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Andersen K, Tjønnfjord GE, Ramslien LF, Panagopoulos I. RUNX1::MIR99AHG Chimera in Acute Myeloid Leukemia. Genes Chromosomes Cancer 2024; 63:e23272. [PMID: 39324493 DOI: 10.1002/gcc.23272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/27/2024] Open
Abstract
RUNX1 fuses with over 70 different partner genes in hematological neoplasms. While common RUNX1 chimeras have been extensively studied and their prognosis is well established, our current understanding of less common RUNX1 chimeras is limited. Here, we present a case of acute myeloid leukemia (AML) with a rare RUNX1 chimera. Bone marrow cells obtained at diagnosis from a 71-year-old patient diagnosed with AML-M5 were studied using G-banding, fluorescence in situ hybridization, array comparative genomic hybridization, RNA sequencing, PCR, and Sanger sequencing. Combined findings from the abovementioned assays suggested three cytogenetic clones: one with a normal karyotype, one with inv(21)(q21q22), and one with two inv(21)(q21q22). The molecular analysis revealed the fusion of RUNX1 with MIR99AHG (at 21q21.1), further supporting the presence of an inv(21)(q21q22). The present case is the third reported AML harboring a RUNX1::MIR99AHG chimera. Similar to the two previously described AML patients, our case also had an FLT3 aberration.
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Affiliation(s)
- Kristin Andersen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Geir E Tjønnfjord
- Department of Haematology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - L Frode Ramslien
- Department of Internal Medicine, Telemark Hospital Trust, Skien, Norway
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, the Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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2
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Guijarro F, Castaño-Díez S, Jiménez-Vicente C, Garrote M, Álamo JR, Gómez-Hernando M, López-Oreja I, Morata J, López-Guerra M, López C, Beà S, Costa D, Colomer D, Díaz-Beyá M, Rozman M, Esteve J. Whole Exome Sequencing of Intermediate-Risk Acute Myeloid Leukemia without Recurrent Genetic Abnormalities Offers Deeper Insights into New Diagnostic Classifications. Int J Mol Sci 2024; 25:8669. [PMID: 39201354 PMCID: PMC11354381 DOI: 10.3390/ijms25168669] [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: 06/17/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Two new diagnostic classifications of acute myeloid leukemia (AML) were published in 2022 to update current knowledge on disease biology. In previous 2017-edition categories of AML with myelodysplasia-related changes, AML was not otherwise specified, but AML with mutated RUNX1 experienced profound changes. We performed whole exome sequencing on a cohort of 69 patients with cytogenetic intermediate-risk AML that belonged to these diagnostic categories to correlate their mutational pattern and copy-number alterations with their new diagnostic distribution. Our results show that 45% of patients changed their diagnostic category, being AML myelodysplasia-related the most enlarged, mainly due to a high frequency of myelodysplasia-related mutations (58% of patients). These showed a good correlation with multilineage dysplasia and/or myelodysplastic syndrome history, but at the same time, 21% of de novo patients without dysplasia also presented them. RUNX1 was the most frequently mutated gene, with a high co-occurrence rate with other myelodysplasia-related mutations. We found a high prevalence of copy-neutral loss of heterozygosity, frequently inducing a homozygous state in particular mutated genes. Mild differences in current classifications explain the diagnostic disparity in 10% of patients, claiming a forthcoming unified classification.
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Affiliation(s)
- Francesca Guijarro
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
| | - Sandra Castaño-Díez
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
| | - Carlos Jiménez-Vicente
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
- Hematology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain
| | - Marta Garrote
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
| | - José Ramón Álamo
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
| | - Marta Gómez-Hernando
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
| | - Irene López-Oreja
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
| | - Jordi Morata
- Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, Spain;
| | - Mònica López-Guerra
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
- Biomedical Research Networking Center on Oncology (CIBERONC), 28029 Madrid, Spain
| | - Cristina López
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
- Biomedical Research Networking Center on Oncology (CIBERONC), 28029 Madrid, Spain
- Facultat de Medicina, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Sílvia Beà
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
- Biomedical Research Networking Center on Oncology (CIBERONC), 28029 Madrid, Spain
- Facultat de Medicina, Universitat de Barcelona, 08007 Barcelona, Spain
| | - Dolors Costa
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
- Biomedical Research Networking Center on Oncology (CIBERONC), 28029 Madrid, Spain
| | - Dolors Colomer
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
- Biomedical Research Networking Center on Oncology (CIBERONC), 28029 Madrid, Spain
| | - Marina Díaz-Beyá
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
- Hematology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain
| | - Maria Rozman
- Hematopathology Section, Pathology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain; (S.C.-D.); (M.G.); (J.R.Á.); (M.G.-H.); (I.L.-O.); (M.L.-G.); (C.L.); (S.B.); (D.C.); (D.C.); (M.R.)
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
| | - Jordi Esteve
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (C.J.-V.); (M.D.-B.); (J.E.)
- Hematology Department, Hospital Clínic Barcelona, 08036 Barcelona, Spain
- Facultat de Medicina, Universitat de Barcelona, 08007 Barcelona, Spain
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3
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Akkari Y, Baughn LB, Kim A, Karaca E, Raca G, Shao L, Mikhail FM. Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes. Genet Med 2024; 26:101054. [PMID: 38349293 DOI: 10.1016/j.gim.2023.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 04/09/2024] Open
Abstract
Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.
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Affiliation(s)
- Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH
| | - Linda B Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Annette Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Ender Karaca
- Department of Pathology, Baylor University Medical Center, Dallas, TX; Texas A&M School of Medicine, Texas A&M University, Dallas, TX
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lina Shao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
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4
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Yuan J, He R, Alkhateeb HB. Sporadic and Familial Acute Myeloid Leukemia with CEBPA Mutations. Curr Hematol Malig Rep 2023; 18:121-129. [PMID: 37261703 PMCID: PMC10484814 DOI: 10.1007/s11899-023-00699-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2023] [Indexed: 06/02/2023]
Abstract
PURPOSE OF REVIEW CCAAT enhancer binding protein A (CEBPA) gene mutation is one of the common genetic alterations in acute myeloid leukemia (AML), which can be associated with sporadic and familial AML. RECENT FINDINGS Due to the recent advances in molecular testing and the prognostic role of CEBPA mutation in AML, the definition for AML with CEBPA mutation (AML-CEBPA) has significantly changed. This review provides the rationale for the updates on classifications, and the impacts on laboratory evaluation and clinical management for sporadic and familial AML-CEBPA patients. In addition, minimal residual disease assessment post therapy to stratify disease risk and stem cell transplant in selected AML-CEBPA patients are discussed. Taken together, the recent progresses have shifted the definition, identification, and management of patients with AML-CEBPA.
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Affiliation(s)
- Ji Yuan
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN USA
| | - Rong He
- Department of Laboratory Medicine and Pathology, Division of Hematopathology, Mayo Clinic, Rochester, MN USA
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5
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Boada M, Catalán AI, Ottati C, Bentancour F, Lens D, Guillermo C, Grille S. Germline CEBPA mutation in familial acute myeloid leukemia. Hematol Rep 2021; 13:9114. [PMID: 34733449 PMCID: PMC8506203 DOI: 10.4081/hr.2021.9114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/17/2021] [Indexed: 11/23/2022] Open
Abstract
Myeloid Neoplasms with germline predisposition become part of 2016 World Health Organization (WHO) classification of hematological malignancies since 2016. CCAAT/enhancer binding protein-alpha (CEBPA) is a myeloid transcription factor located in chromosome 19q. Acute myeloid leukemia (AML) with biallelic mutations of CEBPA AML with recurrent genetic abnormalities according to WHO classification. The inheritance of a germline CEBPA mutation predisposes to the development of AML with autosomal dominant inheritance. Familial CEBPA AML share characteristics with somatic CEBPA AML. However, a higher relapse incidence is reported. We present the case of a 46-years-old male with family history of acute leukemia who was diagnosed with single mutated CEBPA acute myeloid leukemia. The same mutation was found in two of his siblings. The clinical suspicion and proper diagnosis of familial cases is necessary, especially when a related allogenic transplant is indicated in order to select an adequate donor.
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Affiliation(s)
| | - Ana Inés Catalán
- Basic Medicine Department, Hospital de Clínicas Dr. Manuel Quinela, Montevideo, Uruguay
| | - Carolina Ottati
- Basic Medicine Department, Hospital de Clínicas Dr. Manuel Quinela, Montevideo, Uruguay
| | | | - Daniela Lens
- Basic Medicine Department, Hospital de Clínicas Dr. Manuel Quinela, Montevideo, Uruguay
| | | | - Sofía Grille
- Hematology Department.,Basic Medicine Department, Hospital de Clínicas Dr. Manuel Quinela, Montevideo, Uruguay
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6
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Bedair HM, Attia MH, Gohar SF, Khalaf FM, Badr El-DIN S, Rabie H. The prognostic impact of Wilms tumor-1 polymorphism (rs16754) and human myeloid inhibitory C-type lectin-like receptor expression in cytogenetically normal-acute myeloid leukemia. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00183-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
There are several genetic mutations that carry prognostic and predictive values in acute myeloid leukemia (AML). They are also implicated in disease pathogenesis and patient outcome. They can be a target of novel therapies for AML. The aim of the current study was to investigate prognostic value of Wilms’ tumor-1 (WT1) genotypes and human myeloid inhibitory C-type lectin-like (hMICL) receptor expression in normal-cytogenetic group of patients with AML. Genotyping of WT1 mutations was done by Rotor Gene real-time polymerase chain reaction (PCR) while hMICL expression was detected using phycoerythrin (PE)-conjugated mouse monoclonal anti-human (MoAbs) by flow cytometry.
Results
Sixty-three patients with cytogenetically normal AML (CN-AML) were included in the study. The alternate allele of WT1 single nucleotide polymorphism (SNP) rs16754 was found in 26.89%. At day 28 of therapy, complete remission was achieved in 100% of cases harboring mutant AG plus GG genotypes but only in 6.38% of cases harboring wild genotype (AA). After 6 months, 88.23% of patients harboring WT1 mutant genotype maintained complete remission, while only 23.40% of patients with wild type showed complete remission. The overall survival in patients harboring mutant WT1 genotypes was significantly longer than in those who carried the wild type gene (P-value, 0.001). Additionally, hMICL was overexpressed in approximately 87.3% of AML cases and inversely related to complete response. Similarly, overall survival was significantly shorter in patients with positive hMICL (P-value, 0.001).
Conclusion
Mutant WT1 genotypes (SNP rs16754) were conversely, associated with complete response, and hMICL overexpression had poor prognostic value in AML.
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Zhang X, Sjöblom T. Targeting Loss of Heterozygosity: A Novel Paradigm for Cancer Therapy. Pharmaceuticals (Basel) 2021; 14:ph14010057. [PMID: 33450833 PMCID: PMC7828287 DOI: 10.3390/ph14010057] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
Loss of heterozygosity (LOH) is a common genetic event in the development of cancer. In certain tumor types, LOH can affect more than 20% of the genome, entailing loss of allelic variation in thousands of genes. This reduction of heterozygosity creates genetic differences between tumor and normal cells, providing opportunities for development of novel cancer therapies. Here, we review and summarize (1) mutations associated with LOH on chromosomes which have been shown to be promising biomarkers of cancer risk or the prediction of clinical outcomes in certain types of tumors; (2) loci undergoing LOH that can be targeted for development of novel anticancer drugs as well as (3) LOH in tumors provides up-and-coming possibilities to understand the underlying mechanisms of cancer evolution and to discover novel cancer vulnerabilities which are worth a further investigation in the near future.
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8
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Xiao X, He X, Li Q, Zhang W, Zhu H, Yang W, Li Y, Geng L, Liu H, Li L, Wang H, Fu R, Zhao M, Chen Z, Shao Z. Single-Nucleotide Polymorphism Array Technique Generating Valuable Risk-Stratification Information for Patients With Myelodysplastic Syndromes. Front Oncol 2020; 10:962. [PMID: 32733790 PMCID: PMC7358551 DOI: 10.3389/fonc.2020.00962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Chromosomal abnormalities play an important role in the diagnosis and prognosis of patients with myelodysplastic syndromes (MDSs). The single-nucleotide polymorphism array (SNP-A) technique has gained popularity due to its improved resolution compared to that of metaphase cytogenetic (MC) analysis. Methods: A total of 376 individuals were recruited from two medical centers in China, including 350 patients and 26 healthy individuals. Among these patients, 200 were diagnosed with de novo MDS, 25 with myeloproliferative neoplasm (MPN), 63 with primary acute myeloid leukemia (AML), and 62 with idiopathic cytopenia of undetermined significance (ICUS). We evaluated the significance of abnormal chromosomes detected by SNP-A in the diagnosis and prognosis of MDS-related disorders. Results: (1) When certain chromosomal abnormalities could not be detected by conventional MC methods, these abnormalities could be detected more efficiently by the SNP-A method. With SNP-A, the detection rates of submicroscopic or cryptic aberrations in the MDS, MPN, and AML patients with normal MC findings were 32.8, 30.8, and 30%, respectively. (2) The chromosomal abnormalities detected by SNP-A had a very important value for the prognosis of patients with MDSs, especially in the low-risk group. The survival of patients with abnormal chromosomes detected by SNP-A was significantly lower than that of patients with no detected chromosomal abnormalities; this difference was observed in overall survival (OS) (P = 0.001) and progression-free survival (PFS) [24 months vs. not reach (NR); P = 0.008]. The patients with multiple chromosomal abnormalities detected by SNP-A had an inferior prognosis, and SNP-A abnormalities (≥3 per patient) were found to be an independent predictor of poor prognosis in patients with MDSs [hazard ratio (HR) = 2.40, P = 0.002]. (3) Patients with ICUS may progress to myeloid malignancies, but most patients often maintain a stable ICUS status for many years without progression. An ICUS patient found to have an MDS-related karyotype would be rediagnosed with MDS. SNP-A can efficiently detect chromosomal abnormalities, which would be important for assessing the evolution of ICUS. In our study, 17 ICUS patients with SNP-A-detected abnormalities developed typical MDSs. Conclusions: SNP-A can help evaluate the prognosis of patients with MDSs and better assess the risk of disease progression for patients with ICUS.
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Affiliation(s)
- Xia Xiao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Xiaoyuan He
- Department of Clinical Medicine, Nankai University School of Medicine, Tianjin, China
| | - Qing Li
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Wei Zhang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Haibo Zhu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Weihong Yang
- Wuhan Kindstar Diagnostics Co./Kindstar Global Gene (Beijing) Technology, Inc., Wuhan, China
| | - Yuming Li
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Li Geng
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Hui Liu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Lijuan Li
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Huaquan Wang
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Rong Fu
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingfeng Zhao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China.,Department of Clinical Medicine, Nankai University School of Medicine, Tianjin, China
| | - Zhong Chen
- Wuhan Kindstar Diagnostics Co./Kindstar Global Gene (Beijing) Technology, Inc., Wuhan, China
| | - Zonghong Shao
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
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9
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Svobodova K, Lhotska H, Hodanova L, Pavlistova L, Vesela D, Belickova M, Vesela J, Brezinova J, Sarova I, Izakova S, Lizcova L, Siskova M, Jonasova A, Cermak J, Michalova K, Zemanova Z. Cryptic aberrations may allow more accurate prognostic classification of patients with myelodysplastic syndromes and clonal evolution. Genes Chromosomes Cancer 2020; 59:396-405. [PMID: 32170980 DOI: 10.1002/gcc.22841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/03/2020] [Accepted: 02/29/2020] [Indexed: 11/05/2022] Open
Abstract
The karyotype of bone-marrow cells at the time of diagnosis is one of the most important prognostic factors in patients with myelodysplastic syndromes (MDS). In some cases, the acquisition of additional genetic aberrations (clonal evolution [CE]) associated with clinical progression may occur during the disease. We analyzed a cohort of 469 MDS patients using a combination of molecular cytogenomic methods to identify cryptic aberrations and to assess their potential role in CE. We confirmed CE in 36 (8%) patients. The analysis of bone-marrow samples with a combination of cytogenomic methods at diagnosis and after CE identified 214 chromosomal aberrations. The early genetic changes in the diagnostic samples were frequently MDS specific (17 MDS-specific/57 early changes). Most progression-related aberrations identified after CE were not MDS specific (131 non-MDS-specific/155 progression-related changes). Copy number neutral loss of heterozygosity (CN-LOH) was detected in 19% of patients. MDS-specific CN-LOH (4q, 17p) was identified in three patients, and probably pathogenic homozygous mutations were found in TET2 (4q24) and TP53 (17p13.1) genes. We observed a statistically significant difference in overall survival (OS) between the groups of patients divided according to their diagnostic cytogenomic findings, with worse OS in the group with complex karyotypes (P = .021). A combination of cytogenomic methods allowed us to detect many cryptic genomic changes and identify genes and genomic regions that may represent therapeutic targets in patients with progressive MDS.
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Affiliation(s)
- Karla Svobodova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Halka Lhotska
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lucie Hodanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Lenka Pavlistova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Denisa Vesela
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Monika Belickova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jitka Vesela
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jana Brezinova
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Iveta Sarova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Silvia Izakova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Libuse Lizcova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Magda Siskova
- First Medical Department, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Jonasova
- First Medical Department, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jaroslav Cermak
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Kyra Michalova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Zuzana Zemanova
- Center of Oncocytogenomics, Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital and First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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10
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Cottone L, Eden N, Usher I, Lombard P, Ye H, Ligammari L, Lindsay D, Brandner S, Pižem J, Pillay N, Tirabosco R, Amary F, Flanagan AM. Frequent alterations in p16/CDKN2A identified by immunohistochemistry and FISH in chordoma. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2020; 6:113-123. [PMID: 31916407 PMCID: PMC7164370 DOI: 10.1002/cjp2.156] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/19/2022]
Abstract
The expression of p16/CDKN2A, the second most commonly inactivated tumour suppressor gene in cancer, is lost in the majority of chordomas. However, the mechanism(s) leading to its inactivation and contribution to disease progression have only been partially addressed using small patient cohorts. We studied 384 chordoma samples from 320 patients by immunohistochemistry and found that p16 protein was lost in 53% of chordomas and was heterogeneously expressed in these tumours. To determine if CDKN2A copy number loss could explain the absence of p16 protein expression we performed fluorescence in situ hybridisation (FISH) for CDKN2A on consecutive tissue sections. CDKN2A copy number status was altered in 168 of 274 (61%) of samples and copy number loss was the most frequent alteration acquired during clinical disease progression. CDKN2A homozygous deletion was always associated with p16 protein loss but only accounted for 33% of the p16‐negative cases. The remaining immunonegative cases were associated with disomy (27%), monosomy (12%), heterozygous loss (20%) and copy number gain (7%) of CDKN2A, supporting the hypothesis that loss of protein expression might be achieved via epigenetic or post‐transcriptional regulatory mechanisms. We identified that mRNA levels were comparable in tumours with and without p16 protein expression, but other events including DNA promoter hypermethylation, copy number neutral loss of heterozygosity and expression of candidate microRNAs previously implicated in the regulation of CDKN2A expression were not identified to explain the protein loss. The data argue that p16 loss in chordoma is commonly caused by a post‐transcriptional regulatory mechanism that is yet to be defined.
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Affiliation(s)
- Lucia Cottone
- UCL Cancer Institute, University College London, London, UK
| | - Nadia Eden
- UCL Cancer Institute, University College London, London, UK
| | - Inga Usher
- UCL Cancer Institute, University College London, London, UK
| | | | - Hongtao Ye
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | | | - Daniel Lindsay
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Sebastian Brandner
- UCL Queen Square Institute of Neurology, University College London, London, UK.,Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College Hospitals NHS Foundation Trust, London, UK
| | - Jože Pižem
- Institute of Pathology, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | - Nischalan Pillay
- UCL Cancer Institute, University College London, London, UK.,Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Roberto Tirabosco
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Fernanda Amary
- UCL Cancer Institute, University College London, London, UK.,Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | - Adrienne M Flanagan
- UCL Cancer Institute, University College London, London, UK.,Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
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11
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Tuna M, Liu W, Amos CI, Mills GB. Genome-Wide Profiling of Acquired Uniparental Disomy Reveals Prognostic Factors in Head and Neck Squamous Cell Carcinoma. Neoplasia 2019; 21:1102-1109. [PMID: 31734631 PMCID: PMC6889229 DOI: 10.1016/j.neo.2019.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 01/04/2023] Open
Abstract
Acquired uniparental disomy (aUPD) leads to homozygosity facilitating identification of monoallelically expressed genes. We analyzed single-nucleotide polymorphism array-based genotyping data of 448 head and neck squamous cell carcinoma (HNSCC) samples from The Cancer Genome Atlas to determine the frequency and distribution of aUPD regions and their association with survival, as well as to gain a better understanding of their influence on the tumor genome. We used expression data from the same dataset to identify differentially expressed genes between groups with and without aUPD. Univariate and multivariable Cox proportional hazards models were performed for survival analysis. We found that 82.14% of HNSCC samples carried aUPD; the most common regions were in chromosome 17p (31.25%), 9p (30.13%), and 9q (27.46%). In univariate analysis, five independent aUPD regions at chromosome 9p, two regions at chromosome 9q, and the CDKN2A region were associated with poor overall survival in all groups, including training and test sets and human papillomavirus (HPV)-negative samples. Forty-three genes in areas of aUPD including PD-L1 and CDKN2A were differentially expressed in samples with aUPD compared to samples without aUPD. In multivariable analysis, aUPD at the CDKN2A region was a significant predictor of overall survival in the whole cohort and in patients with HPV-negative HNSCC. aUPD at specific regions in the genome influences clinical outcomes of HNSCC and may be beneficial for selection of personalized therapy to prolong survival in patients with this disease.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Medicine, Baylor College of Medicine, Houston, TX.
| | - Wenbin Liu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Cell, Developmental & Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR; Precision Oncology, Knight Cancer Institute, Portland, OR
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12
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Li J, Li J, Li J, Yao H, Liu F, Gusella JF, Shi X, Chen X. A rare case of acquired immunodeficiency associated with myelodysplastic syndrome. Mol Genet Genomic Med 2019; 7:e923. [PMID: 31503426 PMCID: PMC6825869 DOI: 10.1002/mgg3.923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Pediatric myelodysplastic syndromes (MDS) display clonal genomic instability that can lead to acquisition of other hematological disorders, usually by loss of heterozygosity. Immunodeficiency caused by uniparental disomy (UPD) has not previously been reported. METHODS We investigated a 13-year-old boy who suffered from recurrent infections and pancytopenia for 1 year. Both the comet assay and chromosome breakage analysis were normal, but the bone marrow showed evidence of dysplasia characteristic of MDS. With his normal sister as donor, he underwent failed hematopoietic stem cell transplantation (HSCT) with reduced intensity conditioning (RIC) followed by successful HSCT with myeloablative conditioning (MAC). We used single nucleotide polymorphism (SNP) array, targeted gene panel, and whole exome sequencing to investigate the etiology of his disease. RESULTS The molecular analyses revealed multiple regions of homozygosity, one region encompassing a homozygous missense variant of recombination activating gene 1 (RAG1) which was previously associated with severe immunodeficiency in infancy. This RAG1 mutation was heterozygous in the proband's fingernail DNA, but was changed to homozygous in the proband's marrow by somatic acquisition of UPD event. No other pathogenic driver mutation for MDS-related genes was identified. CONCLUSION The hematological phenotype, somatic genomic instability, and response to HSCT MAC but not HSCT RIC deduced to a diagnosis of MDS type refractory cytopenia of children in this patient. His immunodeficiency was secondary to MDS due to somatic acquisition of homozygosity for known pathogenic RAG1 mutation.
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Affiliation(s)
- Juanjuan Li
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Junhui Li
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Jianguo Li
- Department of RheumatologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Hailan Yao
- Department of Molecular ImmunologyCapital Institute of PediatricsBeijingChina
| | - Fang Liu
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingChina
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
| | - Xiaodong Shi
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Xiaoli Chen
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingChina
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13
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Chen C, Heng EYH, Lim AST, Lau LC, Lim TH, Wong GC, Tien SL. Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay. Int J Lab Hematol 2019; 41:561-571. [PMID: 31112375 DOI: 10.1111/ijlh.13052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Conventional cytogenetics (CC) is important in diagnosis, therapy, monitoring of post-transplant bone marrow, and prognosis assessment of acute lymphoblastic leukemia (ALL). However, due to the nature of ALL, CC often encounters difficulties of complex karyotype, poor chromosome morphology, low mitotic index, or normal cells dividing only. In contrast, chromosomal microarray analysis (CMA) showed a specificity >99% and a sensitivity of 100% in chronic lymphocytic leukemia (CLL) patients. Here, we report our experience with CMA on adult ALL patients. METHODS Thirty-three bone marrow/blood samples from ALL patients (aged 18-79 years, median 44) at diagnosis/relapse, analyzed by CC and/or fluorescence in situ hybridization (FISH), were recruited. Chromosomal microarray analysis results were compared with CC. Fluorescence in situ hybridization analysis, if available, was applied when there was a discrepancy. RESULTS Copy-neutral loss-of-heterozygosity (CN-LOH) was found in 8 cases (24.2%). Only CN-LOH at 9p was recurrent (3 cases, 9.1%). Copy number alterations (CNAs) were detected in 6 of 9 cases (66.7%) with normal karyotypes, in 3 of 5 cases (60.0%) with sole "balanced" translocations, and in 18 of 19 cases (94.7%) with complex karyotypes. Common CNAs involved CDKN2A/2B (30.3%), IKZF1 (27.3%), PAX5 (9.1%), RB1 (9.1%), BTG1 (6.7%), and ETV6 (6.7%), which regulate cell cycle, B lymphopoiesis, or act as tumor suppressors in ALL. Copy number alteration detection rate by CMA was 81.8% (27 of 33 cases) as compared to 57.6% (19 of 33 cases) by CC. CONCLUSION Incorporation of CMA as a routine clinical test at the time of diagnosis/relapse, in conjunction with CC and/or FISH, is highly recommended.
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Affiliation(s)
- Chuanfei Chen
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Evelyn Yee Hsieh Heng
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Alvin Soon Tiong Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Lai Ching Lau
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Tse Hui Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Sim Leng Tien
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
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14
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Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group. Cancer Genet 2018; 228-229:218-235. [DOI: 10.1016/j.cancergen.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/19/2022]
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15
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Condorelli DF, Spampinato G, Valenti G, Musso N, Castorina S, Barresi V. Positive Caricature Transcriptomic Effects Associated with Broad Genomic Aberrations in Colorectal Cancer. Sci Rep 2018; 8:14826. [PMID: 30287863 PMCID: PMC6172234 DOI: 10.1038/s41598-018-32884-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
We re-examined the correlation between Broad Genomic Aberrations (BGAs) and transcriptomic profiles in Colorectal Cancer (CRC). Two types of BGAs have been examined: Broad Copy-Number Abnormal regions (BCNAs), distinguished in gain- and loss-type, and Copy-Neutral Loss of Heterozygosities (CNLOHs). Transcripts are classified as “OverT” or “UnderT” if overexpressed or underexpressed comparing CRCs bearing a specific BGA to CRCs not bearing it and as “UpT” or “DownT” if upregulated or downregulated in cancer compared to normal tissue. BGA-associated effects were evaluated by changes in the “Chromosomal Distribution Index” (CDI) of different transcript classes. Data show that UpT are more sensitive than DownT to BCNA-associated gene dosage effects. “Over-UpT” genes are upregulated in cancer and further overexpressed by gene dosage, defining the so called “positive caricature transcriptomic effect”. When Over-UpT genes are ranked according to overexpression, top positions are occupied by genes implicated at the functional and therapeutic level in CRC. We show that cancer-upregulated transcripts are sensitive markers of BCNA-induced effects and suggest that analysis of positive caricature transcriptomic effects can provide clues toward the identification of BCNA-associated cancer driver genes.
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Affiliation(s)
- Daniele F Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy.
| | - Giorgia Spampinato
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy
| | - Giovanna Valenti
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy
| | - Sergio Castorina
- Department of Medical and Surgical Sciences and Advanced Technologies, University of Catania, Catania, (95123), Italy
| | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy.
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16
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Takayanagi S, Mukasa A, Tanaka S, Nomura M, Omata M, Yanagisawa S, Yamamoto S, Ichimura K, Nakatomi H, Ueki K, Aburatani H, Saito N. Differences in genetic and epigenetic alterations between von Hippel-Lindau disease-related and sporadic hemangioblastomas of the central nervous system. Neuro Oncol 2018; 19:1228-1236. [PMID: 28379443 DOI: 10.1093/neuonc/nox034] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Although inactivation of the von Hippel-Lindau gene (VHL), located on chromosome 3p25, is considered to be a major cause of hemangioblastomas (HBs), the incidence of biallelic inactivation of VHL is reportedly low. The aim of this study was to determine the prevalence of VHL alterations in HBs, as well as to identify additional molecular aberrations. Methods Genetic and epigenetic alterations were comprehensively and comparatively analyzed in 11 VHL-related and 21 sporadic HBs. Results VHL alterations detected by sequencing and multiplex ligation-dependent probe amplification (MLPA) analysis were more frequent in VHL-related HBs than in sporadic HBs (100% vs 62%; P = 0.029). VHL alterations were found only in 4 sporadic HBs by direct sequencing; however, targeted deep sequencing detected 9 additional alterations. Loss of heterozygosity (LOH) on chromosome 3 was found in 64% and 57% of VHL-related and sporadic HBs, respectively, by single nucleotide polymorphism (SNP) array analysis. Among 19 tumors with chromosome 3 LOH, 5 were classified as copy-neutral LOH. VHL promoter hypermethylation was detected only in sporadic HBs (33%), indicating that epigenetic suppression of VHL is a common mechanism in sporadic HBs. The rate of biallelic VHL inactivation among VHL-related and sporadic HBs was 64% and 52%, respectively. LOH on either chromosome 6 or 10 was detected only in sporadic HBs (43%). Conclusion Although biallelic inactivation of VHL is a dominant mechanistic cause of the pathogenesis of HB, other unknown mechanisms may also be involved, and such mechanisms may be different between VHL-related and sporadic HB.
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Affiliation(s)
| | - Akitake Mukasa
- Department of Neurosurgery, The University of Tokyo, Tokyo, Japan
| | - Shota Tanaka
- Department of Neurosurgery, The University of Tokyo, Tokyo, Japan
| | - Masashi Nomura
- Department of Neurosurgery, The University of Tokyo, Tokyo, Japan
| | - Mayu Omata
- Department of Neurosurgery, The University of Tokyo, Tokyo, Japan
| | | | - Shogo Yamamoto
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | | | - Keisuke Ueki
- Department of Neurosurgery, Dokkyo Medical University, Mibu, Tochigi,Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, The University of Tokyo, Tokyo, Japan
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17
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Whole-exome sequencing exploration of acquired uniparental disomies in B-cell precursor acute lymphoblastic leukemia. Leukemia 2018; 32:2058-2062. [PMID: 29967378 PMCID: PMC6127080 DOI: 10.1038/s41375-018-0191-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/07/2018] [Accepted: 06/04/2018] [Indexed: 11/08/2022]
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18
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El-Sharkawi D, Sproul D, Allen CG, Feber A, Wright M, Hills RK, Linch DC, Gale RE. Variable outcome and methylation status according to CEBPA mutant type in double-mutated acute myeloid leukemia patients and the possible implications for treatment. Haematologica 2018; 103:91-100. [PMID: 29025912 PMCID: PMC5777194 DOI: 10.3324/haematol.2017.173096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/10/2017] [Indexed: 11/16/2022] Open
Abstract
Although CEBPA double-mutated (CEBPADM) acute myeloid leukemia is considered to be a favorable-risk disease, relapse remains a major cause of treatment failure. Most CEBPADM patients have a classic biallelic mutant combination with an N-terminal mutation leading to production of p30 protein plus a C-terminal loss-of-function in-frame indel mutation (CEBPAClassic-DM), but approximately one-third of cases have one or more non-classic mutations, with diverse combinations reported, and there is little information on the consequences of such mutants. We evaluated outcome in a cohort of 104 CEBPADM patients, 79 CEBPAClassic-DM and 25 with non-classic mutants, and found that the latter may have poorer survival (5-year overall survival 64% vs. 46%; P=0.05), particularly post relapse (41% vs. 0%; P=0.02). However, for this analysis, all non-classic cases were grouped together, irrespective of mutant combination. As CEBPADM cases have been reported to be hypermethylated, we used methylation profiling to assess whether this could segregate the different mutants. We developed a CEBPAClassic-DM methylation signature from a preliminary cohort of 10 CEBPADM (including 8 CEBPAClassic-DM) and 30 CEBPA wild-type (CEBPAWT) samples, and independently validated the signature in 17 CEBPAClassic-DM cases. Assessment of the signature in 16 CEBPADM cases with different non-classic mutant combinations showed that only 31% had a methylation profile equivalent to CEBPAClassic-DM whereas for 69% the profile was either intermediate between CEBPAClassic-DM and CEBPAWT or equivalent to CEBPAWT These results suggest that CEBPADM cases with non-classic mutants may be functionally different from those with CEBPAClassic-DM mutants, and should not automatically be included in the same prognostic group. (AML12 is registered under ISRCTN17833622 and AML15 under ISRCTN17161961).
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Affiliation(s)
| | - Duncan Sproul
- MRC Human Genetics Unit and Edinburgh Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh
| | | | | | | | | | - David C Linch
- Department of Haematology, UCL Cancer Institute, London
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19
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Guinn BA, Mohamedali A, Mills KI, Czepulkowski B, Schmitt M, Greiner J. Leukemia Associated Antigens: Their Dual Role as Biomarkers and Immunotherapeutic Targets for Acute Myeloid Leukemia. Biomark Insights 2017. [DOI: 10.1177/117727190700200015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Leukemia associated antigens (LAAs) are being increasingly identified by methods such as cytotoxic T-lymphocyte (CTL) cloning, serological analysis of recombinant cDNA expression libraries (SEREX) and mass spectrometry (MS). In additional, large scale screening techniques such as microarray, single nucleotide polymorphisms (SNPs), serial analysis of gene expression (SAGE) and 2-dimensional gel electrophoresis (2-DE) have expanded our understanding of the role that tumor antigens play in the biological processes which are perturbed in acute myeloid leukemia (AML). It has become increasingly apparent that these antigens play a dual role, not only as targets for immunotherapy, but also as biomarkers of disease state, stage, response to treatment and survival. We need biomarkers to enable the identification of the patients who are most likely to benefit from specific treatments (conventional and/or novel) and to help clinicians and scientists improve clinical end points and treatment design. Here we describe the LAAs identified in AML, to date, which have already been shown to play a dual role as biomarkers of AML disease.
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Affiliation(s)
- Barbara-ann Guinn
- Department of Haematological Medicine, King's College London School of Medicine, The Rayne Institute, 123 Coldharbour Lane, London, SE5 9NU
| | - Azim Mohamedali
- Department of Haematological Medicine, King's College London School of Medicine, The Rayne Institute, 123 Coldharbour Lane, London, SE5 9NU
| | - Ken I. Mills
- Department of Haematology, University Hospital of Wales, Heath Park, Cardiff, CF4 4XN, U.K
| | - Barbara Czepulkowski
- Department of Haematological Medicine, King's College London School of Medicine, The Rayne Institute, 123 Coldharbour Lane, London, SE5 9NU
| | - Michael Schmitt
- Third Clinic for Internal Medicine, University of Ulm, Germany
| | - Jochen Greiner
- Third Clinic for Internal Medicine, University of Ulm, Germany
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20
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21
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Acquired uniparental disomy in chromosome 6p as a feature of relapse after T-cell replete haploidentical hematopoietic stem cell transplantation using cyclophosphamide tolerization. Bone Marrow Transplant 2017; 52:615-619. [DOI: 10.1038/bmt.2016.324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Rebouissou S, Franconi A, Calderaro J, Letouzé E, Imbeaud S, Pilati C, Nault JC, Couchy G, Laurent A, Balabaud C, Bioulac-Sage P, Zucman-Rossi J. Genotype-phenotype correlation of CTNNB1 mutations reveals different ß-catenin activity associated with liver tumor progression. Hepatology 2016; 64:2047-2061. [PMID: 27177928 DOI: 10.1002/hep.28638] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/08/2016] [Accepted: 05/09/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED CTNNB1 mutations activating ß-catenin are frequent somatic events in hepatocellular carcinoma (HCC) and adenoma (HCA), particularly associated with a risk of malignant transformation. We aimed to understand the relationship between CTNNB1 mutation types, tumor phenotype, and level of ß-catenin activation in malignant transformation. To this purpose, CTNNB1 mutation spectrum was analyzed in 220 HCAs, 373 HCCs, and 17 borderline HCA/HCC lesions. ß-catenin activation level was assessed in tumors by quantitative reverse-transcriptase polymerase chain reaction and immunohistochemistry (IHC), in cellulo by TOP-Flash assay. Overall, ß-catenin activity was higher in malignant mutated tumors, compared to adenomas, and this was related to a different spectrum of CTNNB1 mutations in HCCs and HCAs. In benign tumors, we defined three levels of ß-catenin activation related to specific mutations: (1) S45, K335, and N387 mutations led to weak activation; (2) T41 mutations were related to moderate activity; and (3) highly active mutations included exon 3 deletions and amino acid substitutions within the ß-TRCP binding site (D32-S37). Accordingly, in vitro, K335I and N387K mutants showed a lower activity than S33C. Tumors with highly active mutations demonstrated strong/homogeneous glutamine synthase (GS) staining and were associated with malignancy. In contrast, weak mutants demonstrated heterogeneous pattern of GS staining and were more frequent in HCAs except for the S45 mutants identified similarly in 20% of mutated HCAs and HCCs; however, in most of the HCCs, the weak S45 mutant alleles were duplicated, resulting in a final high ß-catenin activity. CONCLUSION High ß-catenin activity driven by specific CTNNB1 mutations and S45 allele duplication is associated with malignant transformation. Consequently, HCAs with S45 and all high/moderate mutants should be identified with precise IHC criteria or mutation screening. (Hepatology 2016;64:2047-2061).
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Affiliation(s)
- Sandra Rebouissou
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France
| | - Andrea Franconi
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France
| | - Julien Calderaro
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France.,Public Hospitals of Paris, Department of Pathology, CHU Henri Mondor, Créteil, France
| | - Eric Letouzé
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France
| | - Sandrine Imbeaud
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France
| | - Camilla Pilati
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France
| | - Jean-Charles Nault
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France.,Public Hospitals of Paris, University hospital of Paris-Seine Saint-Denis, Site Jean Verdier, Cancerology unit, Department of Hepatology, Bondy, France
| | - Gabrielle Couchy
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France
| | - Alexis Laurent
- Public Hospitals of Paris, Department of Digestive and Hepatobiliary Surgery, CHU Henri Mondor, Créteil, France.,INSERM U955 Henri Mondor Hospital University of Paris-Est Créteil, France
| | - Charles Balabaud
- Inserm, UMR-1053, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Paulette Bioulac-Sage
- Inserm, UMR-1053, Bordeaux, France.,University of Bordeaux, Bordeaux, France.,Hospital of Bordeaux, Pellegrin Hospital, Department of Pathology, Bordeaux, France
| | - Jessica Zucman-Rossi
- Inserm, UMR-1162, Functional Genomics of Solid Tumors, Equipe labellisée Ligue Contre le Cancer, Paris, France.,University of Paris Descartes, Sorbonne Paris Cité, Labex Immuno-oncology, Paris, France.,University of Paris Diderot, Sorbonne Paris Cité, University Institute of Hematology, Paris, France.,University of Paris 13, Sorbonne Paris Cité, Saint-Denis, France.,Public Hospitals of Paris, European Hospital Georges Pompidou, Paris, France
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23
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Mutant allele specific imbalance in oncogenes with copy number alterations: Occurrence, mechanisms, and potential clinical implications. Cancer Lett 2016; 384:86-93. [PMID: 27725226 DOI: 10.1016/j.canlet.2016.10.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 01/16/2023]
Abstract
Mutant allele specific imbalance (MASI) was initially coined to describe copy number alterations associated with the mutant allele of an oncogene. The copy number gain (CNG) specific to the mutant allele can be readily observed in electropherograms. With the development of genome-wide analyses at base-pair resolution with copy number counts, we can now further differentiate MASI into those with CNG, with copy neutral alteration (also termed acquired uniparental disomy; UPD), or with loss of heterozygosity (LOH) due to the loss of the wild-type (WT) allele. Here we summarize the occurrence of MASI with CNG, aUPD, or MASI with LOH in some major oncogenes (such as EGFR, KRAS, PIK3CA, and BRAF). We also discuss how these various classifications of MASI have been demonstrated to impact tumorigenesis, progression, metastasis, prognosis, and potentially therapeutic responses in cancer, notably in lung, colorectal, and pancreatic cancers.
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24
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Olsson L, Zettermark S, Biloglav A, Castor A, Behrendtz M, Forestier E, Paulsson K, Johansson B. The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes. Br J Haematol 2016; 174:292-301. [PMID: 27022003 DOI: 10.1111/bjh.14056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/22/2016] [Indexed: 01/07/2023]
Abstract
Cytogenetic analyses of a consecutive series of 67 paediatric (median age 8 years; range 0-17) de novo acute myeloid leukaemia (AML) patients revealed aberrations in 55 (82%) cases. The most common subgroups were KMT2A rearrangement (29%), normal karyotype (15%), RUNX1-RUNX1T1 (10%), deletions of 5q, 7q and/or 17p (9%), myeloid leukaemia associated with Down syndrome (7%), PML-RARA (7%) and CBFB-MYH11 (5%). Single nucleotide polymorphism array (SNP-A) analysis and exon sequencing of 100 genes, performed in 52 and 40 cases, respectively (39 overlapping), revealed ≥1 aberration in 89%; when adding cytogenetic data, this frequency increased to 98%. Uniparental isodisomies (UPIDs) were detected in 13% and copy number aberrations (CNAs) in 63% (median 2/case); three UPIDs and 22 CNAs were recurrent. Twenty-two genes were targeted by focal CNAs, including AEBP2 and PHF6 deletions and genes involved in AML-associated gene fusions. Deep sequencing identified mutations in 65% of cases (median 1/case). In total, 60 mutations were found in 30 genes, primarily those encoding signalling proteins (47%), transcription factors (25%), or epigenetic modifiers (13%). Twelve genes (BCOR, CEBPA, FLT3, GATA1, KIT, KRAS, NOTCH1, NPM1, NRAS, PTPN11, SMC3 and TP53) were recurrently mutated. We conclude that SNP-A and deep sequencing analyses complement the cytogenetic diagnosis of paediatric AML.
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Affiliation(s)
- Linda Olsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Sofia Zettermark
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Andrea Biloglav
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Anders Castor
- Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Mikael Behrendtz
- Department of Paediatrics, Linköping University Hospital, Linköping, Sweden
| | - Erik Forestier
- Department of Medical Bioscience, University of Umeå, Umeå, Sweden
| | - Kajsa Paulsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Bertil Johansson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
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25
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Svobodova K, Zemanova Z, Lhotska H, Novakova M, Podskalska L, Belickova M, Brezinova J, Sarova I, Izakova S, Lizcova L, Berkova A, Siskova M, Jonasova A, Cermak J, Michalova K. Copy number neutral loss of heterozygosity at 17p and homozygous mutations of TP53 are associated with complex chromosomal aberrations in patients newly diagnosed with myelodysplastic syndromes. Leuk Res 2016; 42:7-12. [DOI: 10.1016/j.leukres.2016.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/16/2015] [Accepted: 01/21/2016] [Indexed: 01/01/2023]
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26
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Lundin KB, Olsson L, Safavi S, Biloglav A, Paulsson K, Johansson B. Patterns and frequencies of acquired and constitutional uniparental isodisomies in pediatric and adult B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2016; 55:472-9. [PMID: 26773847 DOI: 10.1002/gcc.22349] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/11/2016] [Accepted: 01/11/2016] [Indexed: 12/31/2022] Open
Abstract
Single nucleotide polymorphism (SNP) arrays are increasingly being used in clinical routine for genetic analysis of pediatric B-cell precursor acute lymphoblastic leukemias (BCP ALL). Because constitutional DNA is not readily available as a control at the time of diagnosis, it is important to be able to distinguish between acquired and constitutional aberrations in a diagnostic setting. In the present study we focused on uniparental isodisomies (UPIDs). SNP array analyses of 143 pediatric and 38 adult B-cell precursor acute lymphoblastic leukemias and matched remission samples revealed acquired whole chromosome or segmental UPIDs (wUPIDs, sUPIDs) in 32 cases (18%), without any age- or gender-related frequency differences. Acquired sUPIDs were larger than the constitutional ones (mean 35.3 Mb vs. 10.7 Mb; P < 0.0001) and were more often terminally located in the chromosomes (69% vs. 4.5%; P < 0.0001). Chromosomes 3, 5, and 9 were most often involved in acquired wUPIDs, whilst recurrent acquired sUPIDs targeted 6p, 9p, 9q, and 14q. The majority (56%) of sUPID9p was associated with homozygous CDKN2A deletions. In pediatric ALL, all wUPIDs were found in high hyperdiploid (51-67 chromosomes) cases and an extended analysis, also including unmatched diagnostic samples, revealed a higher frequency of wUPID-positivity in higher modal number (56-67 chromosomes) than in lower modal number (51-55 chromosomes) high hyperdiploid cases (34% vs. 11%; P = 0.04), suggesting different underlying mechanisms of formation of these subtypes of high hyperdiploidy. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kristina B Lundin
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Olsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Setareh Safavi
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Andrea Biloglav
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Bertil Johansson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
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27
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Grimwade D, Ivey A, Huntly BJP. Molecular landscape of acute myeloid leukemia in younger adults and its clinical relevance. Blood 2016; 127:29-41. [PMID: 26660431 PMCID: PMC4705608 DOI: 10.1182/blood-2015-07-604496] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 08/04/2015] [Indexed: 01/13/2023] Open
Abstract
Recent major advances in understanding the molecular basis of acute myeloid leukemia (AML) provide a double-edged sword. Although defining the topology and key features of the molecular landscape are fundamental to development of novel treatment approaches and provide opportunities for greater individualization of therapy, confirmation of the genetic complexity presents a huge challenge to successful translation into routine clinical practice. It is now clear that many genes are recurrently mutated in AML; moreover, individual leukemias harbor multiple mutations and are potentially composed of subclones with differing mutational composition, rendering each patient's AML genetically unique. In order to make sense of the overwhelming mutational data and capitalize on this clinically, it is important to identify (1) critical AML-defining molecular abnormalities that distinguish biological disease entities; (2) mutations, typically arising in subclones, that may influence prognosis but are unlikely to be ideal therapeutic targets; (3) mutations associated with preleukemic clones; and (4) mutations that have been robustly shown to confer independent prognostic information or are therapeutically relevant. The reward of identifying AML-defining molecular lesions present in all leukemic populations (including subclones) has been exemplified by acute promyelocytic leukemia, where successful targeting of the underlying PML-RARα oncoprotein has eliminated the need for chemotherapy for disease cure. Despite the molecular heterogeneity and recognizing that treatment options for other forms of AML are limited, this review will consider the scope for using novel molecular information to improve diagnosis, identify subsets of patients eligible for targeted therapies, refine outcome prediction, and track treatment response.
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Affiliation(s)
- David Grimwade
- Department of Medical & Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Adam Ivey
- Department of Medical & Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Brian J P Huntly
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrookes Hospital, University of Cambridge, and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
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28
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Song J, Shao H. SNP Array in Hematopoietic Neoplasms: A Review. MICROARRAYS 2015; 5:microarrays5010001. [PMID: 27600067 PMCID: PMC5003446 DOI: 10.3390/microarrays5010001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/13/2015] [Accepted: 12/14/2015] [Indexed: 12/03/2022]
Abstract
Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH) studies. Single nucleotide polymorphism (SNP) arrays offer high-resolution identification of copy number variants (CNVs) and acquired copy-neutral loss of heterozygosity (LOH)/uniparental disomy (UPD) that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants.
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Affiliation(s)
- Jinming Song
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
| | - Haipeng Shao
- Department of Hematopathology and Laboratory Medicine, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
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29
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Wang L, Wheeler DA, Prchal JT. Acquired uniparental disomy of chromosome 9p in hematologic malignancies. Exp Hematol 2015; 44:644-52. [PMID: 26646991 DOI: 10.1016/j.exphem.2015.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 12/14/2022]
Abstract
Acquired uniparental disomy (aUPD) is a common and recurrent molecular event in human cancers that leads to homozygosity for tumor suppressor genes as well as oncogenes, while retaining the diploid chromosomal complement. Because of the lack of copy number change, aUPD is undetectable by comparative genome hybridization, so the magnitude of this genetic change was underappreciated in the past. 9p aUPD was first described in 2002 in patients with polycythemia vera (PV). Since then, systematic application of genomewide single-nucleotide polymorphism arrays has indicated that 9p aUPD is the most common chromosomal aberration in myeloproliferative neoplasms (MPNs), contributing to discovery of the PV-defining mutation JAK2V617F21. It was also found in other myeloid and lymphoid malignancies, though at a relatively lower frequency. By leading to JAK2V617F 23 homozygosity, 9p aUPD plays a causal role in the development of PV and is also associated with less favorable clinical outcomes. It is also possible that new targets other than JAK2V617F 25 are present within 9p aUPD that may contribute to diversity of PV outcome and phenotype. This review summarizes recent discoveries on 9p aUPD in hematologic malignancies and discusses possible underlying mechanisms and potential roles of 9p aUPD in the pathogenesis of PV, the relationship between 9p aUPD and JAK2V617F29, and possible new cancer-related targets within the 9p aUPD region.
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Affiliation(s)
- Linghua Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Josef T Prchal
- Division of Hematology, University of Utah School of Medicine and VAH, Salt Lake City, Utah.
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30
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Gronseth CM, McElhone SE, Storer BE, Kroeger KA, Sandhu V, Fero ML, Appelbaum FR, Estey EH, Fang M. Prognostic significance of acquired copy-neutral loss of heterozygosity in acute myeloid leukemia. Cancer 2015; 121:2900-8. [PMID: 26033747 DOI: 10.1002/cncr.29475] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/13/2015] [Accepted: 04/21/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Chromosomal abnormalities are important in the diagnosis and prognosis of patients with acute myeloid leukemia (AML). Genomic microarray techniques detect recurrent copy-neutral loss of heterozygosity (cnLOH) in addition to copy number aberrations. However, the clinical utility has not been fully established. Therefore, in the current study, the authors examined the prognostic impact of acquired cnLOH in patients with AML, including complete remission (CR) rate, duration of CR, and overall survival (OS). METHODS A total of 112 consecutive patients with AML who were undergoing chromosome genomic array testing (CGAT) at the Seattle Cancer Care Alliance were included in the current study. DNA from the bone marrow or blood was analyzed with a microarray platform with both single-nucleotide polymorphism (SNP) probes and non-SNP probes to identify acquired cnLOH. Results were correlated with cytogenetic, molecular, immunophenotypic, and other clinicopathological findings. RESULTS Patients with cnLOH demonstrated a shorter duration of CR (hazard ratio, 1.87; P =.04) and worse OS (HR, 1.82; P = .03). Multivariate analyses confirmed the independent predictive value of cnLOH for early disease recurrence (P =.02). These results largely reflected those in patients with intermediate and unfavorable cytogenetics. Most strikingly, 13q cnLOH was found to demonstrate a 6.64-fold higher rate of disease recurrence (P =.006) and 3.45-fold worse OS (P = .02) and was enriched with the FLT3-ITD (Fms-related tyrosine kinase 3-internal tandem duplication) mutation. CONCLUSIONS CnLOH has important prognostic significance in patients with AML. CGAT can replace imbalance fluorescence in situ hybridization and the authors recommend the routine use of CGAT to detect cnLOH, particularly among patients with intermediate-risk cytogenetics.
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Affiliation(s)
| | - Scott E McElhone
- Cytogenetics Department, Seattle Cancer Care Alliance, Seattle, Washington
| | - Barry E Storer
- Clinical Statistics Department, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kathleen A Kroeger
- Cytogenetics Department, Seattle Cancer Care Alliance, Seattle, Washington
| | - Vicky Sandhu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Matthew L Fero
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Frederick R Appelbaum
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Elihu H Estey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Medicine, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
| | - Min Fang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Pathology, University of Washington, Seattle, Washington.,Seattle Cancer Care Alliance, Seattle, Washington
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31
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Abstract
Although the current WHO classification (Swerdlow et al. WHO classification of tumours of haematopoietic and lymphoid tissues. International Agency for Research on Cancer, Lyon, 2008 [1]) for hematolymphoid neoplasms has delineated lymphomas based on the combined morphologic, immunophenotypic, and genotypic findings, further refinement is necessary especially in regard to therapeutics and prognostic implications. High-throughput gene expression profiling (GEP) using microarray technology (Schena et al. Science 270:467-470, 1995 [2]; Augenlicht et al. Proc Natl Acad Sci USA 88:3286-3289, 1991 [3]) was developed about 20 years ago, and further refinement of the technology and analytical approaches has enabled us to routinely evaluate practically the entire transcriptome at a time. GEP has helped to improve the classification and prognostication of non-Hodgkin lymphomas (NHL) as well as improved our understanding of their pathophysiology and response to new therapeutics. In this paper, we will briefly review how this revolutionary tool has transformed our understanding of lymphomas and given us insight into targeted therapeutics. We will also discuss the current efforts in adapting the findings to routine clinical practice, the evolution of the research technology and directions in the future.
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32
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Annesley CE, Brown P. The Biology and Targeting of FLT3 in Pediatric Leukemia. Front Oncol 2014; 4:263. [PMID: 25295230 PMCID: PMC4172015 DOI: 10.3389/fonc.2014.00263] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/08/2014] [Indexed: 12/22/2022] Open
Abstract
Despite remarkable improvement in treatment outcomes in pediatric leukemia over the past several decades, the prognosis for high-risk groups of acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), as well as for relapsed leukemia, remains poor. Intensification of chemotherapy regimens for those at highest risk has improved success rates, but at the cost of significantly increased morbidity and long-term adverse effects. With the success of imatinib in Philadelphia-chromosome-positive leukemia and all-trans retinoic acid in acute promyelocytic leukemia, the quest to find additional molecularly targeted therapies has generated much excitement over recent years. Another such possible target in pediatric acute leukemia is FMS-like tyrosine kinase 3 (FLT3). FLT3 aberrations are among the most frequently identified transforming events in AML, and have significant clinical implications in both high-risk pediatric AML and in certain high-risk groups of pediatric ALL. Therefore, the successful targeting of FLT3 has tremendous potential to improve outcomes in these subsets of patients. This article will give an overview of the molecular function and signaling of the FLT3 receptor, as well as its pathogenic role in leukemia. We review the discovery of targeting FLT3, discuss currently available FLT3 inhibitors in pediatric leukemia and results of clinical trials to date, and finally, consider the future promise and challenges of FLT3 inhibitor therapy.
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Affiliation(s)
- Colleen E. Annesley
- Oncology and Pediatrics, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patrick Brown
- Oncology and Pediatrics, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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33
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Koh KN, Lee JO, Seo EJ, Lee SW, Suh JK, Im HJ, Seo JJ. Clinical significance of previously cryptic copy number alterations and loss of heterozygosity in pediatric acute myeloid leukemia and myelodysplastic syndrome determined using combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray analyses. J Korean Med Sci 2014; 29:926-33. [PMID: 25045224 PMCID: PMC4101780 DOI: 10.3346/jkms.2014.29.7.926] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 04/16/2014] [Indexed: 11/20/2022] Open
Abstract
The combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray (CGH+SNP microarray) platform can simultaneously detect copy number alterations (CNA) and copy-neutral loss of heterozygosity (LOH). Eighteen children with acute myeloid leukemia (AML) (n=15) or myelodysplastic syndrome (MDS) (n=3) were studied using CGH+SNP microarray to evaluate the clinical significance of submicroscopic chromosomal aberrations. CGH+SNP microarray revealed CNAs at 14 regions in 9 patients, while metaphase cytogenetic (MC) analysis detected CNAs in 11 regions in 8 patients. Using CGH+SNP microarray, LOHs>10 Mb involving terminal regions or the whole chromosome were detected in 3 of 18 patients (17%). CGH+SNP microarray revealed cryptic LOHs with or without CNAs in 3 of 5 patients with normal karyotypes. CGH+SNP microarray detected additional cryptic CNAs (n=2) and LOHs (n=5) in 6 of 13 patients with abnormal MC. In total, 9 patients demonstrated additional aberrations, including CNAs (n=3) and/or LOHs (n=8). Three of 15 patients with AML and terminal LOH>10 Mb demonstrated a significantly inferior relapse-free survival rate (P=0.041). This study demonstrates that CGH+SNP microarray can simultaneously detect previously cryptic CNAs and LOH, which may demonstrate prognostic implications.
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Affiliation(s)
- Kyung-Nam Koh
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Ok Lee
- Genome Research Center, Asan Medical Center, Seoul, Korea
| | - Eul Ju Seo
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seong Wook Lee
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Kyung Suh
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho Joon Im
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
| | - Jong Jin Seo
- Division of Pediatric Hematology/Oncology, Asan Medical Center Children's Hospital, Department of Pediatrics, University of Ulsan College of Medicine, Seoul, Korea
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34
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Hemmat M, Chen W, Anguiano A, Naggar ME, Racke FK, Jones D, Wang Y, Strom CM, Chang K, Boyar FZ. Submicroscopic deletion of 5q involving tumor suppressor genes (CTNNA1, HSPA9) and copy neutral loss of heterozygosity associated with TET2 and EZH2 mutations in a case of MDS with normal chromosome and FISH results. Mol Cytogenet 2014; 7:35. [PMID: 25177364 PMCID: PMC4149311 DOI: 10.1186/1755-8166-7-35] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 05/19/2014] [Indexed: 12/24/2022] Open
Abstract
Advances in genome-wide molecular cytogenetics allow identification of novel submicroscopic DNA copy number alterations (aCNAs) and copy-neutral loss of heterozygosity (cnLOH) resulting in homozygosity for known gene mutations in myeloid neoplasms. We describe the use of an oligo-SNP array for genomic profiling of aCNA and cnLOH, together with sequence analysis of recurrently mutated genes, in a patient with myelodysplastic syndrome (MDS) presenting with normal karyotype and FISH results. Oligo-SNP array analysis revealed a hemizygous deletion of 896 kb at chromosome 5q31.2, representing the smallest 5q deletion reported to date. The deletion involved multiple genes, including two tumor suppressor candidate genes (CTNNA1 and HSPA9) that are associated with MDS/AML. The SNP-array study also detected 3 segments of somatic cnLOH: one involved the entire long arm of chromosome 4; the second involved the distal half of the long arm of chromosome 7, and the third encompassed the entire chromosome 22 (UPD 22). Sequence analysis revealed mutations in TET2 (4q), EZH2 (7q), ASXL1 (20q11.21), and RUNX1 (21q22.3). Coincidently, TET2 and EZH2 were located at segments of cnLOH resulting in their homozygosity. Loss of heterozygosity affecting these two chromosomes and mutations in TET2 and EZH2 are indicative of a myelodysplastic syndrome with a poor prognosis. Deletion of the tumor suppressor genes CTNNA1 and HSPA9 is also likely to contribute to a poor prognosis. Furthermore, the original cnLOHs in multiple chromosomes and additional cnLOH 14q in the follow-up study suggest genetic evolution of the disease and poor prognosis. This study attests to the fact that some patients with a myelodysplastic syndrome who exhibit a normal karyotype may have underlying genetic abnormalities detectable by chromosomal microarray and/or targeted mutation analyses.
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Affiliation(s)
- Morteza Hemmat
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Weina Chen
- University of Texas southwestern Medical Center, 5323 Harry Hines Blvd, 75235 Dallas, TX, USA
| | - Arturo Anguiano
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Mohammed El Naggar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Frederick K Racke
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Dan Jones
- Quest Diagnostics Nichols Institute, 14225 Newbrook Drive, 20151 Chantilly, VA, USA
| | - Yongbao Wang
- Quest Diagnostics Nichols Institute, 14225 Newbrook Drive, 20151 Chantilly, VA, USA
| | - Charles M Strom
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Karl Chang
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
| | - Fatih Z Boyar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Hwy, 92675 San Juan Capistrano, CA, USA
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Hahm C, Huh HJ, Mun YC, Seong CM, Chung WS, Huh J. Genomic aberrations of myeloproliferative and myelodysplastic/myeloproliferative neoplasms in chronic phase and during disease progression. Int J Lab Hematol 2014; 37:181-9. [DOI: 10.1111/ijlh.12257] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/14/2014] [Indexed: 01/22/2023]
Affiliation(s)
- C Hahm
- Department of Laboratory Medicine, Ewha Womans University School of Medicine, Seoul, South Korea; Department of Laboratory Medicine, Eone Laboratories, Incheon, South Korea
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Mirza MK, Sukhanova M, Stölzel F, Onel K, Larson RA, Stock W, Ehninger G, Kuithan F, Zöphel K, Reddy P, Joseph L, Raca G. Genomic aberrations in myeloid sarcoma without blood or bone marrow involvement: characterization of formalin-fixed paraffin-embedded samples by chromosomal microarrays. Leuk Res 2014; 38:1091-6. [PMID: 25088808 DOI: 10.1016/j.leukres.2014.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/04/2014] [Indexed: 10/25/2022]
Abstract
Myeloid sarcoma (MS) is a presentation of acute myeloid leukemia (AML) as a tumor mass outside of the bone marrow. Viable cells from MS are frequently unavailable for cytogenetic studies. We therefore investigated whether chromosomal microarray analysis (CMA) using formalin-fixed paraffin-embedded (FFPE) tissues can detect clinically important genetic abnormalities in MS. CMA successfully identified genomic aberrations in six cases of MS, and in two cases it revealed multiple abnormalities equivalent to a complex karyotype, thus predicting a poor outcome. CMA using FFPE material is therefore a feasible and clinically applicable approach for detection of prognostically significant genomic abnormalities in MS.
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Affiliation(s)
- M Kamran Mirza
- Department of Pathology, The University of Chicago, Chicago, USA
| | | | - Friedrich Stölzel
- Department of Internal Medicine, University Hospital Carl Gustav Carus, University of Technology, Dresden, Germany
| | - Kenan Onel
- Department of Pediatrics, The University of Chicago, Chicago, USA
| | | | - Wendy Stock
- Department of Medicine, The University of Chicago, Chicago, USA
| | - Gerhard Ehninger
- Department of Internal Medicine, University Hospital Carl Gustav Carus, University of Technology, Dresden, Germany
| | - Friederike Kuithan
- Department of Pathology, University Hospital Carl Gustav Carus, University of Technology, Dresden, Germany
| | - Klaus Zöphel
- Department of Nuclear Medicine, University Hospital Carl Gustav Carus, University of Technology, Dresden, Germany
| | - Poluru Reddy
- Department of Pathology, The University of Chicago, Chicago, USA
| | - Loren Joseph
- Department of Pathology, The University of Chicago, Chicago, USA
| | - Gordana Raca
- Department of Medicine, The University of Chicago, Chicago, USA.
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Iacobucci I, Lonetti A, Papayannidis C, Martinelli G. Use of single nucleotide polymorphism array technology to improve the identification of chromosomal lesions in leukemia. Curr Cancer Drug Targets 2014; 13:791-810. [PMID: 23941516 PMCID: PMC4104470 DOI: 10.2174/15680096113139990089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 04/05/2013] [Accepted: 07/01/2013] [Indexed: 12/13/2022]
Abstract
Acute leukemias are characterized by recurring chromosomal and genetic abnormalities that disrupt normal development and drive aberrant cell proliferation and survival. Identification of these abnormalities plays important role in diagnosis, risk assessment and patient classification. Until the last decade methods to detect these aberrations have included genome wide approaches, such as conventional cytogenetics, but with a low sensitivity (5-10%), or gene candidate approaches, such as fluorescent in situ hybridization, having a greater sensitivity but being limited to only known regions of the genome. Single nucleotide polymorphism (SNP) technology is a screening method that has revolutionized our way to find genetic alterations, enabling linkage and association studies between SNP genotype and disease as well as the identification of alterations in DNA content on a whole genome scale. The adoption of this approach for the study of lymphoid and myeloid leukemias contributed to the identification of novel genetic alterations, such as losses/gains/uniparental disomy not visible by cytogenetics and implicated in pathogenesis, improving risk assessment and patient classification and in some cases working as targets for tailored therapies. In this review, we reported recent advances obtained in the knowledge of the genomic complexity of chronic myeloid leukemia and acute leukemias thanks to the use of high-throughput technologies, such as SNP array.
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Affiliation(s)
- Ilaria Iacobucci
- Institute of Hematology "L. e A. Seràgnoli" Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy, Via Massarenti, 9 - 40138 Bologna, Italy.
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Walen KH. Haploidization of Human Diploid Metaphase Cells: Is This Genome Reductive Mechanism Opperational in Near-Haploid Leukemia? ACTA ACUST UNITED AC 2014. [DOI: 10.4236/jct.2014.51013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Koszarska M, Meggyesi N, Bors A, Batai A, Csacsovszki O, Lehoczky E, Adam E, Kozma A, Lovas N, Sipos A, Krahling T, Dolgos J, Remenyi P, Fekete S, Masszi T, Tordai A, Andrikovics H. Medium-sizedFLT3internal tandem duplications confer worse prognosis than short and long duplications in a non-elderly acute myeloid leukemia cohort. Leuk Lymphoma 2013; 55:1510-7. [DOI: 10.3109/10428194.2013.850163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Klampfl T, Milosevic JD, Puda A, Schönegger A, Bagienski K, Berg T, Harutyunyan AS, Gisslinger B, Rumi E, Malcovati L, Pietra D, Elena C, Della Porta MG, Pieri L, Guglielmelli P, Bock C, Doubek M, Dvorakova D, Suvajdzic N, Tomin D, Tosic N, Racil Z, Steurer M, Pavlovic S, Vannucchi AM, Cazzola M, Gisslinger H, Kralovics R. Complex patterns of chromosome 11 aberrations in myeloid malignancies target CBL, MLL, DDB1 and LMO2. PLoS One 2013; 8:e77819. [PMID: 24147083 PMCID: PMC3797696 DOI: 10.1371/journal.pone.0077819] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/04/2013] [Indexed: 11/19/2022] Open
Abstract
Exome sequencing of primary tumors identifies complex somatic mutation patterns. Assignment of relevance of individual somatic mutations is difficult and poses the next challenge for interpretation of next generation sequencing data. Here we present an approach how exome sequencing in combination with SNP microarray data may identify targets of chromosomal aberrations in myeloid malignancies. The rationale of this approach is that hotspots of chromosomal aberrations might also harbor point mutations in the target genes of deletions, gains or uniparental disomies (UPDs). Chromosome 11 is a frequent target of lesions in myeloid malignancies. Therefore, we studied chromosome 11 in a total of 813 samples from 773 individual patients with different myeloid malignancies by SNP microarrays and complemented the data with exome sequencing in selected cases exhibiting chromosome 11 defects. We found gains, losses and UPDs of chromosome 11 in 52 of the 813 samples (6.4%). Chromosome 11q UPDs frequently associated with mutations of CBL. In one patient the 11qUPD amplified somatic mutations in both CBL and the DNA repair gene DDB1. A duplication within MLL exon 3 was detected in another patient with 11qUPD. We identified several common deleted regions (CDR) on chromosome 11. One of the CDRs associated with de novo acute myeloid leukemia (P=0.013). One patient with a deletion at the LMO2 locus harbored an additional point mutation on the other allele indicating that LMO2 might be a tumor suppressor frequently targeted by 11p deletions. Our chromosome-centered analysis indicates that chromosome 11 contains a number of tumor suppressor genes and that the role of this chromosome in myeloid malignancies is more complex than previously recognized.
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Affiliation(s)
- Thorsten Klampfl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jelena D. Milosevic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ana Puda
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Schönegger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Klaudia Bagienski
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tiina Berg
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ashot S. Harutyunyan
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bettina Gisslinger
- Division of Hematology and Blood Coagulation, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Elisa Rumi
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Luca Malcovati
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Daniela Pietra
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Chiara Elena
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Matteo Giovanni Della Porta
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Lisa Pieri
- Section of Hematology, University of Florence, Florence, Italy
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michael Doubek
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno, Masaryk University Brno, Brno, Czech Republic, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno, Czech Republic
| | - Dana Dvorakova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno, Masaryk University Brno, Brno, Czech Republic, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno, Czech Republic
| | - Nada Suvajdzic
- Clinic of Hematology, Clinical Center of Serbia, University of Belgrade, School of Medicine, Belgrade, Serbia
| | - Dragica Tomin
- Clinic of Hematology, Clinical Center of Serbia, University of Belgrade, School of Medicine, Belgrade, Serbia
| | - Natasa Tosic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Zdenek Racil
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno, Masaryk University Brno, Brno, Czech Republic, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno, Czech Republic
| | - Michael Steurer
- Division of Hematology and Oncology, Innsbruck University Hospital, Innsbruck, Austria
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Mario Cazzola
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Heinz Gisslinger
- Division of Hematology and Blood Coagulation, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Division of Hematology and Blood Coagulation, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Comprehensive high-resolution genomic profiling and cytogenetics of two pediatric and one adult medulloblastoma. Pathol Res Pract 2013; 209:541-7. [PMID: 23896263 DOI: 10.1016/j.prp.2013.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Medulloblastoma (WHO grade IV) is a rare, malignant, invasive, embryonal tumor which mainly occurs in children and represents less than 1% of all adult brain tumors. Systematic comprehensive genetic analyses on medulloblastomas are rare but necessary to provide more detailed information. Therefore, we performed comprehensive cytogenetic analyses (blood and tissue) of two pediatric and one adult medulloblastoma, using trypsin-Giemsa staining, spectral karyotyping (tissues only), SNP-arrays, and gene expression analyses. We confirmed frequently detected chromosomal aberrations in medulloblastoma, such as +7q, -8p/q, -9q, -11q, -12q, and +17q and identified novel genetic events. Applying SNP-array, we identified constitutional de novo losses 5q21.1, 15q11.2, 17q21.31, 19p12 (pediatric medulloblastoma), 9p21.1, 19p12, 19q13.3, 21q11.2 (adult medulloblastoma) and gains 16p11.1-16p11.2, 18p11.32, Yq11.223-Yq11.23 (pediatric medulloblastoma), Xp22.31 (adult medulloblastoma) possibly representing inherited causal events for medulloblastoma formation. We show evidence for somatic segmental uniparental disomy in regions 1p36, 6q16.3, 6q24.1, 14q21.2, 17p13.3, and 17q22 not previously described for primary medulloblastoma. Gene expression analysis supported classification of the adult medulloblastoma to the WNT-subgroup and classification of pediatric medulloblastomas to group 3 tumors. Analyses of tumors and matched normal tissues (blood) with a combination of complementary techniques will help to further elucidate potentially causal genetic events for medulloblastomas.
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Analysis of acquired genomic copy number aberrations and regions of loss of heterozygosity in acute myelogenous leukemia genomes using Affymetrix SNP 6.0 arrays and supporting software tools. Methods Mol Biol 2013. [PMID: 23412786 DOI: 10.1007/978-1-62703-281-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The application of SNP array technology to the analysis of cancer genomes has greatly advanced our knowledge of the incidence and functional consequences of acquired genomic copy number aberrations (aCNA) and LOH in various malignancies. The major challenges of using SNP arrays are accurately identifying acquired genomic DNA aberrations in the raw array data with very high sensitivity and specificity and meaningfully assessing the associations between these aberrations and biological characteristics or patient outcomes. Critical to the success and valid interpretation of data derived from SNP array profiling are (1) the purity of cells used as a source of template DNA; (2) the analysis of paired DNA samples (tumor and normal); (3) use of validated software tools for data analysis; (4) access to an acceptable gold standard for aCNA and LOH, including FISH data, cytogenetic results, and Q-PCR data; and (5) statistical support to employ or develop algorithmic approaches to SNP array data analysis. Overcalling of lesions including lack of validation and undercalling of lesions that display low fractional allelic representations are common problems. This guide should help the reader establish this powerful technology in the laboratory and aims to stimulate transition of SNP array profiling into clinical applications.
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Kulasekararaj AG, Mohamedali AM, Mufti GJ. Recent advances in understanding the molecular pathogenesis of myelodysplastic syndromes. Br J Haematol 2013; 162:587-605. [PMID: 23869491 DOI: 10.1111/bjh.12435] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The advent of novel genomic sequencing technologies has aided the identification of somatically acquired genetic abnormalities up to 80% of myelodysplastic syndrome (MDS) patients. Novel recurrent genetic mutations in pathways such as RNA splicing, DNA methylation and histone modification and cohesion complexes, underscore the molecular heterogeneity seen in this clinically varied disease. Functional studies to establish a causative link between genomic aberrations and MDS biogenesis are still in their infancy. The deluge of this molecular information, once validated on a larger cohort, will be incorporated into prognostic systems and clinical practise, and also hopefully aid in MDS therapeutics, especially in guiding targeted therapy.
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Affiliation(s)
- Austin G Kulasekararaj
- Department of Haematological Medicine, King's College London School of Medicine, London, UK
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Abstract
Mutations in the nucleophosmin 1 (NPM1) gene are considered a founder event in the pathogenesis of acute myeloid leukemia (AML). To address the role of clonal evolution in relapsed NPM1-mutated (NPM1mut) AML, we applied high-resolution, genome-wide, single-nucleotide polymorphism array profiling to detect copy number alterations (CNAs) and uniparental disomies (UPDs) and performed comprehensive gene mutation screening in 53 paired bone marrow/peripheral blood samples obtained at diagnosis and relapse. At diagnosis, 15 aberrations (CNAs, n = 10; UPDs, n = 5) were identified in 13 patients (25%), whereas at relapse, 56 genomic alterations (CNAs, n = 46; UPDs, n = 10) were detected in 29 patients (55%) indicating an increase in genomic complexity. Recurrent aberrations acquired at relapse included deletions affecting tumor suppressor genes (ETV6 [n = 3], TP53 [n = 2], NF1 [n = 2], WT1 [n = 3], FHIT [n = 2]) and homozygous FLT3 mutations acquired via UPD13q (n = 7). DNMT3A mutations (DNMT3Amut) showed the highest stability (97%). Persistence of DNMT3Amut in 5 patients who lost NPM1mut at relapse suggests that DNMT3Amut may precede NPM1mut in AML pathogenesis. Of note, all relapse samples shared at least 1 genetic aberration with the matched primary AML sample, implying common ancestral clones. In conclusion, our study reveals novel insights into clonal evolution in NPM1mut AML.
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Tyner JW. Rapid Identification of Therapeutic Targets in Hematologic Malignancies via Functional Genomics. Ther Adv Hematol 2013; 2:83-93. [PMID: 23556079 DOI: 10.1177/2040620711403028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The clinical application of gene-targeted drugs has transformed cancer therapy. The hallmark example of this strategy is use of the ABL kinase inhibitor imatinib for treatment of patients with chronic myeloid leukemia (CML). This remarkable clinical success has also stimulated an expansive search for personalized gene targets in all patients to facilitate broad application of targeted therapy for cancer. However, achievement of this objective will require simultaneous work towards several complementary goals. The first step towards broad application of gene-targeted therapy must entail a rapid means to identify target oncogenes in individual patients. Next, we must identify well-tolerated, gene-specific drugs that are collectively effective against a wide diversity of gene targets. Finally, we must develop protocols by which individual patients are matched with appropriate, gene-targeted drugs in a clinically relevant time frame. While these may seem like difficult tasks, we are fortunate to have a wide variety of new and rapidly evolving research tools at our disposal. These include next-generation sequencing of the genome and transcriptome, single nucleotide polymorphism (SNP)/copy number variations (CNV) and gene expression microarrays, and RNAi libraries for the application of functional screens. In this review we discuss the advantages and disadvantages of each of these techniques with the goal of demonstrating that no single technique will be sufficient as a standalone technology, but rather it will be the integration of all techniques that will enable broad application of gene-targeted cancer therapies.
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Hahm C, Mun YC, Seong CM, Han SH, Chung WS, Huh J. Single nucleotide polymorphism array-based karyotyping in acute myeloid leukemia or myelodysplastic syndrome with trisomy 8 as the sole chromosomal abnormality. Acta Haematol 2013. [PMID: 23208021 DOI: 10.1159/000343420] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The clinical heterogeneity of patients with acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS) with trisomy 8 as the sole abnormality may result from cytogenetically undetectable genetic changes. The purpose of this study was to identify hidden genomic aberrations not detected by metaphase cytogenetics (MC) using high-resolution single nucleotide polymorphism array (SNP-A)-based karyotyping in AML/MDS patients with a sole trisomy 8. The study group included 8 patients (3 AML and 5 MDS) and array-based karyotyping was done using whole-genome SNP-A (SNP 6.0 and SNP 2.7M). By SNP-A, additional genomic aberrations not detected by MC were identified in 2 patients: 1 AML patient exhibited a copy-neutral loss of heterozygosity (CN-LOH) of 3q21.1-q29 and 11q13.1-q25 and the other patient with MDS (refractory cytopenia with unilineage dysplasia) had CN-LOH of 2p25.3-p15. In particular, the latter patient progressed to AML 18 months after the diagnosis. In 3 patients, aberrations in addition to trisomy 8 were not identified by SNP-A. In the remaining 3 patients, SNP-A could not detect trisomy 8, while trisomy 8 was found in 25-67% of metaphase cells by MC. This study suggests that additional genomic aberrations may in fact be present even in cases of trisomy 8 as sole abnormality by MC, and SNP-A could be a useful karyotyping tool to identify hidden aberrations such as CN-LOH.
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Affiliation(s)
- Chorong Hahm
- Department of Laboratory Medicine, Ewha Womans University School of Medicine, Seoul, South Korea
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Abstract
Genomic profiling of mantle cell lymphoma (MCL) cells has enabled a better understanding of the complex mechanisms underlying the pathogenesis of disease. Besides the t(11;14)(q13;q32) leading to cyclin D1 overexpression, MCL exhibits a characteristic pattern of DNA copy number aberrations that differs from those detected in other B-cell lymphomas. These genomic changes disrupt selected oncogenes and suppressor genes that are required for lymphoma development and progression, many of which are components of cell cycle, DNA damage response and repair, apoptosis, and cell-signaling pathways. Additionally, some of them may represent effective therapeutic targets. A number of genomic and molecular abnormalities have been correlated with the clinical outcome of patients with MCL and are considered prognostic factors. However, only a few genomic markers have been shown to predict the response to current or novel targeted therapies. One representative example is the high-level amplification of the BCL2 gene, which predicts a good response to pro-apoptotic BH3 mimetic drugs. In summary, genomic analyses have contributed to the substantial advances made in the comprehension of the pathogenesis of MCL, providing a solid basis for the identification of optimal therapeutic targets and for the design of new molecular therapies aiming to cure this fatal disease.
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Affiliation(s)
- Melissa Rieger Menanteau
- Division of Oncology, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
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Grimwade D. The changing paradigm of prognostic factors in acute myeloid leukaemia. Best Pract Res Clin Haematol 2012. [DOI: 10.1016/j.beha.2012.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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50
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Abstract
The finding of somatically acquired uniparental disomy, where both copies of a chromosome pair or parts of chromosomes have originated from one parent, has led to the discovery of several novel mutated genes in myeloproliferative neoplasms and related disorders. This article examines how the development of single nucleotide polymorphism array technology has facilitated the identification of regions of acquired uniparental disomy and has led to a much greater understanding of the molecular pathology of these heterogeneous diseases.
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Affiliation(s)
- Joannah Score
- Faculty of Medicine, University of Southampton, Southampton, UK
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