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Lestringant V, Guermouche-Flament H, Jimenez-Pocquet M, Gaillard JB, Penther D. Cytogenetics in the management of hematological malignancies: An overview of alternative technologies for cytogenetic characterization. Curr Res Transl Med 2024; 72:103440. [PMID: 38447270 DOI: 10.1016/j.retram.2024.103440] [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: 07/10/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Genomic characterization is an essential part of the clinical management of hematological malignancies for diagnostic, prognostic and therapeutic purposes. Although CBA and FISH are still the gold standard in hematology for the detection of CNA and SV, some alternative technologies are intended to complement their deficiencies or even replace them in the more or less near future. In this article, we provide a technological overview of these alternatives. CMA is the historical and well established technique for the high-resolution detection of CNA. For SV detection, there are emerging techniques based on the study of chromatin conformation and more established ones such as RTMLPA for the detection of fusion transcripts and RNA-seq to reveal the molecular consequences of SV. Comprehensive techniques that detect both CNA and SV are the most interesting because they provide all the information in a single examination. Among these, OGM is a promising emerging higher-solution technique that offers a complete solution at a contained cost, at the expense of a relatively low throughput per machine. WGS remains the most adaptable solution, with long-read approaches enabling very high-resolution detection of CAs, but requiring a heavy bioinformatics installation and at a still high cost. However, the development of high-resolution genome-wide detection techniques for CAs allows for a much better description of chromoanagenesis. Therefore, we have included in this review an update on the various existing mechanisms and their consequences and implications, especially prognostic, in hematological malignancies.
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Affiliation(s)
| | | | | | - Jean-Baptiste Gaillard
- Unité de Génétique Chromosomique, Service de Génétique moléculaire et cytogénomique, CHU Montpellier, Montpellier, France
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2
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Levy B, Baughn LB, Akkari Y, Chartrand S, LaBarge B, Claxton D, Lennon PA, Cujar C, Kolhe R, Kroeger K, Pitel B, Sahajpal N, Sathanoori M, Vlad G, Zhang L, Fang M, Kanagal-Shamanna R, Broach JR. Optical genome mapping in acute myeloid leukemia: a multicenter evaluation. Blood Adv 2023; 7:1297-1307. [PMID: 36417763 PMCID: PMC10119592 DOI: 10.1182/bloodadvances.2022007583] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/25/2022] Open
Abstract
Detection of hallmark genomic aberrations in acute myeloid leukemia (AML) is essential for diagnostic subtyping, prognosis, and patient management. However, cytogenetic/cytogenomic techniques used to identify those aberrations, such as karyotyping, fluorescence in situ hybridization (FISH), or chromosomal microarray analysis (CMA), are limited by the need for skilled personnel as well as significant time, cost, and labor. Optical genome mapping (OGM) provides a single, cost-effective assay with a significantly higher resolution than karyotyping and with a comprehensive genome-wide analysis comparable with CMA and the added unique ability to detect balanced structural variants (SVs). Here, we report in a real-world setting the performance of OGM in a cohort of 100 AML cases that were previously characterized by karyotype alone or karyotype and FISH or CMA. OGM identified all clinically relevant SVs and copy number variants (CNVs) reported by these standard cytogenetic methods when representative clones were present in >5% allelic fraction. Importantly, OGM identified clinically relevant information in 13% of cases that had been missed by the routine methods. Three cases reported with normal karyotypes were shown to have cryptic translocations involving gene fusions. In 4% of cases, OGM findings would have altered recommended clinical management, and in an additional 8% of cases, OGM would have rendered the cases potentially eligible for clinical trials. The results from this multi-institutional study indicate that OGM effectively recovers clinically relevant SVs and CNVs found by standard-of-care methods and reveals additional SVs that are not reported. Furthermore, OGM minimizes the need for labor-intensive multiple cytogenetic tests while concomitantly maximizing diagnostic detection through a standardized workflow.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Linda B. Baughn
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Yassmine Akkari
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Brandon LaBarge
- Department of Otolaryngology, Penn State College of Medicine, Hershey, PA
| | - David Claxton
- Department of Hematology and Oncology, Department of Medicine, Penn State College of Medicine, Hershey, PA
| | | | - Claudia Cujar
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA
| | - Kate Kroeger
- Cytogenetics Laboratory, Seattle Cancer Care Alliance, Seattle, WA
| | - Beth Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA
| | | | - George Vlad
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - James R. Broach
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA
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3
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Yurov YB, Vorsanova SG, Iourov IY. FISHing for Chromosome Instability and Aneuploidy in the Alzheimer's Disease Brain. Methods Mol Biol 2022; 2561:191-204. [PMID: 36399271 DOI: 10.1007/978-1-0716-2655-9_10] [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: 11/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is the method of choice for visualizing chromosomal DNA in post-mitotic cells. The availability of chromosome-enumeration (centromeric), site-specific, and multicolor-banding DNA probes offers opportunities to uncover genomic changes, at the chromosomal level, in single interphase nuclei. Alzheimer's disease (AD) has been associated repeatedly with (sub)chromosome instability and aneuploidy, likely affecting the brain. Although the types and rates of chromosome instability in the AD brain remain a matter of debate, molecular cytogenetic analysis of brain cells appears to be important for uncovering mechanisms of neurodegeneration. Here, we describe a FISH protocol for studying chromosome instability and aneuploidy in the AD brain.
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Affiliation(s)
- Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia. .,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia.
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4
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Lyu X, Li T, Zhu D, Cheng Y, Chen Y, He X, Li Z, Li S, Wu W, Geng S, Zhang M, Yao C, Li J, Li Y, Chang Y, Li Y, Zhu Z, Mao M, Song Y. Whole-genome sequencing as an alternative to analyze copy number abnormalities in acute myeloid leukemia and myelodysplastic syndrome. Leuk Lymphoma 2022; 63:2301-2310. [PMID: 35695096 DOI: 10.1080/10428194.2022.2080821] [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: 10/18/2022]
Abstract
Copy number aberrations (CNA) are the core determinants for diagnosis, risk stratification and prognosis in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). In this study, a shallow whole-genome sequencing-based assay, LeukoPrint, was utilized to depict genomic CNA profiles from the bone marrow of 137 newly diagnosed AML/MDS patients. It demonstrated 98.1% concordance of CNA profiles with cytogenetics and/or fluorescence in situ hybridization (FISH). It is advantageous in detecting CNAs of short segments (1 Mb) and from samples with low leukemic cell content, more accurate for describing complex karyotypes and less confounded by subjective bias. LeukoPrint improved the overall diagnostic yield by redefining the risk categories for 16 patients by presenting new information. In summary, LeukoPrint provided an automated, convenient, and cost-effective approach to describe genomic CNA profiles. It brought greater diagnostic yield and risk stratification information by incorporating into the routine cytogenetics based on the CNA-related criteria of standard ELN/IPSS-R guidelines.
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Affiliation(s)
- Xiaodong Lyu
- Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Tao Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dandan Zhu
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Yuexin Cheng
- Department of Hematology, Yancheng No. 1 People's Hospital, Yancheng, China.,Department of Hematology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China
| | - Yan Chen
- Research & Development, SeekIn Inc., Shenzhen, China
| | - Xiangxiang He
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Zhenling Li
- Department of Hematology, China-Japan Friendship Hospital, Beijing, China
| | - Shiyong Li
- Research & Development, SeekIn Inc., Shenzhen, China
| | - Wei Wu
- Research & Development, SeekIn Inc., Shenzhen, China
| | | | - Mengna Zhang
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Chunxiao Yao
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Jingshuai Li
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Yangwei Li
- Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yinyin Chang
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Yuchun Li
- Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zunmin Zhu
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Mao Mao
- Research & Development, SeekIn Inc., Shenzhen, China.,Yonsei Song-Dang Institute for Cancer Research, Yonsei University, Seoul, Korea
| | - Yongping Song
- Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
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5
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Nguyen-Khac F, Bidet A, Daudignon A, Lafage-Pochitaloff M, Ameye G, Bilhou-Nabéra C, Chapiro E, Collonge-Rame MA, Cuccuini W, Douet-Guilbert N, Eclache V, Luquet I, Michaux L, Nadal N, Penther D, Quilichini B, Terre C, Lefebvre C, Troadec MB, Véronèse L. The complex karyotype in hematological malignancies: a comprehensive overview by the Francophone Group of Hematological Cytogenetics (GFCH). Leukemia 2022; 36:1451-1466. [DOI: 10.1038/s41375-022-01561-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 12/16/2022]
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6
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Berglund E, Barbany G, Orsmark-Pietras C, Fogelstrand L, Abrahamsson J, Golovleva I, Hallböök H, Höglund M, Lazarevic V, Levin LÅ, Nordlund J, Norèn-Nyström U, Palle J, Thangavelu T, Palmqvist L, Wirta V, Cavelier L, Fioretos T, Rosenquist R. A Study Protocol for Validation and Implementation of Whole-Genome and -Transcriptome Sequencing as a Comprehensive Precision Diagnostic Test in Acute Leukemias. Front Med (Lausanne) 2022; 9:842507. [PMID: 35402448 PMCID: PMC8987911 DOI: 10.3389/fmed.2022.842507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/17/2022] [Indexed: 12/11/2022] Open
Abstract
Background Whole-genome sequencing (WGS) and whole-transcriptome sequencing (WTS), with the ability to provide comprehensive genomic information, have become the focal point of research interest as novel techniques that can support precision diagnostics in routine clinical care of patients with various cancer types, including hematological malignancies. This national multi-center study, led by Genomic Medicine Sweden, aims to evaluate whether combined application of WGS and WTS (WGTS) is technically feasible and can be implemented as an efficient diagnostic tool in patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). In addition to clinical impact assessment, a health-economic evaluation of such strategy will be performed. Methods and Analysis The study comprises four phases (i.e., retrospective, prospective, real-time validation, and follow-up) including approximately 700 adult and pediatric Swedish AML and ALL patients. Results of WGS for tumor (90×) and normal/germline (30×) samples as well as WTS for tumors only will be compared to current standard of care diagnostics. Primary study endpoints are diagnostic efficiency and improved diagnostic yield. Secondary endpoints are technical and clinical feasibility for routine implementation, clinical utility, and health-economic impact. Discussion Data from this national multi-center study will be used to evaluate clinical performance of the integrated WGTS diagnostic workflow compared with standard of care. The study will also elucidate clinical and health-economic impacts of a combined WGTS strategy when implemented in routine clinical care. Clinical Trial Registration [https://doi.org/10.1186/ISRCTN66987142], identifier [ISRCTN66987142].
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Affiliation(s)
- Eva Berglund
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Christina Orsmark-Pietras
- Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Clinical Genomics Gothenburg, Science for Life Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Abrahamsson
- Clinical Sciences, Queen Silvias Childrens Hospital, Gothenburg, Sweden
| | - Irina Golovleva
- Department of Medical Biosciences, University of Umeå, Umeå, Sweden
| | - Helene Hallböök
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Martin Höglund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Vladimir Lazarevic
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Lars-Åke Levin
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Josefine Palle
- Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Tharshini Thangavelu
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Lars Palmqvist
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Clinical Genomics Gothenburg, Science for Life Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Valtteri Wirta
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics and Pathology, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- *Correspondence: Richard Rosenquist,
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7
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Bi X, French Z, Palmisiano N, Wen KY, Wilde L. The prognostic impact of cigarette smoking on survival in acute myeloid leukemia with TP53 mutations and/or 17p deletions. Ann Hematol 2022; 101:1251-1259. [PMID: 35288759 DOI: 10.1007/s00277-022-04812-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/28/2022] [Indexed: 11/01/2022]
Abstract
Cigarette smoking has been associated with increased risk of developing acute myeloid leukemia (AML) in adults. There is limited data on the impact of smoking in AML patients with certain cytogenetic abnormalities. The aim of this study is to assess whether cigarette smoking affected the survival outcome of patients with newly diagnosed AML with TP53 alterations. We conducted a retrospective study of patients who were diagnosed with AML at the Thomas Jefferson Hospital with presence of TP53 mutations and/or 17p deletions. Patients' sex, age, race, smoking status (ever vs. never), cytogenetics, mutational profile, induction regimen, and induction response were analyzed. A total of 102 patients were included in the study with a median follow-up of 27.8 months. Among 100 patients who had documentation of smoking status, 59 patients (59%) were ever-smokers and 41 (41%) were never-smokers. Kaplan-Meier survival analysis showed that never-smokers did not differ in overall survival (OS) when compared to ever-smokers (P = 0.34). Univariate analysis revealed that age and cytogenetics had a statistically significant impact on survival. In multivariate analysis incorporating sex, age, race, smoking status, cytogenetics, and induction regimen as covariates, cytogenetics and induction regimen were independent prognostic factors for OS. In summary, no significant difference in OS was found between ever- and never-smokers in AML patients with TP53 alterations. Additional studies are needed to examine the prognostic impact of cigarette smoking in AML with specific cytogenetic abnormalities.
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Affiliation(s)
- Xia Bi
- Department of Medical Oncology, Thomas Jefferson University, Sidney Kimmel Cancer Center, 834 Chestnut Street, Suite 308, Philadelphia, PA, 19107, USA.
| | - Zachary French
- Department of Medical Oncology, Thomas Jefferson University, Sidney Kimmel Cancer Center, 834 Chestnut Street, Suite 308, Philadelphia, PA, 19107, USA
| | - Neil Palmisiano
- Department of Medical Oncology, Thomas Jefferson University, Sidney Kimmel Cancer Center, 834 Chestnut Street, Suite 308, Philadelphia, PA, 19107, USA
| | - Kuang-Yi Wen
- Division of Population Science, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Lindsay Wilde
- Department of Medical Oncology, Thomas Jefferson University, Sidney Kimmel Cancer Center, 834 Chestnut Street, Suite 308, Philadelphia, PA, 19107, USA
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8
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Lee WY, Gutierrez-Lanz EA, Xiao H, McClintock D, Chan MP, Bixby DL, Shao L. ERG amplification is a secondary recurrent driver event in myeloid malignancy with complex karyotype and TP53 mutations. Genes Chromosomes Cancer 2022; 61:399-411. [PMID: 35083818 DOI: 10.1002/gcc.23027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 11/09/2022] Open
Abstract
ERG is a transcription factor encoded on chromosome 21q22.2 with important roles in hematopoiesis and oncogenesis of prostate cancer. ERG amplification has been identified as one of the most common recurrent events in acute myeloid leukemia with complex karyotype (AML-CK). In this study, we uncover 3 different modes of ERG amplification in AML-CK. Importantly, we present evidence to show that ERG amplification is distinct from intrachromosomal amplification of chromosome 21 (iAMP21), a hallmark segmental amplification frequently encompassing RUNX1 and ERG in a subset of high-risk B-lymphoblastic leukemia. We also characterize the association with TP53 aberrations and other chromosomal aberrations, including chromothripsis. Lastly, we show that ERG amplification can initially emerge as subclonal events in low grade myeloid neoplasms. These findings demonstrate that ERG amplification is a recurrent secondary driver event in AML and raise the tantalizing possibility of ERG as a therapeutic target. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Winston Y Lee
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Efrain A Gutierrez-Lanz
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Hong Xiao
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - David McClintock
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - May P Chan
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Dale L Bixby
- Division of Hematology and Medical Oncology, Department of Medicine, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Lina Shao
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
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9
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Yang RK, Toruner GA, Wang W, Fang H, Issa GC, Wang L, Quesada AE, Thakral B, Patel KP, Peng G, Liu S, Yin CC, Borthakur G, Tang Z, Wang SA, Miranda RN, Khoury JD, Medeiros LJ, Tang G. CBFB Break-Apart FISH Testing: An Analysis of 1629 AML Cases with a Focus on Atypical Findings and Their Implications in Clinical Diagnosis and Management. Cancers (Basel) 2021; 13:5354. [PMID: 34771519 PMCID: PMC8582369 DOI: 10.3390/cancers13215354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 02/05/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) is a confirmatory test to establish a diagnosis of inv(16)/t(16;16) AML. However, incidental findings and their clinical diagnostic implication have not been systemically studied. We studied 1629 CBFB FISH cases performed in our institution, 262 (16.1%), 1234 (75.7%), and 133 (8.2%) were reported as positive, normal, and abnormal, respectively. The last included CBFB copy number changes (n = 120) and atypical findings such as 3'CBFB deletion (n = 11), 5'CBFB deletion (n = 1), and 5'CBFB gain (n = 1). Correlating with CBFB-MYH11 RT-PCR results, totally 271 CBFB rearrangement cases were identified, including five with discrepancies between FISH and RT-PCR due to new partner genes (n = 3), insertion (n = 1), or rare CBFB-MYH11 variant (n = 1) and eight with 3'CBFB deletion. All cases with atypical findings and/or discrepancies presented clinical diagnostic challenges. Correlating FISH signal patterns and karyotypes, additional chromosome 16 aberrations (AC16As) show impacts on the re-definition of a complex karyotype and prognostic prediction. The CBFB rearrangement but not all AC16As will be detected by NGS-based methods. Therefore, FISH testing is currently still needed to provide a quick and straightforward confirmatory inv(16)/t(16;16) AML diagnosis and additional information related to clinical management.
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Affiliation(s)
- Richard K. Yang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Gokce A. Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Wei Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Hong Fang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Ghayas C. Issa
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.I.); (G.B.)
| | - Lulu Wang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.W.); (G.P.)
| | - Andrés E. Quesada
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Beenu Thakral
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (L.W.); (G.P.)
| | - Shujuan Liu
- Parkview Regional Medical Center, Allied Hospital Pathologists, Fort Wayne, IN 46845, USA;
| | - C. Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Gautam Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.I.); (G.B.)
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Sa A. Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Roberto N. Miranda
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Joseph D. Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - L. Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (R.K.Y.); (G.A.T.); (W.W.); (H.F.); (A.E.Q.); (B.T.); (K.P.P.); (C.C.Y.); (S.A.W.); (R.N.M.); (J.D.K.); (L.J.M.); (G.T.)
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What Is Abnormal in Normal Karyotype Acute Myeloid Leukemia in Children? Analysis of the Mutational Landscape and Prognosis of the TARGET-AML Cohort. Genes (Basel) 2021; 12:genes12060792. [PMID: 34064268 PMCID: PMC8224370 DOI: 10.3390/genes12060792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 01/01/2023] Open
Abstract
Normal karyotype acute myeloid leukemia (NK-AML) constitutes 20–25% of pediatric AML and detailed molecular analysis is essential to unravel the genetic background of this group. Using publicly available sequencing data from the TARGET-AML initiative, we investigated the mutational landscape of NK-AML in comparison with abnormal karyotype AML (AK-AML). In 164 (97.6%) of 168 independent NK-AML samples, at least one somatic protein-coding mutation was identified using whole-genome or targeted capture sequencing. We identified a unique mutational landscape of NK-AML characterized by a higher prevalence of mutated CEBPA, FLT3, GATA2, NPM1, PTPN11, TET2, and WT1 and a lower prevalence of mutated KIT, KRAS, and NRAS compared with AK-AML. Mutated CEBPA often co-occurred with mutated GATA2, whereas mutated FLT3 co-occurred with mutated WT1 and NPM1. In multivariate regression analysis, we identified younger age, WBC count ≥50 × 109/L, FLT3-internal tandem duplications, and mutated WT1 as independent predictors of adverse prognosis and mutated NPM1 and GATA2 as independent predictors of favorable prognosis in NK-AML. In conclusion, NK-AML in children is characterized by a unique mutational landscape which impacts the disease outcome.
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