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Papadopoulou V, Schoumans J, Scarpelli I, Blum S. Description of an Institutional Cohort of Myeloid Neoplasms Carrying ETV6-Locus Deletions or ETV6 Rearrangements. Acta Haematol 2023; 146:401-407. [PMID: 36848872 PMCID: PMC10614221 DOI: 10.1159/000529844] [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: 09/20/2022] [Accepted: 02/20/2023] [Indexed: 03/01/2023]
Abstract
The gene encoding for transcription factor ETV6 presents recurrent lesions in hematologic neoplasms, most notably the ETV6-RUNX1 rearrangement in childhood B-ALL. The role of ETV6 for normal hematopoiesis is unknown, but loss of its function probably participates in oncogenic procedures. In myeloid neoplasms, ETV6-locus (12p13) deletions are rare but recurrent; ETV6 translocations are even rarer, but those reported seem to have phenotype-defining consequences. We herein describe the genetic and hematologic profile of myeloid neoplasms with ETV6 deletions (10 cases), or translocations (4 cases) diagnosed in the last 10 years in our institution. We find complex caryotype to be the most prevalent cytogenetics among patients with 12p13 deletion (8/10 patients), with most frequent coexisting anomalies being monosomy 7 or deletion 7q32 (5/10), monosomy 5 or del5q14-15 (5/10), and deletion/inversion of chromosome 20 (5/10), and most frequent point mutation being TP53 mutation (6/10 patients). Mechanisms of synergy of these lesions are unknown. We describe the entire genetic profile and hematologic phenotype of cases with extremely rare ETV6 translocations, confirming the biphenotypic T/myeloid nature of acute leukemia associated to ETV6-NCOA2 rearrangement, the association of t (1;12) (p36; p13) and of the CHIC2-ETV6 fusion with MDS/AML, and the association of the ETV6-ACSL6 rearrangement with myeloproliferative neoplasm with eosinophilia. Mutation of the intact ETV6 allele was present in two cases and seems to be subclonal to the chromosomal lesions. Decoding the mechanisms of disease related to ETV6 haploinsufficiency or rearrangements is important for the understanding of pathogenesis of myeloid neoplasms and fundamental research must be guided by observational cues.
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Affiliation(s)
- Vasiliki Papadopoulou
- Hematology Division, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Ilaria Scarpelli
- Oncogenetics Laboratory, Lausanne University Hospital, Lausanne, Switzerland
| | - Sabine Blum
- Hematology Division, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
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2
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Ren Y, Lang W, Mei C, Luo Y, Ye L, Wang L, Zhou X, Xu G, Ma L, Jin J, Tong H. Co-mutation landscape and clinical significance of RAS pathway related gene mutations in patients with myelodysplastic syndrome. Hematol Oncol 2023; 41:159-166. [PMID: 36316121 DOI: 10.1002/hon.3099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/06/2022] [Accepted: 10/24/2022] [Indexed: 11/04/2022]
Abstract
Single gene mutations in the RAS pathway are uncommon and of unknown significance in myelodysplastic syndrome (MDS) patients, RAS pathway-related gene mutations (RASwaymut ) as a whole may be significant and require further elucidation. The clinical and molecular data of 370 MDS patients who were newly diagnosed between 1 November 2016 and 31 August 2020 in our hospital were collected and retrospectively reviewed. RASwaymut were detected in 57 (15.41%) patients. Higher median percentage of marrow blasts (2% vs. 1%, P = 0.00), more co-mutated genes (4, interquartile range [IQR]: 2-5. vs. 2, IQR:1-4, P = 0.00), more higher risk patients according to international prognostic scoring system-revised (IPSS-R) (80.70% vs. 59.11%, P = 0.002) as well as higher acute myeloid leukemia transformation rate (35.09% vs. 14.38%, P = 0.02) were observed in patients with RASwaymut when compared to those with wild type RAS pathway-related genes (RASwaywt ). The most frequent co-mutated genes were ASXL1 (28.6%), TET2 (23.2%), U2AF1, RUNX1, TP53 (14.3%); DNMT3A (12.5%), among which ASXL1 mutation rate were significantly higher than those with RASwaywt (p < 0.05). RASwaymut had no significant effect on response to disease-modifying treatment in MDS patients. However, Overall survivals (OS) of RASwaymut patients were significantly shorter than those with RASwaywt (16.05 m. vs. 92.3 m, P = 0.00), especially in patients with marrow blasts less than 5% (P = 0.002), normal karyotype (P = 0.01) and lower risk (P = 0.00). While multivariate prognostic analysis showed that RASwaymut co-mutated with TET2 was an independent poor prognostic factor for all MDS patients (P = 0.00, hazrad ratio [HR] = 4.77 with 95% confidence interval [CI]: 2.4-9.51) and RASwaymut patients (P = 0.02, HR 2.76, 95% CI 1.21-6.29). In conclusion, RASwaymut was associated with higher IPSS-R risk, higher incidence of leukemic transformation thus shorter OS in MDS patients, it could be viewed as a whole to predict poor prognosis. Co-mutation with TET2 may promote disease progression and was an independent poor prognostic factor in MDS patients.
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Affiliation(s)
- Yanling Ren
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Wei Lang
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Chen Mei
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Yingwan Luo
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Li Ye
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Lu Wang
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Xinping Zhou
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Gaixiang Xu
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Liya Ma
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Jie Jin
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
| | - Hongyan Tong
- Myelodysplastic Syndromes Diagnosis and Therapy Center, Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Zhejiang Provincial Clinical Research Center for Hematologic Diseases, Hangzhou, Zhejiang, China
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Czegle I, Gray AL, Wang M, Liu Y, Wang J, Wappler-Guzzetta EA. Mitochondria and Their Relationship with Common Genetic Abnormalities in Hematologic Malignancies. Life (Basel) 2021; 11:1351. [PMID: 34947882 PMCID: PMC8707674 DOI: 10.3390/life11121351] [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: 11/01/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Hematologic malignancies are known to be associated with numerous cytogenetic and molecular genetic changes. In addition to morphology, immunophenotype, cytochemistry and clinical characteristics, these genetic alterations are typically required to diagnose myeloid, lymphoid, and plasma cell neoplasms. According to the current World Health Organization (WHO) Classification of Tumors of Hematopoietic and Lymphoid Tissues, numerous genetic changes are highlighted, often defining a distinct subtype of a disease, or providing prognostic information. This review highlights how these molecular changes can alter mitochondrial bioenergetics, cell death pathways, mitochondrial dynamics and potentially be related to mitochondrial genetic changes. A better understanding of these processes emphasizes potential novel therapies.
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Affiliation(s)
- Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary;
| | - Austin L. Gray
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Minjing Wang
- Independent Researcher, Diamond Bar, CA 91765, USA;
| | - Yan Liu
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Jun Wang
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Edina A. Wappler-Guzzetta
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
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Yang Y, Lin T, Dong T, Wu Y. Myelodysplastic syndrome presenting with central diabetes insipidus is associated with monosomy 7, visible or hidden: report of two cases and literature review. Mol Cytogenet 2021; 14:42. [PMID: 34470671 PMCID: PMC8411536 DOI: 10.1186/s13039-021-00563-0] [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: 04/02/2021] [Accepted: 08/07/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Central diabetes insipidus (CDI) is a rare complication of myelodysplastic syndrome (MDS). Although the cytogenetic features of patients with MDS and CDI are not clear, CDI in patients with acute myeloid leukemia (AML) is associated with chromosome 7 and/or 3 anomalies. CASE PRESENTATION In this report, we describe two patients with MDS and concurrent CDI, and in one of them, CDI was the first manifestation. One patient had monosomy 7 on metaphase cytogenetics (MC). Monosomy 7 and numerous cytogenetic abnormalities were found in the other patient using single-nucleotide polymorphism array (SNP-A) karyotyping, while the MC did not uncover monosomy 7. In this manuscript we also reviewed reported cases of MDS with diabetes insipidus (DI-MDS) to summarize the relationship between DI-MDS and karyotype, and explore the best treatment strategy for DI-MDS. CONCLUSIONS DI-MDS is closely related to monosomy 7. Allogeneic hematopoietic stem cell transplantation may be the only effective treatment for DI-MDS. The SNP-A-based karyotyping is helpful to reveal subtle cytogenetic abnormalities and unveil their roles in the clinical features of MDS.
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Affiliation(s)
- Yunfan Yang
- Department of Hematology, Institute of Hematology, West China Hospital of Sichuan University, Guoxuexiang 37, Chengdu, 610041, People's Republic of China
| | - Ting Lin
- Department of Hematology, Institute of Hematology, West China Hospital of Sichuan University, Guoxuexiang 37, Chengdu, 610041, People's Republic of China
| | - Tian Dong
- Department of Hematology, Institute of Hematology, West China Hospital of Sichuan University, Guoxuexiang 37, Chengdu, 610041, People's Republic of China
| | - Yu Wu
- Department of Hematology, Institute of Hematology, West China Hospital of Sichuan University, Guoxuexiang 37, Chengdu, 610041, People's Republic of China.
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5
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Yao W, Yang Z, Lou X, Mao H, Yan H, Zhang Y. Simultaneous Detection of Ebola Virus and Pathogens Associated With Hemorrhagic Fever by an Oligonucleotide Microarray. Front Microbiol 2021; 12:713372. [PMID: 34394063 PMCID: PMC8363200 DOI: 10.3389/fmicb.2021.713372] [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: 05/22/2021] [Accepted: 07/05/2021] [Indexed: 11/15/2022] Open
Abstract
Ebola virus infection causes severe hemorrhagic fever, and its mortality rates varied from 25 to 90% in the previous outbreaks. The highly infectious and lethal nature of this virus highlights the need for reliable and sensitive diagnostic methods to distinguish it from other diseases present with similar clinical symptoms. Based on multiplex polymerase chain reaction (PCR) and oligonucleotide microarray technology, a cost-effective, multipathogen and high-throughput method was developed for simultaneous detection of Ebola virus and other pathogens associated with hemorrhagic fever, including Marburg virus, Lassa fever virus, Junin virus, Machupo virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever virus, malaria parasite, hantavirus, severe fever with thrombocytopenia syndrome virus, dengue virus, yellow fever virus, Chikungunya virus, influenza A virus, and influenza B virus. This assay had an excellent specificity for target pathogens, without overlap signal between the probes. The limit of detection was approximately 103 pathogen copies/μl. A total of 60 positive nucleic acid samples for different pathogens were detected, a concordance of 100% was observed between microarray assay and real-time PCR analysis. Consequently, the described oligonucleotide microarray may be specific and sensitive assay for diagnosis and surveillance of infections caused by Ebola virus and other species of hemorrhagic fever pathogens.
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Affiliation(s)
- Wenwu Yao
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhangnv Yang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiuyu Lou
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Haiyan Mao
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Hao Yan
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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6
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Genomic variations in patients with myelodysplastic syndrome and karyotypes without numerical or structural changes. Sci Rep 2021; 11:2783. [PMID: 33531543 PMCID: PMC7854738 DOI: 10.1038/s41598-021-81467-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 01/30/2023] Open
Abstract
Myelodysplastic syndrome (MDS) is an onco-hematologic disease with distinct levels of peripheral blood cytopenias, dysplasias in cell differentiation and various forms of chromosomal and cytogenomic alterations. In this study, the Chromosomal Microarray Analysis (CMA) was performed in patients with primary MDS without numerical and/or structural chromosomal alterations in karyotypes. A total of 17 patients was evaluated by GTG banding and eight patients showed no numerical and/or structural alterations. Then, the CMA was carried out and identified gains and losses CNVs and long continuous stretches of homozygosity (LCSHs). They were mapped on chromosomes 1, 2, 3, 4, 5, 6, 7, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, X, and Y. Ninety-one genes that have already been implicated in molecular pathways important for cell viability were selected and in-silico expression analyses demonstrated 28 genes differentially expressed in mesenchymal stromal cells of patients. Alterations in these genes may be related to the inactivation of suppressor genes or the activation of oncogenes contributing to the evolution and malignization of MDS. CMA provided additional information in patients without visible changes in the karyotype and our findings could contribute with additional information to improve the prognostic and personalized stratification for patients.
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Ronaghy A, Yang RK, Khoury JD, Kanagal-Shamanna R. Clinical Applications of Chromosomal Microarray Testing in Myeloid Malignancies. Curr Hematol Malig Rep 2020; 15:194-202. [PMID: 32382988 DOI: 10.1007/s11899-020-00578-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW Knowledge of both somatic mutations and copy number aberrations are important for the understanding of cancer pathogenesis and management of myeloid neoplasms. The currently available standard of care technologies for copy number assessment such as conventional karyotype and FISH are either limited by low resolution or restriction to targeted assessment. RECENT FINDINGS Chromosomal microarray (CMA) is effective in characterization of chromosomal and gene aberrations of diagnostic, prognostic, and therapeutic significance at a higher resolution than conventional karyotyping. These results are complementary to NGS mutation studies. Copy-neutral loss of heterozygosity (CN-LOH), which is prognostic in AML, is currently only identified by CMA. Yet, despite the widespread availability, CMA testing is not routinely performed in diagnostic laboratories due to lack of knowledge on best-testing practices for clinical work-up of myeloid neoplasms. In this review, we provide an overview of the clinical significance of CMA in acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myelodysplastic/myeloproliferative neoplasms (MDS/MPN). We will also elaborate the specific clinical scenarios where CMA can provide additional information essential for management and could potentially alter treatment. Chromosomal microarray (CMA) is an effective technology for characterizing chromosomal copy number changes and copy-neutral loss of heterozygosity of diagnostic, prognostic, and therapeutic significance at a high resolution in myeloid malignancies.
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MESH Headings
- Chromosome Aberrations
- Chromosomes, Human
- Comparative Genomic Hybridization
- DNA Copy Number Variations
- Genetic Predisposition to Disease
- High-Throughput Nucleotide Sequencing
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myelomonocytic, Chronic/diagnosis
- Leukemia, Myelomonocytic, Chronic/genetics
- Loss of Heterozygosity
- Microarray Analysis
- Myelodysplastic Syndromes/diagnosis
- Myelodysplastic Syndromes/genetics
- Polymorphism, Single Nucleotide
- Predictive Value of Tests
- Prognosis
- Reproducibility of Results
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Affiliation(s)
- Arash Ronaghy
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Richard K Yang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 072, Houston, TX, 77030, USA.
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Gao M, Li S, Wang L, Nie S, Pang H, Lu X, Wang X, Wang M, Guo S, Ma Y, Meng F. Identification of a cryptic submicroscopic deletion using a combination of fluorescence in situ hybridization and array comparative genomic hybridization in a t(3;5)(q25;q35)-positive acute myeloid leukemia patient: A case report and review of the literature. Medicine (Baltimore) 2020; 99:e22789. [PMID: 33120794 PMCID: PMC7581054 DOI: 10.1097/md.0000000000022789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RATIONALE The advent of high-resolution genome arrays including array comparative genomic hybridization (aCGH) has enabled the detection of cryptic submicroscopic deletions flanking translocation breakpoints in up to 20% of the apparently "balanced" structural chromosomal rearrangements in hematological disorders. However, reports of submicroscopic deletions flanking the breakpoints of t(3;5)(q25;q35) are rare and the clinical significance of submicroscopic deletions in t(3;5) has not been explicitly identified. PATIENT CONCERNS We present a 47-year-old man with acute myeloid leukemia. G-banding analysis identified t(3;5)(q25;q35). DIAGNOSIS Array CGH-based detection initially confirmed only the deletion of chromosome 3. Further characterization using fluorescence in situ hybridization identified a cryptic submicroscopic deletion including 5' MLF1-3' NPM1 flanking the breakpoint on the derivative chromosome 3. INTERVENTIONS The patient started "7+3" induction chemotherapy with cytosine arabinoside and daunorubicin, and subsequently received 2 cycles of high-dose intermittent acronym of cytosine arabinoside or cytarabine. OUTCOMES The patient did not undergo complete remission and died from an infection due to neutropenia. LESSONS Haploinsufficiency of NPM1 or other deleted genes, including SSR3, may be responsible for the phenotype of t(3;5)(q25;q35)-positive myeloid neoplasms with submicroscopic deletions.
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Affiliation(s)
- Man Gao
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Lina Wang
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Shu Nie
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Hui Pang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Xianglan Lu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Xianfu Wang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Mingwei Wang
- Department of Radiotherapy, Public Health School of Jilin University, Changchun City, Jilin, P.R. China
| | - Shirong Guo
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Yuhan Ma
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
| | - Fanzheng Meng
- Department of Pediatrics, the First Hospital of Jilin University, Changchun City, Jilin
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Laboratory and Clinical Evaluation of DNA Microarray for the Detection of Carbapenemase Genes in Gram-Negative Bacteria from Hospitalized Patients. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8219748. [PMID: 31214618 PMCID: PMC6535891 DOI: 10.1155/2019/8219748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/12/2019] [Accepted: 04/02/2019] [Indexed: 11/23/2022]
Abstract
Background The prevalence of a variety of carbapenemases in Gram-negative bacteria (GNB) has posed a global threat on clinical control and management. Monitoring and controlling the carbapenemase-producing GNB became imperative tasks for many healthcare centers. The aim of this study was to develop a high-throughput, specific, sensitive, and rapid DNA microarray-based method for the diagnosis, phenotypic confirmation, and molecular epidemiological study of carbapenemase genes. Methods We targeted a panel of eight carbapenemase genes, including blaKPC, blaNDM-1, blaOXA-23, blaOXA-48, blaOXA-51, blaIMP, blaVIM, and blaDIM for detection. Ultrasensitive chemiluminescence (CL) detection method was developed and used to simultaneously detect eight carbapenemase genes, and plasmids were established as positive or limit of detection (LOD) reference materials. Antibiotic susceptibility was determined by disk diffusion according to Clinical and Laboratory Standards Institute (CLSI) guidelines in order to screen clinical isolates resistant to carbapenem antibiotics as well as Sanger sequencing which was used to confirm the reliability of the results presented by DNA microarray. Results Eight carbapenemase genes could be detected with high sensitivity and specificity. The absolute LOD of this strategy to detect serially diluted plasmids of eight carbapenemase genes was 102- 103copies/μL. Then, 416 specimens collected from hospital were detected and the results showed 96.6% concordance between the phenotypic and microarray tests. Compared with Sanger sequencing, a specificity and sensitivity of 100% were recorded for blaNDM-1, blaIMP, blaVIM, and blaDIM genes. The specificity for blaKPC, blaOXA-23, blaOXA-48, and blaOXA-51 genes was 100% and the sensitivity was 98.5%, 97.6%, 95.7%, and 97.9%, respectively. The overall consistency rate between the sequencing and microarray is 97.8%. Conclusions The proposed ultrasensitive CL imaging DNA hybridization has high specificity, sensitivity, and reproducibility and could detect and differentiate clinical specimens that carried various carbapenemase genes, suggesting that the method can conveniently be customized for high-throughput detection of the carbapenemase-producing GNB and can be easily adapted for various clinical applications.
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10
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Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genet 2018; 228-229:197-217. [PMID: 30377088 DOI: 10.1016/j.cancergen.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston TX, USA.
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, Cancer Genetics Laboratory, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Shashi Shetty
- Department of Pathology, UHCMC, University Hospitals and Case Western Reserve University, Cleveland, OH, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emma Huxley
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Xinjie Xu
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Sally Jeffries
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Marilyn L Slovak
- TriCore Reference Laboratories, University of New Mexico, Albuquerque, NM, USA
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, NY, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA.
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11
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Peterson JF, Van Dyke DL, Hoppman NL, Kearney HM, Sukov WR, Greipp PT, Ketterling RP, Baughn LB. The Utilization of Chromosomal Microarray Technologies for Hematologic Neoplasms: An ACLPS Critical Review. Am J Clin Pathol 2018; 150:375-384. [PMID: 30052716 DOI: 10.1093/ajcp/aqy076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Chromosome (G-banding) and fluorescence in situ hybridization (FISH) serve as the primary methodologies utilized for detecting genetic aberrations in hematologic neoplasms. Chromosomal microarray can detect copy number aberrations (CNAs) with greater resolution when compared to G-banding and FISH, and can also identify copy-neutral loss of heterozygosity (CN-LOH). The purpose of our review is to highlight a preselected group of hematologic neoplasms for which chromosomal microarray has the greatest clinical utility. METHODS A case-based approach and review of the literature was performed to identify the advantages and disadvantages of utilizing chromosomal microarray for specific hematologic neoplasms. RESULTS Chromosomal microarray identified CNAs and CN-LOH of clinical significance, and could be performed on fresh or paraffin-embedded tissue and liquid neoplasms. Microarray studies could not detect balanced rearrangements, low-level clones, or distinguish independent clones. CONCLUSIONS When utilized appropriately, chromosomal microarray can provide clinically significant information that complements traditional cytogenetic testing methodologies.
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Affiliation(s)
- Jess F Peterson
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Daniel L Van Dyke
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Hutton M Kearney
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Rhett P Ketterling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
| | - Linda B Baughn
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN
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12
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Zhang L, Ren M, Song G, Zhang Y, Liu X, Zhang X, Wang J. Prenatal diagnosis of sex chromosomal inversion, translocation and deletion. Mol Med Rep 2018; 17:2811-2816. [PMID: 29257243 PMCID: PMC5783495 DOI: 10.3892/mmr.2017.8198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 04/27/2017] [Indexed: 11/23/2022] Open
Abstract
The aim of the present study was to perform comprehensive prenatal diagnosis using various detection techniques on a fetus in a high‑risk pregnant woman, and to provide genetic counseling for the patient and her family so as to avoid birth defects. The routine karyotype analysis via amniocentesis, fluorescence in situ hybridization, and whole genome microarray technique were performed for the prenatal diagnosis of the fetus. The fetal karyotype was 46,X,ish der(X) inv(X)(p22.3q28)t(X;Y)(q28;q11.2)(XYqter+,SRY‑,DXZ1+, RP11‑64L19+,STS+,XYpter+); namely, one fetal X chromosome belonged to the derivative imbalanced chromosome and this chromosome demonstrated complex chromosomal rearrangements involving inversion, translocation and deletion. Notably, pericentric inversion between Xp22.3 and Xq28 was identified, and the chromosomal microarray technique confirmed that the long arm q28 of the derivative X chromosome had a 1.241‑Mb deletion in Xq28, which included Online Mendelian Inheritance in Man genes such as coagulation factor VIII, glucose‑6‑phosphate dehydrogenase, inhibitor of nuclear factor‑κB kinase subunit γ, trimethyllysine hydroxylase ε, Ras‑related protein Rab‑39B and chloride intracellular channel 2. In addition, this chromosome also exhibited the local translocation of fragment Yq11.21‑q11.23, which did not include the sex determining region Y gene. This fetus demonstrated deletion, inversion and translocation syndrome, and may exhibit the corresponding clinical phenotypes (e.g., intellectual disability or general delayed development) (1) of such chromosome abnormalities after birth. Therefore, in prenatal diagnosis, a variety of genetic diagnostic techniques should be comprehensively used based on specific clinical situations, which may accurately reveal the nature, sources and manifestations of the derivative chromosome abnormalities and avoid the birth of children with defects.
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Affiliation(s)
- Lin Zhang
- Prenatal Diagnosis Center, People's Hospital of Peking University, Beijing 100044, P.R. China
| | - Meihong Ren
- Prenatal Diagnosis Center, People's Hospital of Peking University, Beijing 100044, P.R. China
| | - Guining Song
- Prenatal Diagnosis Center, People's Hospital of Peking University, Beijing 100044, P.R. China
| | - Yang Zhang
- Prenatal Diagnosis Center, People's Hospital of Peking University, Beijing 100044, P.R. China
| | - Xuexia Liu
- Prenatal Diagnosis Center, People's Hospital of Peking University, Beijing 100044, P.R. China
| | - Xiaohong Zhang
- Prenatal Diagnosis Center, People's Hospital of Peking University, Beijing 100044, P.R. China
| | - Jianliu Wang
- Prenatal Diagnosis Center, People's Hospital of Peking University, Beijing 100044, P.R. China
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13
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Selection of internal references for qRT-PCR assays of human hepatocellular carcinoma cell lines. Biosci Rep 2017; 37:BSR20171281. [PMID: 29180379 PMCID: PMC5741833 DOI: 10.1042/bsr20171281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/13/2022] Open
Abstract
Selecting internal references is important for normalizing the loading quantity of samples in quantitative reverse-transcription PCR (qRT-PCR). In the present study, a systematic evaluation of reference genes among nine hepatocellular carcinoma (HCC) cell lines was conducted. After screening the microarray assay data of ten HCC cell lines, 19 candidate reference genes were preselected and then evaluated by qRT-PCR, together with ACTB, GAPDH, HPRT1 and TUBB The expression evenness of these candidate genes was evaluated using RefFinder. The stabilities of the reference genes were further evaluated under different experimental perturbations in Huh-7 and MHCC-97L, and the applicability of the reference genes was assessed by measuring the mRNA expression of CCND1, CCND3, CDK4 and CDK6 under sorafenib treatment in Huh-7. Results showed that TFG and SFRS4 are among the most reliable reference genes, and ACTB ranks third and acts quite well as a classical choice, whereas GAPDH, HPRT1 and TUBB are not proper reference genes in qRT-PCR assays among the HCC cell lines. SFRS4, YWHAB, SFRS4 and CNPY3 are the most stable reference genes of the MHCC-97L under the perturbations of chemotherapy, oxidative stress, starvation and hypoxia respectively, whereas YWHAB is the most stable one of Huh-7 under all perturbations. GAPDH is recommended as a reference gene under chemotherapy perturbations. YWHAB and UBE2B, TMED2 and TSFM, and GAPDH and TSFM are the two best reference genes under oxidative stress, starvation and hypoxia perturbations respectively. TSFM is stable in both cell lines across all the perturbations.
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14
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Song Q, Chu Y, Yao Y, Peng M, Yang W, Li X, Huang S. Identify latent chromosomal aberrations relevant to myelodysplastic syndromes. Sci Rep 2017; 7:10354. [PMID: 28871208 PMCID: PMC5583229 DOI: 10.1038/s41598-017-10551-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/11/2017] [Indexed: 12/02/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic malignancies. This study aims to identify latent chromosomal abnormalities relevant to MDS, which may optimize the current diagnosis of MDS. Affymetrix CytoScan 750 K microarray platform was utilized to perform a genome-wide detection of chromosomal aberrations in the bone marrow cells of the patients. The findings were compared with the results from traditional karyotypic analysis and FISH to reveal latent chromosomal aberrations. Chromosomal gain, loss, and UPD, and complex karyotypes were identified in those samples. In addition to established cytogenetic aberrations detected by karyotypic analysis, CytoScan 750 K microarray also detected cryptic chromosomal lesions in MDS. Those latent defects underlying multiple gene mutations may construe the clinical variability of MDS. In Conclusion, Affymetrix CytoScan 750 K microarray is efficient in identifying latent chromosomal aberrations in MDS.
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Affiliation(s)
- Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Yuxin Chu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Min Peng
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weihong Yang
- Molecular department, Kindstar global, Wuhan, China
| | - Xiaoqing Li
- Molecular department, Kindstar global, Wuhan, China
| | - Shiang Huang
- Molecular department, Kindstar global, Wuhan, China
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15
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Abstract
Background Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in dysregulation of the RAS/MAPK pathway and are causative of NF1. The major known function of the NF1 gene product neurofibromin is to downregulate RAS. NF1 exhibits variable clinical expression and is characterized by benign cutaneous lesions including neurofibromas and café-au-lait macules, as well as a predisposition to various types of malignancy, such as breast cancer and leukaemia. However, acquired somatic mutations in NF1 are also found in a wide variety of malignant neoplasms that are not associated with NF1. Main body Capitalizing upon the availability of next-generation sequencing data from cancer genomes and exomes, we review current knowledge of somatic NF1 mutations in a wide variety of tumours occurring at a number of different sites: breast, colorectum, urothelium, lung, ovary, skin, brain and neuroendocrine tissues, as well as leukaemias, in an attempt to understand their broader role and significance, and with a view ultimately to exploiting this in a diagnostic and therapeutic context. Conclusion As neurofibromin activity is a key to regulating the RAS/MAPK pathway, NF1 mutations are important in the acquisition of drug resistance, to BRAF, EGFR inhibitors, tamoxifen and retinoic acid in melanoma, lung and breast cancers and neuroblastoma. Other curiosities are observed, such as a high rate of somatic NF1 mutation in cutaneous melanoma, lung cancer, ovarian carcinoma and glioblastoma which are not usually associated with neurofibromatosis type 1. Somatic NF1 mutations may be critical drivers in multiple cancers. The mutational landscape of somatic NF1 mutations should provide novel insights into our understanding of the pathophysiology of cancer. The identification of high frequency of somatic NF1 mutations in sporadic tumours indicates that neurofibromin is likely to play a critical role in development, far beyond that evident in the tumour predisposition syndrome NF1.
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16
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Stevens-Kroef MJ, Olde Weghuis D, ElIdrissi-Zaynoun N, van der Reijden B, Cremers EMP, Alhan C, Westers TM, Visser-Wisselaar HA, Chitu DA, Cunha SM, Vellenga E, Klein SK, Wijermans P, de Greef GE, Schaafsma MR, Muus P, Ossenkoppele GJ, van de Loosdrecht AA, Jansen JH. Genomic array as compared to karyotyping in myelodysplastic syndromes in a prospective clinical trial. Genes Chromosomes Cancer 2017; 56:524-534. [DOI: 10.1002/gcc.22455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/16/2017] [Accepted: 02/16/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Daniel Olde Weghuis
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Bert van der Reijden
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
| | - Eline M. P. Cremers
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Canan Alhan
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Theresia M. Westers
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Heleen A. Visser-Wisselaar
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Dana A. Chitu
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Sonia M. Cunha
- Department of Hematology; Erasmus MC Cancer Institute, HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - Edo Vellenga
- Department of Experimental Hematology; University Medical Center Groningen; Groningen The Netherlands
| | - Saskia K. Klein
- Department of Internal Medicine; Meander Medisch Centrum; Amersfoort The Netherlands
| | - Pierre Wijermans
- Department of Internal Medicine; Haga Ziekenhuis; The Hague The Netherlands
| | - Georgine E. de Greef
- Department of Hematology; Erasmus University Medical Center-Daniel den Hoed; Rotterdam The Netherlands
| | - M. Ron Schaafsma
- Department of Internal Medicine; Medisch Centrum Twente; Enschede The Netherlands
| | - Petra Muus
- Department of Hematology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Gert J. Ossenkoppele
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Arjan A. van de Loosdrecht
- Department of Hematology; VU University Medical Center, Cancer Center Amsterdam; Amsterdam The Netherlands
| | - Joop H. Jansen
- Department of Laboratory Medicine; Radboud University Medical Center; Nijmegen The Netherlands
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17
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Ciabatti E, Valetto A, Bertini V, Ferreri MI, Guazzelli A, Grassi S, Guerrini F, Petrini I, Metelli MR, Caligo MA, Rossi S, Galimberti S. Myelodysplastic syndromes: advantages of a combined cytogenetic and molecular diagnostic workup. Oncotarget 2017; 8:79188-79200. [PMID: 29108298 PMCID: PMC5668031 DOI: 10.18632/oncotarget.16578] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/14/2017] [Indexed: 12/26/2022] Open
Abstract
In this study we present a new diagnostic workup for the myelodysplastic syndromes (MDS) including FISH, aCGH, and somatic mutation assays in addition to the conventional cytogenetics (CC). We analyzed 61 patients by CC, FISH for chromosome 5, 7, 8 and PDGFR rearrangements, aCGH, and PCR for ASXL1, EZH2, TP53, TET2, RUNX1, DNMT3A, SF3B1 somatic mutations. Moreover, we quantified WT1 and RPS14 gene expression levels, in order to find their possible adjunctive value and their possible clinical impact. CC analysis showed 32% of patients with at least one aberration. FISH analysis detected chromosomal aberrations in 24% of patients and recovered 5 cases (13.5%) at normal karyotype (two 5q- syndromes, one del(7) case, two cases with PDGFR rearrangement). The aGCH detected 10 "new" unbalanced cases in respect of the CC, including one with alteration of the ETV6 gene. After mutational analysis, 33 patients (54%) presented at least one mutation and represented the only marker of clonality in 36% of all patients. The statistical analysis confirmed the prognostic role of CC either on overall or on progression-free-survival. In addition, deletions detected by aCGH and WT1 over-expression negatively conditioned survival. In conclusion, our work showed that 1) the addition of FISH (at least for chr. 5 and 7) can improve the definition of the risk score; 2) mutational analysis, especially for the TP53 and SF3B1, could better define the type of MDS and represent a "clinical warning"; 3) the aCGH use could be probably applied to selected cases (with suboptimal response or failure).
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Affiliation(s)
- Elena Ciabatti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy.,GenOMec, University of Siena, Siena, Italy
| | - Angelo Valetto
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Veronica Bertini
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Maria Immacolata Ferreri
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Alice Guazzelli
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Susanna Grassi
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy.,GenOMec, University of Siena, Siena, Italy
| | - Francesca Guerrini
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Iacopo Petrini
- Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Maria Rita Metelli
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Maria Adelaide Caligo
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Simona Rossi
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
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18
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Abstract
Cytogenetic analysis has an essential role in diagnosis, classification, and prognosis of myelodysplastic syndromes (MDS). Some cytogenetic abnormalities are sufficiently characteristic of MDS to be considered MDS defining in the appropriate clinical context. MDS with isolated del(5q) is the only molecularly defined MDS subtype. The genes responsible for many aspects of 5q- syndrome, the distinct clinical phenotype associated with this condition, have now been identified. Cytogenetics forms the cornerstone of the most widely adopted prognostic scoring systems in MDS, the international prognostic scoring system (IPSS) and the revised international prognostic scoring system (IPPS-R). Cytogenetic parameters also have utility in chronic myelomonocytic leukemia (CMML) and have been incorporated into specific prognostic scoring systems for this condition. More recently, it has been appreciated that submicroscopic copy number changes and gene mutations play a significant part in MDS pathogenesis. Integration of molecular genetics and cytogenetics holds much promise for improving clinical care and outcomes for patients with MDS.
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Affiliation(s)
- Meaghan Wall
- Victorian Cancer Cytogenetics Service, St. Vincent's Hospital, 41 Victoria Parade, Fitzroy, Melbourne, VIC, 3065, Australia.
- Department of Medicine, St Vincent's Hospital, The University of Melbourne, Melbourne, Australia.
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19
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Abáigar M, Robledo C, Benito R, Ramos F, Díez-Campelo M, Hermosín L, Sánchez-del-Real J, Alonso JM, Cuello R, Megido M, Rodríguez JN, Martín-Núñez G, Aguilar C, Vargas M, Martín AA, García JL, Kohlmann A, del Cañizo MC, Hernández-Rivas JM. Chromothripsis Is a Recurrent Genomic Abnormality in High-Risk Myelodysplastic Syndromes. PLoS One 2016; 11:e0164370. [PMID: 27741277 PMCID: PMC5065168 DOI: 10.1371/journal.pone.0164370] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022] Open
Abstract
To explore novel genetic abnormalities occurring in myelodysplastic syndromes (MDS) through an integrative study combining array-based comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases. 285 abnormalities were identified in 71 patients (23.6%). Three high-risk MDS cases (1.2%) displayed chromothripsis involving exclusively chromosome 13 and affecting some cancer genes: FLT3, BRCA2 and RB1. All three cases carried TP53 mutations as revealed by NGS. Moreover, in the whole series, the integrative analysis of aCGH and NGS enabled the identification of cryptic recurrent deletions in 2p23.3 (DNMT3A; n = 2.8%), 4q24 (TET2; n = 10%) 17p13 (TP53; n = 8.5%), 21q22 (RUNX1; n = 7%), and Xp11.4 (BCOR; n = 2.8%), while mutations in the non-deleted allele where found only in DNMT3A (n = 1), TET2 (n = 3), and TP53 (n = 4). These cryptic abnormalities were detected mainly in patients with normal (45%) or non-informative (15%) karyotype by conventional cytogenetics, except for those with TP53 deletion and mutation (15%), which had a complex karyotype. In addition to well-known copy number defects, the presence of chromothripsis involving chromosome 13 was a novel recurrent change in high-risk MDS patients. Array CGH analysis revealed the presence of cryptic abnormalities in genomic regions where MDS-related genes, such as TET2, DNMT3A, RUNX1 and BCOR, are located.
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Affiliation(s)
- María Abáigar
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Cristina Robledo
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Rocío Benito
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fernando Ramos
- IBIOMED, Instituto de Biomedicina, Universidad de León, León, Spain
- Servicio de Hematología, Hospital Universitario de León, León, Spain
| | - María Díez-Campelo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Lourdes Hermosín
- Servicio de Hematología, Hospital Jerez de la Frontera, Cádiz, Spain
| | | | - Jose M. Alonso
- Servicio de Hematología, Hospital Río Carrión, Palencia, Spain
| | - Rebeca Cuello
- Servicio de Hematología, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Marta Megido
- Servicio de Hematología, Hospital del Bierzo, Ponferrada, Spain
| | | | | | - Carlos Aguilar
- Servicio de Hematología, Hospital General de Soria, Soria, Spain
| | - Manuel Vargas
- Servicio de Hematología, Hospital Comarcal de Jarrio, Jarrio-Coaña, Spain
| | - Ana A. Martín
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Juan L. García
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Alexander Kohlmann
- AstraZeneca, Personalized Healthcare and Biomarkers, Innovative Medicines and Early Development, Cambridge, United Kingdom
| | - M. Consuelo del Cañizo
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
| | - Jesús M. Hernández-Rivas
- Unidad de Diagnóstico Molecular y Celular del Cáncer, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
- Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
- IBSAL, Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- * E-mail:
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20
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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: 1.5] [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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Schoumans J, Suela J, Hastings R, Muehlematter D, Rack K, van den Berg E, Berna Beverloo H, Stevens-Kroef M. Guidelines for genomic array analysis in acquired haematological neoplastic disorders. Genes Chromosomes Cancer 2016; 55:480-91. [PMID: 26774012 DOI: 10.1002/gcc.22350] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/09/2016] [Accepted: 01/09/2016] [Indexed: 12/19/2022] Open
Abstract
Genetic profiling is important for disease evaluation and prediction of prognosis or responsiveness to therapy in neoplasia. Microarray technologies, including array comparative genomic hybridization and single-nucleotide polymorphism-detecting arrays, have in recent years been introduced into the diagnostic setting for specific types of haematological malignancies and solid tumours. It can be used as a complementary test or depending on the neoplasia investigated, also as a standalone test. However, comprehensive and readable presentation of frequently identified complex genomic profiles remains challenging. To assist diagnostic laboratories, standardization and minimum criteria for clinical interpretation and reporting of acquired genomic abnormalities detected through arrays in neoplastic disorders are presented.
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Affiliation(s)
- Jacqueline Schoumans
- Unité De Génétique Du Cancer, Service De Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, CH-1011, Switzerland
| | - Javier Suela
- Cytogenomics Laboratory, NIMGenetics, Madrid, Spain
| | - Ros Hastings
- Cytogenetic External Quality Assessment, Women's Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Dominique Muehlematter
- Unité De Génétique Du Cancer, Service De Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, CH-1011, Switzerland
| | - Katrina Rack
- Institut De Pathologie Et De Génétique, Gosselies, Belgium
- West Midland Regional Genetic Laboratory, Birmingham Womens Hospital, Birmingham, UK
| | - Eva van den Berg
- Dept Genet, University Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
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Gill H, Leung AYH, Kwong YL. Molecular and Cellular Mechanisms of Myelodysplastic Syndrome: Implications on Targeted Therapy. Int J Mol Sci 2016; 17:440. [PMID: 27023522 PMCID: PMC4848896 DOI: 10.3390/ijms17040440] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/02/2016] [Accepted: 03/07/2016] [Indexed: 12/11/2022] Open
Abstract
Myelodysplastic syndrome (MDS) is a group of heterogeneous clonal hematopoietic stem cell disorders characterized by cytopenia, ineffective hematopoiesis, and progression to secondary acute myeloid leukemia in high-risk cases. Conventional prognostication relies on clinicopathological parameters supplemented by cytogenetic information. However, recent studies have shown that genetic aberrations also have critical impacts on treatment outcome. Moreover, these genetic alterations may themselves be a target for treatment. The mutation landscape in MDS is shaped by gene aberrations involved in DNA methylation (TET2, DNMT3A, IDH1/2), histone modification (ASXL1, EZH2), the RNA splicing machinery (SF3B1, SRSF2, ZRSR2, U2AF1/2), transcription (RUNX1, TP53, BCOR, PHF6, NCOR, CEBPA, GATA2), tyrosine kinase receptor signaling (JAK2, MPL, FLT3, GNAS, KIT), RAS pathways (KRAS, NRAS, CBL, NF1, PTPN11), DNA repair (ATM, BRCC3, DLRE1C, FANCL), and cohesion complexes (STAG2, CTCF, SMC1A, RAD21). A detailed understanding of the pathogenetic mechanisms leading to transformation is critical for designing single-agent or combinatorial approaches in target therapy of MDS.
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Affiliation(s)
- Harinder Gill
- Department of Medicine, Queen Mary Hospital, Hong Kong, China.
| | | | - Yok-Lam Kwong
- Department of Medicine, Queen Mary Hospital, Hong Kong, China.
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23
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Lee EJ, Podoltsev N, Gore SD, Zeidan AM. The evolving field of prognostication and risk stratification in MDS: Recent developments and future directions. Blood Rev 2016; 30:1-10. [DOI: 10.1016/j.blre.2015.06.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/08/2015] [Accepted: 06/15/2015] [Indexed: 01/01/2023]
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Abstract
Neurofibromatosis type 1 (NF1) is a relatively common tumour predisposition syndrome related to germline aberrations of NF1, a tumour suppressor gene. The gene product neurofibromin is a negative regulator of the Ras cellular proliferation pathway, and also exerts tumour suppression via other mechanisms. Recent next-generation sequencing projects have revealed somatic NF1 aberrations in various sporadic tumours. NF1 plays a critical role in a wide range of tumours. NF1 alterations appear to be associated with resistance to therapy and adverse outcomes in several tumour types. Identification of a patient's germline or somatic NF1 aberrations can be challenging, as NF1 is one of the largest human genes, with a myriad of possible mutations. Epigenetic factors may also contribute to inadequate levels of neurofibromin in cancer cells. Clinical trials of NF1-based therapeutic approaches are currently limited. Preclinical studies on neurofibromin-deficient malignancies have mainly been on malignant peripheral nerve sheath tumour cell lines or xenografts derived from NF1 patients. However, the emerging recognition of the role of NF1 in sporadic cancers may lead to the development of NF1-based treatments for other tumour types. Improved understanding of the implications of NF1 aberrations is critical for the development of novel therapeutic strategies.
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25
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Array CGH identifies copy number changes in 11% of 520 MDS patients with normal karyotype and uncovers prognostically relevant deletions. Leukemia 2015; 30:257-60. [PMID: 26392226 DOI: 10.1038/leu.2015.257] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Yin CC, Jain N, Mehrotra M, Zhagn J, Protopopov A, Zuo Z, Pemmaraju N, DiNardo C, Hirsch-Ginsberg C, Wang SA, Medeiros LJ, Chin L, Patel KP, Ravandi F, Futreal A, Bueso-Ramos CE. Identification of a novel fusion gene, IRF2BP2-RARA, in acute promyelocytic leukemia. J Natl Compr Canc Netw 2015; 13:19-22. [PMID: 25583766 DOI: 10.6004/jnccn.2015.0005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Acute promyelocytic leukemia (APL) is characterized by the fusion of retinoic acid receptor alpha (RARA) with promyelocytic leukemia (PML) or, rarely, other gene partners. This report presents a patient with APL with a novel fusion between RARA and the interferon regulatory factor 2 binding protein 2 (IRF2BP2) genes. A bone marrow examination in a 19-year-old woman who presented with ecchymoses and epistaxis showed morphologic and immunophenotypic features consistent with APL. PML oncogenic domain antibody was positive. Results of fluorescence in situ hybridization, conventional cytogenetics, reverse transcription-polymerase chain reaction (RT-PCR), and oligonucleotide microarray for PML-RARA and common APL variant translocations were negative. Next-generation RNA-sequencing analysis followed by RT-PCR and direct sequencing revealed distinct breakpoints within IRF2BP2 exon 2 and RARA intron 2. The patient received all-trans retinoic acid, arsenic, and gemtuzumab ozogamicin, and achieved complete remission. However, the disease relapsed 10 months later, 2 months after consolidation therapy. This is the first report showing involvement of IRF2BP2 in APL, and it expands the list of novel RARA partners identified in APL.
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Affiliation(s)
- C Cameron Yin
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nitin Jain
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Meenakshi Mehrotra
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhagn
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexei Protopopov
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhuang Zuo
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Naveen Pemmaraju
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Courtney DiNardo
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cheryl Hirsch-Ginsberg
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sa A Wang
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lynda Chin
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keyur P Patel
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Farhad Ravandi
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew Futreal
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carlos E Bueso-Ramos
- From the Departments of Hematopathology, Leukemia, Genomic Medicine, and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Peterson JF, Aggarwal N, Smith CA, Gollin SM, Surti U, Rajkovic A, Swerdlow SH, Yatsenko SA. Integration of microarray analysis into the clinical diagnosis of hematological malignancies: How much can we improve cytogenetic testing? Oncotarget 2015; 6:18845-62. [PMID: 26299921 PMCID: PMC4662459 DOI: 10.18632/oncotarget.4586] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/21/2015] [Indexed: 12/14/2022] Open
Abstract
Purpose To evaluate the clinical utility, diagnostic yield and rationale of integrating microarray analysis in the clinical diagnosis of hematological malignancies in comparison with classical chromosome karyotyping/fluorescence in situ hybridization (FISH). Methods G-banded chromosome analysis, FISH and microarray studies using customized CGH and CGH+SNP designs were performed on 27 samples from patients with hematological malignancies. A comprehensive comparison of the results obtained by three methods was conducted to evaluate benefits and limitations of these techniques for clinical diagnosis. Results Overall, 89.7% of chromosomal abnormalities identified by karyotyping/FISH studies were also detectable by microarray. Among 183 acquired copy number alterations (CNAs) identified by microarray, 94 were additional findings revealed in 14 cases (52%), and at least 30% of CNAs were in genomic regions of diagnostic/prognostic significance. Approximately 30% of novel alterations detected by microarray were >20 Mb in size. Balanced abnormalities were not detected by microarray; however, of the 19 apparently “balanced” rearrangements, 55% (6/11) of recurrent and 13% (1/8) of non-recurrent translocations had alterations at the breakpoints discovered by microarray. Conclusion Microarray technology enables accurate, cost-effective and time-efficient whole-genome analysis at a resolution significantly higher than that of conventional karyotyping and FISH. Array-CGH showed advantage in identification of cryptic imbalances and detection of clonal aberrations in population of non-dividing cancer cells and samples with poor chromosome morphology. The integration of microarray analysis into the cytogenetic diagnosis of hematologic malignancies has the potential to improve patient management by providing clinicians with additional disease specific and potentially clinically actionable genomic alterations.
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Affiliation(s)
- Jess F Peterson
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.,Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nidhi Aggarwal
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Clayton A Smith
- Department of Medicine, Division of Hematology, University of Colorado, Denver, CO
| | - Susanne M Gollin
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Urvashi Surti
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aleksandar Rajkovic
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven H Swerdlow
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Svetlana A Yatsenko
- Pittsburgh Cytogenetics Laboratory, Center for Medical Genetics and Genomics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Mishra A, Rollison DE, Brandon TH, Al Ali NH, Corrales-Yepez M, Padron E, Epling-Burnette PK, Lancet JE, List AF, Komrokji RS. Impact of tobacco usage on disease outcome in myelodysplastic syndromes. Leuk Res 2015; 39:673-8. [PMID: 25934048 PMCID: PMC5992898 DOI: 10.1016/j.leukres.2015.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 03/24/2015] [Accepted: 03/27/2015] [Indexed: 11/24/2022]
Abstract
We hypothesized that tobacco usage is an independent prognostic factor in patients with myelodysplastic syndromes (MDS). To evaluate the impact of tobacco usage in this population, we identified patients diagnosed with MDS in our Center's MDS database and reviewed individual charts retrospectively. Of the 767 MDS patients identified, 743 patients (97%) had a known tobacco usage history. Given that the majority of tobacco users were smokers, we stratified patients as having never smoked (never-smoker group) versus current or former smokers (ever-smoker group). Greater than 60% of ever-smokers were risk stratified as having low or intermediate-1 (int-1) risk at diagnosis based on the International Prognostic Scoring System for MDS. In patients with lower-risk MDS, we found that ever-smokers had an increased proportion of poor-risk karyotypes (8.8%) compared with never-smokers (2.4%) (P=0.003). The adverse effect of smoking was greatest in the low-risk and int-1-risk groups, where median overall survival was 69 months (95% CI 42-96) in never-smokers versus 48 months (95% CI 41-55) in ever-smokers (P=0.006). The median overall survival for never-smokers, former smokers, and current smokers was 69 months (95% CI 42-96), 50 months (95% CI 43-57), and 38 months (95% CI 23-53), respectively, in patients risk stratified as lower-risk MDS (P=0.01). Our findings suggest that tobacco usage negatively impacts overall survival in patients with lower-risk MDS.
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Affiliation(s)
- Asmita Mishra
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Dana E Rollison
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Thomas H Brandon
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Najla H Al Ali
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Eric Padron
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Jeffrey E Lancet
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alan F List
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rami S Komrokji
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
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29
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Zhang L, Padron E, Lancet J. The molecular basis and clinical significance of genetic mutations identified in myelodysplastic syndromes. Leuk Res 2015; 39:6-17. [DOI: 10.1016/j.leukres.2014.10.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/25/2014] [Indexed: 01/07/2023]
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30
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Hartmann L, Stephenson CF, Verkamp SR, Johnson KR, Burnworth B, Hammock K, Brodersen LE, de Baca ME, Wells DA, Loken MR, Zehentner BK. Detection of clonal evolution in hematopoietic malignancies by combining comparative genomic hybridization and single nucleotide polymorphism arrays. Clin Chem 2014; 60:1558-68. [PMID: 25320376 DOI: 10.1373/clinchem.2014.227785] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Array comparative genomic hybridization (aCGH) has become a powerful tool for analyzing hematopoietic neoplasms and identifying genome-wide copy number changes in a single assay. aCGH also has superior resolution compared with fluorescence in situ hybridization (FISH) or conventional cytogenetics. Integration of single nucleotide polymorphism (SNP) probes with microarray analysis allows additional identification of acquired uniparental disomy, a copy neutral aberration with known potential to contribute to tumor pathogenesis. However, a limitation of microarray analysis has been the inability to detect clonal heterogeneity in a sample. METHODS This study comprised 16 samples (acute myeloid leukemia, myelodysplastic syndrome, chronic lymphocytic leukemia, plasma cell neoplasm) with complex cytogenetic features and evidence of clonal evolution. We used an integrated manual peak reassignment approach combining analysis of aCGH and SNP microarray data for characterization of subclonal abnormalities. We compared array findings with results obtained from conventional cytogenetic and FISH studies. RESULTS Clonal heterogeneity was detected in 13 of 16 samples by microarray on the basis of log2 values. Use of the manual peak reassignment analysis approach improved resolution of the sample's clonal composition and genetic heterogeneity in 10 of 13 (77%) patients. Moreover, in 3 patients, clonal disease progression was revealed by array analysis that was not evident by cytogenetic or FISH studies. CONCLUSIONS Genetic abnormalities originating from separate clonal subpopulations can be identified and further characterized by combining aCGH and SNP hybridization results from 1 integrated microarray chip by use of the manual peak reassignment technique. Its clinical utility in comparison to conventional cytogenetic or FISH studies is demonstrated.
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31
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Hamdi A, Afrough A, Muzzafar T, Popat UR, Hosing CM, Qazilbash MH, Lu G. Donor cell-derived myelodysplastic syndrome with ring chromosome 7 after allogeneic hematopoietic stem cell transplant in 2 patients with lymphomas as primary disease. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2014; 14:e151-5. [PMID: 25022600 DOI: 10.1016/j.clml.2014.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/30/2014] [Indexed: 01/09/2023]
MESH Headings
- Allografts
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal, Murine-Derived/administration & dosage
- Biomarkers, Tumor
- Bone Marrow/pathology
- Cell Transformation, Neoplastic/genetics
- Chromosome Deletion
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 7/ultrastructure
- Cyclophosphamide/administration & dosage
- Disease Progression
- Female
- Gene Deletion
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myeloid, Acute/etiology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Living Donors
- Lymphoma, Follicular/drug therapy
- Lymphoma, Follicular/therapy
- Lymphoma, Mantle-Cell/drug therapy
- Lymphoma, Mantle-Cell/therapy
- Male
- Middle Aged
- Myelodysplastic Syndromes/etiology
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/pathology
- Neoplasms, Second Primary/etiology
- Neoplasms, Second Primary/pathology
- Peripheral Blood Stem Cell Transplantation
- Proto-Oncogene Proteins c-ets/deficiency
- Proto-Oncogene Proteins c-ets/genetics
- Repressor Proteins/deficiency
- Repressor Proteins/genetics
- Ring Chromosomes
- Rituximab
- Transplantation Chimera/genetics
- Vidarabine/administration & dosage
- Vidarabine/analogs & derivatives
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Amir Hamdi
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Aimaz Afrough
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tariq Muzzafar
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Uday R Popat
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chitra M Hosing
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Muzaffar H Qazilbash
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gary Lu
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX.
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Fetal mesenchymal stromal cells from cryopreserved human chorionic villi: cytogenetic and molecular analysis of genome stability in long-term cultures. Cytotherapy 2014; 15:1340-51. [PMID: 24094486 DOI: 10.1016/j.jcyt.2013.06.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 06/21/2013] [Accepted: 06/27/2013] [Indexed: 12/24/2022]
Abstract
BACKGROUND AIMS First-trimester chorionic villi (CV) are an attractive source of human mesenchymal stromal cells (hMSC) for possible applications in cellular therapy and regenerative medicine. Human MSC from CV were monitored for genetic stability in long-term cultures. METHODS We set up a good manufacturing practice cryopreservation procedure for small amounts of native CV samples. After isolation, hMSC were in vitro cultured and analyzed for biological end points. Genome stability at different passages of expansion was explored by karyotype, genome-wide array-comparative genomic hybridization and microsatellite genotyping. RESULTS Growth curve analysis revealed a high proliferative potential of CV-derived cells. Immunophenotyping showed expression of typical MSC markers and absence of hematopoietic markers. Analysis of multilineage potential demonstrated efficient differentiation into adipocytes, osteocytes, chondrocytes and induction of neuro-glial commitment. In angiogenic experiments, differentiation in endothelial cells was detected by in vitro Matrigel assay after vascular endothelial growth factor stimulation. Data obtained from karyotyping, array-comparative genomic hybridization and microsatellite genotyping comparing early with late DNA passages did not show any genomic variation at least up to passage 10. Aneuploid clones appeared in four of 14 cases at latest passages, immediately before culture growth arrest. CONCLUSIONS Our findings indicate that hCV-MSC are genetically stable in long-term cultures at least up to passage 10 and that it is possible to achieve clinically relevant amounts of hCV-MSC even after few stages of expansion. Genome abnormalities at higher passages can occasionally occur and are always associated with spontaneous growth arrest. Under these circumstances, hCV-MSC could be suitable for therapeutic purposes.
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Abstract
CONTEXT Hematopathology is a dynamic field that has always been on the frontier of clinical research within the scope of pathology. Several recent developments in hematopathology will likely affect its practice clinically. OBJECTIVE To review 5 important recent advances in hematopathology: (1) detection and prognostic implication of MYC in diffuse large B-cell lymphomas, (2) determining origin and prognosis through immunoglobulin gene usage in mature B-cell neoplasms, (3)detecting minimal residual disease in multiple myeloma, (4) using genome-wide analysis in myelodysplastic syndromes, and (5) employing whole-genome sequencing in acute myeloid leukemias. DATA SOURCES Literature review and the authors' experiences in an academic center. CONCLUSIONS These advances will bring hematopathology into a new molecular era and help us to better understand the molecular, pathologic mechanisms of lymphomas, leukemias, myelomas, and myelodysplastic syndromes. They will help us to identify diagnostic and prognostic markers and eventually provide new therapeutic targets and treatments for these diseases.
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Affiliation(s)
- Min Shi
- From the Department of Pathology, UMass Memorial Medical Center, Worcester, Massachusetts
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Piotrowski P, Grobelna MK, Wudarski M, Olesińska M, Jagodziński PP. Genetic variants of DNMT3A and systemic lupus erythematosus susceptibility. Mod Rheumatol 2014; 25:96-9. [PMID: 24716599 DOI: 10.3109/14397595.2014.902296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES A significant increase in DNA methyltransferase 3A (DNMT3A) transcript levels has recently been demonstrated in peripheral blood mononuclear cells from systemic lupus erythematosus (SLE) patients as compared to healthy individuals. METHODS Employing high resolution melting curve analysis (HRM) and PCR-restriction fragment length polymorphism analysis, we assessed the frequency of five single nucleotide polymorphisms (SNPs) of this gene: rs2289195, rs7590760, rs13401241, rs749131 and rs1550117, situated in different linkage disequilibrium blocks of the DNMT3A gene in two hundred and fifty seven women with SLE and six hundred and twenty five controls. RESULTS The lowest p values of the trend test were observed for the DNMT3A -448A> G (rs1550117) SNP (ptrend = 0.0111). We also found that, in a dominant inheritance model, the DNMT3A -448A> G SNP may protect from SLE development [odds ratio (OR) = 0.494 (0.294-0.830), p = 0.0068, pcorr = 0.034]. Furthermore, we observed that the DNMT3A -448A > G SNP in dominant inheritance models may protect from immunologic manifestations of SLE [OR = 0.1753 (95% CI = 0.04976-0.6176, p = 0.0026, pcorr = 0.0468). CONCLUSIONS Our study demonstrates that the DNMT3A -448A> G SNP might protect from SLE and its immunologic manifestations in a sample from the Polish population.
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Affiliation(s)
- Piotr Piotrowski
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences , Poznań , Poland
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35
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Tan Y, Sutanto E, Alleyne AG, Cunningham BT. Photonic crystal enhancement of a homogeneous fluorescent assay using submicron fluid channels fabricated by E-jet patterning. JOURNAL OF BIOPHOTONICS 2014; 7:266-75. [PMID: 24376013 PMCID: PMC4980434 DOI: 10.1002/jbio.201300158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/18/2013] [Accepted: 12/07/2013] [Indexed: 05/21/2023]
Abstract
We demonstrate the enhancement of a liquid-based homogenous fluorescence assay using the resonant electric fields from a photonic crystal (PC) surface. Because evanescent fields are confined to the liquid volume nearest to the photonic crystal, we developed a simple approach for integrating a PC fabricated on a silicon substrate within a fluid channel with submicron height, using electrohydrodynamic jet (e-jet) printing of a light-curable epoxy adhesive to define the fluid channel pattern. The PC is excited by a custom-designed compact instrument that illuminates the PC with collimated light that precisely matches the resonant coupling condition when the PC is covered with aqueous media. Using a molecular beacon nucleic acid fluorescence resonant energy transfer (FRET) probe for a specific miRNA sequence, we demonstrate an 8× enhancement of the fluorescence emission signal, compared to performing the same assay without exciting resonance in the PC detecting a miRNA sequence at a concentration of 62 nM from a liquid volume of only ∼20 nL. The approach may be utilized for any liquid-based fluorescence assay for applications in point-of-care diagnostics, environmental monitoring, or pathogen detection.
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Affiliation(s)
- Yafang Tan
- Department of Electrical and Computer Engineering, 1406 West Green Street
| | - Erick Sutanto
- Department of Mechanical Science and Engineering, 1206 West Green Street
| | - Andrew G. Alleyne
- Department of Mechanical Science and Engineering, 1206 West Green Street
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, 1406 West Green Street
- Department of Bioengineering, 1304 West Springfield Avenue
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Nybakken GE, Bagg A. The genetic basis and expanding role of molecular analysis in the diagnosis, prognosis, and therapeutic design for myelodysplastic syndromes. J Mol Diagn 2014; 16:145-58. [PMID: 24457119 DOI: 10.1016/j.jmoldx.2013.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 11/09/2013] [Accepted: 11/21/2013] [Indexed: 12/31/2022] Open
Abstract
The myelodysplastic syndromes (MDS) are clonal hematopoietic stem cell disorders of ineffective hematopoiesis that characteristically demonstrate peripheral blood cytopenia, bone marrow hypercellularity, and morphologically defined dysplasia of one or more hematopoietic lineages. Classical metaphase cytogenetics and judicious use of fluorescence in situ hybridization play central roles in the contemporary diagnosis and classification of MDS. An abundance of recent molecular studies are beginning to delineate additional genetic and epigenetic aberrations associated with these disorders. These alterations affect diagnosis, prognosis, and therapy, and with this understanding classification systems are evolving from a primarily hematological and morphological basis toward a multifactorial appreciation that includes histomorphology, metaphase cytogenetics, and directed molecular studies. In the present health-care environment, it is critical to develop a cost-effective, efficient testing strategy that maximizes the diagnostic potential of even limited specimens. Here, we briefly review the classical genetic approach to MDS, outline exciting new advances in the molecular understanding of this heterogeneous group of hematological neoplasms, and discuss how these advances are driving the evolution of classification and prognostic systems. Rapidly growing understanding of the genetic basis of MDS holds much promise for testing, and here we provide a frame of reference for discussion of current testing protocols and for addressing testing modalities likely to enter clinical practice in the near future.
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Affiliation(s)
- Grant E Nybakken
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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Abstract
Higher-risk myelodysplastic syndromes (MDS) are defined by patients who fall into higher-risk group categories in the original or revised International Prognostic Scoring System. Survival for these patients is dismal, and treatment should be initiated rapidly. Standard therapies include the hypomethylating agents azacitidine and decitabine, which should be administered for a minimum of 6 cycles, and continued for as long as a patient is responding. Once a drug fails in one of these patients, further treatment options are limited, median survival is <6 months, and consideration should be given to clinical trials. Higher-risk eligible patients should be offered consultation to discuss hematopoietic stem cell transplantation close to the time of diagnosis, depending on patient goals of therapy, with consideration given to proceeding to transplantation soon after an optimal donor is located. In the interim period before transplantation, hypomethylating agent therapy, induction chemotherapy, or enrollment in a clinical trial should be considered to prevent disease progression, although the optimal pretransplantation therapy is unknown.
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Valli R, Pressato B, Marletta C, Mare L, Montalbano G, Curto FL, Pasquali F, Maserati E. Different loss of material in recurrent chromosome 20 interstitial deletions in Shwachman-Diamond syndrome and in myeloid neoplasms. Mol Cytogenet 2013; 6:56. [PMID: 24330778 PMCID: PMC3914702 DOI: 10.1186/1755-8166-6-56] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/04/2013] [Indexed: 12/19/2022] Open
Abstract
Background An interstitial deletion of the long arms of chromosome 20, del(20)(q), is frequent in the bone marrow (BM) of patients with myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), and myeloproliferative neoplasms (MPN), and it is recurrent in the BM of patients with Shwachman-Diamond syndrome (SDS), who have a 30-40% risk of developing MDS and AML. Results We report the results obtained by microarray-based comparative genomic hybridization (a-CGH) in six patients with SDS, and we compare the loss of chromosome 20 material with one patient with MDS, and with data on 92 informative patients with MDS/AML/MPN and del(20)(q) collected from the literature. Conclusions The chromosome material lost in MDS/AML/MPN is highly variable with no identifiable common deleted regions, whereas in SDS the loss is more uniform: in 3/6 patients it was almost identical, and the breakpoints that we defined are probably common to most patients from the literature. In some SDS patients less material may be lost, due to different distal breakpoints, but the proximal breakpoint is in the same region, always leading to the loss of the EIF6 gene, an event which was related to a lower risk of MDS/AML in comparison with other patients.
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Affiliation(s)
| | | | | | | | | | | | | | - Emanuela Maserati
- Dipartimento di Medicina Clinica e Sperimentale, Università dell'Insubria, Via J, H, Dunant, 5, I 21100 Varese, Italy.
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Zeidan AM, Komrokji RS. There's risk, and then there's risk: The latest clinical prognostic risk stratification models in myelodysplastic syndromes. Curr Hematol Malig Rep 2013; 8:351-60. [PMID: 23979829 PMCID: PMC4133773 DOI: 10.1007/s11899-013-0172-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Myelodysplastic syndromes (MDS) include a diverse group of clonal hematopoietic disorders characterized by progressive cytopenias and propensity for leukemic progression. The biologic heterogeneity that underlies MDS translates clinically in wide variations of clinical outcomes. Several prognostic schemes were developed to predict the natural course of MDS, counsel patients, and allow evidence-based, risk-adaptive implementation of therapeutic strategies. The prognostic schemes divide patients into subgroups with similar prognosis, but the extent to which the prognostic prediction applies to any individual patient is more variable. None of these instruments was designed to predict the clinical benefit in relation to any specific MDS therapy. The prognostic impact of molecular mutations is being more recognized and attempts at incorporating it into the current prognostic schemes are ongoing.
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Affiliation(s)
- Amer M Zeidan
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, CRB1 building, room 186, Baltimore, MD, 21287, USA,
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Lukackova R, Gerykova Bujalkova M, Majerova L, Mladosievicova B. Molecular genetic methods in the diagnosis of myelodysplastic syndromes. A review. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2013; 158:339-45. [PMID: 24263214 DOI: 10.5507/bp.2013.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/06/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) represent a heterogeneous group of premalignant hematologic disorders characterized by ineffective hematopoiesis, peripheral blood cytopenias and increased risk of progression to acute leukemia. Cytogenetic analysis still plays a central role in the diagnosis of MDS, as clonal chromosomal abnormalities are observed in 30-50% of MDS patients. Despite their technical limitations, standard karyotyping and fluorescence in situ hybridization (FISH) are routinely used for identifying recurrent chromosomal rearrangements. However, using this approach means that submicroscopic and not targeted chromosomal aberrations, as well as somatic mutations and epigenetic changes remain largely undetected. METHODS AND RESULTS Introduction of methods for the analysis of copy-number variations (CNV), including array-based technologies and Multiplex ligation-dependent probe amplification (MLPA) has provided novel insights into the molecular pathogenesis of MDS and considerably extended possibilities for genetic laboratory testing. Several novel molecular markers have been discovered and used for diagnosis and prognostic evaluation of patients with MDS. At present, mutational analysis is not routinely performed, as the clinical significance of somatic mutations in MDS has only begun to emerge. However, recently introduced Next-generation sequencing (NGS) technologies could help to elucidate the relationship between chromosomal and molecular aberrations in MDS and lead to further improvement in its diagnosis. CONCLUSION This review focuses on the advantages, limitations, clinical applications and future perspectives of three molecular methods (array-based analysis, MLPA and NGS) currently used in genetic testing and/ or translational research of MDS. In conclusion, a brief summary for clinicians from the routine diagnostic point of view is given.
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Affiliation(s)
- Renata Lukackova
- Department of Clinical Genetics, Medirex a.s., Bratislava, Slovak Republic
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Mostowska A, Sajdak S, Pawlik P, Lianeri M, Jagodzinski PP. DNMT1, DNMT3A and DNMT3B gene variants in relation to ovarian cancer risk in the Polish population. Mol Biol Rep 2013; 40:4893-9. [PMID: 23666104 PMCID: PMC3723978 DOI: 10.1007/s11033-013-2589-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 04/29/2013] [Indexed: 12/24/2022]
Abstract
Studies have demonstrated that changes in DNA methylation of cancer related genes can be an elementary process accounting for ovarian tumorigenesis. Therefore, we evaluated the possible association of single nucleotide polymorphisms (SNPs) of DNA methyltransferases (DNMTs) genes, including DNMT1, DNMT3B, and DNMT3A, with ovarian cancer development in the Polish population. Using PCR-RFLP and HRM analyses, we studied the prevalence of the DNMT1 rs8101626, rs2228611 and rs759920, DNMT3A rs2289195, 7590760, rs13401241, rs749131 and rs1550117, and DNMT3B rs1569686, rs2424913 and rs2424932 SNPs in patients with ovarian cancer (n=159) and controls (n=180). The lowest p values of the trend test were observed for the DNMT1 rs2228611 and rs759920 SNPs in patients with ovarian cancer (p trend=0.0118 and p trend=0.0173, respectively). Moreover, we observed, in the recessive inheritance model, that the DNMT1 rs2228611 and rs759920 SNPs are associated with an increased risk of ovarian cancer development [OR 1.836 (1.143-2.949), p=0.0114, p corr=0.0342, and OR 1.932 (1.185-3.152), p=0.0078, p cor=0.0234, respectively]. However, none of other nine studied SNPs displayed significant contribution to the development of ovarian cancer. Furthermore, haplotype and multifactor dimensionality reduction analysis of the studied DNMT1, DNMT3B, and DNMT3A polymorphisms did not reveal either SNP combinations or gene interactions to be associated with the risk of ovarian cancer development. Our results may suggest that DNMT1 variants may be risk factors of ovarian cancer.
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Affiliation(s)
- Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego Street, 60-781 Poznan, Poland
| | - Stefan Sajdak
- Clinic of Gynecological Surgery, Poznań University of Medical Sciences, Poznan, Poland
| | - Piotr Pawlik
- Clinic of Gynecological Surgery, Poznań University of Medical Sciences, Poznan, Poland
| | - Margarita Lianeri
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego Street, 60-781 Poznan, Poland
| | - Paweł P. Jagodzinski
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego Street, 60-781 Poznan, Poland
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Otrock ZK, Tiu RV, Maciejewski JP, Sekeres MA. The need for additional genetic markers for myelodysplastic syndrome stratification: what does the future hold for prognostication? Expert Rev Hematol 2013; 6:59-68. [PMID: 23373781 DOI: 10.1586/ehm.12.67] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Myelodysplastic syndromes (MDS) constitute a heterogeneous group of clonal hematopoietic disorders. Metaphase cytogenetics has been the gold standard for genetic testing in MDS, but it detects clonal cytogenetic abnormalities in only 50% of cases. New karyotyping tests include FISH, array-based comparative genomic hybridization and single-nucleotide polymorphism arrays. These techniques have increased the detected genetic abnormalities in MDS, many of which confer prognostic significance to overall and leukemia-free survival. This has eventually increased our understanding of MDS genetics. With the help of new technologies, we anticipate that the existing prognostic scoring systems will incorporate mutational data into their parameters. This review discusses the progress in MDS diagnosis through the use of array-based technologies. The authors also discuss the recently investigated genetic mutations in MDS and revisit the MDS classification and prognostic scoring systems.
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Affiliation(s)
- Zaher K Otrock
- Leukemia Program, Cleveland Clinic Taussig Cancer Institute, OH 44195, USA
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Modified Array-based Comparative Genomic Hybridization Detects Cryptic and Variant PML-RARA Rearrangements in Acute Promyelocytic Leukemia Lacking Classic Translocations. ACTA ACUST UNITED AC 2013; 22:10-21. [DOI: 10.1097/pdm.0b013e31825b8326] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zhang Y, Liu Q, Wang D, Chen S, Wang S. Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. PLoS One 2013; 8:e57154. [PMID: 23451169 PMCID: PMC3579783 DOI: 10.1371/journal.pone.0057154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 01/18/2013] [Indexed: 12/15/2022] Open
Abstract
Presently, the resistance of Influenza A virus isolates causes great difficulty for the prevention and treatment of influenza A virus infection. It is important to establish a drug-resistance detection method for epidemiological study and personalized medicine in the clinical setting. Consequently, a cost-effective oligonucleotide microarray visualization method, which was based on quantum dot-catalyzed silver deposition, was developed and evaluated for the simultaneous detection of neuraminidase H275Y and E119V; matrix protein 2 V27A and S31N mutations of influenza A (H3N2), seasonal influenza A (H1N1), and 2009 influenza A (H1N1). Then, 307 clinical throat swab specimens were detected and the drug-resistance results showed that 100% (17/17) of influenza A (H3N2) and 100% (259/259) of 2009 influenza A (H1N1) samples were resistant to amantadine and susceptible to oseltamivir; and 100% (5/5) of seasonal influenza A (H1N1) samples were resistant to both amantadine and oseltamivir.
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Affiliation(s)
- Yingjie Zhang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, People's Republic of China
| | - Qiqi Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, People's Republic of China
- Shenzhen Puruikang Biotech Co., Ltd, Shenzhen, People's Republic of China
| | - Dou Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, People's Republic of China
| | - Suhong Chen
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, People's Republic of China
- * E-mail: (SC); (SW)
| | - Shengqi Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, People's Republic of China
- Shenzhen Puruikang Biotech Co., Ltd, Shenzhen, People's Republic of China
- * E-mail: (SC); (SW)
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Schultz RA, Tsuchiya K, Furrow A, Slovak ML, McDaniel LD, Wall M, Crawford E, Ning Y, Saleki R, Fang M, Cawich V, Johnson CE, Minier SL, Neill NJ, Morton SA, Byerly S, Surti U, Brown TC, Ballif BC, Shaffer LG. CGH-based microarray detection of cryptic and novel copy number alterations and balanced translocations in cytogenetically abnormal cases of b-cell all. Health (London) 2013. [DOI: 10.4236/health.2013.55a004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Wall M, Rayeroux KC, MacKinnon RN, Zordan A, Campbell LJ. ETV6 deletion is a common additional abnormality in patients with myelodysplastic syndromes or acute myeloid leukemia and monosomy 7. Haematologica 2012; 97:1933-6. [PMID: 22875624 PMCID: PMC3590101 DOI: 10.3324/haematol.2012.069716] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Meaghan Wall
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital Melbourne, University of Melbourne, Fitzroy, Victoria, Australia
| | - Kathleen C. Rayeroux
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital Melbourne, University of Melbourne, Fitzroy, Victoria, Australia
| | - Ruth N. MacKinnon
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital Melbourne, University of Melbourne, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent’s Hospital Melbourne, University of Melbourne, Fitzroy, Victoria, Australia
| | - Adrian Zordan
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital Melbourne, University of Melbourne, Fitzroy, Victoria, Australia
| | - Lynda J. Campbell
- Victorian Cancer Cytogenetics Service, St Vincent’s Hospital Melbourne, University of Melbourne, Fitzroy, Victoria, Australia
- Department of Medicine, St Vincent’s Hospital Melbourne, University of Melbourne, Fitzroy, Victoria, Australia
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Yan-Fang T, Dong W, Li P, Wen-Li Z, Jun L, Na W, Jian W, Xing F, Yan-Hong L, Jian N, Jian P. Analyzing the gene expression profile of pediatric acute myeloid leukemia with real-time PCR arrays. Cancer Cell Int 2012; 12:40. [PMID: 22958424 PMCID: PMC3495223 DOI: 10.1186/1475-2867-12-40] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/06/2012] [Indexed: 02/06/2023] Open
Abstract
Background The Real-time PCR Array System is the ideal tool for analyzing the expression of a focused panel of genes. In this study, we will analyze the gene expression profile of pediatric acute myeloid leukemia with real-time PCR arrays. Methods Real-time PCR array was designed and tested firstly. Then gene expression profile of 11 pediatric AML and 10 normal controls was analyzed with real-time PCR arrays. We analyzed the expression data with MEV (Multi Experiment View) cluster software. Datasets representing genes with altered expression profile derived from cluster analyses were imported into the Ingenuity Pathway Analysis Tool. Results We designed and tested 88 real-time PCR primer pairs for a quantitative gene expression analysis of key genes involved in pediatric AML. The gene expression profile of pediatric AML is significantly different from normal control; there are 19 genes up-regulated and 25 genes down-regulated in pediatric AML. To investigate possible biological interactions of differently regulated genes, datasets representing genes with altered expression profile were imported into the Ingenuity Pathway Analysis Tool. The results revealed 12 significant networks. Of these networks, Cellular Development, Cellular Growth and Proliferation, Tumor Morphology was the highest rated network with 36 focus molecules and the significance score of 41. The IPA analysis also groups the differentially expressed genes into biological mechanisms that are related to hematological disease, cell death, cell growth and hematological system development. In the top canonical pathways, p53 and Huntington’s disease signaling came out to be the top two most significant pathways with a p value of 1.5E-8 and2.95E-7, respectively. Conclusions The present study demonstrates the gene expression profile of pediatric AML is significantly different from normal control; there are 19 genes up-regulated and 25 genes down-regulated in pediatric AML. We found some genes dyes-regulated in pediatric AML for the first time as FASLG, HDAC4, HDAC7 and some HOX family genes. IPA analysis showed the top important pathways for pediatric AML are p53 and Huntington’s disease signaling. This work may provide new clues of molecular mechanism in pediatric AML.
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Affiliation(s)
- Tao Yan-Fang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
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Abstract
Ras proteins are critical nodes in cellular signaling that integrate inputs from activated cell surface receptors and other stimuli to modulate cell fate through a complex network of effector pathways. Oncogenic RAS mutations are found in ∼25% of human cancers and are highly prevalent in hematopoietic malignancies. Because of their structural and biochemical properties, oncogenic Ras proteins are exceedingly difficult targets for rational drug discovery, and no mechanism-based therapies exist for cancers with RAS mutations. This article reviews the properties of normal and oncogenic Ras proteins, the prevalence and likely pathogenic role of NRAS, KRAS, and NF1 mutations in hematopoietic malignancies, relevant animal models of these cancers, and implications for drug discovery. Because hematologic malignancies are experimentally tractable, they are especially valuable platforms for addressing the fundamental question of how to reverse the adverse biochemical output of oncogenic Ras in cancer.
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49
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Shaffer LG, Schultz RA, Ballif BC. The use of new technologies in the detection of balanced translocations in hematologic disorders. Curr Opin Genet Dev 2012; 22:264-71. [PMID: 22336526 DOI: 10.1016/j.gde.2012.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 01/11/2023]
Abstract
The cytogenetic evaluation of hematologic disease can confirm a diagnosis, determine treatment options, and provide prognostic information to the patient. Among the potential cytogenetic aberrations that can be identified are certain balanced translocations with recurrent breakpoints that provide disease classification and define the sites of disease-causing or disease-promoting genes. In this review, we discuss the importance of balanced translocation identification, the methods traditionally used to identify balanced translocations in the cytogenetics laboratory, and the application of new methodologies such as next generation (NextGen) sequencing and array-based translocation identification through a linear amplification application. These new technologies have the potential to identify all currently known diagnostically and prognostically important rearrangements as well as novel alterations that may provide new therapeutic targets to enhance treatment of hematologic disease.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA.
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