma 2011; 53:451-5. [DOI: 10.3109/10428194.2011.625100] [Citation(s) in RCA: 7] [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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Miniaturized flow cytometry-based BCR-ABL immunoassay in detecting leptomeningeal disease. Leuk Res 2011; 35:1290-3. [DOI: 10.1016/j.leukres.2011.05.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/05/2011] [Accepted: 05/12/2011] [Indexed: 11/21/2022]
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36
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Flow cytometric detection of BCR-ABL in cerebrospinal fluid. Leuk Res 2011; 35:1286-7. [DOI: 10.1016/j.leukres.2011.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 06/04/2011] [Accepted: 06/04/2011] [Indexed: 11/22/2022]
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Dasatinib as first-line treatment for adult patients with Philadelphia chromosome-positive acute lymphoblastic leukemia. Blood 2011; 118:6521-8. [PMID: 21931113 DOI: 10.1182/blood-2011-05-351403] [Citation(s) in RCA: 330] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dasatinib is a potent BCR-ABL inhibitor effective in chronic myeloid leukemia and Ph(+) acute lymphoblastic leukemia (ALL) resistant/intolerant to imatinib. In the GIMEMA LAL1205 protocol, patients with newly diagnosed Ph(+) ALL older than 18 years (with no upper age limit) received dasatinib induction therapy for 84 days combined with steroids for the first 32 days and intrathecal chemotherapy. Postremission therapy was free. Fifty-three patients were evaluable (median age, 53.6 years). All patients achieved a complete hematologic remission (CHR), 49 (92.5%) at day 22. At this time point, 10 patients achieved a BCR-ABL reduction to < 10(-3). At 20 months, the overall survival was 69.2% and disease-free survival was 51.1%. A significant difference in DFS was observed between patients who showed at day 22 a decrease in BCR-ABL levels to < 10(-3) compared with patients who never reached these levels during induction. In multivariate analysis, BCR-ABL levels of < 10(-3) at day 85 correlated with disease-free survival. No deaths or relapses occurred during induction. Twenty-three patients relapsed after completing induction. A T315I mutation was detected in 12 of 17 relapsed cases. Treatment was well tolerated; only 4 patients discontinued therapy during the last phase of the induction when already in CHR. In adult Ph(+) ALL, induction treatment with dasatinib plus steroids is associated with a CHR in virtually all patients, irrespective of age, good compliance, no deaths, and a very rapid debulking of the neoplastic clone.
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Varma N, Naseem S. Application of flow cytometry in pediatric hematology-oncology. Pediatr Blood Cancer 2011; 57:18-29. [PMID: 21462301 DOI: 10.1002/pbc.22954] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 11/09/2010] [Indexed: 11/08/2022]
Abstract
Applications of flow cytometry in pediatric cancers have expanded substantially in recent years. In acute leukemias, the commonest childhood cancer, flow cytometry can now define complex antigenic profiles that are associated with specific cytogenetic/molecular defects and can also directly identify BCR-ABL fusion protein. Flow cytometry based scoring system has been described for diagnosis of myelodysplastic syndromes. In solid tumors, flow cytometry was previously used mainly to determine DNA content for prognosis; however, recent studies in children with neuroblastoma and Ewing sarcoma have identified its diagnostic utility. In this review, we will discuss the current and future applications of flow cytometry in pediatric hematology-oncology.
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Affiliation(s)
- Neelam Varma
- Department of Hematology, Postgraduate Institute of Medical Education and Research, India.
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Acute myeloid leukemia with the t(8;21) translocation: clinical consequences and biological implications. J Biomed Biotechnol 2011; 2011:104631. [PMID: 21629739 PMCID: PMC3100545 DOI: 10.1155/2011/104631] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/31/2011] [Accepted: 02/22/2011] [Indexed: 12/20/2022] Open
Abstract
The t(8;21) abnormality occurs in a minority of acute myeloid leukemia (AML) patients. The translocation results in an in-frame fusion of two genes, resulting in a fusion protein of one N-terminal domain from the AML1 gene and four C-terminal domains from the ETO gene. This protein has multiple effects on the regulation of the proliferation, the differentiation, and the viability of leukemic cells. The translocation can be detected as the only genetic abnormality or as part of more complex abnormalities. If t(8;21) is detected in a patient with bone marrow pathology, the diagnosis AML can be made based on this abnormality alone. t(8;21) is usually associated with a good prognosis. Whether the detection of the fusion gene can be used for evaluation of minimal residual disease and risk of leukemia relapse remains to be clarified. To conclude, detection of t(8;21) is essential for optimal handling of these patients as it has both diagnostic, prognostic, and therapeutic implications.
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Mizutani T, Kondo T, Darmanin S, Tsuda M, Tanaka S, Tobiume M, Asaka M, Ohba Y. A novel FRET-based biosensor for the measurement of BCR-ABL activity and its response to drugs in living cells. Clin Cancer Res 2010; 16:3964-75. [PMID: 20670950 DOI: 10.1158/1078-0432.ccr-10-0548] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To develop a novel diagnostic method for the assessment of drug efficacy in chronic myeloid leukemia (CML) patients individually, we generated a biosensor that enables the evaluation of BCR-ABL kinase activity in living cells using the principle of fluorescence resonance energy transfer (FRET). EXPERIMENTAL DESIGN To develop FRET-based biosensors, we used CrkL, the most characteristic substrate of BCR-ABL, and designed a protein in which CrkL is sandwiched between Venus, a variant of YFP, and enhanced cyan fluorescent protein, so that CrkL intramolecular binding of the SH2 domain to phosphorylated tyrosine (Y207) increases FRET efficiency. After evaluation of the properties of this biosensor by comparison with established methods including Western blotting and flow cytometry, BCR-ABL activity and its response to drugs were examined in CML patient cells. RESULTS After optimization, we obtained a biosensor that possesses higher sensitivity than that of established techniques with respect to measuring BCR-ABL activity and its suppression by imatinib. Thanks to its high sensitivity, this biosensor accurately gauges BCR-ABL activity in relatively small cell numbers and can also detect <1% minor drug-resistant populations within heterogeneous ones. We also noticed that this method enabled us to predict future onset of drug resistance as well as to monitor the disease status during imatinib therapy, using patient cells. CONCLUSION In consideration of its quick and practical nature, this method is potentially a promising tool for the prediction of both current and future therapeutic responses in individual CML patients, which will be surely beneficial for both patients and clinicians.
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MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Antineoplastic Agents/therapeutic use
- Benzamides
- Biosensing Techniques/methods
- Blotting, Western
- Cell Separation
- Drug Resistance, Neoplasm/drug effects
- Flow Cytometry
- Fluorescence Resonance Energy Transfer/methods
- Fusion Proteins, bcr-abl/analysis
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Luminescent Agents
- Nuclear Proteins/metabolism
- Phosphorylation
- Piperazines/therapeutic use
- Pyrimidines/therapeutic use
- Sensitivity and Specificity
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Affiliation(s)
- Tatsuaki Mizutani
- Laboratory of Pathophysiology and Signal Transduction, Hokkaido University Graduate School of Medicine, Kira-ku, Sapporo, Japan
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Detection of fusion genes at the protein level in leukemia patients via the flow cytometric immunobead assay. Best Pract Res Clin Haematol 2010; 23:333-45. [PMID: 21123134 DOI: 10.1016/j.beha.2010.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nowadays, the presence of specific genetic aberrations is progressively used for classification and treatment stratification, because acute leukemias with the same oncogenetic aberration generally form a clinically and diagnostically homogenous disease entity with comparable prognosis. Many oncogenetic aberrations in acute leukemias result in a fusion gene, which is transcribed into fusion transcripts and translated into fusion proteins, which are assumed to play a critical role in the oncogenetic process. Fusion gene aberrations are detected by karyotyping, FISH, or RT-PCR analysis. However, these molecular genetic techniques are laborious and time consuming, which is in contrast to flow cytometric techniques. Therefore we developed a flow cytometric immunobead assay for detection of fusion proteins in lysates of leukemia cell samples by use of a bead-bound catching antibody against one side of the fusion protein and fluorochrome-conjugated detection antibody. So far, we have been able to design such fusion protein immunobead assays for BCR-ABL, PML-RARA, TEL-AML1, E2A-PBX1, MLL-AF4, AML1-ETO and CBFB-MYH11. The immunobead assay for detection of fusion proteins can be performed within 3 to 4 hours in a routine diagnostic setting, without the need of special equipment other than a flow cytometer. The novel immunobead assay will enable fast and easy classification of acute leukemia patients that express fusion proteins. Such patients can be included at an early stage in the right treatment protocols, much faster than by use of current molecular techniques. The immunobead assay can be run in parallel to routine immunophenotyping and is particularly attractive for clinical settings without direct access to molecular diagnostics.
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Paietta E. Surrogate marker profiles for genetic lesions in acute leukemias. Best Pract Res Clin Haematol 2010; 23:359-68. [PMID: 21112035 DOI: 10.1016/j.beha.2010.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The basic hypothesis of surrogate marker profiles is that individual genetic lesions result in characteristic distortions of the cellular phenotype with some predictable consistency that can be exploited by sophisticated immunophenotyping. While cytogenetic and molecular aberrancies currently are accepted prognostic predictors in acute leukemias, single antigen expression and even antigenic profiles rarely impact on prognosis. However, increasingly, phenotypes are delineated which can serve as surrogates for underlying genetic aberrations of clinical importance. This development is of particular significance as antileukemic therapy becomes available that targets any component of the disturbed molecular pathways associated with these genetic lesions. This chapter will focus on established surrogate marker profiles, such as those for PML/RARα, AML1/ETO, FLT3-gene mutated acute lymphocytic leukemia (ALL), and BCR/ABL(POS) ALL. As the list of therapeutic targets grows, the role of surrogate antigen profiles will grow, as they can predict for the efficacy of targeted approaches in lieu of expensive, time-consuming and not always accessible genetic analyses.
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Affiliation(s)
- Elisabeth Paietta
- Montefiore Medical Center-North Division, Immunology Laboratory, Cancer Center, 600 East 233rd Street, Bronx, NY 10466, USA.
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Aptamer-based and DNAzyme-linked colorimetric detection of cancer cells. Protein Cell 2010; 1:842-6. [PMID: 21203926 DOI: 10.1007/s13238-010-0110-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 09/06/2010] [Indexed: 12/22/2022] Open
Abstract
This paper reports a novel method to detect human leukemic lymphoblasts (CCRF-CEM cells). While the aptamer of the cancer cells was employed as the recognition element to target cancer cells, peroxidase-active DNAzyme was used as the sensing element to produce catalysis-induced colorimetric signals. The elegant architecture integrating the aptamer and DNAzyme made it feasible to detect cancer cells easily and rapidly by the color change of the substrate for DNAzyme. Experimental results showed that 500 cells can well indicate the cancer, while as control, 250,000 Islet Island Beta cells only show tiny signals, suggesting that the method proposed in this paper has considerable sensitivity and selectivity. Furthermore, since it does not require expensive apparatus, or modification or label of DNA chains, the method we present here is also cost-effective and conveniently operated, implying potential applications in future cancer diagnosis.
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GUILLAUME N, PENTHER D, VAIDA I, GRUSON B, HARRIVEL V, CLAISSE J.F, CAPIOD JC, LEFRERE JJ, DAMAJ G. CD66c expression in B-cell acute lymphoblastic leukemia: strength and weakness. Int J Lab Hematol 2010; 33:92-6. [DOI: 10.1111/j.1751-553x.2010.01254.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hjelle SM, Forthun RB, Haaland I, Reikvam H, Sjøholt G, Bruserud O, Gjertsen BT. Clinical proteomics of myeloid leukemia. Genome Med 2010; 2:41. [PMID: 20587003 PMCID: PMC2905101 DOI: 10.1186/gm162] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Myeloid leukemias are a heterogeneous group of diseases originating from bone marrow myeloid progenitor cells. Patients with myeloid leukemias can achieve long-term survival through targeted therapy, cure after intensive chemotherapy or short-term survival because of highly chemoresistant disease. Therefore, despite the development of advanced molecular diagnostics, there is an unmet need for efficient therapy that reflects the advanced diagnostics. Although the molecular design of therapeutic agents is aimed at interacting with specific proteins identified through molecular diagnostics, the majority of therapeutic agents act on multiple protein targets. Ongoing studies on the leukemic cell proteome will probably identify a large number of new biomarkers, and the prediction of response to therapy through these markers is an interesting avenue for future personalized medicine. Mass spectrometric protein detection is a fundamental technique in clinical proteomics, and selected tools are presented, including stable isotope labeling with amino acids in cell culture (SILAC), isobaric tags for relative and absolute quantification (iTRAQ) and multiple reaction monitoring (MRM), as well as single cell determination. We suggest that protein analysis will play not only a supplementary, but also a prominent role in future molecular diagnostics, and we outline how accurate knowledge of the molecular therapeutic targets can be used to monitor therapy response.
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Affiliation(s)
- Sigrun M Hjelle
- Institute of Medicine, Hematology Section, University of Bergen, Haukeland University Hospital, N-5021 Bergen, Norway.
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Szczepański T, Harrison CJ, van Dongen JJM. Genetic aberrations in paediatric acute leukaemias and implications for management of patients. Lancet Oncol 2010; 11:880-9. [PMID: 20435517 DOI: 10.1016/s1470-2045(09)70369-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The process of malignant transformation in paediatric acute leukaemias is complex, requiring at least two deleterious events resulting in DNA damage. This damage ranges from point-mutations to double-strand DNA breaks leading to various types of chromosomal rearrangements. In this review we summarise the most common genetic aberrations for the three main subtypes of paediatric acute leukaemia: B-cell-precursor acute lymphoblastic leukaemia, T-cell acute lymphoblastic leukaemia and acute myeloid leukaemia. Several genetic aberrations are independent prognostic factors, and are now used in risk stratification for treatment. Molecular pathways activated by genetic aberrations could provide potential molecular targets for novel therapies. Some genetic aberrations represent sensitive targets for molecular detection of minimal residual disease. This provides hope for the development of targeted therapies, effective against leukaemic cells.
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Affiliation(s)
- Tomasz Szczepański
- Department of Pediatric Haematology and Oncology, Medical University of Silesia, Zabrze, Poland.
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Bridgeman JS, Blaylock M, Hawkins RE, Gilham DE. Development of a flow cytometric co-immunoprecipitation technique for the study of multiple protein-protein interactions and its application to T-cell receptor analysis. Cytometry A 2010; 77:338-46. [DOI: 10.1002/cyto.a.20840] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Buldini B, Zangrando A, Michielotto B, Veltroni M, Giarin E, Tosato F, Cazzaniga G, Biondi A, Basso G. Identification of immunophenotypic signatures by clustering analysis in pediatric patients with Philadelphia chromosome-positive acute lymphoblastic leukemia. Am J Hematol 2010; 85:138-41. [PMID: 20095033 DOI: 10.1002/ajh.21595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Raponi S, De Propris MS, Wai H, Intoppa S, Elia L, Diverio D, Vitale A, Foà R, Guarini A. An accurate and rapid flow cytometric diagnosis of BCR-ABL positive acute lymphoblastic leukemia. Haematologica 2009; 94:1767-70. [PMID: 19608682 DOI: 10.3324/haematol.2009.010900] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Tyrosine kinase inhibitors have profoundly modified the treatment and prognosis of chronic myeloid leukemia and Ph(+) acute lymphoblastic leukemia. A rapid and accurate detection of the BCR-ABL fusion protein is paramount today for an optimal management of Ph(+) acute lymphoblastic leukemia. We have utilized a recently described and commercialized immunoassay that identifies qualitatively the presence of the BCR-ABL protein in leukemic cell lysates. The BCR-ABL fusion protein is captured and detected by a cytometric bead assay and analyzed by flow cytometry. The assay was applied to 101 primary patient samples (94 acute leukemias and 7 chronic myeloid leukemia blast crisis) and the results of the immunoassay were concordant with those obtained by conventional molecular techniques. The method proved reliable, reproducible, of simple execution and it was successfully completed within four hours. This flow cytometric immunoassay has important implications for perfecting the management of Ph(+) acute lymphoblastic leukemia patients worldwide.
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Affiliation(s)
- Sara Raponi
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
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