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Mareschal S, Ruminy P, Alcantara M, Villenet C, Figeac M, Dubois S, Bertrand P, Bouzelfen A, Viailly PJ, Penther D, Tilly H, Bastard C, Jardin F. Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma. Bioinformatics 2018; 33:2977-2985. [PMID: 28481978 DOI: 10.1093/bioinformatics/btx309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/06/2017] [Indexed: 12/15/2022] Open
Abstract
Motivation Although sequencing-based technologies are becoming the new reference in genome analysis, comparative genomic hybridization arrays (aCGH) still constitute a simple and reliable approach for copy number analysis. The most powerful algorithms to analyze such data have been freely provided by the scientific community for many years, but combining them is a complex scripting task. Results The cghRA framework combines a user-friendly graphical interface and a powerful object-oriented command-line interface to handle a full aCGH analysis, as is illustrated in an original series of 107 Diffuse Large B-Cell Lymphomas. New algorithms for copy-number calling, polymorphism detection and minimal common region prioritization were also developed and validated. While their performances will only be demonstrated with aCGH, these algorithms could actually prove useful to any copy-number analysis, whatever the technique used. Availability and implementation R package and source for Linux, MS Windows and MacOS are freely available at http://bioinformatics.ovsa.fr/cghRA. Contact mareschal@ovsa.fr or fabrice.jardin@chb.unicancer.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sylvain Mareschal
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Philippe Ruminy
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Marion Alcantara
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Céline Villenet
- Plate-Forme de Génomique Fonctionnelle et Structurale, Université de Lille II, 59000 Lille, France
| | - Martin Figeac
- Plate-Forme de Génomique Fonctionnelle et Structurale, Université de Lille II, 59000 Lille, France.,Cellule de Bioinformatique du Plateau Commun de Séquençage, CHRU de Lille, 59000 Lille, France
| | - Sydney Dubois
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Philippe Bertrand
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Abdelilah Bouzelfen
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Pierre-Julien Viailly
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Dominique Penther
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Hervé Tilly
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France
| | - Christian Bastard
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
| | - Fabrice Jardin
- INSERM U1245 Team "Genomics and Biomarkers in Lymphoma and Solid Tumors," Centre Henri Becquerel, 76000 Rouen, France.,Normandie Université, 14000 Caen, France
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Bastida-Lertxundi N, López-López E, Piñán MA, Puiggros A, Navajas A, Solé F, García-Orad A. Errors in the interpretation of copy number variations due to the use of public databases as a reference. Cancer Genet 2014; 207:164-7. [DOI: 10.1016/j.cancergen.2014.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 02/07/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
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Erdogan B, Bosompem A, Peng D, Han L, Smith E, Kennedy ME, Alford CE, Wu H, Zhao Z, Mosse CA, El-Rifai W, Kim AS. Methylation of promoters of microRNAs and their host genes in myelodysplastic syndromes. Leuk Lymphoma 2013; 54:2720-7. [PMID: 23547841 DOI: 10.3109/10428194.2013.790542] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Myelodysplastic syndromes (MDS) are a group of hematopoietic malignancies characterized by ineffective hematopoiesis. Recently, we identified MDS-associated microRNAs (miRNAs) that are down-regulated in MDS. This study examines possible explanations for that observed down-regulation of miRNA expression in MDS. Since genomic losses are insufficient to explain the down-regulation of all our MDS-associated miRNAs, we explored other avenues. We demonstrate that these miRNAs are predominantly intragenic, and that, in many cases, they and their host genes are expressed in a similar pattern during myeloid maturation, suggesting their co-regulation. This co-regulation is further supported by the down-regulation of several of the host genes in MDS and increased methylation of the shared promoters of several miRNAs and their respective host genes. These studies identify a role of hypermethylation of miRNA promoters in the down-regulation of MDS-associated miRNAs, unifying research on miRNAs in MDS and epigenetic regulation in MDS into a common pathway.
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Affiliation(s)
- Begum Erdogan
- Department of Pathology, Immunology, and Microbiology
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MASL1 induces erythroid differentiation in human erythropoietin-dependent CD34+ cells through the Raf/MEK/ERK pathway. Blood 2013; 121:3216-27. [PMID: 23327923 DOI: 10.1182/blood-2011-10-385252] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human erythropoiesis is a dynamic and complex multistep process involving differentiation of early erythroid progenitors into enucleated RBCs. The mechanisms underlying erythropoiesis still remain incompletely understood. We previously demonstrated that erythropoietin-stimulated clone-1, which is selectively expressed in normal human erythroid-lineage cells, shares 99.5% identity with malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1 (MASL1). In this study, we hypothesized that the MASL1 gene plays a role in erythroid differentiation, and used a human erythroid cell culture system to explore this concept. MASL1 mRNA and protein expression levels were significantly increased during the erythroid differentiation of CD34(+) cells following erythropoietin (EPO) treatment. Conversely, MASL1 knockdown reduced erythroid differentiation in EPO-treated CD34(+) cells. In addition, MASL1 knockdown interrupted the Raf/MEK/ERK signaling pathway in CD34(+) cells. MASL1 mutant-transfected CD34(+) cells also showed decreased erythroid differentiation. Furthermore, inhibition of the SH3 domain of Son of Sevenless, which is an upstream adapter protein in EPO-induced erythroid differentiation, also reduced MASL1 expression and phosphorylation of Raf/MEK/ERK kinases that consequently reduced erythroid differentiation of EPO-induced CD34(+) cells. Importantly, we also demonstrated that MASL1 interacts physically with Raf1. Taken together, our data provide novel insights into MASL1 regulation of erythropoiesis through the Raf/MEK/ERK pathway.
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Simons A, Sikkema-Raddatz B, de Leeuw N, Konrad NC, Hastings RJ, Schoumans J. Genome-wide arrays in routine diagnostics of hematological malignancies. Hum Mutat 2012; 33:941-8. [PMID: 22488943 DOI: 10.1002/humu.22057] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 02/03/2012] [Indexed: 11/10/2022]
Abstract
Over the last three decades, cytogenetic analysis of malignancies has become an integral part of disease evaluation and prediction of prognosis or responsiveness to therapy. In most diagnostic laboratories, conventional karyotyping, in conjunction with targeted fluorescence in situ hybridization analysis, is routinely performed to detect recurrent aberrations with prognostic implications. However, the genetic complexity of cancer cells requires a sensitive genome-wide analysis, enabling the detection of small genomic changes in a mixed cell population, as well as of regions of homozygosity. The advent of comprehensive high-resolution genomic tools, such as molecular karyotyping using comparative genomic hybridization or single-nucleotide polymorphism microarrays, has overcome many of the limitations of traditional cytogenetic techniques and has been used to study complex genomic lesions in, for example, leukemia. The clinical impact of the genomic copy-number and copy-neutral alterations identified by microarray technologies is growing rapidly and genome-wide array analysis is evolving into a diagnostic tool, to better identify high-risk patients and predict patients' outcomes from their genomic profiles. Here, we review the added clinical value of an array-based genome-wide screen in leukemia, and discuss the technical challenges and an interpretation workflow in applying arrays in the acquired cytogenetic diagnostic setting.
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Affiliation(s)
- Annet Simons
- Laboratory of Tumor Genetics, Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
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Merkerova MD, Bystricka D, Belickova M, Krejcik Z, Zemanova Z, Polak J, Hajkova H, Brezinova J, Michalova K, Cermak J. From cryptic chromosomal lesions to pathologically relevant genes: integration of SNP-array with gene expression profiling in myelodysplastic syndrome with normal karyotype. Genes Chromosomes Cancer 2012; 51:419-28. [PMID: 22250017 DOI: 10.1002/gcc.21927] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 12/08/2011] [Indexed: 01/26/2023] Open
Abstract
Myelodysplastic syndrome (MDS), a clonal disorder originating from hematopoietic stem cell, is characterized by a progressive character often leading to transformation to acute myeloid leukemia. We used single nucleotide polymorphism arrays (SNP-A) to identify previously cryptic chromosomal abnormalities such as copy number alterations and uniparental disomies (UPD) in cytogenetically normal MDS. In the aberrant regions, we attempted to localize candidate genes with potential relevance to the disease. Using SNP-A, we analyzed peripheral blood granulocytes from 37 MDS patients. The analysis identified 13 cryptic chromosomal defects in 10 patients (27%). Four UPD (affecting chromosomes 3q, 7q, 17q, and 20p), 5 deletions and 4 duplications were detected. Gene expression data measured on CD34+ cells were available for 4 patients with and 6 patients without SNP-A lesions. We performed an integrative analysis of genotyping and gene expression microarrays and found several genes with an altered expression located in the aberrant regions. The expression microarrays suggested BMP2 and TRIB3 located in 20p UPD as potential candidate genes contributing to MDS. We showed that the genome-wide integrative approach is beneficial to the comprehension of molecular backgrounds of diseases with incompletely understood etiopathology.
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Costa ARS, Belangero SI, Melaragno MI, Chauffaille MDL. Additional chromosomal abnormalities detected by array comparative genomic hybridization in AML. Med Oncol 2011; 29:2083-7. [PMID: 22116774 DOI: 10.1007/s12032-011-0108-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/01/2011] [Indexed: 12/30/2022]
Abstract
Improved outcome of acute myeloid leukemia (AML) depends on the better differentiation of subtypes to predict treatment response and the identification of new target for treatment. In this study, array comparative genomic hybridization (aCGH) was used to distinguish eight cases of AML cases. Validation was performed by FISH and quantitative genomic PCR. The aCGH revealed new large and small recurrent genomic imbalances, such as gains of 1p36, 10q26, 11p15, 20q13, 22q23, harboring many proto-oncogenes. These results better define genetically the studied cases and could be used to understand the multiple phenomena involved in leukemogenesis.
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Affiliation(s)
- Ana Rosa S Costa
- Division of Hematology and Hemotherapy, UNIFESP/Escola Paulista de Medicina, Rua Botucatu740, 3º andar, São Paulo CEP: 04023-900, Brazil
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van der Veken LT, Buijs A. Array CGH in human leukemia: from somatics to genetics. Cytogenet Genome Res 2011; 135:260-70. [PMID: 21893961 DOI: 10.1159/000330629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During the past decade, array CGH has been applied to study copy number alterations in the genome in human leukemia in relation to prediction of prognosis or responsiveness to therapy. In the first segment of this review, we will focus on the identification of acquired mutations by array CGH, followed by studies on the pathogenesis of leukemia associated with germline genetic variants, phenotypic presentation and response to treatment. In the last section, we will discuss constitutional genomic aberrations causally related to myeloid leukemogenesis.
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Affiliation(s)
- L T van der Veken
- Section of Genome Diagnostics, Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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