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Abstract
Myelodysplastic syndromes (MDS) are a family of myeloid cancers with diverse genotypes and phenotypes characterized by ineffective haematopoiesis and risk of transformation to acute myeloid leukaemia (AML). Some epidemiological data indicate that MDS incidence is increasing in resource-rich regions but this is controversial. Most MDS cases are caused by randomly acquired somatic mutations. In some patients, the phenotype and/or genotype of MDS overlaps with that of bone marrow failure disorders such as aplastic anaemia, paroxysmal nocturnal haemoglobinuria (PNH) and AML. Prognostic systems, such as the revised International Prognostic Scoring System (IPSS-R), provide reasonably accurate predictions of survival at the population level. Therapeutic goals in individuals with lower-risk MDS include improving quality of life and minimizing erythrocyte and platelet transfusions. Therapeutic goals in people with higher-risk MDS include decreasing the risk of AML transformation and prolonging survival. Haematopoietic cell transplantation (HCT) can cure MDS, yet fewer than 10% of affected individuals receive this treatment. However, how, when and in which patients with HCT for MDS should be performed remains controversial, with some studies suggesting HCT is preferred in some individuals with higher-risk MDS. Advances in the understanding of MDS biology offer the prospect of new therapeutic approaches.
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2
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Gao M, Li S, Wang L, Nie S, Pang H, Lu X, Wang X, Wang M, Guo S, Ma Y, Meng F. Identification of a cryptic submicroscopic deletion using a combination of fluorescence in situ hybridization and array comparative genomic hybridization in a t(3;5)(q25;q35)-positive acute myeloid leukemia patient: A case report and review of the literature. Medicine (Baltimore) 2020; 99:e22789. [PMID: 33120794 PMCID: PMC7581054 DOI: 10.1097/md.0000000000022789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
RATIONALE The advent of high-resolution genome arrays including array comparative genomic hybridization (aCGH) has enabled the detection of cryptic submicroscopic deletions flanking translocation breakpoints in up to 20% of the apparently "balanced" structural chromosomal rearrangements in hematological disorders. However, reports of submicroscopic deletions flanking the breakpoints of t(3;5)(q25;q35) are rare and the clinical significance of submicroscopic deletions in t(3;5) has not been explicitly identified. PATIENT CONCERNS We present a 47-year-old man with acute myeloid leukemia. G-banding analysis identified t(3;5)(q25;q35). DIAGNOSIS Array CGH-based detection initially confirmed only the deletion of chromosome 3. Further characterization using fluorescence in situ hybridization identified a cryptic submicroscopic deletion including 5' MLF1-3' NPM1 flanking the breakpoint on the derivative chromosome 3. INTERVENTIONS The patient started "7+3" induction chemotherapy with cytosine arabinoside and daunorubicin, and subsequently received 2 cycles of high-dose intermittent acronym of cytosine arabinoside or cytarabine. OUTCOMES The patient did not undergo complete remission and died from an infection due to neutropenia. LESSONS Haploinsufficiency of NPM1 or other deleted genes, including SSR3, may be responsible for the phenotype of t(3;5)(q25;q35)-positive myeloid neoplasms with submicroscopic deletions.
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Affiliation(s)
- Man Gao
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Lina Wang
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Shu Nie
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Hui Pang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Xianglan Lu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Xianfu Wang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Mingwei Wang
- Department of Radiotherapy, Public Health School of Jilin University, Changchun City, Jilin, P.R. China
| | - Shirong Guo
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Yuhan Ma
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Fanzheng Meng
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
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3
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Clofarabine Improves Relapse-Free Survival of Acute Myeloid Leukemia in Younger Adults with Micro-Complex Karyotype. Cancers (Basel) 2019; 12:cancers12010088. [PMID: 31905904 PMCID: PMC7017244 DOI: 10.3390/cancers12010088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/26/2019] [Accepted: 12/27/2019] [Indexed: 12/21/2022] Open
Abstract
Acute myeloid leukemia (AML) encompasses heterogeneous entities with dismal outcomes. Intermediate and unfavorable-risk AML represent the most difficult-to-treat entities. We recently reported the benefit of the clofarabine-based consolidation (CLARA) regimen compared to the standard high-dose cytarabine (HDAC) regimen in younger AML patients. Here, we aimed at assessing the clinical significance of single-nucleotide polymorphism (SNP)-array alterations and their interactions with chemotherapy regimens. A SNP-array was successfully performed in 187 out of the 221 intent-to-treat patients (CLARA arm: n = 92 patients, HDAC arm: n = 95 patients). The CLARA regimen did not significantly improve relapse-free survival (RFS) among patients who displayed a complex karyotype when compared to the HDAC regimen (4-year RFS (4y-RFS): 36.4% vs. 18.8%, respectively; p = 0.134). Defining micro-complex karyotypes from at least four SNP-array lesions enabled us to refine and enlarge the subset of adverse patients. In such patients, the CLARA regimen significantly improved RFS compared to the HDAC regimen (4y-RFS: 44.4% vs. 13.8%, respectively; p = 0.004). From our study cohort, 8% of patients displayed TP53 mutations, which were associated with an impaired RFS (4y-RFS: 20.0% vs 43.7%; p = 0.029). In a multivariate analysis, micro-complex karyotypes remained the sole poor prognostic factor in the HDAC arm (hazard ratio (HR) = 2.324 (95% confidence interval (CI) = 1.337–4.041), p = 0.003). The SNP array represents a powerful and reproductive approach to refine adverse AML patients that may benefit from alternative consolidation regimens.
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4
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Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genet 2018; 228-229:197-217. [PMID: 30377088 DOI: 10.1016/j.cancergen.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston TX, USA.
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, Cancer Genetics Laboratory, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Shashi Shetty
- Department of Pathology, UHCMC, University Hospitals and Case Western Reserve University, Cleveland, OH, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emma Huxley
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Xinjie Xu
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Sally Jeffries
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Marilyn L Slovak
- TriCore Reference Laboratories, University of New Mexico, Albuquerque, NM, USA
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, NY, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA.
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5
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Voisset E, Moravcsik E, Stratford EW, Jaye A, Palgrave CJ, Hills RK, Salomoni P, Kogan SC, Solomon E, Grimwade D. Pml nuclear body disruption cooperates in APL pathogenesis and impairs DNA damage repair pathways in mice. Blood 2018; 131:636-648. [PMID: 29191918 PMCID: PMC5805489 DOI: 10.1182/blood-2017-07-794784] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/26/2017] [Indexed: 01/20/2023] Open
Abstract
A hallmark of acute promyelocytic leukemia (APL) is altered nuclear architecture, with disruption of promyelocytic leukemia (PML) nuclear bodies (NBs) mediated by the PML-retinoic acid receptor α (RARα) oncoprotein. To address whether this phenomenon plays a role in disease pathogenesis, we generated a knock-in mouse model with NB disruption mediated by 2 point mutations (C62A/C65A) in the Pml RING domain. Although no leukemias developed in PmlC62A/C65A mice, these transgenic mice also expressing RARα linked to a dimerization domain (p50-RARα model) exhibited a doubling in the rate of leukemia, with a reduced latency period. Additionally, we found that response to targeted therapy with all-trans retinoic acid in vivo was dependent on NB integrity. PML-RARα is recognized to be insufficient for development of APL, requiring acquisition of cooperating mutations. We therefore investigated whether NB disruption might be mutagenic. Compared with wild-type cells, primary PmlC62A/C65A cells exhibited increased sister-chromatid exchange and chromosome abnormalities. Moreover, functional assays showed impaired homologous recombination (HR) and nonhomologous end-joining (NHEJ) repair pathways, with defective localization of Brca1 and Rad51 to sites of DNA damage. These data directly demonstrate that Pml NBs are critical for DNA damage responses, and suggest that Pml NB disruption is a central contributor to APL pathogenesis.
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MESH Headings
- Animals
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- DNA Damage/genetics
- DNA End-Joining Repair/genetics
- DNA Repair/genetics
- Intranuclear Inclusion Bodies/genetics
- Intranuclear Inclusion Bodies/metabolism
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Mice
- Mice, Transgenic
- Mutagenesis/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promyelocytic Leukemia Protein/genetics
- Promyelocytic Leukemia Protein/physiology
- Signal Transduction/genetics
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Affiliation(s)
- Edwige Voisset
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Eva Moravcsik
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Eva W Stratford
- Department of Tumor Biology, The Norwegian Radium Hospital/Oslo University Hospital, Oslo, Norway
| | - Amie Jaye
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | | | - Robert K Hills
- Centre for Trials Research, College of Biomedical & Life Sciences, Cardiff University, Cardiff, United Kingdom
| | | | - Scott C Kogan
- Helen Diller Family Comprehensive Cancer Center and
- Department of Laboratory Medicine, University of California, San Francisco, CA
| | - Ellen Solomon
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Grimwade
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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6
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Song Q, Peng M, Chu Y, Huang S. Techniques for detecting chromosomal aberrations in myelodysplastic syndromes. Oncotarget 2017; 8:62716-62729. [PMID: 28977983 PMCID: PMC5617543 DOI: 10.18632/oncotarget.17698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/19/2017] [Indexed: 11/25/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic diseases. Chromosomal aberrations are important for the initiation, development, and progression of MDS. Detection of chromosomal abnormalities in MDS is important for categorization, risk stratification, therapeutic selection, and prognosis evaluation of the disease. Recent progress of multiple techniques has brought powerful molecular cytogenetic information to reveal copy number variation, uniparental disomy, and complex chromosomal aberrations in MDS. In this review, we will introduce some common chromosomal aberrations in MDS and their clinical significance. Then we will explain the application, advantages, and limitations of different techniques for detecting chromosomal abnormalities in MDS. The information in this review may be helpful for clinicians to select appropriate methods in patient-related decision making.
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Affiliation(s)
- Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Peng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shiang Huang
- Molecular department, Kindstar Global, Wuhan, China
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7
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Mohanty P, Korgaonkar S, Shanmukhaiah C, Ghosh K, Vundinti BR. Cytogenetic abnormalities and genomic copy number variations in EPO (7q22) and SEC-61(7p11) genes in primary myelodysplastic syndromes. Blood Cells Mol Dis 2016; 59:52-7. [PMID: 27282568 DOI: 10.1016/j.bcmd.2016.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/11/2016] [Indexed: 10/21/2022]
Abstract
Myelodysplastic syndromes (MDSs) are heterogeneous clonal haematopoeitic stem cell disorders characterized by ineffective haematopoeisis, cytopenias and risk of progression to AML. We studied 150 MDS patients for cytogenetic aberrations and 60 patients with normal karyotype and 40 patients harboring cytogenetic abnormalities for copy number variations (CNVs). Cytogenetic abnormalities were detected in 46% of patients with a majority of patients harboring abnormalities of chromosome 7 and del (20q) at frequencies of 16% and 12% respectively. We explored the potential of quantitative multiplex PCR assay of short fluorescent fragments (QMPSF) to identify CNVs and correlated the findings with cytogenetic data and disease prognosis. CNVs (n=31) were detected in 28.3% of karyotypically normal and 23% patients with abnormal karyotype. Genetic losses or deletions (n=26) were more frequent than duplications (n=5). EPO (7q22) and SEC-61(7p11) emerged as new candidate genes susceptible to genetic losses with 57.7% deletions identified in regions on chromosome 7. The CNVs correlated with International Prognostic Scoring System (IPSS) intermediate disease risk group. Our integrative cytogenetic and copy number variation study suggests that abnormalities of chromosome 7 are predominant in Indian population and that they may play a secondary role in disease progression and should be evaluated further for asserting their clinical significance and influence on disease prognosis.
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Affiliation(s)
- Purvi Mohanty
- Department of Cytogenetics, National Institute of Immunohaematology, 13th Floor, New Multistoried Building, KEM Hospital Campus, Parel, Mumbai 400012, India
| | - Seema Korgaonkar
- Department of Cytogenetics, National Institute of Immunohaematology, 13th Floor, New Multistoried Building, KEM Hospital Campus, Parel, Mumbai 400012, India
| | - Chandrakala Shanmukhaiah
- Department of Haematology, 10th Floor, New Multistoried Building, KEM Hospital, Parel, Mumbai 400012, India
| | - Kanjaksha Ghosh
- Department of Cytogenetics, National Institute of Immunohaematology, 13th Floor, New Multistoried Building, KEM Hospital Campus, Parel, Mumbai 400012, India
| | - Babu Rao Vundinti
- Department of Cytogenetics, National Institute of Immunohaematology, 13th Floor, New Multistoried Building, KEM Hospital Campus, Parel, Mumbai 400012, India.
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8
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Jiang X, Hu C, Arnovitz S, Bugno J, Yu M, Zuo Z, Chen P, Huang H, Ulrich B, Gurbuxani S, Weng H, Strong J, Wang Y, Li Y, Salat J, Li S, Elkahloun AG, Yang Y, Neilly MB, Larson RA, Le Beau MM, Herold T, Bohlander SK, Liu PP, Zhang J, Li Z, He C, Jin J, Hong S, Chen J. miR-22 has a potent anti-tumour role with therapeutic potential in acute myeloid leukaemia. Nat Commun 2016; 7:11452. [PMID: 27116251 PMCID: PMC5477496 DOI: 10.1038/ncomms11452] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/23/2016] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs are subject to precise regulation and have key roles in tumorigenesis. In contrast to the oncogenic role of miR-22 reported in myelodysplastic syndrome (MDS) and breast cancer, here we show that miR-22 is an essential anti-tumour gatekeeper in de novo acute myeloid leukaemia (AML) where it is significantly downregulated. Forced expression of miR-22 significantly suppresses leukaemic cell viability and growth in vitro, and substantially inhibits leukaemia development and maintenance in vivo. Mechanistically, miR-22 targets multiple oncogenes, including CRTC1, FLT3 and MYCBP, and thus represses the CREB and MYC pathways. The downregulation of miR-22 in AML is caused by TET1/GFI1/EZH2/SIN3A-mediated epigenetic repression and/or DNA copy-number loss. Furthermore, nanoparticles carrying miR-22 oligos significantly inhibit leukaemia progression in vivo. Together, our study uncovers a TET1/GFI1/EZH2/SIN3A/miR-22/CREB-MYC signalling circuit and thereby provides insights into epigenetic/genetic mechanisms underlying the pathogenesis of AML, and also highlights the clinical potential of miR-22-based AML therapy.
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Affiliation(s)
- Xi Jiang
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45219, USA.,Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Chao Hu
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45219, USA.,Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.,Department of Hematology, The First Affiliated Hospital Zhejiang University, Hangzhou, 310003 Zhejiang, China
| | - Stephen Arnovitz
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Jason Bugno
- Department of Biopharmaceutical Sciences College of Pharmacy, The University of Illinois, Chicago, Illinois 60612, USA
| | - Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637, USA
| | - Zhixiang Zuo
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45219, USA.,Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060 Guangzhou, China
| | - Ping Chen
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Hao Huang
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Bryan Ulrich
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Sandeep Gurbuxani
- Department of Pathology, University of Chicago, Chicago, Illinois 60637, USA
| | - Hengyou Weng
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45219, USA.,Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Jennifer Strong
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45219, USA
| | - Yungui Wang
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45219, USA.,Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.,Department of Hematology, The First Affiliated Hospital Zhejiang University, Hangzhou, 310003 Zhejiang, China
| | - Yuanyuan Li
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Justin Salat
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Shenglai Li
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Abdel G Elkahloun
- Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
| | - Yang Yang
- Department of Biopharmaceutical Sciences College of Pharmacy, The University of Illinois, Chicago, Illinois 60612, USA
| | - Mary Beth Neilly
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Richard A Larson
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Michelle M Le Beau
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Tobias Herold
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1142, New Zealand
| | - Paul P Liu
- Division of Intramural Research, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
| | - Jiwang Zhang
- Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, Illinois 60153, USA
| | - Zejuan Li
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.,Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637, USA
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital Zhejiang University, Hangzhou, 310003 Zhejiang, China
| | - Seungpyo Hong
- Department of Biopharmaceutical Sciences College of Pharmacy, The University of Illinois, Chicago, Illinois 60612, USA.,Integrated Science and Engineering Division, Underwood International College, Yonsei University, Incheon 406-840, Korea
| | - Jianjun Chen
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45219, USA.,Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
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9
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Hussaini M. Biomarkers in Hematological Malignancies: A Review of Molecular Testing in Hematopathology. Cancer Control 2016; 22:158-66. [PMID: 26068760 DOI: 10.1177/107327481502200206] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Molecular interrogation of genetic information has transformed our understanding of disease and is now routinely integrated into the workup and monitoring of hematological malignancies. In this article, a brief but comprehensive review is presented of state-of-the-art testing in hematological disease. METHODS The primary medical literature and standard textbooks in the field were queried and reviewed to assess current practices and trends for molecular testing in hematopathology by disease. RESULTS Pertinent materials were summarized under appropriate disease categories. CONCLUSION Molecular testing is well entrenched in the diagnostic and therapeutic pathways for hematological malignancies, with rapid growth and insights emerging following the integration of next-generation sequencing into the clinical workflow.
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Affiliation(s)
- Mohammad Hussaini
- Department of Hematopathology and Laboratory Medicine, Moffitt Cancer Center, Tampa, FL 33612, USA.
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10
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Mäbert K, Cojoc M, Peitzsch C, Kurth I, Souchelnytskyi S, Dubrovska A. Cancer biomarker discovery: current status and future perspectives. Int J Radiat Biol 2014; 90:659-77. [PMID: 24524284 DOI: 10.3109/09553002.2014.892229] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
PURPOSE Cancer is a multigene disease which arises as a result of mutational and epigenetic changes coupled with activation of complex signaling networks. The use of biomarkers for early cancer detection, staging and individualization of therapy might improve patient care. A few fundamental issues such as tumor heterogeneity, a highly dynamic nature of the intrinsic and extrinsic determinants of radio- and chemoresistance, along with the plasticity and diversity of cancer stem cells (CSC) make biomarker development a challenging task. In this review we outline the preclinical strategies of cancer biomarker discovery including genomic, proteomic, metabolomic and microRNomic profiling, comparative genome hybridization (CGH), single nucleotide polymorphism (SNP) analysis, high throughput screening (HTS) and next generation sequencing (NGS). Other promising approaches such as assessment of circulating tumor cells (CTC), analysis of CSC-specific markers and cell-free circulating tumor DNA (ctDNA) are also discussed. CONCLUSIONS The emergence of powerful proteomic and genomic technologies in conjunction with advanced bioinformatic tools allows the simultaneous analysis of thousands of biological molecules. These techniques yield the discovery of new tumor signatures, which are sensitive and specific enough for early cancer detection, for monitoring disease progression and for proper treatment selection, paving the way to individualized cancer treatment.
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Affiliation(s)
- Katrin Mäbert
- OncoRay-National Center for Radiation Research in Oncology, Medical Faculty Dresden Carl Gustav Carus , TU Dresden , Germany
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11
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De Braekeleer E, Douet-Guilbert N, De Braekeleer M. Genetic diagnosis in malignant hemopathies: from cytogenetics to next-generation sequencing. Expert Rev Mol Diagn 2014; 14:127-9. [PMID: 24437978 DOI: 10.1586/14737159.2014.872563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the first specific chromosomal abnormality was identified in leukemia more than 50 years ago, technology has much evolved, now allowing the deciphering of cancer genomes in ever-greater detail. However, much has still to be learned as we have not yet completely dissected all the genomic aberrations driving the genesis and the evolution of malignant hemopathies. The first techniques that have been developed allowed 'gross' chromosomal abnormalities to be identified. They include conventional and molecular cytogenetics and microarray-based techniques. However, these techniques can only reveal part of the problem, as genes can be altered in a number of ways (mutations, methylation and so on). This led to the development of what is now known as next-generation sequencing (NGS). Each method has advantages and limits. At present, no single method can decipher all the mechanisms involved in leukemogenesis. Therefore, in our view, it is unlikely that a particular technique will become the 'gold standard'.
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Affiliation(s)
- Etienne De Braekeleer
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) & Heidelberg Institute for Stem Cell Technology and Experimental Medicine GmbH (HI-STEM), Heidelberg, Germany
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Ozer HG, Usubalieva A, Dorrance A, Yilmaz AS, Caligiuri M, Marcucci G, Huang K. Identification of medium-sized copy number alterations in whole-genome sequencing. Cancer Inform 2014; 13:105-11. [PMID: 25788829 PMCID: PMC4356486 DOI: 10.4137/cin.s14023] [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: 06/04/2014] [Revised: 12/29/2014] [Accepted: 01/04/2015] [Indexed: 11/05/2022] Open
Abstract
The genome-wide discoveries such as detection of copy number alterations (CNA) from high-throughput whole-genome sequencing data enabled new developments in personalized medicine. The CNAs have been reported to be associated with various diseases and cancers including acute myeloid leukemia. However, there are multiple challenges to the use of current CNA detection tools that lead to high false-positive rates and thus impede widespread use of such tools in cancer research. In this paper, we discuss these issues and propose possible solutions. First, since the entire genome cannot be mapped due to some regions lacking sequence uniqueness, current methods cannot be appropriately adjusted to handle these regions in the analyses. Thus, detection of medium-sized CNAs is also being directly affected by these mappability problems. The requirement for matching control samples is also an important limitation because acquiring matching controls might not be possible or might not be cost efficient. Here we present an approach that addresses these issues and detects medium-sized CNAs in cancer genomes by (1) masking unmappable regions during the initial CNA detection phase, (2) using pool of a few normal samples as control, and (3) employing median filtering to adjust CNA ratios to its surrounding coverage and eliminate false positives.
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Affiliation(s)
- Hatice Gulcin Ozer
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Aisulu Usubalieva
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Adrienne Dorrance
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, OH, USA
| | - Ayse Selen Yilmaz
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Michael Caligiuri
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, OH, USA
| | - Guido Marcucci
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, OH, USA
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
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Abstract
Higher-risk myelodysplastic syndromes (MDS) are defined by patients who fall into higher-risk group categories in the original or revised International Prognostic Scoring System. Survival for these patients is dismal, and treatment should be initiated rapidly. Standard therapies include the hypomethylating agents azacitidine and decitabine, which should be administered for a minimum of 6 cycles, and continued for as long as a patient is responding. Once a drug fails in one of these patients, further treatment options are limited, median survival is <6 months, and consideration should be given to clinical trials. Higher-risk eligible patients should be offered consultation to discuss hematopoietic stem cell transplantation close to the time of diagnosis, depending on patient goals of therapy, with consideration given to proceeding to transplantation soon after an optimal donor is located. In the interim period before transplantation, hypomethylating agent therapy, induction chemotherapy, or enrollment in a clinical trial should be considered to prevent disease progression, although the optimal pretransplantation therapy is unknown.
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Lukackova R, Gerykova Bujalkova M, Majerova L, Mladosievicova B. Molecular genetic methods in the diagnosis of myelodysplastic syndromes. A review. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2013; 158:339-45. [PMID: 24263214 DOI: 10.5507/bp.2013.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/06/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) represent a heterogeneous group of premalignant hematologic disorders characterized by ineffective hematopoiesis, peripheral blood cytopenias and increased risk of progression to acute leukemia. Cytogenetic analysis still plays a central role in the diagnosis of MDS, as clonal chromosomal abnormalities are observed in 30-50% of MDS patients. Despite their technical limitations, standard karyotyping and fluorescence in situ hybridization (FISH) are routinely used for identifying recurrent chromosomal rearrangements. However, using this approach means that submicroscopic and not targeted chromosomal aberrations, as well as somatic mutations and epigenetic changes remain largely undetected. METHODS AND RESULTS Introduction of methods for the analysis of copy-number variations (CNV), including array-based technologies and Multiplex ligation-dependent probe amplification (MLPA) has provided novel insights into the molecular pathogenesis of MDS and considerably extended possibilities for genetic laboratory testing. Several novel molecular markers have been discovered and used for diagnosis and prognostic evaluation of patients with MDS. At present, mutational analysis is not routinely performed, as the clinical significance of somatic mutations in MDS has only begun to emerge. However, recently introduced Next-generation sequencing (NGS) technologies could help to elucidate the relationship between chromosomal and molecular aberrations in MDS and lead to further improvement in its diagnosis. CONCLUSION This review focuses on the advantages, limitations, clinical applications and future perspectives of three molecular methods (array-based analysis, MLPA and NGS) currently used in genetic testing and/ or translational research of MDS. In conclusion, a brief summary for clinicians from the routine diagnostic point of view is given.
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Affiliation(s)
- Renata Lukackova
- Department of Clinical Genetics, Medirex a.s., Bratislava, Slovak Republic
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Otrock ZK, Tiu RV, Maciejewski JP, Sekeres MA. The need for additional genetic markers for myelodysplastic syndrome stratification: what does the future hold for prognostication? Expert Rev Hematol 2013; 6:59-68. [PMID: 23373781 DOI: 10.1586/ehm.12.67] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Myelodysplastic syndromes (MDS) constitute a heterogeneous group of clonal hematopoietic disorders. Metaphase cytogenetics has been the gold standard for genetic testing in MDS, but it detects clonal cytogenetic abnormalities in only 50% of cases. New karyotyping tests include FISH, array-based comparative genomic hybridization and single-nucleotide polymorphism arrays. These techniques have increased the detected genetic abnormalities in MDS, many of which confer prognostic significance to overall and leukemia-free survival. This has eventually increased our understanding of MDS genetics. With the help of new technologies, we anticipate that the existing prognostic scoring systems will incorporate mutational data into their parameters. This review discusses the progress in MDS diagnosis through the use of array-based technologies. The authors also discuss the recently investigated genetic mutations in MDS and revisit the MDS classification and prognostic scoring systems.
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Affiliation(s)
- Zaher K Otrock
- Leukemia Program, Cleveland Clinic Taussig Cancer Institute, OH 44195, USA
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