1
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García R, Alkayyali T, Gomez LM, Wright C, Chen W, Oliver D, Koduru P. Recurrent cytogenetic abnormalities reveal alterations that promote progression and transformation in myelodysplastic syndrome. Cancer Genet 2024; 288-289:92-105. [PMID: 39499993 DOI: 10.1016/j.cancergen.2024.10.002] [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: 09/11/2023] [Revised: 07/05/2024] [Accepted: 10/14/2024] [Indexed: 12/10/2024]
Abstract
OBJECTIVE To illustrate patterns of cytogenetic abnormalities that promote progression and/or transformation in myelodysplastic syndrome. METHODS In this study we evaluated three different data sets to identify recurrent cytogenetic abnormalities (RCAs) to delineate the cytogenetic evolutionary trajectories and their clinical significance. RESULTS Datasets 1 and 2 were 2402 cross sectional samples from Mitelman database of Chromosome Aberrations and Gene Fusions in Cancer; these were used to discover RCAs and to validate them. Dataset 3 was a cohort of 163 institutional patients with serial samples from 35 % of them. This was used to further validate RCAs identified in the cross-sectional data, and their clinical impact. We identified MDS subtype associated RCAs, and some exclusive RCAs (Xp-, 2q-, 17q-, 21q-) that led to disease progression or transformation to leukemia. Evolutionary pathway analysis had shown temporal acquisition of RCAs. Therefore, presence of two or more RCAs suggests cooperative or complementary role in disease progression or transformation. Patients with one or more of these RCAs had poor prognosis and high risk for transformation. Genes frequently altered in MDS are mapped to some of the RCAs and suggest a close correlation between RCAs and molecular alterations in MDS. Karyotypic complexity, clonal evolution, loss of 17p had poor clinical outcomes. CONCLUSION This study identified a unique combination of RCAs that are components in distinct cytogenetic trajectories. Some of these were primary changes while others were secondary or tertiary changes. Acquiring specific additional aberrations predicts progression or transformation to leukemia.
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Affiliation(s)
- Rolando García
- Department of Pathology, UT Southwestern Medical Center, Dallas TX, United States.
| | - Tasnim Alkayyali
- Department of Pathology, UT Southwestern Medical Center, Dallas TX, United States
| | - Luis Mosquera Gomez
- Department of Pathology, UT Southwestern Medical Center, Dallas TX, United States
| | - Carter Wright
- Department of Pathology, UT Southwestern Medical Center, Dallas TX, United States
| | - Weina Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas TX, United States
| | - Dwight Oliver
- Department of Pathology, UT Southwestern Medical Center, Dallas TX, United States
| | - Prasad Koduru
- Department of Pathology, UT Southwestern Medical Center, Dallas TX, United States
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2
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Lam J, van den Bosch M, Wegrzyn J, Parker J, Ibrahim R, Slowski K, Chang L, Martinez-Høyer S, Condorelli G, Boldin M, Deng Y, Umlandt P, Fuller M, Karsan A. miR-143/145 differentially regulate hematopoietic stem and progenitor activity through suppression of canonical TGFβ signaling. Nat Commun 2018; 9:2418. [PMID: 29925839 PMCID: PMC6010451 DOI: 10.1038/s41467-018-04831-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 05/24/2018] [Indexed: 02/07/2023] Open
Abstract
Expression of miR-143 and miR-145 is reduced in hematopoietic stem/progenitor cells (HSPCs) of myelodysplastic syndrome patients with a deletion in the long arm of chromosome 5. Here we show that mice lacking miR-143/145 have impaired HSPC activity with depletion of functional hematopoietic stem cells (HSCs), but activation of progenitor cells (HPCs). We identify components of the transforming growth factor β (TGFβ) pathway as key targets of miR-143/145. Enforced expression of the TGFβ adaptor protein and miR-145 target, Disabled-2 (DAB2), recapitulates the HSC defect seen in miR-143/145-/- mice. Despite reduced HSC activity, older miR-143/145-/- and DAB2-expressing mice show elevated leukocyte counts associated with increased HPC activity. A subset of mice develop a serially transplantable myeloid malignancy, associated with expansion of HPC. Thus, miR-143/145 play a cell context-dependent role in HSPC function through regulation of TGFβ/DAB2 activation, and loss of these miRNAs creates a preleukemic state.
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Grants
- R01 AI125615 NIAID NIH HHS
- This work was supported by grants from the Terry Fox Research Institute, the Canadian Institutes of Health Research (CIHR), and the Cancer Research Society. The following agencies provided salary support: CIHR (J.L., J.W., L.C., R.I.), European Molecular Biology Organization (J.W.), US Department of Defense (L.C.), the Michael Smith Foundation for Health Research (J.W., L.C.), the University of British Columbia (J.L.), Natural Sciences and Engineering Research Council (K.S.), and the Centre for Blood Research (K.S.). A.K. is the recipient of the John Auston BC Cancer Foundation award.
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Affiliation(s)
- Jeffrey Lam
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Marion van den Bosch
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Joanna Wegrzyn
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jeremy Parker
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
| | - Rawa Ibrahim
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Kate Slowski
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Linda Chang
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Sergio Martinez-Høyer
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Gianluigi Condorelli
- Department of Cardiovascular Medicine, Humanitas Clinical and Research Center, 20089, Rozzano, MI, Italy
| | - Mark Boldin
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Yu Deng
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Patricia Umlandt
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
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3
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Hergueta-Redondo M, Sarrio D, Molina-Crespo Á, Vicario R, Bernadó-Morales C, Martínez L, Rojo-Sebastián A, Serra-Musach J, Mota A, Martínez-Ramírez Á, Castilla MÁ, González-Martin A, Pernas S, Cano A, Cortes J, Nuciforo PG, Peg V, Palacios J, Pujana MÁ, Arribas J, Moreno-Bueno G. Gasdermin B expression predicts poor clinical outcome in HER2-positive breast cancer. Oncotarget 2018; 7:56295-56308. [PMID: 27462779 PMCID: PMC5302915 DOI: 10.18632/oncotarget.10787] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 07/06/2016] [Indexed: 01/03/2023] Open
Abstract
Around, 30–40% of HER2-positive breast cancers do not show substantial clinical benefit from the targeted therapy and, thus, the mechanisms underlying resistance remain partially unknown. Interestingly, ERBB2 is frequently co-amplified and co-expressed with neighbour genes that may play a relevant role in this cancer subtype. Here, using an in silico analysis of data from 2,096 breast tumours, we reveal a significant correlation between Gasdermin B (GSDMB) gene (located 175 kilo bases distal from ERBB2) expression and the pathological and clinical parameters of poor prognosis in HER2-positive breast cancer. Next, the analysis of three independent cohorts (totalizing 286 tumours) showed that approximately 65% of the HER2-positive cases have GSDMB gene amplification and protein over-expression. Moreover, GSDMB expression was also linked to poor therapeutic responses in terms of lower relapse free survival and pathologic complete response as well as positive lymph node status and the development of distant metastasis under neoadjuvant and adjuvant treatment settings, respectively. Importantly, GSDMB expression promotes survival to trastuzumab in different HER2-positive breast carcinoma cells, and is associated with trastuzumab resistance phenotype in vivo in Patient Derived Xenografts. In summary, our data identifies the ERBB2 co-amplified and co-expressed gene GSDMB as a critical determinant of poor prognosis and therapeutic response in HER2-positive breast cancer.
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Affiliation(s)
- Marta Hergueta-Redondo
- Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - David Sarrio
- Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - Ángela Molina-Crespo
- Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - Rocío Vicario
- Preclinical Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Cristina Bernadó-Morales
- Preclinical Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lidia Martínez
- Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | | | - Jordi Serra-Musach
- Breast Cancer and Systems Biology Unit, ProCURE, Catalan Institute of Oncology, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - Alba Mota
- Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain.,Translational Research Laboratory, MD Anderson Internacional Foundation, Madrid, Spain
| | | | - Mª Ángeles Castilla
- Pathology Department, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| | | | - Sonia Pernas
- Breast Cancer and Systems Biology Unit, ProCURE, Catalan Institute of Oncology, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - Amparo Cano
- Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - Javier Cortes
- Clinical Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autonoma de Barcelona, Barcelona, Spain.,Oncology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Paolo G Nuciforo
- Molecular Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vicente Peg
- Pathology Department, Hospital Vall d'Hebron University, Barcelona, Spain
| | - José Palacios
- Pathology Department, Hospital Universitario Virgen del Rocío, Sevilla, Spain.,Pathology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Miguel Ángel Pujana
- Breast Cancer and Systems Biology Unit, ProCURE, Catalan Institute of Oncology, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - Joaquín Arribas
- Preclinical Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain.,Clinical Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autonoma de Barcelona, Barcelona, Spain.,Molecular Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Gema Moreno-Bueno
- Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain.,Translational Research Laboratory, MD Anderson Internacional Foundation, Madrid, Spain
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4
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Sabatino R, Aquino G, Pinto A, Piris MA, Marra L, Napolitano M, De Chiara A, Franco R. B-cell lymphoblastic lymphoma presenting as solitary temporal mass with amplification of AML1/RUNX1: case report. Hematol Oncol 2017; 35:380-384. [PMID: 28933515 DOI: 10.1002/hon.2269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 09/18/2015] [Accepted: 09/27/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Rocco Sabatino
- Pathology Unit, Istituto Nazionale Tumori " Fondazione 'G. Pascale", Napoli, Italy
| | - Gabriella Aquino
- Pathology Unit, Istituto Nazionale Tumori " Fondazione 'G. Pascale", Napoli, Italy
| | - Antonio Pinto
- Haematology- Oncology and Stem Cell Transplantation Unit, Istituto Nazionale Tumori Fondazione " G. Pascale", Napoli, Italy
| | - Miguel Angel Piris
- Pathology Unit, Hospital Universitario Marques de Valdecilla IDIVAL, Santander, Spain
| | - Laura Marra
- Pathology Unit, Istituto Nazionale Tumori " Fondazione 'G. Pascale", Napoli, Italy
| | - Maria Napolitano
- Immunology- Oncology Unit, Istituto Nazionale Tumori Fondazione " G. Pascale", Napoli, Italy
| | | | - Renato Franco
- Pathology Unit, Istituto Nazionale Tumori " Fondazione 'G. Pascale", Napoli, Italy
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5
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Ades L, Prebet T, Stamatoullas A, Recher C, Guieze R, Raffoux E, Bouabdallah K, Hunault M, Wattel E, Stalnikiewicz L, Toma A, Dombret H, Vey N, Sebert M, Gardin C, Chaffaut C, Chevret S, Fenaux P. Lenalidomide combined with intensive chemotherapy in acute myeloid leukemia and higher-risk myelodysplastic syndrome with 5q deletion. Results of a phase II study by the Groupe Francophone Des Myélodysplasies. Haematologica 2016; 102:728-735. [PMID: 28034993 PMCID: PMC5395113 DOI: 10.3324/haematol.2016.151894] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 12/16/2016] [Indexed: 12/26/2022] Open
Abstract
Patients with acute myeloblastic leukemia or higher risk myelodysplastic syndromes with 5q deletion (generally within a complex karyotype) respond poorly to intensive chemotherapy and have very poor survival. In this population, we evaluated escalating doses of lenalidomide combined with intensive chemotherapy in a phase II study. Treatment consisted of daunorubicin (45 mg/m2/day, days 1–3 in cohort 1, escalated to 60 mg/m2/day, days 1–3 in cohorts 2 and 3) combined with cytosine arabinoside (200 mg/m2/day, days 1–7) and lenalidomide (10 mg/day, days 1–21 in cohorts 1 and 2, escalated to 25 mg/day, days 1–21 in cohort 3). Eighty-two patients with 5q deletion were enrolled, including 62 with acute myeloblastic leukemia, 62/79 (78%) of whom had a complex karyotype (median 7 cytogenetic abnormalities, all but 2 of them monosomal) and three had unknown karyotypes. Thirty-eight patients (46%) achieved complete remission and the overall response rate was 58.5%. Among the 62 patients with a complex karyotype, 27 achieved complete remission (44%) and 21 had cytogenetic responses. A lower response rate was observed in patients with acute myeloblastic leukemia but other pretreatment factors, including cytogenetic complexity and treatment cohort, did not significantly influence response. Fifteen patients underwent allogeneic stem cell transplantation, including 11 patients in first remission. The 1-year cumulative incidence of relapse was 64.6% and the median overall survival was 8.2 months. By comparison with conventional intensive chemotherapy, the treatment protocol we used appeared to produce higher hematologic and cytogenetic complete remission rates in patients with very poor cytogenetics, but response duration was short in this very poor risk population, highlighting the need for better post-induction strategies. Clinical trial registry number: NCT00885508
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Affiliation(s)
- Lionel Ades
- Hôpital St Louis, Assistance Publique-Hôpitaux de Paris and Paris 7 University, Paris, France
| | | | | | | | | | | | - Krimo Bouabdallah
- Service d'Hématologie Clinique et de Thérapie Cellulaire, CHU de Bordeaux Hôpital du Haut-Lévêque, Pessac, France
| | | | | | | | | | | | | | - Marie Sebert
- Hôpital St Louis, Assistance Publique-Hôpitaux de Paris and Paris 7 University, Paris, France
| | | | | | | | - Pierre Fenaux
- Hôpital St Louis, Assistance Publique-Hôpitaux de Paris and Paris 7 University, Paris, France
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6
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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: 2.8] [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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7
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Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, Woodland H, Amaral FMR, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nat Commun 2016; 7:12846. [PMID: 27667448 PMCID: PMC5052684 DOI: 10.1038/ncomms12846] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 08/05/2016] [Indexed: 12/14/2022] Open
Abstract
Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new insights, but requires further human curation. Here we report a crowdsourcing project to annotate and reanalyse a large number of gene expression profiles from Gene Expression Omnibus (GEO). Through a massive open online course on Coursera, over 70 participants from over 25 countries identify and annotate 2,460 single-gene perturbation signatures, 839 disease versus normal signatures, and 906 drug perturbation signatures. All these signatures are unique and are manually validated for quality. Global analysis of these signatures confirms known associations and identifies novel associations between genes, diseases and drugs. The manually curated signatures are used as a training set to develop classifiers for extracting similar signatures from the entire GEO repository. We develop a web portal to serve these signatures for query, download and visualization.
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Affiliation(s)
- Zichen Wang
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Caroline D. Monteiro
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Kathleen M. Jagodnik
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
- Fluid Physics and Transport Processes Branch, NASA Glenn Research Center, 21000 Brookpark Rd, Cleveland, Ohio 44135, USA
- Center for Space Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
| | - Nicolas F. Fernandez
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Gregory W. Gundersen
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Andrew D. Rouillard
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Axel S. Feldmann
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Kevin S. Hu
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Michael G. McDermott
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Qiaonan Duan
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Neil R. Clark
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Matthew R. Jones
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Yan Kou
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Troy Goff
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | | | - Fabio M R. Amaral
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Gregory L. Szeto
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- The Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Oliver Fuchs
- Paediatric Allergology and Pulmonology, Dr von Hauner University Children's Hospital, Ludwig-Maximilians-University of Munich, Member of the German Centre for Lung Research (DZL), Lindwurmstrasse 4, Munich 80337, Germany
| | - Sophia M. Schüssler-Fiorenza Rose
- Spinal Cord Injury Service, Veteran Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
- Department of Neurosurgery, Stanford School of Medicine, Stanford, California 94304, USA
| | - Shvetank Sharma
- Department of Research, Institute of Liver & Biliary Sciences, D1, Vasant Kunj, New Delhi 110070, India
| | - Uwe Schwartz
- Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Xabier Bengoetxea Bausela
- Department of Pharmacology and Toxicology, University of Navarra, Pamplona, Irunlarrea 1, Pamplona 31008, Spain
| | - Maciej Szymkiewicz
- Warsaw School of Information Technology under the auspices of the Polish Academy of Sciences, 6 Newelska St, Warsaw 01–447, Poland
| | | | - Anton Salykin
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - Carolina M. Barra
- IMIM-Hospital Del Mar, PRBB Barcelona, Dr Aiguader, Barcelona 88.08003, Spain
| | | | - Nicholas J. Bongio
- Department of Biology, Shenandoah University, 1460 University Dr Winchester, Winchester, Virginia 22601, USA
| | | | | | - Udi E. Rubin
- Department of Biological Sciences, 600 Fairchild Center, Mail Code 2402, Columbia University, New York, New York 10032, USA
| | - Apostolos Malatras
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, Paris 75013, France
| | - Carl T. Fulp
- 13-1, Higashi 4-chome Shibuya-ku, Tokyo 150-0011, Japan
| | - John A. Galindo
- Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Cr. 30 # 45-08, Colombia
| | - Ruta Motiejunaite
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, 3 Blackfan Circle, Boston, Massachusetts 02115, USA
| | - Christoph Jüschke
- Department of Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, Oldenburg 26129, Germany
| | | | - Katharina Lahl
- Technical University of Denmark, National Veterinary Institute, Bülowsvej 27 Building 2-3, Frederiksberg C 1870, Denmark
| | - Mohieddin Jafari
- Protein Chemistry and Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, No. 358, 12th Farwardin Ave, Jomhhoori St, Tehran 13164, Iran
- School of Biological Sciences, Institute for Researches in Fundamental Sciences, Niavaran Square, P.O.Box, Tehran 19395-5746, Iran
| | - Sara Aibar
- University of Salamanca, Salamanca, Madrid 37008, Spain
| | - Apostolos Zaravinos
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, level 7, Stockholm SE141 86, Sweden
- Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenes Str. Engomi, P.O.Box 22006, Nicosia 1516, Cyprus
| | | | | | | | - Fernando de Andres Segura
- CICAB, Clinical Research Centre, Extremadura University Hospital, Elvas Av., s/n. 06006 Badajoz 06006, Spain
| | | | - Vicente Pérez-García
- Consejo Superior de Investigaciones Científicas, Centro Nacional de Biotecnología, Department of Immunology and Oncology, c/Darwin, 3 Madrid 28049, Spain
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
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8
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Mota A, Triviño JC, Rojo-Sebastian A, Martínez-Ramírez Á, Chiva L, González-Martín A, Garcia JF, Garcia-Sanz P, Moreno-Bueno G. Intra-tumor heterogeneity in TP53 null High Grade Serous Ovarian Carcinoma progression. BMC Cancer 2015; 15:940. [PMID: 26620706 PMCID: PMC4666042 DOI: 10.1186/s12885-015-1952-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 11/23/2015] [Indexed: 12/20/2022] Open
Abstract
Background High grade serous ovarian cancer is characterised by high initial response to chemotherapy but poor outcome in the long term due to acquired resistance. One of the main genetic features of this disease is TP53 mutation. The majority of TP53 mutated tumors harbor missense mutations in this gene, correlated with p53 accumulation. TP53 null tumors constitute a specific subgroup characterised by nonsense, frameshift or splice-site mutations associated to complete absence of p53 expression. Different studies show that this kind of tumors may have a worse prognosis than other TP53 mutated HGSC. Methods In this study, we sought to characterise the intra-tumor heterogeneity of a TP53 null HGSC consisting of six primary tumor samples, two intra-pelvic and four extra-pelvic recurrences using exome sequencing and comparative genome hybridisation. Results Significant heterogeneity was found among the different tumor samples, both at the mutational and copy number levels. Exome sequencing identified 102 variants, of which only 42 were common to all three samples; whereas 7 of the 18 copy number changes found by CGH analysis were presented in all samples. Sanger validation of 20 variants found by exome sequencing in additional regions of the primary tumor and the recurrence allowed us to establish a sequence of the tumor clonal evolution, identifying those populations that most likely gave rise to recurrences and genes potentially involved in this process, like GPNMB and TFDP1. Using functional annotation and network analysis, we identified those biological functions most significantly altered in this tumor. Remarkably, unexpected functions such as microtubule-based movement and lipid metabolism emerged as important for tumor development and progression, suggesting its potential interest as therapeutic targets. Conclusions Altogether, our results shed light on the clonal evolution of the distinct tumor regions identifying the most aggressive subpopulations and at least some of the genes that may be implicated in its progression and recurrence, and highlights the importance of considering intra-tumor heterogeneity when carrying out genetic and genomic studies, especially when these are aimed to diagnostic procedures or to uncover possible therapeutic strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1952-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alba Mota
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain. .,MD Anderson International Foundation, Madrid, Spain.
| | | | | | | | - Luis Chiva
- Department of Gynecologic Oncology, MD Anderson Cancer Center, Madrid, Spain.
| | | | - Juan F Garcia
- MD Anderson International Foundation, Madrid, Spain. .,Department of Pathology, MD Anderson Cancer Center, Madrid, Spain.
| | - Pablo Garcia-Sanz
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain. .,MD Anderson International Foundation, Madrid, Spain.
| | - Gema Moreno-Bueno
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain. .,MD Anderson International Foundation, Madrid, Spain.
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9
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Tyrosine kinome profiling: oncogenic mutations and therapeutic targeting in cancer. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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10
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Cherian S, Bagg A. The genetics of the myelodysplastic syndromes: Classical cytogenetics and recent molecular insights. Hematology 2013; 11:1-13. [PMID: 16522543 DOI: 10.1080/10245330500276691] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are a complex group of clonal hematopoietic disorders with an attendant diverse array of associated genetic changes. Conventional cytogenetics plays a prominent and well-established role in determining the contemporary diagnosis and prognosis of these disorders. More recently, molecular approaches have been useful in further characterizing this group of diseases, albeit in a largely experimental context, with the detection of changes at the single gene level including mutations, amplification and epigenetic phenomena. Nevertheless, we remain largely ignorant of the genetic underpinnings of MDS. Here we briefly review the established role of cytogenetics in MDS, and emphasize recent advances in unraveling the genetics of MDS, with a view towards how such findings might facilitate our ability to understand, diagnose and treat these disorders in a more rational manner.
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Affiliation(s)
- Sindhu Cherian
- University of Washington Medical Center, Department of Laboratory Medicine, Seattle, 98195, USA.
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11
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Kim BR, Kim JE, Woo KS, Kim KH, Kim JM, Lee S, Shaffer LG, Han JY. A case of near-triploidy in myelodysplastic syndrome with del(5q) combined with del(1p) and del(13q). Ann Lab Med 2012; 32:294-7. [PMID: 22779072 PMCID: PMC3384812 DOI: 10.3343/alm.2012.32.4.294] [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: 09/14/2011] [Revised: 01/09/2012] [Accepted: 02/17/2012] [Indexed: 11/29/2022] Open
Abstract
Numerical and structural chromosomal abnormalities are common in hematological malignancies. Near-triploidy (58-80 chromosomes) is a numerical abnormality observed in 3% of adult cases of acute lymphoblastic leukemia. Near-triploidy is rare in myeloid lineage hematologic malignancies and compared to near-triploidy in lymphoid malignancies, near-triploidy in myeloid malignancies is associated with poor outcomes. Few studies on near-triploidy in myelodysplastic syndrome (MDS) have been reported, and the clinicopathologic significance of this condition is still unclear. Here, we report a novel case of MDS with near-triploidy and multiple structural chromosomal abnormalities: del(5q) combined with del(1p) and del(13q). These abnormalities were detected by cytogenetic analysis with array comparative genomic hybridization (CGH). Our results suggest that array CGH can be a useful tool for detecting chromosomal abnormalities in patients with MDS.
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Affiliation(s)
- Bo-Ram Kim
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
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12
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Wei Y, Gañán-Gómez I, Salazar-Dimicoli S, McCay SL, Garcia-Manero G. Histone methylation in myelodysplastic syndromes. Epigenomics 2012; 3:193-205. [PMID: 22122281 DOI: 10.2217/epi.11.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Histone methylation is a type of epigenetic modification that is critical for the regulation of gene expression. Numerous studies have demonstrated that abnormalities of this newly characterized epigenetic modification are involved in the development of multiple diseases, including cancer. There is also emerging evidence for a link between histone methylation and the pathogenesis of myeloid neoplasms, including myelodysplastic syndromes (MDS). This article provides an overview of recent progress in the studies of histone methylation in myeloid malignancies, with an emphasis on MDS. We cover each type of histone methylation modification and their regulatory mechanisms, as well as their abnormalities in MDS or potential connections to MDS. We also summarize the recent progress in the development of inhibitors targeting histone methylation and their applications as potential therapeutic agents.
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Affiliation(s)
- Yue Wei
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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13
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Genomic profiling in high hyperdiploid acute myeloid leukemia: a retrospective study of 19 cases. Cancer Genet 2012; 204:516-21. [PMID: 22018275 DOI: 10.1016/j.cancergen.2011.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 08/26/2011] [Accepted: 09/03/2011] [Indexed: 11/22/2022]
Abstract
Among patients with acute myeloid leukemia (AML), the rare group of complex aberrant karyotypes characterized by high hyperdiploidy (HH) is a subset with poor prognosis. Because of their rarity, few conventional cytogenetic studies have specifically addressed these patients. To identify DNA copy number aberrations at the submicroscopic level, we applied array-based comparative genomic hybridization (aCGH) to samples from 19 AML patients with complex karyotypes characterized by HH (≥49 chromosomes). We found a total of 155 imbalances (average: 8.2 per patient), and a high proportion of these imbalances involved whole chromosomes (n = 75). The chromosomes most commonly gained were chromosomes 8 (58%), 21 (42%), and 19 (32%). We identified 80 segmental genomic aberrations, and losses (n = 47) were more frequent than gains (n = 33). We identified common deleted regions at 5q, 15q, 18p, and 19p. The tumor suppressor gene L3MBTL4 and zinc finger proteins reside within 18p and 19p, respectively. The aCGH analysis added new information to the karyotypic interpretations in 16 of the 19 HH AML cases (84%), leading to a significantly higher detection rate of abnormalities.
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14
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Borze I, Scheinin I, Siitonen S, Elonen E, Juvonen E, Knuutila S. miRNA expression profiles in myelodysplastic syndromes reveal Epstein-Barr virus miR-BART13 dysregulation. Leuk Lymphoma 2011; 52:1567-73. [PMID: 21649547 DOI: 10.3109/10428194.2011.568652] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Recently, the microRNA (miRNA) signature has been used for better characterization and understanding of the pathogenesis of different malignancies, including myelodysplastic syndromes (MDS). MDS are a heterogeneous group of stem cell disorders in which the genetic and molecular defects are not well defined. In the present study, we applied array based miRNA profiling to study 19 bone marrow cell samples of de novo MDS compared with eight healthy individuals. In addition, integration of the miRNA profiling data with our previous array comparative genomic hybridization data, from the same cohort of patients, was performed. We observed up-regulation of hsa-miR-720 and hsa-miR-21, and down-regulation of hsa-miR-671-5p and one human virus miRNA (Epstein-Barr virus miR-BART13) in MDS samples compared with normal samples. In our study, the copy number alteration harboring miRNA was not affecting miRNA expression, but a distinct microRNA expression pattern was observed, not only in MDS compared with controls, but also between MDS entities.
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Affiliation(s)
- Ioana Borze
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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15
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Herry A, Douet-Guilbert N, Morel F, Le Bris MJ, Guéganic N, Berthou C, De Braekeleer M. Isochromosome 5p and related anomalies: a novel recurrent chromosome abnormality in myeloid disorders. ACTA ACUST UNITED AC 2010; 200:134-9. [PMID: 20620596 DOI: 10.1016/j.cancergencyto.2010.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/17/2010] [Accepted: 04/07/2010] [Indexed: 12/14/2022]
Abstract
Loss of material from chromosome arm 5q is a common finding in patients with myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML). Fluorescence in situ hybridization with a panel of different types of probes, used as a complement to conventional cytogenetics, revealed that 7 of 148 patients (4.7%) with abnormalities of chromosome 5 had an i(5)(p10), an idic(5)(q11), or a structurally rearranged i(5)(p10). Three patients had MDS and four had AML. Six of the patients were female, and one was male; age at diagnosis ranged from 56 to 85 years. All patients but one had a complex karyotype. Isochromosome of the short arm of chromosome 5 and its related abnormalities such as idic(5)(q11) and structurally rearranged i(5)(p10) are rare but recurrent abnormalities; their identification requires a combination of conventional and molecular cytogenetic techniques. The biological and clinical significance cannot yet be assessed, not only because too few cases have been described but also because these abnormalities are usually part of a complex karyotype.
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Affiliation(s)
- Angèle Herry
- Laboratory of Histology, Embryology, and Cytogenetics, Faculty of Medicine and Health Sciences, Université de Bretagne Occidentale, 22 avenue Camille Desmoulins, Brest cedex 3l, France
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16
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Array comparative genomic hybridization analysis of adult acute leukemia patients. ACTA ACUST UNITED AC 2010; 197:122-9. [PMID: 20193845 DOI: 10.1016/j.cancergencyto.2009.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 11/22/2009] [Accepted: 11/25/2009] [Indexed: 12/27/2022]
Abstract
We have performed a retrospective array-based comparative hybridization (array-CGH) study on 41 acute leukemia samples [n=17 acute lymphoblastic leukemia (ALL) patients only at diagnosis, n=3 ALL patients both at diagnosis and relapse; n=20 acute myeloid leukemia (AML) patients only at diagnosis and n=1 AML patient both at diagnosis and relapse] using an Agilent 44K array. In addition to previously detected cytogenetic aberrations, we observed cryptic aberrations in 95% of ALL and 90.5% of AML cases. ALL-specific recurrent abnormalities were RB1 (n=3), PAX5 (n=4), and CDKN2B (n=3) deletions; AML-specific recurrent abnormalities were HOXA9 and HOXA10 (n=2) deletions and NOTCH1 duplication (n=2). Recurrent duplication of the ELK1 oncogene was observed in both ALL (n=2) and AML (n=3) cases. Our results demonstrate that oligo-array CGH (oaCGH) is an effective method for defining copy number alterations and identification of novel recurring unbalanced abnormalities. At least for now, however, the use of oaCGH for routine diagnosis still has some restrictions.
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17
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High-resolution oligonucleotide array comparative genomic hybridization study and methylation status of the RPS14 gene in de novo myelodysplastic syndromes. ACTA ACUST UNITED AC 2010; 197:166-73. [PMID: 20193850 DOI: 10.1016/j.cancergencyto.2009.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 10/23/2009] [Accepted: 11/19/2009] [Indexed: 11/22/2022]
Abstract
In myelodysplastic syndromes (MDS), close to one half of patients do not have any visible karyotypic change. In order to study submicroscopic genomic alterations, we applied high-resolution array comparative genomic hybridization techniques (aCGH) in 37 patients with de novo MDS. Furthermore, we studied the methylation status of the RPS14 gene in 5q deletion (5q21.3q33.1) in 24 patients. In all, 21 of the 37 patients (57%) had copy number alterations. The most frequent copy number losses with minimal common overlapping areas were 5q21.3q33.1 (21%) and 7q22.1q33 (19%); the most frequent copy number gain was gain of the whole chromosome 8 (8%). Recurrent, but less frequent copy number losses were detected in two cases each: 11q14.1q22.1, 11q22.3q24.2, 12p12.2p13.31, 17p13.2, 18q12.1q12.2, 18q12.3q21.3, 18q21.2qter, and 20q11.23q12; the gains 8p23.2pter, 8p22p23.1, 8p12p21.1, and 8p11.21q21.2 were similarly found in two cases each. No homozygous losses or amplifications were observed. The RPS14 gene was not methylated in any of the patients.
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18
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Kim JE, Woo KS, Kim KE, Kim SH, Park JI, Shaffer LG, Han JY. Duplications of the long arm of both chromosome 1, dup(1)(q21q32), leading to tetrasomy 1q in myelodysplastic syndrome. Leuk Res 2010; 34:e210-2. [PMID: 20299094 DOI: 10.1016/j.leukres.2010.02.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 02/09/2010] [Accepted: 02/22/2010] [Indexed: 11/17/2022]
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19
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Starczynowski DT, Kuchenbauer F, Argiropoulos B, Sung S, Morin R, Muranyi A, Hirst M, Hogge D, Marra M, Wells RA, Buckstein R, Lam W, Humphries RK, Karsan A. Identification of miR-145 and miR-146a as mediators of the 5q- syndrome phenotype. Nat Med 2010; 16:49-58. [PMID: 19898489 DOI: 10.1038/nm.2054] [Citation(s) in RCA: 510] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 09/30/2009] [Indexed: 12/30/2022]
Abstract
5q- syndrome is a subtype of myelodysplastic syndrome characterized by severe anemia and variable neutropenia but normal or high platelet counts with dysplastic megakaryocytes. We examined expression of microRNAs (miRNAs) encoded on chromosome 5q as a possible cause of haploinsufficiency. We show that deletion of chromosome 5q correlates with loss of two miRNAs that are abundant in hematopoietic stem/progenitor cells (HSPCs), miR-145 and miR-146a, and we identify Toll-interleukin-1 receptor domain-containing adaptor protein (TIRAP) and tumor necrosis factor receptor-associated factor-6 (TRAF6) as respective targets of these miRNAs. TIRAP is known to lie upstream of TRAF6 in innate immune signaling. Knockdown of miR-145 and miR-146a together or enforced expression of TRAF6 in mouse HSPCs resulted in thrombocytosis, mild neutropenia and megakaryocytic dysplasia. A subset of mice transplanted with TRAF6-expressing marrow progressed either to marrow failure or acute myeloid leukemia. Thus, inappropriate activation of innate immune signals in HSPCs phenocopies several clinical features of 5q- syndrome.
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20
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Rayeroux KC, Campbell LJ. Gene amplification in myeloid leukemias elucidated by fluorescence in situ hybridization. ACTA ACUST UNITED AC 2009; 193:44-53. [PMID: 19602463 DOI: 10.1016/j.cancergencyto.2009.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 04/10/2009] [Indexed: 12/28/2022]
Abstract
Gene amplification in hematologic malignancies is uncommon. When karyotyping leukemia cells, gene amplification is generally seen as double-minute (dmin) chromosomes and homogeneously staining regions (hsr). One of the more commonly amplified regions is MYC at 8q24.21, but amplification of MLL at 11q23 and regions on 9p, 19q, and elsewhere on 11q have been reported. Increased copy number of these genes has been associated with poor prognosis. Over an 11-year period, we identified 31 cases of possible gene amplification, 27 of which had enough sample material for further investigations. A total of 17 cases had dmin only, 13 cases had hsr only, and 1 case had both dmin and hsr in the karyotype. Fluorescence in situ hybridization (FISH) analysis identified amplification of MYC in 12 cases, all on dmin, and amplification of MLL in eight cases, all on hsr. Regions other than MYC and MLL were amplified in eight cases and, using multicolor FISH and multicolor banding, we identified a number of novel regions of amplification: 13q11 approximately q12.1, 15q26.1 approximately q26.3, and 17q12. We also identified one case where two different chromosomal regions were simultaneously amplified in the same cell line.
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Affiliation(s)
- Kathleen C Rayeroux
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital Melbourne, P.O. Box 2900, Fitzroy, Victoria 3065, Australia.
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21
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Zatkova A, Merk S, Wendehack M, Bilban M, Muzik EM, Muradyan A, Haferlach C, Haferlach T, Wimmer K, Fonatsch C, Ullmann R. AML/MDS with 11q/MLLamplification show characteristic gene expression signature and interplay of DNA copy number changes. Genes Chromosomes Cancer 2009; 48:510-20. [DOI: 10.1002/gcc.20658] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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22
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Ou JJ, Bagg A. Diagnostic challenges in the myelodysplastic syndromes: the current and future role of genetic and immunophenotypic studies. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2009; 3:275-91. [PMID: 23488463 DOI: 10.1517/17530050902813947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Myelodysplastic syndromes (MDS) comprise a clinically and pathologically diverse collection of hematopoietic neoplasms, most commonly presenting with peripheral cytopenias typically in the context of bone marrow hypercellularity. Mechanistically, at least in the early phases of the disease, this apparently paradoxical picture is primarily due to ineffective hematopoiesis, which is accompanied by a variety of morphologic abnormalities in hematopoietic cells. The identification of recurrent, clinically relevant cytogenetic defects in MDS has spurred the research of molecular mechanisms that contribute to its inception as well as to the development of heterogeneous subtypes. Although conventional cytogenetic analyses remain a diagnostic mainstay in MDS, the application of contemporary techniques including molecular cytogenetics, microarray technologies and multiparametric flow cytometry may ultimately reveal new diagnostic parameters that are theoretically more objective and sensitive than current morphologic approaches. This review aims to outline the role of genetic and immunophenotypic studies in the evaluation of MDS, including findings that may potentially influence future diagnostic classifications, which could refine prognostication and ultimately facilitate the growth of targeted therapies.
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Affiliation(s)
- Joyce J Ou
- University of Pennsylvania, Department of Pathology and Laboratory Medicine, 3400 Spruce Street, 6 Founders Pavilion, PA 19406-4283, USA
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Gelsi-Boyer V, Trouplin V, Adélaïde J, Bonansea J, Cervera N, Carbuccia N, Lagarde A, Prebet T, Nezri M, Sainty D, Olschwang S, Xerri L, Chaffanet M, Mozziconacci MJ, Vey N, Birnbaum D. Mutations of polycomb-associated gene ASXL1 in myelodysplastic syndromes and chronic myelomonocytic leukaemia. Br J Haematol 2009; 145:788-800. [PMID: 19388938 DOI: 10.1111/j.1365-2141.2009.07697.x] [Citation(s) in RCA: 460] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The myelodysplastic syndromes (MDSs) are a heterogeneous group of clonal haematological diseases characterized by ineffective haematopoiesis and predisposition to acute myeloid leukaemia (AML). The pathophysiology of MDSs remains unclear. A definition of the molecular biology of MDSs may lead to a better classification, new prognosis indicators and new treatments. We studied a series of 40 MDS/AML samples by high-density array-comparative genome hybridization (aCGH). The genome of MDSs displayed a few alterations that can point to candidate genes, which potentially regulate histone modifications and WNT pathways (e.g. ASXL1, ASXL2, UTX, CXXC4, CXXC5, TET2, TET3). To validate some of these candidates we studied the sequence of ASXL1. We found mutations in the ASXL1 gene in four out of 35 MDS patients (11%). To extend these results we searched for mutations of ASXL1 in a series of chronic myelomonocytic leukaemias, a disease classified as MDS/Myeloproliferative disorder, and found mutations in 17 out of 39 patients (43%). These results show that ASXL1 might play the role of a tumour suppressor in myeloid malignancies.
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Affiliation(s)
- Véronique Gelsi-Boyer
- Centre de Recherche en Cancérologie de Marseille, Département d'Oncologie Moléculaire, UMR891 Inserm, Institut Paoli-Calmettes, France
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24
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High-resolution whole genome tiling path array CGH analysis of CD34+ cells from patients with low-risk myelodysplastic syndromes reveals cryptic copy number alterations and predicts overall and leukemia-free survival. Blood 2008; 112:3412-24. [PMID: 18663149 DOI: 10.1182/blood-2007-11-122028] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Abstract
Myelodysplastic syndromes (MDSs) pose an important diagnostic and treatment challenge because of the genetic heterogeneity and poorly understood biology of the disease. To investigate initiating genomic alterations and the potential prognostic significance of cryptic genomic changes in low-risk MDS, we performed whole genome tiling path array comparative genomic hybridization (aCGH) on CD34+ cells from 44 patients with an International Prognostic Scoring System score less than or equal to 1.0. Clonal copy number differences were detected in cells from 36 of 44 patients. In contrast, cells from only 16 of the 44 patients displayed karyotypic abnormalities. Although most patients had normal karyotype, aCGH identified 21 recurring copy number alterations. Examples of frequent cryptic alterations included gains at 11q24.2-qter, 17q11.2, and 17q12 and losses at 2q33.1-q33.2, 5q13.1-q13.2, and 10q21.3. Maintenance of genomic integrity defined as less than 3 Mb total disruption of the genome correlated with better overall survival (P = .002) and was less frequently associated with transformation to acute myeloid leukemia (P = .033). This study suggests a potential role for the use of aCGH in the clinical workup of MDS patients.
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25
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Puces à ADN (CGH-array) : application pour le diagnostic de déséquilibres cytogénétiques cryptiques. ACTA ACUST UNITED AC 2008; 56:368-74. [DOI: 10.1016/j.patbio.2008.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 04/16/2008] [Indexed: 01/05/2023]
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26
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Calasanz MJ, Cigudosa JC. Molecular cytogenetics in translational oncology: when chromosomes meet genomics. Clin Transl Oncol 2008; 10:20-9. [DOI: 10.1007/s12094-008-0149-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Mackinnon RN, Campbell LJ. Dicentric chromosomes and 20q11.2 amplification in MDS/AML with apparent monosomy 20. Cytogenet Genome Res 2008; 119:211-20. [PMID: 18253031 DOI: 10.1159/000112063] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2007] [Indexed: 01/15/2023] Open
Abstract
FISH analysis of 41 previously karyotyped cases of MDS and AML with apparent monosomy of chromosome 20 revealed a variety of dicentric abnormalities involving chromosome 20. These usually, but not always, involved a breakpoint in the long arm of chromosome 20 and loss of the common deleted region at 20q12. Not one case of true monosomy 20 was confirmed. We found evidence for dicentric chromosome formation in 21 of 24 unbalanced translocations containing chromosome 20 and that were studied in more detail. Subsequent loss of one of the centromeres had occurred in eight of these 24 cases, and was more frequent than centromere inactivation as a means of resolving the inherent instability of a dicentric chromosome. In the three cases with dicentric chromosomes from which proximal 20q had been excised along with the 20 centromere, the excised segment was retained, and in two of these it was amplified. Proximal 20q was clearly retained in all but three cases, and present in three or more copies in 17 of 41 cases. The retention and amplification of proximal 20q provides support for the hypothesis that there is an oncogene located in this region of 20q that is activated in cases of MDS/AML with del(20q). Apparent monosomy 20 in MDS/AML should be treated as evidence of unidentified chromosome 20 abnormalities, and familiarity with the typical G-banded morphology of these derivatives can help with their identification. The reported incidence of dicentric chromosomes is clearly an under-estimate but is increasing in myeloid disorders as more cases are studied with methods allowing their detection.
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Affiliation(s)
- R N Mackinnon
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital, University of Melbourne, Melbourne, Australia.
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28
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Suela J, Alvarez S, Cigudosa JC. DNA profiling by arrayCGH in acute myeloid leukemia and myelodysplastic syndromes. Cytogenet Genome Res 2007; 118:304-9. [PMID: 18000384 DOI: 10.1159/000108314] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Accepted: 11/09/2006] [Indexed: 12/20/2022] Open
Affiliation(s)
- J Suela
- Molecular Cytogenetics Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
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29
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Herry A, Douet-Guilbert N, Morel F, Le Bris MJ, De Braekeleer M. Redefining monosomy 5 by molecular cytogenetics in 23 patients with MDS/AML. Eur J Haematol 2007; 78:457-67. [PMID: 17391336 DOI: 10.1111/j.1600-0609.2007.00847.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Deletion of the long arm of chromosome 5 [del(5q)] or loss of a whole chromosome 5 (-5) is a common finding, arising de novo in 10% of patients with myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML) and in 40% of patients with therapy-related MDS or AML. We investigated by molecular cytogenetics 23 MDS/AML patients for whom conventional cytogenetics detected a monosomy 5. Monosomy 5 was redefined as unbalanced or balanced translocation and ring of chromosome 5. Loss of 5q material was identified in all 23 patients, but one. One copy of EGR1(5q31) or CSF1R(5q33-34) genes was lost in 22 of the 23 patients. Chromosome 5p material was a constant chromosomal component of derivative chromosomes or rings in all patients, but one. Sequential fluorescent in situ hybridization studies with whole chromosome paints and region-specific probes, used as a complement to conventional cytogenetic analysis, allow a better interpretation of karyotypes in MDS/AML patients.
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Affiliation(s)
- Angèle Herry
- Laboratoire d'Histologie, Embryologie et Cytogénétique, Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale, Brest, France
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30
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Suela J, Alvarez S, Cifuentes F, Largo C, Ferreira BI, Blesa D, Ardanaz M, García R, Marquez JA, Odero MD, Calasanz MJ, Cigudosa JC. DNA profiling analysis of 100 consecutive de novo acute myeloid leukemia cases reveals patterns of genomic instability that affect all cytogenetic risk groups. Leukemia 2007; 21:1224-31. [PMID: 17377590 DOI: 10.1038/sj.leu.2404653] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have carried out a high-resolution whole genome DNA profiling analysis on 100 bone marrow samples from a consecutive series of de novo acute myeloid leukemia (AML) cases. After discarding copy number changes that are known to be genetic polymorphisms, we found that genomic aberrations (GA) in the form of gains or losses of genetic material were present in 74% of the samples, with a median of 2 GA per case (range 0-35). In addition to the cytogenetically detected aberration, GA were present in cases from all cytogenetic prognostic groups: 79% in the favorable group, 60% in the intermediate group (including 59% of cases with normal karyotype) and 83% in the adverse group. Five aberrant deleted regions were recurrently associated with cases with a highly aberrant genome (e.g., a 1.5 Mb deletion at 17q11.2 and a 750 kb deletion at 5q31.1). Different degrees of genomic instability showed a statistically significant impact on survival curves, even within the normal karyotype cases. This association was independent of other clinical and genetic parameters. Our study provides, for the first time, a detailed picture of the nature and frequency of DNA copy number aberrations in de novo AML.
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Affiliation(s)
- J Suela
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncologicas, Madrid, Spain
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31
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Brezinová J, Zemanová Z, Ransdorfová S, Pavlistová L, Babická L, Housková L, Melichercíková J, Sisková M, Cermák J, Michalová K. Structural aberrations of chromosome 7 revealed by a combination of molecular cytogenetic techniques in myeloid malignancies. ACTA ACUST UNITED AC 2007; 173:10-6. [PMID: 17284364 DOI: 10.1016/j.cancergencyto.2006.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Revised: 08/21/2006] [Accepted: 09/01/2006] [Indexed: 10/23/2022]
Abstract
In bone marrow cells of 33 patients with myelodysplastic syndrome and acute myeloid leukemia, structural rearrangements of chromosome 7 were found with conventional G-banding: 8 with deletions 7q and 25 with translocations. In 29 of the patients, complex karyotypes were confirmed using multicolor fluorescence in situ hybridization (mFISH). Commercial probes (Abbot Molecular) were used for 7q22, 7q31, and 7q35, the regions most frequently deleted in myeloid malignancies. In three cases without deletions, high-resolution multicolor banding (mBAND) for chromosome 7 revealed other aberrations. Five groups of chromosomal rearrangements were established: (a) deletion 7q as a sole aberration (2 cases), (b) deletion 7q and complex karyotypes (6 cases), (c) combined translocations and deletions of 7q (17 cases), (d) combined translocation and deletion 7p (5 cases), and (e) translocation of chromosomes 7 without deletion 7p or 7q (3 cases). Deletions of all three FISH-screened regions were the most frequent, with heterogeneous breakpoints. The region 7p13.2 approximately p15.2 was most commonly deleted. Most of the deletions were cryptic, not detectable with conventional cytogenetics. Aberrations of chromosome 7 are associated with a very poor outcome; survival time in our cohort was short (median 7 months).
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Affiliation(s)
- Jana Brezinová
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 128 20 Prague 2, Czech Republic.
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32
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Strefford JC, Worley H, Barber K, Wright S, Stewart ARM, Robinson HM, Bettney G, van Delft FW, Atherton MG, Davies T, Griffiths M, Hing S, Ross FM, Talley P, Saha V, Moorman AV, Harrison CJ. Genome complexity in acute lymphoblastic leukemia is revealed by array-based comparative genomic hybridization. Oncogene 2007; 26:4306-18. [PMID: 17237825 DOI: 10.1038/sj.onc.1210190] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromosomal abnormalities are important for the classification and risk stratification of patients with acute lymphoblastic leukemia (ALL). However, approximately 30% of childhood and 50% of adult patients lack abnormalities with clinical relevance. Here, we describe the use of array-based comparative genomic hybridization (aCGH) to identify copy number alterations (CNA) in 58 ALL patients. CNA were identified in 83% of cases, and most frequently involved chromosomes 21 (n=42), 9 (n=21), 6 (n=16), 12 (n=11), 15 (n=11), 8 (n=10) and 17 (n=10). Deletions of 6q (del(6q)) were heterogeneous in size, in agreement with previous data, demonstrating the sensitivity of aCGH to measure CNA. Although 9p deletions showed considerable variability in both the extent and location, all encompassed the CDKN2A locus. Six patients showed del(12p), with a common region encompassing the ETV6 gene. Complex CNA were observed involving chromosomes 6 (n=2), 15 (n=2) and 21 (n=11) with multiple regions of loss and gain along each chromosome. Chromosome 21 CNA shared a common region of gain, with associated subtelomeric deletions. Other recurrent findings included dim(13q), dim(16q) and enh(17q). This is the first report of genome-wide detection of CNA in ALL patients using aCGH, and it has demonstrated a higher level of karyotype complexity than anticipated from conventional cytogenetic analysis.
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Affiliation(s)
- J C Strefford
- Leukaemia Research Cytogenetics Group, Cancer Sciences Division, University of Southampton, UK.
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33
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Zatkova A, Schoch C, Speleman F, Poppe B, Mannhalter C, Fonatsch C, Wimmer K. GAB2 is a novel target of 11q amplification in AML/MDS. Genes Chromosomes Cancer 2006; 45:798-807. [PMID: 16736498 DOI: 10.1002/gcc.20344] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Chromosome arm 11q amplifications involving the mixed lineage leukemia gene (MLL) locus are rare but recurrent aberrations in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). We have recently shown that in addition to the MLL core amplicon, independent sequences in 11q23-24 and/or 11q13.5 are coamplified within the same cytogenetic markers in 90% and 60% of patients, respectively. Here we further narrow down the minimal amplicon in 11q13.5 to 1.17 Mb by means of semi-quantitative PCR and FISH analyses. The newly defined amplicon contains seven genes, including the GRB2-associated binding protein 2 (GAB2). Using real-time RT-PCR we show a significant transcriptional upregulation of GAB2 in the patients who have GAB2 coamplified with MLL. Thus, the adaptor molecule GAB2 that has already been shown to enhance oncogenic signaling in other neoplasias appears as a novel target of 11q amplification in AML/MDS.
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Affiliation(s)
- Andrea Zatkova
- Abteilung für Humangenetik, Klinisches Institut für Medizinische und Chemische Labor Diagnostik (KIMCL), Medizinische Universität Wien, Währinger Strasse 10, A-1090 Vienna, Austria.
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34
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Stamatoullas A, Callat MP, Marreiros S, Tilly H, Bastard C. Unusual complex hyperdiploid karyotypes in myelodysplastic syndromes. ACTA ACUST UNITED AC 2006; 170:129-32. [PMID: 17011983 DOI: 10.1016/j.cancergencyto.2006.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 05/08/2006] [Accepted: 05/10/2006] [Indexed: 12/24/2022]
Abstract
Over an 18-year period, 10 myelodysplastic syndrome (MDS) patients with complex hyperdiploid karyotypes were identified. According to the FAB classification, the 10 patients were subclassified as three refractory anemias (RA), three refractory anemias with excess blasts (RAEB), two RAEB in transformation (RAEB-t), and two unclassified MDS. According to the WHO classification, the diagnoses were two RA, one refractory cytopenia with multilineage dysplasia, two RAEB-1, one RAEB-2, two unclassified MDS, and two acute myeloid leukemia. Six were secondary MDS. Four patients showed marked dyserythropoiesis; three of these were secondary MDS. The chromosome number ranged from 47 to 62, and clonal evolution or composite karyotypes were noted in 7 patients. Seven patients had at least one clone with >50 chromosomes. Recurrent defects included chromosome 5, 17, and 13 abnormalities. Notably, trisomy 8 and monosomy 7 were rare in that group of patients. Three of four patients with marked dyserythropoiesis shared abnormalities of both chromosomes 13 and 17.
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Affiliation(s)
- Aspasia Stamatoullas
- Groupe d'Etude des Proliferations Lymphoïdes, Centre Henri Becquerel, Département d'Hématologie INSERM U 614, IFR 23, Rouen, France.
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35
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Gelsi-Boyer V, Vey N. Avancées dans la prise en charge des syndromes myélodysplasiques. Rev Med Interne 2006; 27:600-9. [PMID: 16713027 DOI: 10.1016/j.revmed.2006.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Accepted: 02/03/2006] [Indexed: 11/22/2022]
Abstract
OBJECTIVES Myelodysplastic syndromes (MDS) are a group of clonal hematologic disorder, which combine ineffective hematopoiesis and evolution to acute myeloid leukemia. Significant progress has been made in the understanding of the disease pathogenesis, diagnostics and classification. Promising new agents and innovative therapeutic strategies are currently used. In this article we will review these achievements and their impact on the treatment of MDS. CURRENT KNOWLEDGE AND KEY POINTS The pathogenesis of MDS involves abnormalities of the MDS clone itself such as abnormal apoptosis, signalling or epigenetic regulation and abnormalities of the microenvironment such as immune deregulation or increased angiogenesis, which represent potential therapeutic targets. There is currently no standard treatment for MDS and allogeneic stem cell transplantation remains the only curative strategy. However, besides conventional chemotherapy and growth factors, new agents including hypomethylating agents, antiangiogenic drugs, immune modulatory agents have proved effective. FUTURE PROSPECTS AND PROJECTS The interesting results achieved with these new agents show that it is necessary to continue investigation in order to improve therapeutic strategies in MDS.
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Affiliation(s)
- V Gelsi-Boyer
- Département de biopathologie, 232, boulevard Sainte-Marguerite, 13009 Marseille, France
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36
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Strefford JC, van Delft FW, Robinson HM, Worley H, Yiannikouris O, Selzer R, Richmond T, Hann I, Bellotti T, Raghavan M, Young BD, Saha V, Harrison CJ. Complex genomic alterations and gene expression in acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Proc Natl Acad Sci U S A 2006; 103:8167-72. [PMID: 16702559 PMCID: PMC1472447 DOI: 10.1073/pnas.0602360103] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Indexed: 12/13/2022] Open
Abstract
We have previously identified a unique subtype of acute lymphoblastic leukemia (ALL) associated with a poor outcome and characterized by intrachromosomal amplification of chromosome 21 including the RUNX1 gene (iAMP21). In this study, array-based comparative genomic hybridization (aCGH) (n = 10) detected a common region of amplification (CRA) between 33.192 and 39.796 Mb and a common region of deletion (CRD) between 43.7 and 47 Mb in 100% and 70% of iAMP21 patients, respectively. High-resolution genotypic analysis (n = 3) identified allelic imbalances in the CRA. Supervised gene expression analysis showed a distinct signature for eight patients with iAMP21, with 10% of overexpressed genes located within the CRA. The mean expression of these genes was significantly higher in iAMP21 when compared to other ALL samples (n = 45). Although genomic copy number correlated with overall gene expression levels within areas of loss or gain, there was considerable individual variation. A unique subset of differentially expressed genes, outside the CRA and CRD, were identified when gene expression signatures of iAMP21 were compared to ALL samples with ETV6-RUNX1 fusion (n = 21) or high hyperdiploidy with additional chromosomes 21 (n = 23). From this analysis, LGMN was shown to be overexpressed in patients with iAMP21 (P = 0.0012). Genomic and expression data has further characterized this ALL subtype, demonstrating high levels of 21q instability in these patients leading to proposals for mechanisms underlying this clinical phenotype and plausible alternative treatments.
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Affiliation(s)
- Jon C Strefford
- Leukaemia Research Cytogenetics Group, Cancer Sciences Division, University of Southampton, Southampton SO16 6YD, United Kingdom.
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37
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Abstract
In all organisms, cell proliferation is orchestrated by coordinated patterns of gene expression. Transcription results from the activity of the RNA polymerase machinery and depends on the ability of transcription activators and repressors to access chromatin at specific promoters. During the last decades, increasing evidence supports aberrant transcription regulation as contributing to the development of human cancers. In fact, transcription regulatory proteins are often identified in oncogenic chromosomal rearrangements and are overexpressed in a variety of malignancies. Most transcription regulators are large proteins, containing multiple structural and functional domains some with enzymatic activity. These activities modify the structure of the chromatin, occluding certain DNA regions and exposing others for interaction with the transcription machinery. Thus, chromatin modifiers represent an additional level of transcription regulation. In this review we focus on several families of transcription activators and repressors that catalyse histone post-translational modifications (acetylation, methylation, phosphorylation, ubiquitination and SUMOylation); and how these enzymatic activities might alter the correct cell proliferation program, leading to cancer.
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Affiliation(s)
- Helena Santos-Rosa
- The Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK
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38
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Alvarez S, Cigudosa JC. Gains, losses and complex karyotypes in myeloid disorders: a light at the end of the tunnel. Hematol Oncol 2005; 23:18-25. [PMID: 16142824 DOI: 10.1002/hon.744] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Complex karyotypes are seen in approximately 15% of de novo MDS/AML and in up to 50% of therapy-related MDS/AML. These patients represent a therapeutic challenge for which no current treatment approach is satisfactory. Therefore, a large number of genetic studies using cytogenetic molecular techniques have been performed to better define the chromosomal abnormalities in this poor-prognosis group. On the basis of the available data from several studies of AML with complex karyotypes, similar findings on recurrent breakpoints and frequently lost and gained chromosomal regions have been observed. The most frequent rearrangements, in all the published series, were unbalanced translocations leading to loss of chromosomal material. Overall, loss of 5q and/or 7q chromosomal material seemed the more common event, and losses of 5q, 7q, and 17p in combination were observed in many cases. Overrepresented chromosomal material from 8q, 11q23, 21q and 22q was found recurrently and in several cases this was due to the amplification of the MLL (located at 11q23) and AML1/RUNX1 (located at 22q22) genes. As a result of these findings, the presence of MLL copy gain/amplifications or losses of the short arm of chromosome 17, in association with 5/5q, have been found to be indicators of an extremely poor prognosis. Interestingly, this non-random pattern of DNA gains and losses, that characterizes AML cases with complex karyotypes, affects the gene expression pattern, and a specific expression profile, characterized by the upregulation of genes involved in the DNA repair and chromosome segregation pathways, has been recently reported. Therefore, a comprehensive genome-wide analysis of patients with AML or MDS with complex karyotypes has led to a better characterization of chromosomal aberrations. These specific alterations could be used in the near future as therapeutic targets or markers for the risk stratification of patients, detection of minimal residual disease and the development of new therapeutic interventions.
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MESH Headings
- Chromosome Segregation/genetics
- Chromosomes, Human/genetics
- Chromosomes, Human/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- DNA Repair/genetics
- Gene Amplification/genetics
- Gene Expression Profiling/methods
- Gene Expression Regulation, Leukemic/genetics
- Genome, Human/genetics
- Histone-Lysine N-Methyltransferase
- Humans
- Karyotyping
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/therapy
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/metabolism
- Myelodysplastic Syndromes/therapy
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Neoplasm, Residual/genetics
- Neoplasm, Residual/metabolism
- Neoplasm, Residual/therapy
- Risk Factors
- Translocation, Genetic
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Affiliation(s)
- Sara Alvarez
- Cytogenetics Unit, Centro Nacional de de Investigaciones Oncológicas (CNIO), Madrid, Spain
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