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Salaverria I, Siebert R, Mrózek K. Appraisal of current technologies for the study of genetic alterations in hematologic malignancies with a focus on chromosome analysis and structural variants. MED GENET-BERLIN 2024; 36:13-20. [PMID: 38835966 PMCID: PMC11006330 DOI: 10.1515/medgen-2024-2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
During the last five decades, chromosome analysis identified recurring translocations and inversions in leukemias and lymphomas, which led to cloning of genes at the breakpoints that contribute to oncogenesis. Such molecular cytogenetic methods as fluorescence in situ hybridization (FISH), copy number (CN) arrays or optical genome mapping (OGM) have augmented standard chromosome analysis. The use of both cytogenetic and molecular methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and next generation sequencing (NGS), including whole-genome sequencing (WGS), discloses alterations that not only delineate separate WHO disease entities but also constitute independent prognostic factors, whose use in the clinic improves management of patients with hematologic neoplasms.
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Affiliation(s)
- Itziar Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer Barcelona Spain
| | - Reiner Siebert
- Ulm University Medical Center, Ulm University Institute of Human Genetics Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research Columbus USA
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2
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Boyd RJ, Murry JB, Morsberger LA, Klausner M, Chen S, Gocke CD, McCallion AS, Zou YS. Ring Chromosomes in Hematological Malignancies Are Associated with TP53 Gene Mutations and Characteristic Copy Number Variants. Cancers (Basel) 2023; 15:5439. [PMID: 38001699 PMCID: PMC10670249 DOI: 10.3390/cancers15225439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/28/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Ring chromosomes (RC) are present in <10% of patients with hematological malignancies and are associated with poor prognosis. Until now, only small cohorts of patients with hematological neoplasms and concomitant RCs have been cytogenetically characterized. Here, we performed a conventional chromosome analysis on metaphase spreads from >13,000 patients diagnosed with hematological malignancies at the Johns Hopkins University Hospital and identified 98 patients with RCs-90 with myeloid malignancies and 8 with lymphoid malignancies. We also performed a targeted Next-Generation Sequencing (NGS) assay, using a panel of 642 cancer genes, to identify whether these patients harbor relevant pathogenic variants. Cytogenetic analyses revealed that RCs and marker chromosomes of unknown origin are concurrently present in most patients by karyotyping, and 93% of patients with NGS data have complex karyotypes. A total of 72% of these individuals have pathogenic mutations in TP53, most of whom also possess cytogenetic abnormalities resulting in the loss of 17p, including the loss of TP53. All patients with a detected RC and without complex karyotypes also lack TP53 mutations but have pathogenic mutations in TET2. Further, 70% of RCs that map to a known chromosome are detected in individuals without TP53 mutations. Our data suggest that RCs in hematological malignancies may arise through different mechanisms, but ultimately promote widespread chromosomal instability.
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Affiliation(s)
- Rachel J. Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.J.B.); (A.S.M.)
| | - Jaclyn B. Murry
- Johns Hopkins Genomics, Baltimore, MD 21205, USA; (J.B.M.); (L.A.M.); (M.K.); (S.C.); (C.D.G.)
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cytogenetics Laboratory, Johns Hopkins Medicine, Baltimore, MD 21205, USA
| | - Laura A. Morsberger
- Johns Hopkins Genomics, Baltimore, MD 21205, USA; (J.B.M.); (L.A.M.); (M.K.); (S.C.); (C.D.G.)
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cytogenetics Laboratory, Johns Hopkins Medicine, Baltimore, MD 21205, USA
| | - Melanie Klausner
- Johns Hopkins Genomics, Baltimore, MD 21205, USA; (J.B.M.); (L.A.M.); (M.K.); (S.C.); (C.D.G.)
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cytogenetics Laboratory, Johns Hopkins Medicine, Baltimore, MD 21205, USA
| | - Suping Chen
- Johns Hopkins Genomics, Baltimore, MD 21205, USA; (J.B.M.); (L.A.M.); (M.K.); (S.C.); (C.D.G.)
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christopher D. Gocke
- Johns Hopkins Genomics, Baltimore, MD 21205, USA; (J.B.M.); (L.A.M.); (M.K.); (S.C.); (C.D.G.)
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew S. McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.J.B.); (A.S.M.)
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ying S. Zou
- Johns Hopkins Genomics, Baltimore, MD 21205, USA; (J.B.M.); (L.A.M.); (M.K.); (S.C.); (C.D.G.)
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cytogenetics Laboratory, Johns Hopkins Medicine, Baltimore, MD 21205, USA
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Srivastava VM, Nair SC, Sappani M, Manipadam MT, Kulkarni UP, Devasia AJ, Fouzia NA, Korula A, Lakshmi KM, Abraham A, Srivastava A. Cytogenetic profile of 1791 adult acute myeloid leukemia in India. Mol Cytogenet 2023; 16:24. [PMID: 37716945 PMCID: PMC10504794 DOI: 10.1186/s13039-023-00653-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Cytogenetic analysis continues to have an important role in the management of acute myeloid leukemia (AML) because it is essential for prognostication. It is also necessary to diagnose specific categories of AML and to determine the most effective form of treatment. Reports from South Asia are few because the availability of cytogenetic services is relatively limited. METHODS We performed a retrospective analysis of the cytogenetic findings in adults with AML seen consecutively in a single centre in India. The results were categorised according to the 2022 World Health Organisation (WHO), International Consensus Classification (ICC) and European LeukemiaNet (ELN) classifications. RESULTS There were 1791 patients aged 18-85 years (median age 42, 1086 males). Normal karyotypes were seen in 646 (36%) patients. The 1145 (64%) abnormal karyotypes comprised 585 (32.7%) with recurrent genetic abnormalities (RGA), 403 (22.5%) with myelodysplasia-related cytogenetic abnormalities (MRC), and 157 (8.8%) with other abnormalities. There were 567 (31.7%) patients with solitary abnormalities and 299 (16.7%) with two abnormalities. Among the 279 (15.6%) patients with ≥ 3 abnormalities, 200 (11.2%) had complex karyotypes (CK) as per the WHO/ICC and 184 (10.3%), as per the ELN definition. There were 158 (8.8%) monosomal karyotypes (MK). Patients with normal karyotypes had a higher median age (45 years) than those with abnormal karyotypes (40 years, p < 0.001), and those with ≥ 3 abnormalities (43 years), than those with fewer abnormalities (39 years, p = 0.005). Patients with CK (WHO/ICC) and monosomal karyotypes had a median age of 48 years. Those with RGA had a lower median age (35 years, p < 0.001) than MRC (46 years) or other abnormalities (44 years). The t(15;17) was the most common abnormality (16.7%),followed by trisomy 8 (11.6%), monosomy 7/del 7q (9.3%), t(8;21) (7.2%), monosomy 5/del 5q (6.7%) and monosomy 17/del 17p (5.2%). CONCLUSION Our findings confirm the lower age profile of AML in India and show similarities and differences with respect to the frequencies of individual abnormalities compared to the literature. The frequencies of the t(15;17), trisomy 8 and the high-risk abnormalities monosomy 7 and monosomy 5/del 5q were higher, and that of the inv(16), lower than in most reports.
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Affiliation(s)
- Vivi M Srivastava
- Department of Cytogenetics, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
| | - Sukesh Chandran Nair
- Department of Transfusion Medicine and Immunohaematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
| | - Marimuthu Sappani
- Department of Biostatistics, Christian Medical College, Vellore, Tamil Nadu, 632002, India
| | - Marie-Therese Manipadam
- Department of General Pathology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
- Department of Cellular Pathology, Maidstone Hospital, Hermitage Lane, Maidstone, ME169QQ, UK
| | - Uday P Kulkarni
- Department of Clinical Haematology, Christian Medical College, Vellore, 632501, Tamil Nadu, India
| | - Anup J Devasia
- Department of Clinical Haematology, Christian Medical College, Vellore, 632501, Tamil Nadu, India
- On leave at Princess Margaret Cancer Centre, Toronto, Canada
| | - N A Fouzia
- Department of Clinical Haematology, Christian Medical College, Vellore, 632501, Tamil Nadu, India
| | - Anu Korula
- Department of Clinical Haematology, Christian Medical College, Vellore, 632501, Tamil Nadu, India
- NCCCR, Doha, Qatar
| | - Kavitha M Lakshmi
- Department of Clinical Haematology, Christian Medical College, Vellore, 632501, Tamil Nadu, India
| | - Aby Abraham
- Department of Clinical Haematology, Christian Medical College, Vellore, 632501, Tamil Nadu, India
| | - Alok Srivastava
- Department of Clinical Haematology, Christian Medical College, Vellore, 632501, Tamil Nadu, India
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Schandl CA, Mazzoni S, Znoyko I, Nahhas GJ, Chung D, Ding Y, Hess B, Wolff DJ. Novel high-risk acute myeloid leukemia subgroup with ERG amplification and Biallelic loss of TP53. Cancer Genet 2023; 272-273:23-28. [PMID: 36657266 DOI: 10.1016/j.cancergen.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
ETS-related gene (ERG) amplification, observed in 4-6% of acute myeloid leukemia (AML), is associated with unfavorable prognosis. To determine coincident effects of additional genomic abnormalities in AML with ERG amplification (ERGamp), we examined 11 ERGamp cases of 205 newly diagnosed AML using chromosomal microarray analysis and next generation sequencing. ERGamp cases demonstrated a distinct pattern of high genetic complexity: loss of 5q, chromothripsis and TP53 loss of function variants. Remarkably, allelic TP53 loss or loss of heterozygosity (LOH) co-occurring with TP53 inactivating mutation dramatically effected ERGamp tumor patient outcome. In the presence of homozygous TP53 loss of function, ERGamp patients demonstrated no response to induction chemotherapy with median overall survival (OS) of 3.8 months (N = 9). Two patients with heterozygous loss of TP53 function underwent alloSCT without evidence of relapse at one year. Similarly, a validation TCGA cohort, 6 of the 8 ERGamp cases with TP53 loss of function demonstrated median OS of 2.5 months. This suggests that with TP53 mutant ERGamp AML, successive loss of the second TP53 allele, typically by 17p deletion or LOH identifies a specific high-risk subtype of AML patients who are resistant to standard induction chemotherapy and need novel approaches to avert the very poor prognosis.
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Affiliation(s)
- Cynthia A Schandl
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Sandra Mazzoni
- Departmant of Hematology and Oncology, Cleveland Clinic Taussig Cancer Center, Cleveland, OH, USA.
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Georges J Nahhas
- Department of Public Health-Division of Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Dongjun Chung
- Department of Public Health-Division of Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Yanna Ding
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Brian Hess
- Department of Hematology and Oncology, Medical University of South Carolina Hollings Cancer Center, Charleston, SC, USA
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
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Wang J, Chen Z, He F, Lee T, Cai W, Chen W, Miao N, Zeng Z, Hussain G, Yang Q, Guo Q, Sun T. Single-Cell Transcriptomics of Cultured Amniotic Fluid Cells Reveals Complex Gene Expression Alterations in Human Fetuses With Trisomy 18. Front Cell Dev Biol 2022; 10:825345. [PMID: 35392164 PMCID: PMC8980718 DOI: 10.3389/fcell.2022.825345] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
Trisomy 18, commonly known as Edwards syndrome, is the second most common autosomal trisomy among live born neonates. Multiple tissues including cardiac, abdominal, and nervous systems are affected by an extra chromosome 18. To delineate the complexity of anomalies of trisomy 18, we analyzed cultured amniotic fluid cells from two euploid and three trisomy 18 samples using single-cell transcriptomics. We identified 6 cell groups, which function in development of major tissues such as kidney, vasculature and smooth muscle, and display significant alterations in gene expression as detected by single-cell RNA-sequencing. Moreover, we demonstrated significant gene expression changes in previously proposed trisomy 18 critical regions, and identified three new regions such as 18p11.32, 18q11 and 18q21.32, which are likely associated with trisomy 18 phenotypes. Our results indicate complexity of trisomy 18 at the gene expression level and reveal genetic reasoning of diverse phenotypes in trisomy 18 patients.
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Affiliation(s)
- Jing Wang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
- College of Materials Science and Engineering, Huaqiao University, Xiamen, China
| | - Zixi Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco- Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Fei He
- Genergy Bio-Technology (Shanghai) Co., Ltd, Shanghai, China
| | - Trevor Lee
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, New York, NY, United States
| | - Wenjie Cai
- Department of Radiation Oncology, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Wanhua Chen
- Department of Clinical Laboratory, First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - Zhiwei Zeng
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - Ghulam Hussain
- Neurochemical Biology and Genetics Laboratory, Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Qingwei Yang
- Department of Neurology, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Qiwei Guo
- United Diagnostic and Research Center for Clinical Genetics, School of Medicine and School of Public Health, Women and Children’s Hospital, Xiamen University, Xiamen, China
- *Correspondence: Qiwei Guo, ; Tao Sun,
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
- *Correspondence: Qiwei Guo, ; Tao Sun,
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Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML. Blood Adv 2021; 5:1003-1016. [PMID: 33591326 DOI: 10.1182/bloodadvances.2020002517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022] Open
Abstract
Although copy number alterations (CNAs) and translocations constitute the backbone of the diagnosis and prognostication of acute myeloid leukemia (AML), techniques used for their assessment in routine diagnostics have not been reconsidered for decades. We used a combination of 2 next-generation sequencing-based techniques to challenge the currently recommended conventional cytogenetic analysis (CCA), comparing the approaches in a series of 281 intensively treated patients with AML. Shallow whole-genome sequencing (sWGS) outperformed CCA in detecting European Leukemia Net (ELN)-defining CNAs and showed that CCA overestimated monosomies and suboptimally reported karyotype complexity. Still, the concordance between CCA and sWGS for all ELN CNA-related criteria was 94%. Moreover, using in silico dilution, we showed that 1 million reads per patient would be enough to accurately assess ELN-defining CNAs. Total genomic loss, defined as a total loss ≥200 Mb by sWGS, was found to be a better marker for genetic complexity and poor prognosis compared with the CCA-based definition of complex karyotype. For fusion detection, the concordance between CCA and whole-transcriptome sequencing (WTS) was 99%. WTS had better sensitivity in identifying inv(16) and KMT2A rearrangements while showing limitations in detecting lowly expressed PML-RARA fusions. Ligation-dependent reverse transcription polymerase chain reaction was used for validation and was shown to be a fast and reliable method for fusion detection. We conclude that a next-generation sequencing-based approach can replace conventional CCA for karyotyping, provided that efforts are made to cover lowly expressed fusion transcripts.
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Jain H, Shetty D, Roy Moulik N, Narula G, Subramanian PG, Banavali S. A novel case of intrachromosomal amplification and insertion of RUNX1 on derivative chromosome 2 in pediatric AML. Cancer Genet 2021; 254-255:65-69. [PMID: 33647813 DOI: 10.1016/j.cancergen.2021.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/15/2021] [Accepted: 02/08/2021] [Indexed: 11/18/2022]
Abstract
Intrachromosomal amplification of RUNX1 gene on chromosome 21 (iAMP21) is a rare occurrence in acute myeloid leukemia (AML). Herein, we describe a case of AML with amplification of RUNX1 and its insertion on chromosome 2 detected by conventional karyotyping and confirmed by metaphase FISH. A six-year-old female was diagnosed as acute myeloid leukemia with monocytic differentiation. The patient's bone marrow revealed 74% blasts which were MPO negative. Conventional karyotyping revealed a complex karyotype, with rearrangements in chromosomes 1, 2, 7, 8 and hsr(21). FISH on interphase cells with LSI RUNX1-RUNX1T1 dual colour dual fusion translocation probe showed 6-7 copies of RUNX1 signal. Metaphase FISH with LSI RUNX1-RUNX1T1 probe confirmed amplification of RUNX1 and insertion of amplified RUNX1 sequences on long arm of chromosome 2. Induction chemotherapy was initiated, however, the patient died within one month of diagnosis suggesting poor outcome associated with this novel finding. Insertion of amplified RUNX1 on another chromosome has not yet been reported so far.
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Affiliation(s)
- Hemani Jain
- Cancer Cytogenetics Department, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Sector-22, Kharghar, Navi Mumbai 410210, India.
| | - Dhanlaxmi Shetty
- Cancer Cytogenetics Department, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Sector-22, Kharghar, Navi Mumbai 410210, India.
| | - Nirmalya Roy Moulik
- Department of Pediatric Oncology, Tata Memorial Hospital, Dr. E. Borges Road, Parel. Mumbai 400012, India; Cancer Cytogenetics Department, Room No. 6, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210 India.
| | - Gaurav Narula
- Department of Pediatric Oncology, Tata Memorial Hospital, Dr. E. Borges Road, Parel. Mumbai 400012, India; Cancer Cytogenetics Department, Room No. 6, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210 India.
| | - P G Subramanian
- Hematopathology Department, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210, India; Cancer Cytogenetics Department, Room No. 6, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210 India.
| | - Sripad Banavali
- Department of Pediatric Oncology, Tata Memorial Hospital, Dr. E. Borges Road, Parel. Mumbai 400012, India; Cancer Cytogenetics Department, Room No. 6, CCE building, Advanced Centre for Treatment, Research & Education in Cancer (ACTREC), Tata Memorial Centre, Sector-22, Kharghar, Navi Mumbai 410210 India.
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iAMP21 in acute myeloid leukemia is associated with complex karyotype, TP53 mutation and dismal outcome. Mod Pathol 2020; 33:1389-1397. [PMID: 32034282 DOI: 10.1038/s41379-020-0494-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
Acute myeloid leukemia (AML) with intrachromosomal amplification of chromosome 21 (iAMP21) is rare and has not been well characterized. We report 13 patients, 7 men and 6 women, with a median age of 65 years. Eleven patients presented with AML with myelodysplasia-related changes, and two patients had therapy-related AML. Cytopenias were detected in all patients (11 pancytopenia and two bi-lineage cytopenia). Myelodysplastic changes were observed in all 11 patients with adequate cells to evaluate. Myelofibrosis was present in ten patients. All patients had a complex karyotype, including abnormalities of chromosomes 5, 7, 17, and hsr(21)(q22), and ten patients showed TP53 deletion and/or mutation. Eleven patients received AML-based chemotherapy, one of whom also received hematopoietic stem cell transplant. By the end of the last follow-up, eight patients died with median survival of 3.2 months, four patients were alive with persistent AML, and one was in complete remission. The median overall survival was 6 months for all patients. We conclude that AML with iAMP21 is often associated with cytopenias, myelodysplasia, a complex karyotype, TP53 mutation/deletion, and a poor prognosis despite current therapies.
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Mowery CT, Reyes JM, Cabal-Hierro L, Higby KJ, Karlin KL, Wang JH, Kimmerling RJ, Cejas P, Lim K, Li H, Furusawa T, Long HW, Pellman D, Chapuy B, Bustin M, Manalis SR, Westbrook TF, Lin CY, Lane AA. Trisomy of a Down Syndrome Critical Region Globally Amplifies Transcription via HMGN1 Overexpression. Cell Rep 2019; 25:1898-1911.e5. [PMID: 30428356 PMCID: PMC6321629 DOI: 10.1016/j.celrep.2018.10.061] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 08/21/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute normalization unmasks global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulates transcriptional changes seen with triplication of a Down syndrome critical region on distal chromosome 21, and HMGN1 is necessary for B cell phenotypes in DS models. Absolute exogenous-normalized chromatin immunoprecipitation sequencing (ChIP-Rx) also reveals a global increase in histone H3K27 acetylation caused by HMGN1. Transcriptional amplification downstream of HMGN1 is enriched for stage-specific programs of B cells and B cell acute lymphoblastic leukemia, dependent on the developmental cellular context. These data offer a mechanistic explanation for DS transcriptional patterns and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted. How trisomy 21 contributes to Down syndrome phenotypes, including increased leukemia risk, is not well understood. Mowery et al. use per-cell normalization approaches to reveal global transcriptional amplification in Down syndrome models. HMGN1 overexpression is sufficient to induce these alterations and promotes lineage-associated transcriptional programs, signaling, and B cell progenitor phenotypes.
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Affiliation(s)
- Cody T Mowery
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jaime M Reyes
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lucia Cabal-Hierro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kelly J Higby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kristen L Karlin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Jarey H Wang
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Robert J Kimmerling
- Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hubo Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Takashi Furusawa
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Bjoern Chapuy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Department of Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, USA
| | - Scott R Manalis
- Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas F Westbrook
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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10
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Abubakar SD. Characterization of Chromosomal Abnormalities in Cancer by Spectral Karyotyping. MEDICAL LABORATORY JOURNAL 2019. [DOI: 10.29252/mlj.13.6.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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11
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Nguyen D, Li Y, Safah H, Brown TC. RUNX1 deletion/amplification in therapy-related acute myeloid leukemia: A case report and review of the literature. Cancer Genet 2019; 238:37-43. [DOI: 10.1016/j.cancergen.2019.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/16/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022]
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12
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Mrózek K, Eisfeld AK, Kohlschmidt J, Carroll AJ, Walker CJ, Nicolet D, Blachly JS, Bill M, Papaioannou D, Wang ES, Uy GL, Kolitz JE, Powell BL, Blum W, Stone RM, Byrd JC, Bloomfield CD. Complex karyotype in de novo acute myeloid leukemia: typical and atypical subtypes differ molecularly and clinically. Leukemia 2019; 33:1620-1634. [PMID: 30737482 PMCID: PMC6609457 DOI: 10.1038/s41375-019-0390-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/17/2018] [Accepted: 01/09/2019] [Indexed: 02/04/2023]
Abstract
Complex karyotype (CK) with ≥ 3 abnormalities is detected in 10-12% of patients with acute myeloid leukemia (AML) and associated with poor prognosis. The most common unbalanced abnormalities found in CK result in loss of material from the 5q, 7q, and/or 17p chromosome arms. The presence of 5q, 7q, and/or 17p abnormalities denotes typical CK and their absence denotes atypical CK. Since molecular features of CK-AML are not well characterized, we investigated mutational status of 81 leukemia/cancer-associated genes in 160 clinically well-characterized patients. They included 136 patients with ≥ 3 exclusively unbalanced chromosome abnormalities, 96 of whom had a typical CK and 40 atypical CK, and 24 patients with ≥ 1 balanced abnormality in addition to ≥ 2 unbalanced ones. Patients with atypical CK-AML differed from those with typical CK-AML: they carried TP53 mutations less often (P < 0.001) and more often PHF6 (P = 0.008), FLT3-TKD (P = 0.02), MED12 (P = 0.02), and NPM1 (P = 0.02) mutations. They were younger (P = 0.007), had higher WBC (P = 0.001) and percentages of marrow (P < 0.001) and blood (P = 0.006) blasts, higher complete remission rates (P = 0.02), and longer overall survival (P < 0.001), thus indicating that atypical and typical CK-AMLs constitute distinct disease subtypes. We also identified smaller patient subsets within both typical and atypical CK-AML that differed molecularly and clinically.
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Affiliation(s)
- Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
| | | | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | | | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Marius Bill
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Eunice S Wang
- Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Geoffrey L Uy
- Washington University School of Medicine in St. Louis, Siteman Cancer Center, St. Louis, MO, USA
| | - Jonathan E Kolitz
- Monter Cancer Center, Hofstra Northwell School of Medicine, Lake Success, NY, USA
| | - Bayard L Powell
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - William Blum
- Emory University School of Medicine, Atlanta, GA, USA
| | | | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Clara D Bloomfield
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
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13
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Ornellas MHF, Maioli MCP, de Lucena SBSG, Bastos EF, Chaves TS, de Melo KV, Ribeiro-Carvalho MDM, Liehr T, Alves G. Complex karyotype including ring chromosome 11 in a patient with acute myeloid leukemia: case report. SAO PAULO MED J 2018; 136:361-367. [PMID: 28832804 PMCID: PMC9881703 DOI: 10.1590/1516-3180.2016.0252150217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 02/15/2017] [Indexed: 02/02/2023] Open
Abstract
CONTEXT Complex karyotypes in acute myeloid leukemia (AML) are characterized by an overall low response rate with frequent relapses after clinical treatment. CASE REPORT Here, we describe the case of a 61-year-old obese female with clinically diagnosed AML who presented a complex karyotype involving an uncommon abnormality: ring chromosome 11. Immunophenotypic analysis confirmed the diagnosis. Classical and molecular cytogenetic analyses, using GTG banding and FISH (fluorescence in situ hybridization), revealed the presence of complex structural rearrangement involving r(11), add(12)(p13), der(5) and der(13). CONCLUSIONS Molecular cytogenetic analysis is suitable for better identification and characterization of chromosomal rearrangements in AML. Case reports like this, as well as population-based studies, are necessary for understanding the karyotypic changes that occur in humans.
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Affiliation(s)
- Maria Helena Faria Ornellas
- Associate Professor, Pathology Service, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro (RJ), Brazil.
| | | | - Stella Beatriz Sampaio Gonçalves de Lucena
- Associate Professor, Hematology Service, Universidade do Estado do Rio de Janeiro (UERJ), and Postdoctoral Research, Research Coordination, Instituto Nacional de Câncer (INCA), Rio de Janeiro (RJ), Brazil.
| | - Elenice Ferreira Bastos
- Biologist, Hematology Department, Universidade do Estado do Rio de Janeiro (UERJ), and Supervisor, Medical Genetics Department, Instituto Fernandes Figueira (IFF), Rio de Janeiro (RJ), Brazil.
| | - Tatiana Silva Chaves
- Biologist, Hematology Service, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro (RJ), Brazil.
| | - Karina Vieira de Melo
- Medical Sciences Master’s Student, Hematology Service, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro (RJ), Brazil.
| | - Marilza de Moura Ribeiro-Carvalho
- Biologist and Postdoctoral Researcher, Pathology Department, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro (RJ), Brazil.
| | - Thomas Liehr
- Biologist and Head of Molecular Cytogenetics Laboratory, Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Thüringen, Germany.
| | - Gilda Alves
- Biologist and Professor, Universidade do Estado do Rio de Janeiro (UERJ), and Researcher, Research Coordination, Instituto Nacional de Câncer (INCA), Rio de Janeiro (RJ), Brazil.
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14
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Sabatino R, Aquino G, Pinto A, Piris MA, Marra L, Napolitano M, De Chiara A, Franco R. B-cell lymphoblastic lymphoma presenting as solitary temporal mass with amplification of AML1/RUNX1: case report. Hematol Oncol 2017; 35:380-384. [PMID: 28933515 DOI: 10.1002/hon.2269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 09/18/2015] [Accepted: 09/27/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Rocco Sabatino
- Pathology Unit, Istituto Nazionale Tumori " Fondazione 'G. Pascale", Napoli, Italy
| | - Gabriella Aquino
- Pathology Unit, Istituto Nazionale Tumori " Fondazione 'G. Pascale", Napoli, Italy
| | - Antonio Pinto
- Haematology- Oncology and Stem Cell Transplantation Unit, Istituto Nazionale Tumori Fondazione " G. Pascale", Napoli, Italy
| | - Miguel Angel Piris
- Pathology Unit, Hospital Universitario Marques de Valdecilla IDIVAL, Santander, Spain
| | - Laura Marra
- Pathology Unit, Istituto Nazionale Tumori " Fondazione 'G. Pascale", Napoli, Italy
| | - Maria Napolitano
- Immunology- Oncology Unit, Istituto Nazionale Tumori Fondazione " G. Pascale", Napoli, Italy
| | | | - Renato Franco
- Pathology Unit, Istituto Nazionale Tumori " Fondazione 'G. Pascale", Napoli, Italy
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15
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Weber S, Haferlach C, Jeromin S, Nadarajah N, Dicker F, Noël L, Zenger M, Alpermann T, Kern W, Haferlach T, Schnittger S. Gain of chromosome 21 or amplification of chromosome arm 21q is one mechanism for increased ERG expression in acute myeloid leukemia. Genes Chromosomes Cancer 2015; 55:148-57. [PMID: 26542308 DOI: 10.1002/gcc.22321] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/19/2023] Open
Abstract
In acute myeloid leukemia (AML), acquired genomic gains and losses are common and lead to altered expression of genes located within or nearby the affected regions. Increased expression of the ETS-related transcription factor gene ERG has been described in myeloid malignancies with chromosomal rearrangements involving chromosome band 21q22, but also in cytogenetically normal AML, where it is associated with adverse prognosis. In this study, fluorescence in situ hybridization on interphase nuclei disclosed an amplification of the ERG gene (more than six copies) in 33 AML patients with structural rearrangements of 21q22. Array comparative genomic hybridization of these cases disclosed a minimal amplified region at the position 39.6-40.0 Mbp from pter that harbors ERG as the only gene. Analysis by quantitative real-time reverse transcription polymerase chain reaction revealed significantly higher ERG mRNA expression in these patients and in a group of 95 AML patients with complete or partial gain of chromosome 21 (three to six copies) compared with 351 AML patients without gain of chromosome 21. Quantification of ERG DNA copy numbers revealed a strong correlation with ERG mRNA expression. Furthermore, in patients with gain of chromosome 21, higher ERG expression was found to be associated with RUNX1 mutations. Our results suggest that acquired gain of chromosome 21 or amplification of chromosome arm 21q is one mechanism contributing to increased ERG expression in AML.
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Affiliation(s)
| | | | | | | | | | - Louisa Noël
- MLL Munich Leukemia Laboratory, Munich, Germany
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16
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Involvement of deleted chromosome 5 in complex chromosomal aberrations in newly diagnosed myelodysplastic syndromes (MDS) is correlated with extremely adverse prognosis. Leuk Res 2014; 38:537-44. [DOI: 10.1016/j.leukres.2014.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/21/2014] [Accepted: 01/24/2014] [Indexed: 01/25/2023]
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17
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Aref S, Al Khodary T, Zeed TA, El Sadiek A, El Menshawy N, Al Ashery R. The Prognostic Relevance of BAALC and ERG Expression Levels in Cytogenetically Normal Pediatric Acute Myeloid Leukemia. Indian J Hematol Blood Transfus 2014; 31:21-8. [PMID: 25548440 DOI: 10.1007/s12288-014-0395-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 04/16/2014] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED Cytogenetic aberrations are important prognostic factors in acute myeloid leukemia (AML). About 45 % of de novo adult AML and 20 % of pediatric AML lack cytogenetic abnormalities, so identification of predictive molecular markers might improve therapy. Mutation status of FLT3, NPM1 genes and gene expression levels of ERG, BAALC have been postulated as possible prognostic markers in pediatric AML with normal karyotype. Pretreatment blood samples from 47 cytogenetically normal AML patients were analysed for BAALC and ERG expression using real time RT-PCR. The patients were dichotomized at BAALC and ERG mean expression into low and high expression based on the median expression as cutoff. BAALC showed high expression in (24/47; 51.1 %) of patients and ERG high expression was detected in (22/47; 46.6 %). With follow-up for 1 year, patients with high BAALC and high ERG had inferior EFS (P = 0.001, P = 0.017 respectively), overall survival (P = 0.001, 0.08 respectively), and low rates of induction remission (P = 0.001, P = 0.0017 respectively) as compared to those with low expression. Also there was significant positive association between high expression of BAALC; ERG and FLT-ITD mutations (P = 0.016; P = 0.007 respectively). Multivariable analysis confirmed that high BAALC expression is an independent risk factor for EFS [HR for EFS 1.9(1.04-3.46) P = 0.037]; and OS [HR OS 1.55(1.7-3.36) P = 0.03]. IN CONCLUSION Over expression of BAALC could predict adverse clinical outcome and may define important risk factor in cytogenetically normal pediatric AML.
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Affiliation(s)
- Salah Aref
- Hematology Unit, Clinical Pathology Department, Mansoura Faculty of Medicine, Mansoura Cancer Institute, Mansoura, Egypt
| | - Tawfik Al Khodary
- Medical Oncology Unit, Mansoura Faculty of Medicine, Mansoura Cancer Institute, Mansoura, Egypt
| | - Tarek Abou Zeed
- Clinical Hematology Unit, Mansoura Faculty of Medicine, Mansoura Cancer Institute, Mansoura, Egypt
| | - Amre El Sadiek
- Hematology Unit, Clinical Pathology Department, Mansoura Faculty of Medicine, Mansoura Cancer Institute, Mansoura, Egypt
| | - Nadia El Menshawy
- Hematology Unit, Clinical Pathology Department, Mansoura Faculty of Medicine, Mansoura Cancer Institute, Mansoura, Egypt
| | - Rasha Al Ashery
- Pediatric Oncology Unit, Mansoura Faculty of Medicine, Mansoura Cancer Institute, Mansoura, Egypt
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18
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Guo B, Han X, Wu Z, Da W, Zhu H. Spectral karyotyping: an unique technique for the detection of complex genomic rearrangements in leukemia. Transl Pediatr 2014; 3:135-9. [PMID: 26835331 PMCID: PMC4729104 DOI: 10.3978/j.issn.2224-4336.2014.01.02] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Spectral karyotyping (SKY) is a novel cytogenetic technique, has been developed to unambiguously display and identify all 24 humans chromosomes at one time without a priori knowledge of any abnormalities involved. SKY can discern the aberrations that can't be detected very well by conventional banding technique and Fluorescent in situ hybridization (FISH). So SKY is hyper accurate, hypersensitive, and hyper intuitionist. We will review the elements and application of SKY in leukemia.
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Affiliation(s)
- Bo Guo
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Xiaoping Han
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Zhanhe Wu
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Wanming Da
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Hongli Zhu
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
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19
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Manabe M, Okita J, Tarakuwa T, Harada N, Aoyama Y, Kumura T, Ohta T, Furukawa Y, Mugitani A. der(5;17)(p10;q10) is a recurrent but rare whole-arm translocation in patients with hematological neoplasms: a report of three cases. Acta Haematol 2014; 132:134-9. [PMID: 24556628 DOI: 10.1159/000357111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 10/29/2013] [Indexed: 01/22/2023]
Abstract
We report the cases of 3 patients with hematological malignancies and complex karyotypes involving der(5; 17) (p10;q10), which results in the loss of 5q and 17p. Although deletions of 5q and 17p are recurrent abnormalities in hematological disease, only about 20 cases harboring der(5; 17) (p10;q10) have been reported. We address the tumorigenesis and morphological characteristics of hematological malignancies involving der(5; 17)(p10;q10), along with a review of the literature.
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MESH Headings
- Aged
- Aged, 80 and over
- Anemia, Refractory, with Excess of Blasts/drug therapy
- Anemia, Refractory, with Excess of Blasts/genetics
- Anemia, Refractory, with Excess of Blasts/pathology
- Aneuploidy
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Bone Marrow Cells/ultrastructure
- Cell Transformation, Neoplastic/genetics
- Chromosome Aberrations
- Chromosome Banding
- Chromosomes, Human, Pair 17/ultrastructure
- Chromosomes, Human, Pair 5/ultrastructure
- Contraindications
- Fatal Outcome
- Female
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/pathology
- Humans
- Karyotype
- Lenalidomide
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/pathology
- Lymphoma, T-Cell, Peripheral/drug therapy
- Male
- Megakaryocytes/ultrastructure
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/pathology
- Neoplasms, Second Primary/genetics
- Neoplasms, Second Primary/pathology
- Recurrence
- Remission Induction
- Thalidomide/analogs & derivatives
- Translocation, Genetic
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20
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Walker A, Mrózek K, Kohlschmidt J, Rao KW, Pettenati MJ, Sterling LJ, Marcucci G, Carroll AJ, Bloomfield CD. New recurrent balanced translocations in acute myeloid leukemia and myelodysplastic syndromes: cancer and leukemia group B 8461. Genes Chromosomes Cancer 2013; 52:385-401. [PMID: 23225546 PMCID: PMC3874732 DOI: 10.1002/gcc.22036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 10/31/2012] [Indexed: 12/16/2022] Open
Abstract
Acquired chromosome abnormalities in patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are among the most valuable determinants of diagnosis and prognosis. In search of new recurrent balanced translocations, we reviewed the Cancer and Leukemia Group B (CALGB) cytogenetics database containing pretreatment and relapse karyotypes of 4,701 adults with AML and 565 with MDS who were treated on CALGB trials. We identified all cases with balanced structural rearrangements occurring as a sole abnormality or in addition to one other abnormality, excluded abnormalities known to be recurrent, and then reviewed the literature to determine whether any of what we considered unique, previously unknown abnormalities had been reported. As a result, we identified seven new recurrent balanced translocations in AML or MDS: t(7;11)(q22;p15.5), t(10;11)(q23;p15), t(2;12)(p13;p13), t(12;17)(p13;q12), t(2;3)(p21;p21), t(5;21)(q31;q22), and t(8;14)(q24.1;q32.2), and additionally, t(10;12)(p11;q15), a new translocation in AML previously reported in a case of acute lymphoblastic leukemia. Herein, we report hematologic and clinical characteristics and treatment outcomes of patients with these newly recognized recurrent translocations. We also report 52 unique balanced translocations, together with the clinical data of patients harboring them, which to our knowledge have not been previously published. We hope that once the awareness of their existence is increased, some of these translocations may become recognized as novel recurring abnormalities. Identification of additional cases with both the new recurrent and the unique balanced translocations will enable determination of their prognostic significance and help to provide insights into the mechanisms of disease pathogenesis in patients with these rare abnormalities.
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Affiliation(s)
- Alison Walker
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| | - Krzysztof Mrózek
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| | - Jessica Kohlschmidt
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN
| | - Kathleen W. Rao
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mark J. Pettenati
- Comprehensive Cancer Center Wake Forest University, Winston-Salem, NC
| | - Lisa J. Sterling
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| | - Guido Marcucci
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
| | | | - Clara D. Bloomfield
- Division of Hematology and Oncology, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH
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21
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Wawrzyniak E, Wierzbowska A, Kotkowska A, Siemieniuk-Rys M, Robak T, Knopinska-Posluszny W, Klonowska A, Iliszko M, Woroniecka R, Pienkowska-Grela B, Ejduk A, Wach M, Duszenko E, Jaskowiec A, Jakobczyk M, Mucha B, Kosny J, Pluta A, Grosicki S, Holowiecki J, Haus O. Different prognosis of acute myeloid leukemia harboring monosomal karyotype with total or partial monosomies determined by FISH: Retrospective PALG study. Leuk Res 2013; 37:293-9. [DOI: 10.1016/j.leukres.2012.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/25/2012] [Accepted: 10/27/2012] [Indexed: 10/27/2022]
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22
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Evidence for phenotypic plasticity in aggressive triple-negative breast cancer: human biology is recapitulated by a novel model system. PLoS One 2012; 7:e45684. [PMID: 23049838 PMCID: PMC3458110 DOI: 10.1371/journal.pone.0045684] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 08/24/2012] [Indexed: 12/15/2022] Open
Abstract
Breast cancers with a basal-like gene signature are primarily triple-negative, frequently metastatic, and carry a poor prognosis. Basal-like breast cancers are enriched for markers of breast cancer stem cells as well as markers of epithelial-mesenchymal transition (EMT). While EMT is generally thought to be important in the process of metastasis, in vivo evidence of EMT in human disease remains rare. Here we report a novel model of human triple-negative breast cancer, the DKAT cell line, which was isolated from an aggressive, treatment-resistant triple-negative breast cancer that demonstrated morphological and biochemical evidence suggestive of phenotypic plasticity in the patient. The DKAT cell line displays a basal-like phenotype in vitro when cultured in serum-free media, and undergoes phenotypic changes consistent with EMT/MET in response to serum-containing media, a unique property among the breast cancer cell lines we tested. This EMT is marked by increased expression of the transcription factor Zeb1, and Zeb1 is required for the enhanced migratory ability of DKAT cells in the mesenchymal state. DKAT cells also express progenitor-cell markers, and single DKAT cells are able to generate tumorspheres containing both epithelial and mesenchymal cell types. In vivo, as few as ten DKAT cells are capable of forming xenograft tumors which display a range of epithelial and mesenchymal phenotypes. The DKAT model provides a novel model to study the molecular mechanisms regulating phenotypic plasticity and the aggressive biology of triple-negative breast cancers.
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23
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Grimwade D, Mrózek K. Diagnostic and prognostic value of cytogenetics in acute myeloid leukemia. Hematol Oncol Clin North Am 2012; 25:1135-61, vii. [PMID: 22093581 DOI: 10.1016/j.hoc.2011.09.018] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The last 4 decades have seen major advances in understanding the genetic basis of acute myeloid leukemia (AML), and substantial improvements in survival of children and young adults with the disease. A key step forward was the discovery that AML cells harbor recurring cytogenetic abnormalities. The identification of the genes involved in chromosomal rearrangements has provided insights into the regulation of normal hematopoiesis and how disruption of key transcription factors and epigenetic modulators promote leukemic transformation. Cytogenetics has been widely adopted to provide the framework for development of risk-stratified treatment approaches to patient management.
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Affiliation(s)
- David Grimwade
- Cancer Genetics Laboratory, Department of Medical & Molecular Genetics, Guy's Hospital, King's College London School of Medicine, 8th Floor, Guy's Tower, London SE1 9RT, UK.
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24
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Hong WJ, Medeiros BC. Unfavorable-risk cytogenetics in acute myeloid leukemia. Expert Rev Hematol 2011; 4:173-84. [PMID: 21495927 DOI: 10.1586/ehm.11.10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cytogenetic analysis at diagnosis is one of the most significant prognostic factors in acute myeloid leukemia (AML). AML patients with unfavorable-risk cytogenetic abnormalities account for 16-30% of younger adult patients and have poor response to standard treatment, with only 32-55% achieving a complete response. Overall survival is also extremely poor with only 5-12% patients alive at 5-10 years after diagnosis. Owing to the poor response in this subset of patients, risk-adapted treatment has been investigated. Allogeneic stem cell transplant has been shown to provide a survival benefit in patients with unfavorable-risk cytogenetic abnormalities in complement receptor 1. Other risk-adapted treatment strategies, such as reduced-intensity conditioning regimens prior to allogeneic stem cell transplant for older patients with AML, have also shown some survival benefit, without increasing treatment-related toxicities. Risk-stratification models that include cytogenetic abnormalities, as well as other molecular markers, are being developed to allow for individualized risk-adapted treatment for patients with AML. Prospective multicenter trials will be needed to validate these prognostic models.
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Affiliation(s)
- Wan-Jen Hong
- Stanford Cancer Center, 875 Blake Wilbur Drive, Stanford, CA 94305-5821, USA
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25
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BAALC and ERG expression levels are associated with outcome and distinct gene and microRNA expression profiles in older patients with de novo cytogenetically normal acute myeloid leukemia: a Cancer and Leukemia Group B study. Blood 2010; 116:5660-9. [PMID: 20841507 DOI: 10.1182/blood-2010-06-290536] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BAALC and ERG expression levels are prognostic markers in younger (< 60 years) cytogenetically normal acute myeloid leukemia (CN-AML) adults; their prognostic impact in older (≥ 60 years) patients requires further investigation. We evaluated pretreatment expression of BAALC and ERG in 158 de novo patients treated on cytarabine/daunorubicin-based protocols. The patients were also characterized for other established molecular prognosticators. Low BAALC and ERG expression levels were associated with better outcome in univariable and multivariable analyses. Expression levels of both BAALC and ERG were the only factors significantly associated with overall survival upon multivariable analysis. To gain biological insights, we derived gene expression signatures associated with BAALC and ERG expression in older CN-AML patients. Furthermore, we derived the first microRNA expression signatures associated with the expression of these 2 genes. In low BAALC expressers, genes associated with undifferentiated hematopoietic precursors and unfavorable outcome predictors were down-regulated, whereas HOX genes and HOX-gene-embedded microRNAs were up-regulated. Low ERG expressers presented with down-regulation of genes involved in the DNA-methylation machinery, and up-regulation of miR-148a, which targets DNMT3B. We conclude that in older CN-AML patients, low BAALC and ERG expression associates with better outcome and distinct gene and microRNA expression signatures that could aid in identifying new targets and novel therapeutic strategies for older patients.
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Wald D, Vermaat JM, Peleg G, Tse W. Genetic abnormalities in acute myelogenous leukemia with normal cytogenetics. Curr Hematol Malig Rep 2010; 3:83-8. [PMID: 20425451 DOI: 10.1007/s11899-008-0013-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Acute myelogenous leukemia (AML) results from a differentiation block of hematopoietic progenitor cells along with uncontrolled proliferation. The cytogenetic abnormality at initial diagnosis is the single most important prognostic factor classifying AML patients into three prognostic categories: favorable, intermediate, and poor risk. Currently, favorable-risk AML patients are usually treated with contemporary chemotherapy, and poor-risk AML patients receive allogeneic stem cell transplantation if suitable stem cell donors exist. The approximately 40% of AML patients without identifiable cytogenetic abnormalities (NC AML) are classified as intermediate risk. The optimal therapeutic strategies for these patients are largely unclear. Emerging data recently suggested that molecular study of the mutations of NPM1, FLT3, MLL, and CEBPalpha and alterations in expression levels of BAALC, MN1, and ERG may identify poor-risk patients with NC AML. Further prospective studies are needed to confirm whether NC AML patients with poor risk have improved clinical outcomes after more aggressive therapy.
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Affiliation(s)
- David Wald
- Department of Medicine, Division of Hematology/Oncology, Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH 44106, USA
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Sivendran S, Gruenstein S, Malone AK, Najfeld V. Ring chromosome 18 abnormality in acute myelogenous leukemia: the clinical dilemma. J Hematol Oncol 2010; 3:25. [PMID: 20649984 PMCID: PMC2917391 DOI: 10.1186/1756-8722-3-25] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 07/22/2010] [Indexed: 11/10/2022] Open
Abstract
The ring chromosome is a circular, structural abnormality composed of either multiple chromosomes or a single chromosome with loss of genetic material at one or both ends. This chromosomal rearrangement is often unstable with frequent recombinations and may be accompanied by either loss or amplification of genetic material[1]. Considering that ring chromosomes are rare in acute myelogenous leukemia (AML), it is difficult to risk stratify patient prognosis, particularly when the ring chromosome occurs as the sole abnormality. Here we report a case of a ring chromosome 18 abnormality in a patient with newly diagnosed AML with monocytic differentiation. Cytogenetic analysis demonstrated 46, XY, r(18)(p11q21) karyotype in 19 of 34 evaluated metaphase cells. The patient received induction chemotherapy and subsequent allogeneic cord blood transplant from a sex-matched donor, and remained in hematologic and cytogenetic remission for 120 days post transplant. Soon after, he developed post transplant lymphoproliferative disorder and died of multi-organ failure. Although r(18) chromosomal abnormalities were not classified in the recent updated evidence-and expert opinion-based recommendations for the diagnosis and management of AML (likely due to the small number of reported cases), the patient was treated as high risk with stem cell transplantation. This was based on the unstable nature of the ring chromosome and the poor outcomes described in the literature of patients with sole ring 18 abnormalities.
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Affiliation(s)
- Shanthi Sivendran
- Division of Hematology/Oncology, Department of Medicine, The Tisch Cancer Institute, The Mount Sinai School of Medicine, New York, NY, USA
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Mrózek K, Harper DP, Aplan PD. Cytogenetics and molecular genetics of acute lymphoblastic leukemia. Hematol Oncol Clin North Am 2009; 23:991-1010, v. [PMID: 19825449 PMCID: PMC3607311 DOI: 10.1016/j.hoc.2009.07.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acute lymphoblastic leukemia (ALL) is a malignant disease that often features nonrandom numerical or structural chromosome aberrations that can be detected microscopically. The application of contemporary genome-wide molecular analyses is revealing additional genetic alterations that are not detectable cytogenetically. This article describes the cytogenetic methodology and summarizes major cytogenetic findings and their clinical relevance in ALL. The article provides a review of modern molecular techniques and their application in the research on the genetics and epigenetics of ALL.
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Affiliation(s)
- Krzysztof Mrózek
- Division of Hematology and Oncology, Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - David P. Harper
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Peter D. Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
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Tchinda J, Volpert S, McNeil N, Neumann T, Kennerknecht I, Ried T, Büchner T, Serve H, Berdel WE, Horst J, Hilgenfeld E. Multicolor Karyotyping in Acute Myeloid Leukemia. Leuk Lymphoma 2009; 44:1843-53. [PMID: 14738135 DOI: 10.1080/10428190310001603605] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cytogenetic data have significantly contributed to our understanding of the heterogeneity of acute myeloid leukemia (AML). In AML, numerous recurrent chromosomal aberrations have been identified, and several of them, e.g. t(8;21)(q22;q22), t(15;17)(q22;q11-12), inv(16)(p13q22), are specific for distinct subgroups. Furthermore, chromosomal aberrations have proved to be of paramount prognostic importance for remission induction and survival. Chromosome analysis using classical cytogenetic banding techniques often fails to completely resolve complex karyotypes and cryptic translocations not identifiable by these techniques have been detected using molecular cytogenetic methods. While fluorescence in situ hybridization (FISH) has become an indispensable tool for screening and follow-up of known aberrations, the techniques of spectral karyotyping (SKY) and multiplex-fluorescence in situ hybridization (M-FISH) allow for the simultaneous visualization of all chromosomes of a metaphase in a single hybridization step, and thereby enable screening for the aberrations present without their prior knowledge. Therefore, with the introduction of these techniques in 1996 the comprehensive analysis of complex karyotypes and the identification of new, hitherto cryptic translocations and, ultimately, the identification of new disease subgroups seemed possible. Since, more than 600 cases of AML and MDS have been analyzed. Herein, we attempt to summarize the data published and discuss what has been achieved towards realization of these goals.
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Affiliation(s)
- Joëlle Tchinda
- Institut für Humangenetik, Universitätsklinikum Münster, Vesaliusweg 12-14, 48129 Münster, Germany.
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Gregory TK, Wald D, Chen Y, Vermaat JM, Xiong Y, Tse W. Molecular prognostic markers for adult acute myeloid leukemia with normal cytogenetics. J Hematol Oncol 2009; 2:23. [PMID: 19490647 PMCID: PMC2700131 DOI: 10.1186/1756-8722-2-23] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 06/02/2009] [Indexed: 12/23/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogenous disorder that results from a block in the differentiation of hematopoietic progenitor cells along with uncontrolled proliferation. In approximately 60% of cases, specific recurrent chromosomal aberrations can be identified by modern cytogenetic techniques. This cytogenetic information is the single most important tool to classify patients at their initial diagnosis into three prognostic categories: favorable, intermediate, and poor risk. Currently, favorable risk AML patients are usually treated with contemporary chemotherapy while poor risk AML patients receive allogeneic stem cell transplantation if suitable stem cell donors exist. The largest subgroup of AML patients (aproximately 40%) have no identifiable cytogenetic abnormalities and are classified as intermediate risk. The optimal therapeutic strategies for these patients are still largely unclear. Recently, it is becoming increasingly evident that it is possible to identify a subgroup of poorer risk patients among those with normal cytogenic AML (NC-AML). Molecular risk stratification for NC-AML patients may be possible due to mutations of NPM1, FLT3, MLL, and CEBPalpha as well as alterations in expression levels of BAALC, MN1, ERG, and AF1q. Further prospective studies are needed to confirm if poorer risk NC-AML patients have improved clinical outcomes after more aggressive therapy.
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MESH Headings
- Adult
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Cytogenetics
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Genetic Markers/physiology
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Neoplasm, Residual
- Nuclear Proteins/genetics
- Nuclear Proteins/physiology
- Nucleophosmin
- Prognosis
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/physiology
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Affiliation(s)
- Tara K Gregory
- Division of Medical Oncology, University of Colorado Cancer Center, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - David Wald
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yichu Chen
- Division of Medical Oncology, University of Colorado Cancer Center, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Johanna M Vermaat
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yin Xiong
- Division of Medical Oncology, University of Colorado Cancer Center, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - William Tse
- Division of Medical Oncology, University of Colorado Cancer Center, University of Colorado School of Medicine, Aurora, Colorado, USA
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Abstract
Patients with acute myeloid leukemia (AML) harboring three or more acquired chromosome aberrations in the absence of the prognostically favorable t(8;21)(q22;q22), inv(16)(p13q22)/t(6;16)(p13;q22), and t(15;17)(q22;q21) aberrations form a separate category - AML with a complex karyotype. They constitute 10% to 12% of all AML patents, with the incidence of complex karyotypes increasing with the more advanced age. Recent studies using molecular-cytogenetic techniques (spectral karyotyping [SKY], multiplex fluorescence in situ hybridization [M-FISH]) and array comparative genomic hybridization (a-CGH) considerably improved characterization of previously unidentified, partially identified, or cryptic chromosome aberrations, and allowed precise delineation of genomic imbalances. The emerging nonrandom pattern of abnormalities includes relative paucity, but not absence, of balanced rearrangements (translocations, insertions, or inversions), predominance of aberrations leading to loss of chromosome material (monosomies, deletions, and unbalanced translocations) that involve, in decreasing order, chromosome arms 5q, 17p, 7q, 18q, 16q, 17q, 12p, 20q, 18p, and 3p, and the presence of recurrent, albeit less frequent and often hidden (in marker chromosomes and unbalanced translocations) aberrations leading to overrepresentation of segments from 8q, 11q, 21q, 22q, 1p, 9p, and 13q. Several candidate genes have been identified as targets of genomic losses, for example, TP53, CTNNA1, NF1, ETV6, and TCF4, and amplifications, for example, ERG, ETS2, APP, ETS1, FLI1, MLL, DDX6, GAB2, MYC, TRIB1, and CDX2. Treatment outcomes of complex karyotype patients receiving chemotherapy are very poor. They can be improved to some extent by allogeneic stem cell transplantation in younger patients. It is hoped that better understanding of genomic alterations will result in identification of novel therapeutic targets and improved prognosis in patients with complex karyotypes.
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Mackinnon RN, Campbell LJ. Dicentric chromosomes and 20q11.2 amplification in MDS/AML with apparent monosomy 20. Cytogenet Genome Res 2008; 119:211-20. [PMID: 18253031 DOI: 10.1159/000112063] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2007] [Indexed: 01/15/2023] Open
Abstract
FISH analysis of 41 previously karyotyped cases of MDS and AML with apparent monosomy of chromosome 20 revealed a variety of dicentric abnormalities involving chromosome 20. These usually, but not always, involved a breakpoint in the long arm of chromosome 20 and loss of the common deleted region at 20q12. Not one case of true monosomy 20 was confirmed. We found evidence for dicentric chromosome formation in 21 of 24 unbalanced translocations containing chromosome 20 and that were studied in more detail. Subsequent loss of one of the centromeres had occurred in eight of these 24 cases, and was more frequent than centromere inactivation as a means of resolving the inherent instability of a dicentric chromosome. In the three cases with dicentric chromosomes from which proximal 20q had been excised along with the 20 centromere, the excised segment was retained, and in two of these it was amplified. Proximal 20q was clearly retained in all but three cases, and present in three or more copies in 17 of 41 cases. The retention and amplification of proximal 20q provides support for the hypothesis that there is an oncogene located in this region of 20q that is activated in cases of MDS/AML with del(20q). Apparent monosomy 20 in MDS/AML should be treated as evidence of unidentified chromosome 20 abnormalities, and familiarity with the typical G-banded morphology of these derivatives can help with their identification. The reported incidence of dicentric chromosomes is clearly an under-estimate but is increasing in myeloid disorders as more cases are studied with methods allowing their detection.
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Affiliation(s)
- R N Mackinnon
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital, University of Melbourne, Melbourne, Australia.
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Herry A, Douet-Guilbert N, Morel F, Le Bris MJ, Morice P, Abgrall JF, Berthou C, De Braekeleer M. Evaluation of chromosome 5 aberrations in complex karyotypes of patients with myeloid disorders reveals their contribution to dicentric and tricentric chromosomes, resulting in the loss of critical 5q regions. ACTA ACUST UNITED AC 2007; 175:125-31. [PMID: 17556068 DOI: 10.1016/j.cancergencyto.2007.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 02/16/2007] [Accepted: 02/26/2007] [Indexed: 10/23/2022]
Abstract
Dicentric chromosomes have often been observed in complex karyotypes in previously reported studies of therapy-related myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Fluorescence in situ hybridization (FISH) has now made the characterization of these rearrangements much easier. Dicentric and tricentric chromosomes were identified in 21 patients (9 MDS and 12 AML) among the 133 consecutive MDS/AML patients (17%) who had a structural or numerical aberration of chromosome 5 using conventional cytogenetic analysis. One third (7/21) of the patients had received alkylating drugs for a previously diagnosed cancer or chronic myeloproliferative disease. Loss of 5q material was identified in all 21 patients. One copy of the EGR1 (5q31) or the CSF1R (5q33 approximately q34) genes was lost in 20 of the 21 patients. Dicentric and tricentric chromosomes involving chromosome 5 are frequently observed in complex karyotypes among patients with de novo or therapy-related MDS/AML. They lead to deletions of various parts of the long arm of chromosome 5.
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Affiliation(s)
- Angèle Herry
- Laboratory of Histology, Embryology, and Cytogenetics, Faculty of Medicine and Health Sciences, Université de Bretagne Occidentale, 22, avenue Camille Desmoulins, CS 93837, F-29238 Brest cedex 3, France
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Baldus CD, Mrózek K, Marcucci G, Bloomfield CD. Clinical outcome of de novo acute myeloid leukaemia patients with normal cytogenetics is affected by molecular genetic alterations: a concise review. Br J Haematol 2007; 137:387-400. [PMID: 17488484 DOI: 10.1111/j.1365-2141.2007.06566.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Normal cytogenetics are detected pretreatment in approximately 45% of patients with de novo acute myeloid leukaemia (AML); thus this constitutes the single largest cytogenetic group of AML. Recently, molecular genetic alterations with prognostic significance have been reported in these patients. They include internal tandem duplication of the FLT3 gene, partial tandem duplication of the MLL gene, mutations of the CEBPA and NPM1 genes and aberrant expression of the BAALC, ERG and MN1 genes. Additionally, gene-expression profiling has been applied to identify prognostically relevant subgroups. Substantial progress has been made in the understanding of molecular pathways deregulated in leukaemogenesis and how these defects can be targeted by novel therapeutic compounds. Here we critically review the molecular heterogeneity among AML patients with normal cytogenetics and discuss how these data may translate into a prognostic, molecular-based treatment stratification that may improve the currently unsatisfactory outcome of these patients.
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Affiliation(s)
- Claudia D Baldus
- Department of Haematology and Oncology, Charité, Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
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35
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Mrózek K, Döhner H, Bloomfield CD. Influence of new molecular prognostic markers in patients with karyotypically normal acute myeloid leukemia: recent advances. Curr Opin Hematol 2007; 14:106-14. [PMID: 17255787 DOI: 10.1097/moh.0b013e32801684c7] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE OF REVIEW Molecular study of cytogenetically normal acute myeloid leukemia is among the most active areas of leukemia research. Despite having the same normal karyotype, adults with de-novo cytogenetically normal acute myeloid leukemia who constitute the largest cytogenetic group of acute myeloid leukemia, are very diverse with respect to acquired gene mutations and gene expression changes. These genetic alterations affect clinical outcome and may assist in selection of proper treatment. Herein we critically summarize recent clinically relevant molecular genetic studies of cytogenetically normal acute myeloid leukemia. RECENT FINDINGS NPM1 gene mutations causing aberrant cytoplasmic localization of nucleophosmin have been demonstrated to be the most frequent submicroscopic alterations in cytogenetically normal acute myeloid leukemia and to confer improved prognosis, especially in patients without a concomitant FLT3 gene internal tandem duplication. Overexpressed BAALC, ERG and MN1 genes and expression of breast cancer resistance protein have been shown to confer poor prognosis. A gene-expression signature previously suggested to separate cytogenetically normal acute myeloid leukemia patients into prognostic subgroups has been validated on a different microarray platform, although gene-expression signature-based classifiers predicting outcome for individual patients with greater accuracy are still needed. SUMMARY The discovery of new prognostic markers has increased our understanding of leukemogenesis and may lead to improved prognostication and generation of novel risk-adapted therapies.
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Affiliation(s)
- Krzysztof Mrózek
- Division of Hematology and Oncology, Department of Internal Medicine, Comprehensive, Cancer Center, The Ohio State University, Columbus, Ohio 43210-1228, USA.
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Mrózek K, Marcucci G, Paschka P, Whitman SP, Bloomfield CD. Clinical relevance of mutations and gene-expression changes in adult acute myeloid leukemia with normal cytogenetics: are we ready for a prognostically prioritized molecular classification? Blood 2007; 109:431-48. [PMID: 16960150 PMCID: PMC1785102 DOI: 10.1182/blood-2006-06-001149] [Citation(s) in RCA: 406] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Accepted: 08/20/2006] [Indexed: 12/17/2022] Open
Abstract
Recent molecular analyses of leukemic blasts from pretreatment marrow or blood of patients with acute myeloid leukemia (AML) and a normal karyotype, the largest cytogenetic subset (ie, 40%-49%) of AML, have revealed a striking heterogeneity with regard to the presence of acquired gene mutations and changes in gene expression. Multiple submicroscopic genetic alterations with prognostic significance have been discovered, including internal tandem duplication of the FLT3 gene, mutations in the NPM1 gene, partial tandem duplication of the MLL gene, high expression of the BAALC gene, and mutations in the CEBPA gene. Application of gene-expression profiling has also identified a gene-expression signature that appears to separate cytogenetically normal AML patients into prognostic subgroups, although gene-expression signature-based classifiers predicting outcome for individual patients with greater accuracy are needed. These and similar future findings are likely to have a major impact on the clinical management of cytogenetically normal AML not only in prognostication but also in selection of appropriate treatment, since many of the identified genetic alterations already constitute or will potentially become targets for specific therapeutic intervention. In this report, we review prognostic genetic findings in karyotypically normal AML and discuss their clinical implications.
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Affiliation(s)
- Krzysztof Mrózek
- Department of Internal Medicine, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Room 1248B, The Ohio State University, 300 West Tenth Ave, Columbus, OH 43210-1228, USA.
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Olney HJ, Le Beau MM. Evaluation of recurring cytogenetic abnormalities in the treatment of myelodysplastic syndromes. Leuk Res 2006; 31:427-34. [PMID: 17161457 DOI: 10.1016/j.leukres.2006.10.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Revised: 10/16/2006] [Accepted: 10/18/2006] [Indexed: 11/28/2022]
Abstract
Myelodysplastic syndromes (MDS) are clinically heterogeneous, but the presence of specific cytogenetic abnormalities can predict disease manifestations, provide a basis for prognosis, and direct treatment. Conventional cytogenetic analysis is instrumental in identifying chromosomal abnormalities in MDS and novel genetic methods may provide supplementary information. Treatment with lenalidomide was recently shown to be effective in MDS, particularly in those cases with del(5q), resulting in durable cytogenetic remission and hematological responses. In this paradigm, diagnosis of the del(5q) abnormality would be essential to predicting response to therapy.
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Affiliation(s)
- Harold J Olney
- Université de Montréal, CHUM Hospital Notre-Dame, 1560 Sherbrooke St E, Montréal, Québec, H2L 4M1, Canada.
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38
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Zatkova A, Schoch C, Speleman F, Poppe B, Mannhalter C, Fonatsch C, Wimmer K. GAB2 is a novel target of 11q amplification in AML/MDS. Genes Chromosomes Cancer 2006; 45:798-807. [PMID: 16736498 DOI: 10.1002/gcc.20344] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Chromosome arm 11q amplifications involving the mixed lineage leukemia gene (MLL) locus are rare but recurrent aberrations in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). We have recently shown that in addition to the MLL core amplicon, independent sequences in 11q23-24 and/or 11q13.5 are coamplified within the same cytogenetic markers in 90% and 60% of patients, respectively. Here we further narrow down the minimal amplicon in 11q13.5 to 1.17 Mb by means of semi-quantitative PCR and FISH analyses. The newly defined amplicon contains seven genes, including the GRB2-associated binding protein 2 (GAB2). Using real-time RT-PCR we show a significant transcriptional upregulation of GAB2 in the patients who have GAB2 coamplified with MLL. Thus, the adaptor molecule GAB2 that has already been shown to enhance oncogenic signaling in other neoplasias appears as a novel target of 11q amplification in AML/MDS.
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Affiliation(s)
- Andrea Zatkova
- Abteilung für Humangenetik, Klinisches Institut für Medizinische und Chemische Labor Diagnostik (KIMCL), Medizinische Universität Wien, Währinger Strasse 10, A-1090 Vienna, Austria.
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39
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Kearney L. Multiplex-FISH (M-FISH): technique, developments and applications. Cytogenet Genome Res 2006; 114:189-98. [PMID: 16954655 DOI: 10.1159/000094202] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 04/06/2006] [Indexed: 01/08/2023] Open
Abstract
Multiplex FISH (M-FISH) represents one of the most significant developments in molecular cytogenetics of the past decade. Originally designed to generate 24 colour karyotyping, the technique has spawned many variations and an equally diverse range of applications. In tumour and leukaemia cytogenetics, the two groups that have been targeted represent both ends of the cytogenetic spectrum: those with an apparently normal karyotype (suspected of harbouring small rearrangements not detectable by conventional cytogenetics) and those with a complex aberrant karyotype (which are difficult to karyotype accurately due to the sheer number of aberrations). In research, mouse M-FISH provides a powerful tool to characterize mouse models of a disease. In addition, the ability to accurately karyotype single metaphases without selection makes M-FISH the perfect tool in chromosome breakage studies and for characterizing clonal evolution of tumours. Finally, M-FISH has emerged as the perfect partner for the developing genomic microarray (array CGH) technologies, providing a powerful approach to gene discovery.
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Affiliation(s)
- L Kearney
- Section of Haemato-Oncology, Institute of Cancer Research, London, UK.
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40
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Schrock E, Zschieschang P, O'Brien P, Helmrich A, Hardt T, Matthaei A, Stout-Weider K. Spectral karyotyping of human, mouse, rat and ape chromosomes--applications for genetic diagnostics and research. Cytogenet Genome Res 2006; 114:199-221. [PMID: 16954656 DOI: 10.1159/000094203] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 05/19/2006] [Indexed: 01/30/2023] Open
Abstract
Spectral karyotyping (SKY) is a widely used methodology to identify genetic aberrations. Multicolor fluorescence in situ hybridization using chromosome painting probes in individual colors for all metaphase chromosomes at once is combined with a unique spectral measurement and analysis system to automatically classify normal and aberrant chromosomes. Based on countless studies and investigations in many laboratories worldwide, numerous new chromosome translocations and other aberrations have been identified in clinical and tumor cytogenetics. Thus, gene identification studies have been facilitated resulting in the dissection of tumor development and progression. For example, different translocation partners of the TEL/ETV6 transcription factor that is specially required for hematopoiesis within the bone marrow were identified. Also, the correct classification of complex karyotypes of solid tumors supports the prognostication of cancer patients. Important accomplishments for patients with genetic diseases, leukemias and lymphomas, mesenchymal tumors and solid cancers are summarized and exemplified. Furthermore, studies of disease mechanisms such as centromeric DNA breakage, DNA double strand break repair, telomere shortening and radiation-induced neoplastic transformation have been accompanied by SKY analyses. Besides the hybridization of human chromosomes, mouse karyotyping has also contributed to the comprehensive characterization of mouse models of human disease and for gene therapy studies.
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Affiliation(s)
- E Schrock
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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Rücker FG, Bullinger L, Schwaenen C, Lipka DB, Wessendorf S, Fröhling S, Bentz M, Miller S, Scholl C, Schlenk RF, Radlwimmer B, Kestler HA, Pollack JR, Lichter P, Döhner K, Döhner H. Disclosure of candidate genes in acute myeloid leukemia with complex karyotypes using microarray-based molecular characterization. J Clin Oncol 2006; 24:3887-94. [PMID: 16864856 DOI: 10.1200/jco.2005.04.5450] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE To identify novel genomic regions of interest in acute myeloid leukemia (AML) with complex karyotypes, we applied comparative genomic hybridization to microarrays (array-CGH), allowing high-resolution genome-wide screening of genomic imbalances. PATIENTS AND METHODS Sixty AML cases with complex karyotypes were analyzed using array-CGH; parallel analysis of gene expression was performed in a subset of cases. RESULTS Genomic losses were found more frequently than gains. The most frequent losses affected 5q (77%), 17p (55%), and 7q (45%), and the most frequent genomic gains 11q (40%) and 8q (38%). Critical segments could be delineated to genomic fragments of only 0.8 to a few megabase-pairs of DNA. In lost/gained regions, gene expression profiling detected a gene dosage effect with significant lower/higher average gene expression levels across the genes located in the respective regions. Furthermore, high-level DNA amplifications were identified in several regions: 11q23.3-q24.1 (n = 7), 21q22 (n = 6), 11q23.3 (n = 5), 13q12 (n = 3), 8q24 (n = 3), 9p24 (n = 2), 12p13 (n = 2), and 20q11 (n = 2). Parallel analysis of gene expression in critical amplicons displayed overexpressed candidate genes (eg, C8FW and MYC in 8q24). CONCLUSION In conclusion, a large spectrum of genomic imbalances, including novel recurring changes in AML with complex karyotypes, was identified using array-CGH. In addition, the combined analysis of array-CGH data with gene expression profiles allowed the detection of candidate genes involved in the pathogenesis of AML.
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MESH Headings
- Acute Disease
- Allelic Imbalance
- Chromosome Aberrations
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 20
- Chromosomes, Human, Pair 5
- Chromosomes, Human, Pair 7
- Chromosomes, Human, Pair 8
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genetic Linkage
- Genomic Instability
- Humans
- Karyotyping
- Leukemia, Myeloid/genetics
- Loss of Heterozygosity
- Microarray Analysis
- Nucleic Acid Amplification Techniques
- Nucleic Acid Hybridization
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Affiliation(s)
- Frank G Rücker
- Department of Neural Information Processing, University Hospital of Ulm, Ulm, Germany
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42
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Shali W, Hélias C, Fohrer C, Struski S, Gervais C, Falkenrodt A, Leymarie V, Lioure B, Raby P, Herbrecht R, Lessard M. Cytogenetic studies of a series of 43 consecutive secondary myelodysplastic syndromes/acute myeloid leukemias: conventional cytogenetics, FISH, and multiplex FISH. ACTA ACUST UNITED AC 2006; 168:133-45. [PMID: 16843103 DOI: 10.1016/j.cancergencyto.2006.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Revised: 01/31/2006] [Accepted: 02/07/2006] [Indexed: 12/01/2022]
Abstract
We report a series of 43 consecutive therapy-related myelodysplastic syndromes (t-MDS) or acute myeloid leukemias (t-AML) observed for 6 years. This series consisted of 26 women and 17 men, ages ranging from 9 to 85 years. These cases were classified into three groups according to the primary diagnosis. Conventional cytogenetic and fluorescent in situ hybridization (FISH)/ multiplex FISH (M-FISH) methods were used to analyze cytogenetic characteristics of secondary MDS/AML. The features of chromosomal abnormalities were linked to the nature of the therapy and protocols used. A considerable proportion of recurrent balanced translocations characterized t-AML secondary to therapy. FISH techniques showed that conventional cytogenetics often underestimated associated translocations; some deletions were in fact derivative chromosomes associated with deletions. After treatment for lymphomas and chronic myeloproliferative diseases, there were more complex unbalanced abnormalities than the control group. Compared to other series, recurrent translocations appeared to be more numerous (25%), probably reflecting an evolution of therapeutic modalities.
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Affiliation(s)
- Wei Shali
- Laboratoire d'Hématologie, Hôpitaux Universitaires de Strasbourg, Avenue Moliére, 67098 Strasbourg, France
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43
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Bloomfield CD, Mrózek K, Caligiuri MA. Cancer and Leukemia Group B Leukemia Correlative Science Committee: Major Accomplishments and Future Directions: Table 1. Clin Cancer Res 2006; 12:3564s-71s. [PMID: 16740786 DOI: 10.1158/1078-0432.ccr-06-9002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Cancer and Leukemia Group B (CALGB) Leukemia Correlative Science Committee (LCSC) has a remarkable history of outstanding productivity and has been at the cutting edge of correlative science for adult leukemia for almost 25 years. Its work, initially focused on the use of immunophenotyping for diagnosis and prognosis of acute lymphoblastic leukemia and acute myeloid leukemia, has, for the last 15 years, focused on the clinical use of cytogenetic and molecular genetic markers in acute myeloid leukemia and acute lymphoblastic leukemia as well as in chronic lymphocytic leukemia. Numerous CALGB LCSC studies have had a major effect on the way we currently diagnose, predict outcome, select appropriate treatment, document complete remission, and monitor residual disease in adults with acute leukemia. In part as a result of the work of the CALGB LCSC, we are increasingly moving toward molecularly targeted therapy in acute and chronic leukemias. In this report, we briefly review those contributions from the CALGB LCSC that have had, or are likely to have in the future, a major effect on how we currently manage leukemia and outline directions of ongoing and future research conducted by the CALGB LCSC.
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Affiliation(s)
- Clara D Bloomfield
- Division of Hematology and Oncology, Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA.
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44
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Preiss BS, Kerndrup GB, Pedersen RK, Hasle H, Pallisgaard N. Contribution of multiparameter genetic analysis to the detection of genetic alterations in hematologic neoplasia. An evaluation of combining G-band analysis, spectral karyotyping, and multiplex reverse-transcription polymerase chain reaction (multiplex RT-PCR). ACTA ACUST UNITED AC 2006; 165:1-8. [PMID: 16490591 DOI: 10.1016/j.cancergencyto.2005.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/20/2005] [Accepted: 07/26/2005] [Indexed: 01/25/2023]
Abstract
We investigated 150 acute myeloid leukemia (AML) patients and 48 acute lymphoblastic leukemia (ALL) patients by multiplex RT-PCR to 7evaluate the adjuvant diagnostic effect, vis-à-vis G-banding and spectral karyotyping (SKY), and the potentials of this method for providing means for monitoring residual disease by real-time quantitative RT-PCR. An abnormal G-banded karyotype was found in 57% of AML and 68% of ALL cases. Ninety-six patients were investigated by SKY in parallel which extended or confirmed the G-banding finding in 94/96 cases. In patients with an abnormal G-banded karyotype, classification of chromosomes involved in structural aberrations by SKY was possible in 98% of the cases and SKY extended the G-banded karyotype in 34% of cases. In 32 cases, an mRNA hybrid was detected by PCR. These cases constitute 16% of the cases investigated at diagnosis (AML: 11% and ALL: 31%). In 13 of these cases, we detected an mRNA hybrid the equivalent of which was not found by G-banding or SKY (AML: 4% and ALL: 13%). By including multiplex RT-PCR, we were able to detect abnormalities in 62% of the investigated patients as opposed to 59% by G-banding. Genetic techniques complement each other and selection of relevant and targeted primer kits for the multiplex RT-PCR assay is recommended.
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Affiliation(s)
- Birgitte S Preiss
- Institute of Pathology-Laboratory of Molecular Pathology and Chromosome Laboratory, Odense University Hospital, Odense C. DK-5000, Denmark
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45
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Strefford JC, van Delft FW, Robinson HM, Worley H, Yiannikouris O, Selzer R, Richmond T, Hann I, Bellotti T, Raghavan M, Young BD, Saha V, Harrison CJ. Complex genomic alterations and gene expression in acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Proc Natl Acad Sci U S A 2006; 103:8167-72. [PMID: 16702559 PMCID: PMC1472447 DOI: 10.1073/pnas.0602360103] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have previously identified a unique subtype of acute lymphoblastic leukemia (ALL) associated with a poor outcome and characterized by intrachromosomal amplification of chromosome 21 including the RUNX1 gene (iAMP21). In this study, array-based comparative genomic hybridization (aCGH) (n = 10) detected a common region of amplification (CRA) between 33.192 and 39.796 Mb and a common region of deletion (CRD) between 43.7 and 47 Mb in 100% and 70% of iAMP21 patients, respectively. High-resolution genotypic analysis (n = 3) identified allelic imbalances in the CRA. Supervised gene expression analysis showed a distinct signature for eight patients with iAMP21, with 10% of overexpressed genes located within the CRA. The mean expression of these genes was significantly higher in iAMP21 when compared to other ALL samples (n = 45). Although genomic copy number correlated with overall gene expression levels within areas of loss or gain, there was considerable individual variation. A unique subset of differentially expressed genes, outside the CRA and CRD, were identified when gene expression signatures of iAMP21 were compared to ALL samples with ETV6-RUNX1 fusion (n = 21) or high hyperdiploidy with additional chromosomes 21 (n = 23). From this analysis, LGMN was shown to be overexpressed in patients with iAMP21 (P = 0.0012). Genomic and expression data has further characterized this ALL subtype, demonstrating high levels of 21q instability in these patients leading to proposals for mechanisms underlying this clinical phenotype and plausible alternative treatments.
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Affiliation(s)
- Jon C Strefford
- Leukaemia Research Cytogenetics Group, Cancer Sciences Division, University of Southampton, Southampton SO16 6YD, United Kingdom.
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Trost D, Hildebrandt B, Beier M, Müller N, Germing U, Royer-Pokora B. Molecular cytogenetic profiling of complex karyotypes in primary myelodysplastic syndromes and acute myeloid leukemia. ACTA ACUST UNITED AC 2006; 165:51-63. [PMID: 16490597 DOI: 10.1016/j.cancergencyto.2005.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Revised: 09/20/2005] [Accepted: 09/21/2005] [Indexed: 11/26/2022]
Abstract
Complex chromosomal aberrations are present in < or =30% of patients with primary myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) and are associated with a poor prognosis. Specific alterations in complex karyotypes are difficult to define by conventional cytogenetics alone. To obtain a more comprehensive view of the recurrent aberrations, we performed spectral karyotyping (SKY) and fluorescence in situ hybridization (FISH) with selected probes on bone marrow samples from 17 patients with primary MDS and 3 with primary AML. All cases had chromosome 5 alterations. Two different types of 5q loss were identified: unbalanced translocations and interstitial deletions, or del(5q), each occurring in 10 patients. The most frequent additional chromosome aberrations were -3/-3p/-3q, -7/7q-, +8, 13q-, -16, 17p-, -18/18p-, -20/20q-, and +21q, each occurring in 25%. In the five cases with gain of 21q, involvement of the AML1 gene was excluded. Unbalanced 5q translocations occurred more often in combination with monosomy 3 and 7 and with gain of 21q, whereas del(5q) was associated more often with -1p and trisomy 8. A detailed analysis of specific breakpoints and deletions revealed recurrent involvement of specific chromosomal bands harboring known tumor suppressor genes or oncogenes. Analysis of large numbers of MDS and AML cases in a similar detailed manner with SKY and FISH will reveal whether new subgroups can be identified according to their genetic alterations. Correlation with clinical parameters may reveal the prognostic significance of these genetic subgroups.
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Affiliation(s)
- Detlef Trost
- Institute of Human Genetics and Anthropology, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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Mrózek K, Bloomfield CD. Chromosome aberrations, gene mutations and expression changes, and prognosis in adult acute myeloid leukemia. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2006:169-77. [PMID: 17124057 DOI: 10.1182/asheducation-2006.1.169] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pretreatment clinical features and prognosis of patients with acute myeloid leukemia (AML) are strongly influenced by acquired genetic alterations in leukemic cells, which include microscopically detectable chromosome aberrations and, increasingly, submicroscopic gene mutations and changes in gene expression. Cytogenetic findings separate AML patients into three broad prognostic categories: favorable, intermediate and adverse. The cytogenetic-risk classifications differ somewhat for younger adult patients and those aged 60 years or older. In many instances, patients with specific cytogenetic findings, e.g., those with a normal karyotype or those with either t(8;21)(q22;q22) or inv(16)(p13q22)/t(16;16)(p13;q22) [collectively referred to as core-binding factor (CBF) AML] can be further subdivided into prognostic categories based on the presence or absence of particular gene mutations or changes in gene expression. Importantly, many of these molecular genetic alterations constitute potential targets for risk-adapted therapies. In this article, we briefly review major cytogenetic prognostic categories and discuss molecular genetic findings of prognostic significance in two of the largest cytogenetic groups of patients with AML, namely AML with a normal karyotype and CBF AML.
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Affiliation(s)
- Krzysztof Mrózek
- Division of Hematology and Oncology and the Comprehensive Cancer Center, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, 300 West Tenth Avenue, Columbus, OH 43210, USA.
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48
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MacKinnon RN, Campbell LJ. A comparison of two contrasting recurrent isochromosomes 20 found in myelodysplastic syndromes suggests that retention of proximal 20q is a significant factor in myeloid malignancies. ACTA ACUST UNITED AC 2005; 163:176-9. [PMID: 16337864 DOI: 10.1016/j.cancergencyto.2005.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Revised: 05/20/2005] [Accepted: 06/02/2005] [Indexed: 02/03/2023]
Abstract
We compare two different isochromosomes of chromosome 20 in myelodysplastic syndromes (MDS): an isochromosome of the short arm of chromosome 20, idic(20)(q11), and an isochromosome of the long arm of a deleted chromosome 20, ider(20)(q10)del(20)(q11.2). The isochromosomes are of contrasting morphology, because opposite arms are duplicated, but they both show loss of the critical region at 20q12, as well as retention and duplication of the centromere and proximal long arm (20q11). We speculate that a region of proximal 20q is preferentially retained during deletions of the critical region in MDS and acute myeloid leukemia.
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Affiliation(s)
- Ruth N MacKinnon
- Victorian Cancer Cytogenetics Service, Department of Medicine, St. Vincent's Hospital Melbourne and University of Melbourne, Fitzroy Vic, Australia.
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49
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Abstract
In all organisms, cell proliferation is orchestrated by coordinated patterns of gene expression. Transcription results from the activity of the RNA polymerase machinery and depends on the ability of transcription activators and repressors to access chromatin at specific promoters. During the last decades, increasing evidence supports aberrant transcription regulation as contributing to the development of human cancers. In fact, transcription regulatory proteins are often identified in oncogenic chromosomal rearrangements and are overexpressed in a variety of malignancies. Most transcription regulators are large proteins, containing multiple structural and functional domains some with enzymatic activity. These activities modify the structure of the chromatin, occluding certain DNA regions and exposing others for interaction with the transcription machinery. Thus, chromatin modifiers represent an additional level of transcription regulation. In this review we focus on several families of transcription activators and repressors that catalyse histone post-translational modifications (acetylation, methylation, phosphorylation, ubiquitination and SUMOylation); and how these enzymatic activities might alter the correct cell proliferation program, leading to cancer.
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Affiliation(s)
- Helena Santos-Rosa
- The Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK
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50
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MacKinnon RN, Zordan A, Campbell LJ. Recurrent duplication of Xq27∼qter in hematological malignancies revealed by multicolor fluorescence in situ hybridization and multicolor banding. ACTA ACUST UNITED AC 2005; 161:125-9. [PMID: 16102582 DOI: 10.1016/j.cancergencyto.2005.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 01/28/2005] [Accepted: 02/07/2005] [Indexed: 01/18/2023]
Abstract
Multicolor fluorescence in situ hybridization (M-FISH) experiments were performed to determine the composition of abnormal complex karyotypes in 15 cases of hematological malignancy. Four cases were found to have unsuspected unbalanced X chromosome translocations, which resulted in the presence of extra X chromosome material. We determined the identity of the duplicated chromosome regions using the multicolor banding (mBAND) technique. Xq27-qter was duplicated in three of the four male cases with an X chromosome abnormality (i.e., in one third of male cases and one fifth of all cases). These preliminary results may point to the existence of a recurrent chromosome abnormality, either translocation at a specific Xq27 locus or duplication of Xq27-qter.
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Affiliation(s)
- Ruth N MacKinnon
- University of Melbourne Department of Medicine, St Vincent's Hospital, Melbourne, Victoria, Australia.
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