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WT1 Gene Mutations, rs16754 Variant, and WT1 Overexpression as Prognostic Factors in Acute Myeloid Leukemia Patients. J Clin Med 2022; 11:jcm11071873. [PMID: 35407481 PMCID: PMC9000045 DOI: 10.3390/jcm11071873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
(1) Background: The aim of our study was the complex assessment of WT1 variants and their expression in relation to chromosomal changes and molecular prognostic markers in acute myeloid leukemia (AML). It is the first multidimensional study in Polish AML patients; (2) Methods: Bone marrow aspirates of 90 AML patients were used for cell cultures (banding techniques and fluorescence in situ hybridization), and to isolate DNA (WT1 genotyping, array comparative genomic hybridization), and RNA (WT1 expression). Peripheral blood samples from 100 healthy blood donors were used to analyze WT1 rs16754; (3) Results: Allele frequency and distribution of WT1 variant rs16754 (A;G) did not differ significantly among AML patients and controls. Higher expression of WT1 gene was observed in AA genotype (of rs16754) in comparison with GA or GG genotypes—10,556.7 vs. 25,836.5 copies (p = 0.01), respectively. WT1 mutations were more frequent in AML patients under 65 years of age (p < 0.0001) and affected relapse-free survival (RFS). The presence of NPM1 or CEBPA mutations decreased the risk of WT1 mutation presence, odds ratio (OR) = 0.11, 95% CI 0.02−0.46, p = 0.002 or OR = 0.05, 95% CI 0.006−0.46, p = 0.002, respectively. We observed significantly higher WT1 expression in AML CD34+ vs. CD34−, −20,985 vs. 8304 (p = 0.039), respectively. The difference in WT1 expression between patients with normal and abnormal karyotype was statistically insignificant; (4) Conclusions: WT1 gene expression and its rs16754 variant at diagnosis did not affect AML outcome. WT1 mutation may affect RFS in AML.
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Evans AG, Ahmad A, Burack WR, Iqbal MA. Combined comparative genomic hybridization and single-nucleotide polymorphism array detects cryptic chromosomal lesions in both myelodysplastic syndromes and cytopenias of undetermined significance. Mod Pathol 2016; 29:1183-99. [PMID: 27389314 DOI: 10.1038/modpathol.2016.104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 12/28/2022]
Abstract
The diagnosis of myelodysplastic syndrome (MDS) can be challenging, and may be facilitated by correlation with cytogenetic testing. Microarray analysis using comparative genomic hybridization and/or single-nucleotide polymorphism array can detect chromosomal abnormalities not seen by standard metaphase cytogenetics. We examined the ability of combined comparative genomic hybridization and single-nucleotide polymorphism analysis (hereafter referred to as 'combined array') to detect changes among 83 patients with unexplained cytopenias undergoing pathologic evaluation for MDS and compared results with 18 normal bone marrow controls. Thirty-seven patients (45%) were diagnosed with MDS, 12 patients (14%) were demonstrated to have 'indeterminate dyspoiesis' (insufficient for classification of MDS), 27 (33%) were essentially normal, and 7 patients (8%) had alternative pathologic diagnoses. Twenty-one MDS patients (57% of diagnoses) had effectively normal metaphase cytogenetics, but combined array showed that 5 of these (13% of MDS patients) harbored major cryptic chromosomal aberrations. Furthermore, nearly half of patients with 'indeterminate dyspoiesis' and 1 with normal morphology had clonal cytopenia(s) of undetermined significance by combined array analysis. Cryptic array findings among MDS patients and those with clonal cytopenias(s) included large-scale copy-neutral loss of heterozygosity (up to 118 Mb) and genomic deletion of loci implicated in MDS pathogenesis (eg, TET2 (4q22) and NUP98 (11p15)). By comparison, in MDS patients with abnormal metaphase cytogenetics, microarray mostly recapitulated findings seen by routine karyotype. Combined array analysis has considerable diagnostic yield in detecting cryptic chromosomal aberrations in MDS and in demonstrating aberrant clonal hematopoiesis in cytopenic patients with indeterminate morphologic dysplasia.
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Affiliation(s)
- Andrew G Evans
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ausaf Ahmad
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - W Richard Burack
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - M Anwar Iqbal
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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Mehrotra M, Luthra R, Ravandi F, Sargent RL, Barkoh BA, Abraham R, Mishra BM, Medeiros LJ, Patel KP. Identification of clinically important chromosomal aberrations in acute myeloid leukemia by array-based comparative genomic hybridization. Leuk Lymphoma 2015; 55:2538-48. [PMID: 24446873 DOI: 10.3109/10428194.2014.883073] [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] [Indexed: 12/14/2022]
Abstract
Array-based comparative genomic hybridization (aCGH) chromosomal analysis facilitates rapid detection of cytogenetic abnormalities previously undetectable by conventional cytogenetics. In this study, we analyzed 48 uniformly treated patients with acute myeloid leukemia (AML) by 44K aCGH and correlated the findings with clinical outcome. aCGH identified previously undetected aberrations, as small as 5 kb, of currently unknown significance. The 36.7 Mb minimally deleted region on chromosome 5 lies between 5q14.3 and 5q33.3 and contains 634 genes and 15 microRNAs, whereas loss of chromosome 17 spans 3194 kb and involves 342 genes and 12 microRNAs. Loss of a 155 kb region on 5q33.3 (p < 0.05) was associated with achievement of complete remission (CR). In contrast, loss of 17p11.2-q11.1 was associated with a lower CR rate and poorer overall survival (Kaplan-Meier analysis, p < 0.0096). aCGH detected loss of 17p in 12/48 patients as compared to 9/48 by conventional karyotyping. In conclusion, aCGH analysis adds to the prognostic stratification of patients with AML.
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Affiliation(s)
- Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas M. D. Anderson Cancer Center , Houston, TX , USA
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Involvement of deleted chromosome 5 in complex chromosomal aberrations in newly diagnosed myelodysplastic syndromes (MDS) is correlated with extremely adverse prognosis. Leuk Res 2014; 38:537-44. [DOI: 10.1016/j.leukres.2014.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/21/2014] [Accepted: 01/24/2014] [Indexed: 01/25/2023]
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5
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Venkataswamy E, Nargund AR, Prabhudesai S, Patil GV, Chandra RJ, Veldore VH, Patil S, Verma A, Sahoo R, Ajaikumar BS, Prasannakumari. An uncommon case of an adult with del(5)(q) in acute lymphoblastic leukemia. INDIAN JOURNAL OF HUMAN GENETICS 2013; 18:349-51. [PMID: 23716946 PMCID: PMC3656527 DOI: 10.4103/0971-6866.108028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Del(5)(q) is a common chromosomal abnormality with favourable prognosis in Myelodysplastic Syndrome (MDS) and Acute myeloid leukemia (AML). However, del(5)(q) is also seen rarely in Acute lymphoblastic leukemia (ALL) and its significance remains poorly understood. We present here, a case report of diagnosis of an adult 75 year old patient of ALL with a cytogenetic abnormality of del(5)(q32). His clinical features, morphology and immunophenotyping findings were suggestive of T-ALL. Relevant literature has been reviewed and discussed.
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Affiliation(s)
- E Venkataswamy
- Department of Molecular Biology, Triesta Reference Laboratory, HealthCare Global Enterprises Ltd, Bangalore, India
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Mallo M, del Rey M, Ibáñez M, Calasanz MJ, Arenillas L, Larráyoz MJ, Pedro C, Jerez A, Maciejewski J, Costa D, Nomdedeu M, Diez-Campelo M, Lumbreras E, González-Martínez T, Marugán I, Such E, Cervera J, Cigudosa JC, Álvarez S, Florensa L, Hernández JM, Solé F. Response to lenalidomide in myelodysplastic syndromes with del(5q): influence of cytogenetics and mutations. Br J Haematol 2013; 162:74-86. [DOI: 10.1111/bjh.12354] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/12/2013] [Indexed: 12/15/2022]
Affiliation(s)
| | - Mónica del Rey
- Servicio de Hematología; Centro de Investigación del Cáncer; IBSAL (Instituto de Biomedicina de Salamanca) y IBMCC; Universidad de Salamanca; Salamanca; Spain
| | - Mariam Ibáñez
- Servicio de Hematología; Hospital Universitario La Fe; Valencia; Spain
| | - Mª José Calasanz
- Departamento de Genética; Universidad de Navarra; Pamplona; Spain
| | - Leonor Arenillas
- Laboratori de Citogenètica Molecular; Laboratori de Citologia Hematològica; Servei de Patologia; Hospital del Mar; GRETNHE; IMIM (Hospital del Mar Research Institute); Barcelona; Spain
| | - Mª José Larráyoz
- Departamento de Genética; Universidad de Navarra; Pamplona; Spain
| | - Carmen Pedro
- Servei d'Hematologia Clínica; Hospital del Mar; GRETNHE; IMIM (Hospital del Mar Research Institute); Barcelona; Spain
| | - Andrés Jerez
- Department of Translational Hematology and Oncology Research; Taussig Cancer Institute; Cleveland Clinic; Cleveland; OH; USA
| | - Jaroslaw Maciejewski
- Department of Translational Hematology and Oncology Research; Taussig Cancer Institute; Cleveland Clinic; Cleveland; OH; USA
| | - Dolors Costa
- Servei d'Hematopatologia; Hospital Clínic; Barcelona; Spain
| | | | - María Diez-Campelo
- Servicio de Hematología; Centro de Investigación del Cáncer; IBSAL (Instituto de Biomedicina de Salamanca) y IBMCC; Universidad de Salamanca; Salamanca; Spain
| | - Eva Lumbreras
- Servicio de Hematología; Centro de Investigación del Cáncer; IBSAL (Instituto de Biomedicina de Salamanca) y IBMCC; Universidad de Salamanca; Salamanca; Spain
| | - Teresa González-Martínez
- Citoxenética-oncohematolóxica; Fundación Pública Galega de Medicina Xenómica Hospital Clínico Universitario; Santiago de Compostela; Spain
| | - Isabel Marugán
- Servicio de Hematología y Oncología Médica; Hospital Clínico Universitario de Valencia; Valencia; Spain
| | - Esperanza Such
- Servicio de Hematología; Hospital Universitario La Fe; Valencia; Spain
| | - José Cervera
- Servicio de Hematología; Hospital Universitario La Fe; Valencia; Spain
| | - Juan C. Cigudosa
- Grupo de Citogenética Molecular; Centro Nacional de Investigaciones Oncológicas; Madrid; Spain
| | - Sara Álvarez
- Grupo de Citogenética Molecular; Centro Nacional de Investigaciones Oncológicas; Madrid; Spain
| | - Lourdes Florensa
- Laboratori de Citogenètica Molecular; Laboratori de Citologia Hematològica; Servei de Patologia; Hospital del Mar; GRETNHE; IMIM (Hospital del Mar Research Institute); Barcelona; Spain
| | - Jesús Mª Hernández
- Servicio de Hematología; Centro de Investigación del Cáncer; IBSAL (Instituto de Biomedicina de Salamanca) y IBMCC; Universidad de Salamanca; Salamanca; Spain
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Busch M, Leube B, Thiel A, Schanze I, Beier M, Royer-Pokora B. Evaluation of chromosome 11p imbalances in aniridia and Wilms tumor patients. Am J Med Genet A 2013; 161A:958-64. [PMID: 23494989 DOI: 10.1002/ajmg.a.35818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/21/2012] [Indexed: 11/10/2022]
Abstract
Newborn sporadic aniridia patients with an 11p13 deletion including the WT1 gene have an increased risk to develop Wilms tumor. At present a risk for Wilms tumor cannot be estimated in patients with deletions not extending into, but ending close to WT1. Therefore, it is important to determine the distance of deletion endpoints from the WT1 gene and survey these patients for a longer follow-up time to obtain a more defined risk estimation. Using molecular methods, such as Multiplex Ligation-dependent Probe Amplification (MLPA), deletion endpoints can be mapped more accurately than with FISH. We describe here the analysis of six aniridia patients, in two of these the deletions extend close to the 3' end of WT1. At the ages of 3.8 and 4 years they have not developed a Wilms tumor, suggesting a low tumor risk in such patients. In addition we have studied 24 non-AN cases with a higher likelihood for WT1 alterations with MLPA and found no deletions. In conclusion newborns with aniridia should be studied with molecular methods that can determine deletion endpoints in 11p13 exactly. For a better Wilms tumor risk estimation cases with deletion endpoints close to WT1 should be followed for at least 4-5 years. Furthermore germ line intragenic deletions affecting WT1 in patients with a higher likelihood for a WT1 association, for example, bilateral tumors, genitourinary aberrations, or nephrotic syndrome, were not found in this study, suggesting that deletions are rare events.
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Affiliation(s)
- Maike Busch
- Institute of Human Genetics and Anthropology, Medical Faculty, Heinrich-Heine-University of Duesseldorf, Duesseldorf, Germany
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Verburgh E, Hagemeijer A, Delforge M, Verhoef G, Vandenberghe P. Patients with myelodysplastic syndrome and two clones with different interstitial deletions of the long arm of chromosome 5. Leuk Lymphoma 2013; 54:2314-7. [PMID: 23373968 DOI: 10.3109/10428194.2013.772296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Estelle Verburgh
- Department of Hematology, University Hospitals, University of Leuven , Leuven , Belgium
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9
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Cannizzaro LA. Fluorescent in situ hybridization of DNA probes in the interphase and metaphase stages of the cell cycle. Methods Mol Biol 2013. [PMID: 23179826 DOI: 10.1007/978-1-62703-128-8_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In the past decade, fluorescent in situ hybridization (FISH) has been used routinely in detecting molecular abnormalities in the interphase and metaphase stages of the cell cycle. Many of the molecular anomalies which are detected in this manner are diagnostic of a prenatal, postnatal, or neoplastic genetic disorder. With the continuous isolation of commercially available DNA probes specific to a particular chromosome region, FISH analysis has become standardized in its ability to detect characteristic chromosomal anomalies in association with genetic and neoplastic diseases. In recent years, FISH has also become automated to accommodate the increased volume of slide preparations necessary for the number of DNA probes needed to detect characteristic molecular anomalies in cancer tissues and bone marrow samples. FISH technology provides essential information to the physician regarding the diagnosis, response to treatment, and ultimately the prognosis of their patients' disorder. It has become an important source of information routinely used in conjunction with chromosome analyses, and presently to confirm molecular alterations detected by array comparative genomic hybridization (aCGH) analyses. In this chapter we describe the methods for performing FISH analyses in order to determine the presence or the absence of genetic abnormalities which define whether the patient has either a genetic syndrome or malignant disease.
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Affiliation(s)
- Linda A Cannizzaro
- Department of Pathology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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Shaffer LG, Ballif BC, Schultz RA. The use of cytogenetic microarrays in myelodysplastic syndrome characterization. Methods Mol Biol 2013; 973:69-85. [PMID: 23412784 DOI: 10.1007/978-1-62703-281-0_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Various microarray platforms, including BAC, oligonucleotide, and SNP arrays, have been shown to -provide clinically useful diagnostic and prognostic information for patients with myelodysplastic syndromes (MDS). Clinically useful arrays are designed with specific purposes in mind and with attention to genomic content and probe density. All array types have been shown to detect genomic copy gains and losses, with SNP arrays having the added advantage of detecting copy neutral loss of heterozygosity (CNLOH). The finding of CNLOH has led to the identification of certain disease genes implicated in the initiation or progression of myeloid diseases. In addition, SNP karyotyping alone, or in conjunction with routine cytogenetics, can affect the outcome prediction and improve prognostic stratification of patients with MDS. Patients who were reclassified after array testing as having adverse-risk chromosomal findings correlated with poor survival. Results of over 25 published studies support the use of arrays in MDS testing. Because few balanced translocations are found in MDS, this disease is particularly amenable to microarray testing, and studies have shown better disease classification, identification of cryptic changes, and prognostication in this heterogeneous group of disorders. Novel genomic alterations identified by array testing may lead to better targeted therapies for treating patients with MDS.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer Inc., Spokane, WA, USA.
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11
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Abstract
To study genomic imbalances potentially involved in disease development and/or progression of childhood MDS, array-based comparative genomic hybridization (aCGH) is a helpful tool. Copy number alterations (CNA) of subtle chromosomal regions containing potential candidate genes, e.g., TP53 or RUNX1 can be detected. However, characterizing small and/or heterogeneous tumor subpopulations by high-resolution aCGH within a majority of normal cells is a challenge in MDS and requires validation by independent methods like FISH or quantitative PCR. For the identification of tumor-relevant CNA, the analysis of DNA isolated from purified granulocytes or myeloid populations instead of DNA from whole bone marrow (BM) cells is helpful to overcome some of these limitations.
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Affiliation(s)
- Marcel Tauscher
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
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12
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Abstract
Myelodysplastic syndromes (MDS) are malignant clonal disorders of haematopoietic stem cells and their microenvironment, affecting older individuals (median age ∼70 years). Unique features that are associated with MDS - but which are not necessarily present in every patient with MDS - include excessive apoptosis in maturing clonal cells, a pro-inflammatory bone marrow microenvironment, specific chromosomal abnormalities, abnormal ribosomal protein biogenesis, the presence of uniparental disomy, and mutations affecting genes involved in proliferation, methylation and epigenetic modifications. Although emerging insights establish an association between molecular abnormalities and the phenotypic heterogeneity of MDS, their origin and progression remain enigmatic.
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Affiliation(s)
- Azra Raza
- Myelodysplastic Syndromes Center, Columbia University Medical Center, Milstein Hospital Building, 6N-435, 177 Fort Washington Avenue, New York, New York 10032, USA.
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Hahm C, Mun YC, Seong CM, Chung WS, Huh J. Additional genomic aberrations identified by single nucleotide polymorphism array-based karyotyping in an acute myeloid leukemia case with isolated del(20q) abnormality. Ann Lab Med 2012; 32:445-9. [PMID: 23130347 PMCID: PMC3486942 DOI: 10.3343/alm.2012.32.6.445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 08/13/2012] [Accepted: 09/20/2012] [Indexed: 11/19/2022] Open
Abstract
Prognosis is known to be better in cases with isolated chromosomal abnormalities than in those with complex karyotypes. Accordingly, del(20q) as an isolated abnormality must be distinguished from cases in which it is associated with other chromosomal rearrangements for a better stratification of prognosis. We report a case of an isolated del(20q) abnormality with additional genomic aberrations identified using whole-genome single nucleotide polymorphism array (SNP-A)-based karyotyping. A 39-yr-old man was diagnosed with AML without maturation. Metaphase cytogenetic analysis (MC) revealed del(20)(q11.2) as the isolated abnormality in 100% of metaphase cells analyzed, and FISH analysis using D20S108 confirmed the 20q deletion in 99% of interphase cells. Using FISH, other rearrangements such as BCR/ABL1, RUNX1/RUNX1T1, PML/RARA, CBFB/MYH11, and MLL were found to be negative. SNP-A identified an additional copy neutral loss of heterozygosity (CN-LOH) in the 11q13.1-q25 region. Furthermore, SNP-A allowed for a more precise definition of the breakpoints of the 20q deletion (20q11.22-q13.31). Unexpectedly, the terminal regions showed gain on chromosome 20q. The patient did not achieve complete remission; 8 months later, he died from complications of leukemic cell infiltrations into the central nervous system. This study suggests that a presumably isolated chromosomal abnormality by MC may have additional genomic aberrations, including CN-LOH, which could be associated with a poor prognosis. SNP-A-based karyotyping may be helpful for distinguishing true isolated cases from cases in combination with additional genomic aberrations not detected by MC.
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Affiliation(s)
- Chorong Hahm
- Department of Laboratory Medicine, Ewha Womans University School of Medicine, Seoul, Korea
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Abstract
Sustained clinical cytopenia is a frequent laboratory finding in ambulatory and hospitalized patients. For pathologists and hematopathologists who examine the bone marrow (BM), a diagnosis of cytopenia secondary to an infiltrative BM process or acute leukemia can be readily established based on morphologic evaluation and flow cytometry immunophenotyping. However, it can be more challenging to establish a diagnosis of myelodysplastic syndrome (MDS). In this article, the practical approaches for establishing or excluding a diagnosis of MDS (especially low-grade MDS) in patients with clinical cytopenia are discussed along with the current diagnostic recommendations provided by the World Health Organization and the International Working Group for MDS.
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Mackinnon RN, Selan C, Zordan A, Wall M, Nandurkar H, Campbell LJ. CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens. Mol Cytogenet 2012; 5:10. [PMID: 22300816 PMCID: PMC3296743 DOI: 10.1186/1755-8166-5-10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 02/02/2012] [Indexed: 01/13/2023] Open
Abstract
Background The analysis of nucleic acids is limited by the availability of archival specimens and the quality and amount of the extracted material. Archived cytogenetic preparations are stored in many laboratories and are a potential source of total genomic DNA for array karyotyping and other applications. Array CGH using DNA from fixed cytogenetic preparations has been described, but it is not known whether it can be used for SNP arrays. Diagnostic bone marrow specimens taken during the assessment of hematological malignancies are also a potential source of DNA, but it is generally assumed that DNA must be extracted, or the specimen frozen, within a day or two of collection, to obtain DNA suitable for further analysis. We have assessed DNA extracted from these materials for both SNP array and array CGH. Results We show that both SNP array and array CGH can be performed on genomic DNA extracted from cytogenetic specimens stored in Carnoy's fixative, and from bone marrow which has been stored unfrozen, at 4°C, for at least 36 days. We describe a procedure for extracting a usable concentration of total genomic DNA from cytogenetic suspensions of low cellularity. Conclusions The ability to use these archival specimens for DNA-based analysis increases the potential for retrospective genetic analysis of clinical specimens. Fixed cytogenetic preparations and long-term refrigerated bone marrow both provide DNA suitable for array karyotyping, and may be suitable for a wider range of analytical procedures.
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Affiliation(s)
- Ruth N Mackinnon
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital (Melbourne), Fitzroy, Vic, Australia.
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Germing U, Lauseker M, Hildebrandt B, Symeonidis A, Cermak J, Fenaux P, Kelaidi C, Pfeilstöcker M, Nösslinger T, Sekeres M, Maciejewski J, Haase D, Schanz J, Seymour J, Kenealy M, Weide R, Lübbert M, Platzbecker U, Valent P, Götze K, Stauder R, Blum S, Kreuzer KA, Schlenk R, Ganser A, Hofmann WK, Aul C, Krieger O, Kündgen A, Haas R, Hasford J, Giagounidis A. Survival, prognostic factors and rates of leukemic transformation in 381 untreated patients with MDS and del(5q): A multicenter study. Leukemia 2012; 26:1286-92. [PMID: 22289990 DOI: 10.1038/leu.2011.391] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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van der Veken LT, Buijs A. Array CGH in human leukemia: from somatics to genetics. Cytogenet Genome Res 2011; 135:260-70. [PMID: 21893961 DOI: 10.1159/000330629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During the past decade, array CGH has been applied to study copy number alterations in the genome in human leukemia in relation to prediction of prognosis or responsiveness to therapy. In the first segment of this review, we will focus on the identification of acquired mutations by array CGH, followed by studies on the pathogenesis of leukemia associated with germline genetic variants, phenotypic presentation and response to treatment. In the last section, we will discuss constitutional genomic aberrations causally related to myeloid leukemogenesis.
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Affiliation(s)
- L T van der Veken
- Section of Genome Diagnostics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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A cryptic deletion in 5q31.2 provides further evidence for a minimally deleted region in myelodysplastic syndromes. Cancer Genet 2011; 204:187-94. [PMID: 21536236 DOI: 10.1016/j.cancergen.2011.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 02/02/2011] [Accepted: 02/03/2011] [Indexed: 12/19/2022]
Abstract
Recurrent deletions of 5q in myeloid malignancies encompass two separate regions: deletion of 5q33, which is associated with the 5q− syndrome and haploinsufficiency of RPS14, and deletion of a more proximal locus at 5q31. We present a case with a cryptic 1.3 Mb deletion in 5q31.2 identified by array comparative genomic hybridization that places the proximal boundary of the deletion proximal and close to the candidate EGR1 gene. The patient was diagnosed initially with a myelodysplastic syndrome, with a del(20)(q11.2q13.3) as the sole abnormality identified by karyotyping. The patient progressed to acute myeloid leukemia with no change to the G-banded karyotype. The 1.3 Mb deletion on the long arm of one chromosome 5 was confirmed to have been present both at presentation with myelodysplastic syndrome and at transformation. This is an interesting case because there are few array studies identifying cryptic 5q deletions, and the study of these small deletions helps to refine the common deleted region. This case, together with previously published studies, suggests that the proximal boundary of the common deleted region may lie within the KDM3B gene.
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Itzhar N, Dessen P, Toujani S, Auger N, Preudhomme C, Richon C, Lazar V, Saada V, Bennaceur A, Bourhis JH, de Botton S, Bernheim A. Chromosomal minimal critical regions in therapy-related leukemia appear different from those of de novo leukemia by high-resolution aCGH. PLoS One 2011; 6:e16623. [PMID: 21339820 PMCID: PMC3038855 DOI: 10.1371/journal.pone.0016623] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 01/07/2011] [Indexed: 12/25/2022] Open
Abstract
Therapy-related acute leukemia (t-AML), is a severe complication of cytotoxic therapy used for primary cancer treatment. The outcome of these patients is poor, compared to people who develop de novo acute leukemia (p-AML). Cytogenetic abnormalities in t-AML are similar to those found in p-AML but present more frequent unfavorable karyotypes depending on the inducting agent. Losses of chromosome 5 or 7 are observed after alkylating agents while balanced translocations are found after topoisomerase II inhibitors. This study compared t-AML to p-AML using high resolution array CGH in order to find copy number abnormalities (CNA) at a higher resolution than conventional cytogenetics. More CNAs were observed in 30 t-AML than in 36 p-AML: 104 CNAs were observed with 63 losses and 41 gains (mean number 3.46 per case) in t-AML, while in p-AML, 69 CNAs were observed with 32 losses and 37 gains (mean number of 1.9 per case). In primary leukemia with a previously "normal" karyotype, 18% exhibited a previously undetected CNA, whereas in the (few) t-AML with a normal karyotype, the rate was 50%. Several minimal critical regions (MCRs) were found in t-AML and p-AML. No common MCRs were found in the two groups. In t-AML a 40 kb deleted MCR pointed to RUNX1 on 21q22, a gene coding for a transcription factor implicated in frequent rearrangements in leukemia and in familial thrombocytopenia. In de novo AML, a 1 Mb MCR harboring ERG and ETS2 was observed from patients with complex aCGH profiles. High resolution cytogenomics obtained by aCGH and similar techniques already published allowed us to characterize numerous non random chromosome abnormalities. This work supports the hypothesis that they can be classified into several categories: abnormalities common to all AML; those more frequently found in t-AML and those specifically found in p-AML.
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Affiliation(s)
- Nathalie Itzhar
- Institut de la Santé et de la Reherche Médicale U985, Génétique des tumeurs, Institut Gustave Roussy, Villejuif, France
- Université Paris XI, Paris Sud, Orsay, France
- Molecular Pathology, Villejuif, France
| | - Philippe Dessen
- Institut de la Santé et de la Reherche Médicale U985, Génétique des tumeurs, Institut Gustave Roussy, Villejuif, France
- Université Paris XI, Paris Sud, Orsay, France
- Institut Gustave Roussy, Functional Genomics Unit, Institut Gustave Roussy, Villejuif, France
| | - Saloua Toujani
- Institut de la Santé et de la Reherche Médicale U985, Génétique des tumeurs, Institut Gustave Roussy, Villejuif, France
- Université Paris XI, Paris Sud, Orsay, France
| | - Nathalie Auger
- Institut de la Santé et de la Reherche Médicale U985, Génétique des tumeurs, Institut Gustave Roussy, Villejuif, France
- Université Paris XI, Paris Sud, Orsay, France
- Molecular Pathology, Villejuif, France
| | - Claude Preudhomme
- Department of Hematology, Centre de Biologie-Pathologie, Centre Hospitalier Régional Universitaire de Lille, Lille, France
| | - Catherine Richon
- Institut Gustave Roussy, Functional Genomics Unit, Institut Gustave Roussy, Villejuif, France
| | - Vladimir Lazar
- Molecular Pathology, Villejuif, France
- Institut Gustave Roussy, Functional Genomics Unit, Institut Gustave Roussy, Villejuif, France
| | - Véronique Saada
- Molecular Pathology, Villejuif, France
- Department of Hematology, Institut Gustave Roussy, Villejuif, France
| | - Anelyse Bennaceur
- Molecular Pathology, Villejuif, France
- Department of Hematology, Institut Gustave Roussy, Villejuif, France
| | | | | | - Alain Bernheim
- Institut de la Santé et de la Reherche Médicale U985, Génétique des tumeurs, Institut Gustave Roussy, Villejuif, France
- Université Paris XI, Paris Sud, Orsay, France
- Molecular Pathology, Villejuif, France
- * E-mail:
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Comprehensive array CGH of normal karyotype myelodysplastic syndromes reveals hidden recurrent and individual genomic copy number alterations with prognostic relevance. Leukemia 2011; 25:387-99. [DOI: 10.1038/leu.2010.293] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Bajaj R, Xu F, Xiang B, Wilcox K, Diadamo AJ, Kumar R, Pietraszkiewicz A, Halene S, Li P. Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia. Mol Cytogenet 2011; 4:3. [PMID: 21251322 PMCID: PMC3031273 DOI: 10.1186/1755-8166-4-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 01/20/2011] [Indexed: 12/16/2022] Open
Abstract
Background To evaluate the clinical validity of genome-wide oligonucleotide array comparative genomic hybridization (aCGH) for detecting somatic abnormalities, we have applied this genomic analysis to 30 cases (13 MDS and 17 AML) with clonal chromosomal abnormalities detected in more than 50% of analyzed metaphase cells. Results The aCGH detected all numerical chromosomal gains and losses from the mainline clones and 113 copy number alterations (CNAs) ranging from 0.257 to 102.519 megabases (Mb). Clinically significant recurrent deletions of 5q (involving the RPS14 gene), 12p12.3 (ETV6 gene), 17p13 (TP53 gene), 17q11.2 (NF1 gene) and 20q, double minutes containing the MYC gene and segmental amplification involving the MLL gene were further characterized with defined breakpoints and gene contents. Genomic features of microdeletions at 17q11.2 were confirmed by FISH using targeted BAC clones. The aCGH also defined break points in a derivative chromosome 6, der(6)t(3;6)(q21.3;p22.2), and an isodicentric X chromosome. However, chromosomally observed sideline clonal abnormalities in five cases were not detected by aCGH. Conclusions Our data indicated that an integrated cytogenomic analysis will be a better diagnostic scheme to delineate genomic contents of chromosomal and cryptic abnormalities in patients with MDS and AML. An evidence-based approach to interpret somatic genomic findings was proposed.
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Affiliation(s)
- Renu Bajaj
- Molecular Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA.
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22
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Praulich I, Tauscher M, Göhring G, Glaser S, Hofmann W, Feurstein S, Flotho C, Lichter P, Niemeyer CM, Schlegelberger B, Steinemann D. Clonal heterogeneity in childhood myelodysplastic syndromes--challenge for the detection of chromosomal imbalances by array-CGH. Genes Chromosomes Cancer 2010; 49:885-900. [PMID: 20589934 DOI: 10.1002/gcc.20797] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
To evaluate whether copy number alterations (CNAs) are present that may contribute to disease development and/or progression of childhood myelodysplastic syndromes (MDS), 36 pediatric MDS patients were analyzed using array-based comparative genome hybridization (aCGH). In addition to monosomy 7, the most frequent chromosome aberration in childhood MDS, novel recurrent CNAs were detected. They included a loss of 3p14.3-p12.3, which contains the putative tumor suppressor gene FHIT, a loss of 7p21.3-p15.3, a loss of 9q33.3-q34.3 (D184) and microdeletions in 17p11.2, 6q23 containing MYB, and 17p13 containing TP53. In this small patient cohort, patients without CNA, patients with monosomy 7 only and patients with one CNA in addition to monosomy 7 did not differ in their survival. As expected, all patients with complex karyotypes, including two patients with deletions of TP53, died. A challenge inherent to aCGH analysis of MDS is the low percentage of tumor cells. We evaluated several approaches to overcome this limitation. Genomic profiles from isolated granulocytes were of higher quality than those from bone marrow mononuclear cells. Decreased breakpoint calling stringency increased recognition of CNAs present in small clonal populations. However, further analysis using a custom-designed array showed that these CNAs often did not confirm the findings from 244k arrays. In contrast, constitutional CNVs were reliably detected on both arrays. Moreover, aCGH on amplified DNA from distinct myeloid clusters is a new approach to determine CNAs in small subpopulations. Our results clearly emphasize the need to verify array-CGH results by independent methods like FISH or quantitative PCR.
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Affiliation(s)
- Inka Praulich
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
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23
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Abstract
Sustained clinical cytopenia is a frequent laboratory finding in ambulatory and hospitalized patients. For pathologists and hematopathologists who examine the bone marrow (BM), a diagnosis of cytopenia secondary to an infiltrative BM process or acute leukemia can be readily established based on morphologic evaluation and flow cytometry immunophenotyping. However, it can be more challenging to establish a diagnosis of myelodysplastic syndrome (MDS). In this article, the practical approaches for establishing or excluding a diagnosis of MDS (especially low-grade MDS) in patients with clinical cytopenia are discussed along with the current diagnostic recommendations provided by the World Health Organization and the International Working Group for MDS.
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Affiliation(s)
- Sa A Wang
- Department of Hematopathology, University of Texas, MD Anderson Cancer Center, Unit 72, 1515 Holcombe Boulevard, Houston, TX 77030-4009, USA.
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24
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Neukirchen J, Haas R, Germing U. Prognostic molecular markers in myelodysplastic syndromes. Expert Rev Hematol 2010; 2:563-75. [PMID: 21083021 DOI: 10.1586/ehm.09.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cytogenetic findings in myelodysplastic syndromes play an important role in diagnosis, prognostication and clinical decision making. Therefore, they became an important aspect in scoring systems such as the International Prognostic Scoring System (IPSS) and the WHO-adapted Prognostic Scoring System (WPSS). Ongoing efforts to refine the categorization of karyotypes with regard to prognosis and therapeutic options will change scoring systems in the near future. In order to learn more about the pathophysiology of myelodysplastic syndromes, various molecular genetic aberrations are identified and their impact on prognosis discussed. New screening methods such as gene expression or single nucleotide polymorphism analysis are good candidates to find entrance in clinical practice in the future as they are useful tools in further elucidation of the underlying defects in myelodysplastic syndromes and the development of more specific classifications of the disease concerning risk assessment.
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Affiliation(s)
- Judith Neukirchen
- Department of Hematology, Oncology and Clinical Immunology, Heinrich-Heine-University of Duesseldorf, Moorenstraße 5, Düesseldorf, Germany.
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25
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Assessing karyotype precision by microarray-based comparative genomic hybridization in the myelodysplastic/myeloproliferative syndromes. Mol Cytogenet 2010; 3:23. [PMID: 21078186 PMCID: PMC3000833 DOI: 10.1186/1755-8166-3-23] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 11/15/2010] [Indexed: 11/11/2022] Open
Abstract
Background Recent genome-wide microarray-based research investigations have revealed a high frequency of submicroscopic copy number alterations (CNAs) in the myelodysplastic syndromes (MDS), suggesting microarray-based comparative genomic hybridization (aCGH) has the potential to detect new clinically relevant genomic markers in a diagnostic laboratory. Results We performed an exploratory study on 30 cases of MDS, myeloproliferative neoplasia (MPN) or evolving acute myeloid leukemia (AML) (% bone marrow blasts ≤ 30%, range 0-30%, median, 8%) by aCGH, using a genome-wide bacterial artificial chromosome (BAC) microarray. The sample data were compared to corresponding cytogenetics, fluorescence in situ hybridization (FISH), and clinical-pathological findings. Previously unidentified imbalances, in particular those considered submicroscopic aberrations (< 10 Mb), were confirmed by FISH analysis. CNAs identified by aCGH were concordant with the cytogenetic/FISH results in 25/30 (83%) of the samples tested. aCGH revealed new CNAs in 14/30 (47%) patients, including 28 submicroscopic or hidden aberrations verified by FISH studies. Cryptic 344-kb RUNX1 deletions were found in three patients at time of AML transformation. Other hidden CNAs involved 3q26.2/EVI1, 5q22/APC, 5q32/TCERG1,12p13.1/EMP1, 12q21.3/KITLG, and 17q11.2/NF1. Gains of CCND2/12p13.32 were detected in two patients. aCGH failed to detect a balanced translocation (n = 1) and low-level clonality (n = 4) in five karyotypically aberrant samples, revealing clinically important assay limitations. Conclusions The detection of previously known and unknown genomic alterations suggests that aCGH has considerable promise for identification of both recurring microscopic and submicroscopic genomic imbalances that contribute to myeloid disease pathogenesis and progression. These findings suggest that development of higher-resolution microarray platforms could improve karyotyping in clinical practice.
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26
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Array comparative genomic hybridization analysis of adult acute leukemia patients. ACTA ACUST UNITED AC 2010; 197:122-9. [PMID: 20193845 DOI: 10.1016/j.cancergencyto.2009.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 11/22/2009] [Accepted: 11/25/2009] [Indexed: 12/27/2022]
Abstract
We have performed a retrospective array-based comparative hybridization (array-CGH) study on 41 acute leukemia samples [n=17 acute lymphoblastic leukemia (ALL) patients only at diagnosis, n=3 ALL patients both at diagnosis and relapse; n=20 acute myeloid leukemia (AML) patients only at diagnosis and n=1 AML patient both at diagnosis and relapse] using an Agilent 44K array. In addition to previously detected cytogenetic aberrations, we observed cryptic aberrations in 95% of ALL and 90.5% of AML cases. ALL-specific recurrent abnormalities were RB1 (n=3), PAX5 (n=4), and CDKN2B (n=3) deletions; AML-specific recurrent abnormalities were HOXA9 and HOXA10 (n=2) deletions and NOTCH1 duplication (n=2). Recurrent duplication of the ELK1 oncogene was observed in both ALL (n=2) and AML (n=3) cases. Our results demonstrate that oligo-array CGH (oaCGH) is an effective method for defining copy number alterations and identification of novel recurring unbalanced abnormalities. At least for now, however, the use of oaCGH for routine diagnosis still has some restrictions.
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27
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High-resolution oligonucleotide array comparative genomic hybridization study and methylation status of the RPS14 gene in de novo myelodysplastic syndromes. ACTA ACUST UNITED AC 2010; 197:166-73. [PMID: 20193850 DOI: 10.1016/j.cancergencyto.2009.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 10/23/2009] [Accepted: 11/19/2009] [Indexed: 11/22/2022]
Abstract
In myelodysplastic syndromes (MDS), close to one half of patients do not have any visible karyotypic change. In order to study submicroscopic genomic alterations, we applied high-resolution array comparative genomic hybridization techniques (aCGH) in 37 patients with de novo MDS. Furthermore, we studied the methylation status of the RPS14 gene in 5q deletion (5q21.3q33.1) in 24 patients. In all, 21 of the 37 patients (57%) had copy number alterations. The most frequent copy number losses with minimal common overlapping areas were 5q21.3q33.1 (21%) and 7q22.1q33 (19%); the most frequent copy number gain was gain of the whole chromosome 8 (8%). Recurrent, but less frequent copy number losses were detected in two cases each: 11q14.1q22.1, 11q22.3q24.2, 12p12.2p13.31, 17p13.2, 18q12.1q12.2, 18q12.3q21.3, 18q21.2qter, and 20q11.23q12; the gains 8p23.2pter, 8p22p23.1, 8p12p21.1, and 8p11.21q21.2 were similarly found in two cases each. No homozygous losses or amplifications were observed. The RPS14 gene was not methylated in any of the patients.
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Makishima H, Rataul M, Gondek LP, Huh J, Cook JR, Theil KS, Sekeres MA, Kuczkowski E, O'Keefe C, Maciejewski JP. FISH and SNP-A karyotyping in myelodysplastic syndromes: improving cytogenetic detection of del(5q), monosomy 7, del(7q), trisomy 8 and del(20q). Leuk Res 2009; 34:447-53. [PMID: 19758696 DOI: 10.1016/j.leukres.2009.08.023] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 08/15/2009] [Accepted: 08/17/2009] [Indexed: 11/17/2022]
Abstract
Cytogenetic aberrations identified by metaphase cytogenetics (MC) have important diagnostic, prognostic and therapeutic roles in myelodysplastic syndromes (MDS). Fluorescence in situ hybridization (FISH) complements MC by the ability to evaluate large numbers of both interphase and metaphase nuclei. However, clinically practical FISH strategies are limited to detection of known lesions. Single nucleotide polymorphism array (SNP-A)-based karyotyping can reveal unbalanced defects with superior resolution over MC and FISH and identify segmental uniparental disomy (UPD) undetectable by either method. Using a standardized approach, we focused our investigation on detection of -5/del(5q), -7/del(7q), trisomy 8 and del(20q) in patients with MDS (N=52), MDS/myeloproliferative overlap syndromes (N=7) and acute myeloid leukemia (N=15) using MC, FISH and SNP-A karyotyping. The detection rate for del(5q) was 30, 32 and 32% by MC, FISH, and SNP-A, respectively. No single method detected all defects, and detection rates improved when all methods were used. The rate for detection of del(5q) increased incrementally to 35% (MC+FISH), 38% (MC+SNP-A), 38% (FISH+SNP-A) and 39% (all three methods). Similar findings were observed for -7/del(7q), trisomy 8 and -20/del(20q). We conclude that MC, FISH and SNP-A are complementary techniques that, when applied and interpreted together, can improve the diagnostic yield for identifying genetic lesions in MDS and contribute to the better description of abnormal karyotypes.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Chromosome Deletion
- Chromosomes, Human, Pair 20
- Chromosomes, Human, Pair 5
- Chromosomes, Human, Pair 7
- Chromosomes, Human, Pair 8
- DNA Mutational Analysis/methods
- Female
- Humans
- In Situ Hybridization, Fluorescence
- Karyotyping/methods
- Male
- Middle Aged
- Monosomy/diagnosis
- Myelodysplastic Syndromes/diagnosis
- Myelodysplastic Syndromes/genetics
- Polymorphism, Single Nucleotide
- Trisomy/diagnosis
- Young Adult
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Affiliation(s)
- Hideki Makishima
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
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29
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Valent P, Wieser R. Update on genetic and molecular markers associated with myelodysplastic syndromes. Leuk Lymphoma 2009; 50:341-8. [PMID: 19263296 DOI: 10.1080/10428190902756107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid neoplasms defined by morphologic dysplasia, peripheral cytopenia and clonal instability with enhanced risk of transformation into acute myeloid leukemia. The prognosis and clinical picture in MDS vary depending on patient-related factors (age, gender, comorbidity), the disease variant, cell types affected and genes involved in the malignant process. In fact, more and more data suggest that cytogenetic and molecular defects and gene variants are associated with the clinical course and prognosis in MDS. Although certain molecular defects are indicative of distinct cytogenetic abnormalities, others represent point mutations in critical target genes (RUNX1, N-RAS, JAK2, KIT, others) and sometimes are associated with a particular type of MDS, an overlap disease, a co-existing hematopoietic neoplasm or disease progression. Although most are somatic mutations, germ line mutations and gene polymorphisms have also been described in MDS. Some of these mutations may influence the natural course of disease, iron accumulation or disease progression. The present article provides a summary of our current knowledge about molecular and genetic markers in MDS, with special reference to their potential prognostic and therapeutic implications.
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Affiliation(s)
- Peter Valent
- Division of Hematology and Hemostaseology, Department of Internal Medicine I, Medical University of Vienna, Vienna, Austria.
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30
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Eisenmann KM, Dykema KJ, Matheson SF, Kent NF, DeWard AD, West RA, Tibes R, Furge KA, Alberts AS. 5q– myelodysplastic syndromes: chromosome 5q genes direct a tumor-suppression network sensing actin dynamics. Oncogene 2009; 28:3429-41. [DOI: 10.1038/onc.2009.207] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Zatkova A, Merk S, Wendehack M, Bilban M, Muzik EM, Muradyan A, Haferlach C, Haferlach T, Wimmer K, Fonatsch C, Ullmann R. AML/MDS with 11q/MLLamplification show characteristic gene expression signature and interplay of DNA copy number changes. Genes Chromosomes Cancer 2009; 48:510-20. [DOI: 10.1002/gcc.20658] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Ou JJ, Bagg A. Diagnostic challenges in the myelodysplastic syndromes: the current and future role of genetic and immunophenotypic studies. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2009; 3:275-91. [PMID: 23488463 DOI: 10.1517/17530050902813947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Myelodysplastic syndromes (MDS) comprise a clinically and pathologically diverse collection of hematopoietic neoplasms, most commonly presenting with peripheral cytopenias typically in the context of bone marrow hypercellularity. Mechanistically, at least in the early phases of the disease, this apparently paradoxical picture is primarily due to ineffective hematopoiesis, which is accompanied by a variety of morphologic abnormalities in hematopoietic cells. The identification of recurrent, clinically relevant cytogenetic defects in MDS has spurred the research of molecular mechanisms that contribute to its inception as well as to the development of heterogeneous subtypes. Although conventional cytogenetic analyses remain a diagnostic mainstay in MDS, the application of contemporary techniques including molecular cytogenetics, microarray technologies and multiparametric flow cytometry may ultimately reveal new diagnostic parameters that are theoretically more objective and sensitive than current morphologic approaches. This review aims to outline the role of genetic and immunophenotypic studies in the evaluation of MDS, including findings that may potentially influence future diagnostic classifications, which could refine prognostication and ultimately facilitate the growth of targeted therapies.
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Affiliation(s)
- Joyce J Ou
- University of Pennsylvania, Department of Pathology and Laboratory Medicine, 3400 Spruce Street, 6 Founders Pavilion, PA 19406-4283, USA
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33
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Tefferi A, Sirhan S, Sun Y, Lasho T, Finke CM, Weisberger J, Bale S, Compton J, LeDuc CA, Pardanani A, Thorland EC, Shevchenko Y, Grodman M, Chung WK. Oligonucleotide array CGH studies in myeloproliferative neoplasms: Comparison with JAK2V617F mutational status and conventional chromosome analysis. Leuk Res 2009; 33:662-4. [DOI: 10.1016/j.leukres.2008.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 09/08/2008] [Accepted: 09/09/2008] [Indexed: 11/27/2022]
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34
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Eckstein N, Servan K, Hildebrandt B, Pölitz A, von Jonquières G, Wolf-Kümmeth S, Napierski I, Hamacher A, Kassack MU, Budczies J, Beier M, Dietel M, Royer-Pokora B, Denkert C, Royer HD. Hyperactivation of the insulin-like growth factor receptor I signaling pathway is an essential event for cisplatin resistance of ovarian cancer cells. Cancer Res 2009; 69:2996-3003. [PMID: 19318572 DOI: 10.1158/0008-5472.can-08-3153] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Platinum plays a central role in the therapy of ovarian cancer, and the emergence of platinum resistance is a major obstacle for clinical management of the disease. We treated A2780 ovarian cancer cells by weekly cycles of cisplatin over a period of 6 months and unveiled that enhanced insulin-like growth factor I receptor (IGF-IR) expression and autocrine IGF-I are associated with hyperactivation of the IGF-IR and phosphatidylinositol-3-OH kinase (PI3K) pathways in cisplatin-resistant cells. IGF-IR expression levels increased during treatment cycles and correlated with cisplatin resistance. Purified IGF-I induced cisplatin resistance in diverse ovarian cancer cell lines, and small molecule inhibitors proved that IGF-IR and PI3K are essential for cisplatin resistance. Similar results were obtained with BG-1 ovarian cancer cells. Cytogenetic and array comparative genomic hybridization analyses revealed selection and de novo formation of chromosomal alterations during resistance development. An analysis of gene expression profiles of primary ovarian carcinomas identified the regulatory subunit PIK3R2 of PI3-kinase as a significant negative prognosis factor for ovarian cancer. We conclude that targeting the IGF-IR and the PI3K pathways is a promising new strategy to treat cisplatin-resistant ovarian carcinomas.
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Affiliation(s)
- Niels Eckstein
- Center of Advanced European Studies and Research (caesar), Bonn, Germany
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36
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Abstract
Over the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders. Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities. Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, including a need for cell culture. Whole genome scanning using comparative genomic hybridization and single nucleotide polymorphism arrays (CGH-A; SNP-A) can be used for analysis of somatic or clonal unbalanced chromosomal defects. In SNP-A, the combination of copy number detection and genotyping enables diagnosis of copy-neutral loss of heterozygosity, a lesion that cannot be detected using MC but may have important pathogenetic implications. Overall, whole genome scanning arrays, despite the drawback of an inability to detect balanced translocations, allow for discovery of chromosomal defects in a higher proportion of patients with hematologic malignancies. Newly detected chromosomal aberrations, including somatic uniparental disomy, may lead to more precise prognostic schemes in many diseases.
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