1
|
Paulsson K. Chromosomal Gains as a Favorable Prognostic Factor in Pediatric ALL. J Clin Oncol 2023; 41:5433-5436. [PMID: 37820292 DOI: 10.1200/jco.23.01760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 10/13/2023] Open
Affiliation(s)
- Kajsa Paulsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| |
Collapse
|
2
|
Tamburri S, Conway E, Pasini D. Polycomb-dependent histone H2A ubiquitination links developmental disorders with cancer. Trends Genet 2021; 38:333-352. [PMID: 34426021 DOI: 10.1016/j.tig.2021.07.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022]
Abstract
Cell identity is tightly controlled by specific transcriptional programs which require post-translational modifications of histones. These histone modifications allow the establishment and maintenance of active and repressed chromatin domains. Histone H2A lysine 119 ubiquitination (H2AK119ub1) has an essential role in building repressive chromatin domains during development. It is regulated by the counteracting activities of the Polycomb repressive complex 1 (PRC1) and the Polycomb repressive-deubiquitinase (PR-DUB) complexes, two multi-subunit ensembles that write and erase this modification, respectively. We have catalogued the recurrent genetic alterations in subunits of the PRC1 and PR-DUB complexes in both neurodevelopmental disorders and cancer. These genetic lesions are often shared across disorders, and we highlight common mechanisms of H2AK119ub1 dysregulation and how they affect development in multiple disease contexts.
Collapse
Affiliation(s)
- Simone Tamburri
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via Antonio di Rudinì 8, 20142 Milan, Italy.
| | - Eric Conway
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via Antonio di Rudinì 8, 20142 Milan, Italy.
| |
Collapse
|
3
|
Lajoie M, Drouin S, Caron M, St-Onge P, Ouimet M, Gioia R, Lafond MH, Vidal R, Richer C, Oualkacha K, Droit A, Sinnett D. Specific expression of novel long non-coding RNAs in high-hyperdiploid childhood acute lymphoblastic leukemia. PLoS One 2017; 12:e0174124. [PMID: 28346506 PMCID: PMC5367703 DOI: 10.1371/journal.pone.0174124] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/22/2017] [Indexed: 12/31/2022] Open
Abstract
Pre-B cell childhood acute lymphoblastic leukemia (pre-B cALL) is a heterogeneous disease involving many subtypes typically stratified using a combination of cytogenetic and molecular-based assays. These methods, although widely used, rely on the presence of known chromosomal translocations, which is a limiting factor. There is therefore a need for robust, sensitive, and specific molecular biomarkers unaffected by such limitations that would allow better risk stratification and consequently better clinical outcome. In this study we performed a transcriptome analysis of 56 pre-B cALL patients to identify expression signatures in different subtypes. In both protein-coding and long non-coding RNAs (lncRNA), we identified subtype-specific gene signatures distinguishing pre-B cALL subtypes, particularly in t(12;21) and hyperdiploid cases. The genes up-regulated in pre-B cALL subtypes were enriched in bivalent chromatin marks in their promoters. LncRNAs is a new and under-studied class of transcripts. The subtype-specific nature of lncRNAs suggests they may be suitable clinical biomarkers to guide risk stratification and targeted therapies in pre-B cALL patients.
Collapse
Affiliation(s)
- Mathieu Lajoie
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Simon Drouin
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Maxime Caron
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Pascal St-Onge
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Manon Ouimet
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Romain Gioia
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Marie-Hélène Lafond
- Mathematics and Statistics Department, University of Quebec at Montreal (UQAM), 201 President-Kennedy Av., Montreal, QC, Canada
| | - Ramon Vidal
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Chantal Richer
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Karim Oualkacha
- Mathematics and Statistics Department, University of Quebec at Montreal (UQAM), 201 President-Kennedy Av., Montreal, QC, Canada
| | - Arnaud Droit
- Department of Endocrinology and Nephrology, Laval University, 2705 Laurier Blvd., Quebec City, QC, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
- * E-mail:
| |
Collapse
|
4
|
Nagel S, Meyer C, Kaufmann M, Drexler HG, MacLeod RAF. Aberrant expression of homeobox gene SIX1 in Hodgkin lymphoma. Oncotarget 2016; 6:40112-26. [PMID: 26473286 PMCID: PMC4741883 DOI: 10.18632/oncotarget.5556] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/29/2015] [Indexed: 12/17/2022] Open
Abstract
In Hodgkin lymphoma (HL) we recently identified deregulated expression of homeobox genes MSX1 and OTX2 which are physiologically involved in development of the embryonal neural plate border region. Here, we examined in HL homeobox gene SIX1 an additional regulator of this embryonal region mediating differentiation of placodal precursors. SIX1 was aberrantly activated in 12 % of HL patient samples in silico, indicating a pathological role in a subset of this B-cell malignancy. In addition, SIX1 expression was detected in HL cell lines which were used as models to reveal upstream factors and target genes of this basic developmental regulator. We detected increased copy numbers of the SIX1 locus at chromosome 14q23 correlating with enhanced expression while chromosomal translocations were absent. Moreover, comparative expression profiling data and pertinent gene modulation experiments indicated that the WNT-signalling pathway and transcription factor MEF2C regulate SIX1 expression. Genes encoding the transcription factors GATA2, GATA3, MSX1 and SPIB – all basic lymphoid regulators - were identified as targets of SIX1 in HL. In addition, cofactors EYA1 and TLE4, respectively, contrastingly mediated activation and suppression of SIX1 target gene expression. Thus, the protein domain interfaces may represent therapeutic targets in SIX1-positive HL subsets. Collectively, our data reveal a gene regulatory network with SIX1 centrally deregulating lymphoid differentiation and support concordance of lymphopoiesis/lymphomagenesis and developmental processes in the neural plate border region.
Collapse
Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
5
|
Zaliova M, Hovorkova L, Vaskova M, Hrusak O, Stary J, Zuna J. Slower early response to treatment and distinct expression profile of childhood high hyperdiploid acute lymphoblastic leukaemia with DNA index < 1.16. Genes Chromosomes Cancer 2016; 55:727-37. [PMID: 27163296 DOI: 10.1002/gcc.22374] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/04/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023] Open
Abstract
Acute lymphoblastic leukaemias (ALL) with 51-67 chromosomes are defined as high hyperdiploid (HHD) and are generally associated with good prognosis. However, several studies show heterogeneity in HHD ALL and suggest that the favourable prognosis is associated rather with higher ploidy defined by DNA index (DNAi) ≥ 1.16 or with a presence of specific single or combined trisomies. HHD ALL with DNAi < 1.16 are only rarely studied separately. Using single nucleotide polymorphism array, we analysed 89 childhood HHD ALL patients divided into groups with lower (<1.16; n = 34) and higher (≥1.16; n = 55) DNAi. We assessed treatment response, presence of secondary aberrations, mutations in RAS pathway genes and CREBBP and also gene expression profile (GEP) to reveal differences between the two subgroups. Cases with 51-54 chromosomes had DNAi 1.1-1.16 and cases with 55-67 chromosomes had DNAi ≥ 1.16. The groups with lower and higher DNAi had distinct response to early treatment and distinct GEP. The better response of the group with higher DNAi was associated with specific trisomies (trisomy of chromosome 10 or combined with trisomies 4 and/or 17). Our results suggest that cytogenetically defined HHD ALL can in fact be divided into two biologically distinguishable subgroups and that DNAi 1.16 is a relevant value to separate between the two. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Marketa Zaliova
- CLIP, Childhood Leukaemia Investigation Prague, Departmentof Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.,Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Lenka Hovorkova
- CLIP, Childhood Leukaemia Investigation Prague, Departmentof Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.,Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Martina Vaskova
- CLIP, Childhood Leukaemia Investigation Prague, Departmentof Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.,Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Ondrej Hrusak
- CLIP, Childhood Leukaemia Investigation Prague, Departmentof Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.,Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Stary
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jan Zuna
- CLIP, Childhood Leukaemia Investigation Prague, Departmentof Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic.,Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| |
Collapse
|
6
|
Paulsson K. High hyperdiploid childhood acute lymphoblastic leukemia: Chromosomal gains as the main driver event. Mol Cell Oncol 2015; 3:e1064555. [PMID: 27308574 DOI: 10.1080/23723556.2015.1064555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
High hyperdiploid childhood acute lymphoblastic leukemia is characterized by multiple chromosomal gains. Recent results show that this subtype harbors relatively few genetic abnormalities besides the extra chromosomes, which appear to arise early and are likely the main driver event. Secondary hits primarily target genes in the rat sarcoma (RAS) signaling pathway and histone modifiers.
Collapse
Affiliation(s)
- Kajsa Paulsson
- Division of Clinical Genetics, Lund University , Lund, Sweden
| |
Collapse
|
7
|
The genomic landscape of high hyperdiploid childhood acute lymphoblastic leukemia. Nat Genet 2015; 47:672-6. [PMID: 25961940 DOI: 10.1038/ng.3301] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/16/2015] [Indexed: 12/16/2022]
Abstract
High hyperdiploid (51-67 chromosomes) acute lymphoblastic leukemia (ALL) is one of the most common childhood malignancies, comprising 30% of all pediatric B cell-precursor ALL. Its characteristic genetic feature is the nonrandom gain of chromosomes X, 4, 6, 10, 14, 17, 18 and 21, with individual trisomies or tetrasomies being seen in over 75% of cases, but the pathogenesis remains poorly understood. We performed whole-genome sequencing (WGS) (n = 16) and/or whole-exome sequencing (WES) (n = 39) of diagnostic and remission samples from 51 cases of high hyperdiploid ALL to further define the genomic landscape of this malignancy. The majority of cases showed involvement of the RTK-RAS pathway and of histone modifiers. No recurrent fusion gene-forming rearrangement was found, and an analysis of mutations on trisomic chromosomes indicated that the chromosomal gains were early events, strengthening the notion that the high hyperdiploid pattern is the main driver event in this common pediatric malignancy.
Collapse
|
8
|
Othman MAK, Melo JB, Carreira IM, Rincic M, Alhourani E, Wilhelm K, Gruhn B, Glaser A, Liehr T. MLLT10 and IL3 rearrangement together with a complex four-way translocation and trisomy 4 in a patient with early T-cell precursor acute lymphoblastic leukemia: A case report. Oncol Rep 2014; 33:625-30. [PMID: 25435396 DOI: 10.3892/or.2014.3624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/13/2014] [Indexed: 11/06/2022] Open
Abstract
Cytogenetic classification of acute lymphoblastic leukemia (ALL) is primarily based on numerical and structural chromosomal abnormalities. In T-cell ALL (T-ALL), chromosomal rearrangements are identified in up to 70% of the patients while the remaining patients show a normal karyotype. In the present study, a 16-year-old male was diagnosed with T-precursor cell ALL and a normal karyotype after standard GTG-banding, was studied retrospectively (>10 years after diagnosis) in frame of a research project by molecular approaches. In addition to molecular cytogenetics, multiplex ligation-dependent probe amplification (MLPA) and high resolution array-comparative genomic hybridization (aCGH) were also applied. Thus, the following yet unrecognized balanced chromosomal aberrations were detected: der(3)t(3;5)(p23;q31.1), der(5)t(3;5)(p23;q35.3), der(5)t(5;10)(q31.1;p12.3) and der(10)t(5;10)(q35.3;p12.3). The oncogene MLLT10 was involved in this rearrangement as was the IL3 gene; in addition, trisomy 4 was present. All of these clonal aberrations were found in 40% of the cells. Even if this complex karyotype would have been identified at the time of diagnosis, most likely no other protocol of anticancer therapy (ALL-BFM 95) would have been applied. Three months after the end of a successful 2-year treatment, the patient suffered from isolated bone marrow relapse and died of sepsis during ALL-REZ-BFM protocol treatment.
Collapse
Affiliation(s)
- Moneeb A K Othman
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Joana B Melo
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel M Carreira
- Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Martina Rincic
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Eyad Alhourani
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Kathleen Wilhelm
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Bernd Gruhn
- Department of Pediatrics (Oncology and Hematology), Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Anita Glaser
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| |
Collapse
|
9
|
High hyperdiploidy among adolescents and adults with acute lymphoblastic leukaemia (ALL): cytogenetic features, clinical characteristics and outcome. Leukemia 2013; 28:1511-8. [DOI: 10.1038/leu.2013.379] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 01/09/2023]
|
10
|
Oksenberg N, Ahituv N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet 2013; 29:600-8. [PMID: 24008202 DOI: 10.1016/j.tig.2013.08.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 12/31/2022]
Abstract
The autism susceptibility candidate 2 (AUTS2) gene is associated with multiple neurological diseases, including autism, and has been implicated as an important gene in human-specific evolution. Recent functional analysis of this gene has revealed a potential role in neuronal development. Here, we review the literature regarding AUTS2, including its discovery, expression, association with autism and other neurological and non-neurological traits, implication in human evolution, function, regulation, and genetic pathways. Through progress in clinical genomic analysis, the medical importance of this gene is becoming more apparent, as highlighted in this review, but more work needs to be done to discover the precise function and the genetic pathways associated with AUTS2.
Collapse
Affiliation(s)
- Nir Oksenberg
- Department of Bioengineering and Therapeutic Sciences, and Institute for Human Genetics, University of California, San Francisco (UCSF), 1550 4th Street, San Francisco, CA 94158, USA
| | | |
Collapse
|
11
|
Genetic landscape of high hyperdiploid childhood acute lymphoblastic leukemia. Proc Natl Acad Sci U S A 2010; 107:21719-24. [PMID: 21098271 DOI: 10.1073/pnas.1006981107] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High hyperdiploid acute lymphoblastic leukemia (ALL) is one of the most common malignancies in children. It is characterized by gain of chromosomes, typically +X, +4, +6, +10, +14, +17, +18, and +21,+21; little is known about additional genetic aberrations. Approximately 20% of the patients relapse; therefore it is clinically important to identify risk-stratifying markers. We used SNP array analysis to investigate a consecutive series of 74 cases of high hyperdiploid ALL. We show that the characteristic chromosomal gains are even more frequent than previously believed, indicating that karyotyping mistakes are common, and that almost 80% of the cases display additional abnormalities detectable by SNP array analysis. Subclonality analysis strongly implied that the numerical aberrations were primary and arose before structural events, suggesting that step-wise evolution of the leukemic clone is common. An association between duplication of 1q and +5 was seen (P = 0.003). Other frequent abnormalities included whole-chromosome uniparental isodisomies (wUPIDs) 9 and 11, gain of 17q not associated with isochromosome formation, extra gain of part of 21q, deletions of ETS variant 6 (ETV6), cyclin-dependent kinase inhibitor 2A (CKDN2A) and paired box 5 (PAX5), and PAN3 poly(A) specific ribonuclease subunit homolog (PAN3) microdeletions. Comparison of whole-chromosome and partial UPID9 suggested different pathogenetic outcomes, with the former not involving CDKN2A. Finally, two cases had partial deletions of AT rich interactive domain 5B (ARID5B), indicating that acquired as well as constitutional variants in this locus may be associated with pediatric ALL. Here we provide a comprehensive characterization of the genetic landscape of high hyperdiploid childhood ALL, including the heterogeneous pattern of secondary genetic events.
Collapse
|
12
|
Sagaert X, Tousseyn T, Vanhentenrijk V, Van Loo P, Baens M, Marynen P, De Hertogh G, Geboes K, De Wolf-Peeters C. Comparative expressed sequence hybridization studies of t(11;18)(q21;q21)-positive and -negative gastric MALT lymphomas reveal both unique and overlapping gene programs. Mod Pathol 2010; 23:458-69. [PMID: 20081812 DOI: 10.1038/modpathol.2009.182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Among the genetic abnormalities reported to occur in MALT lymphomas, the translocation t(11;18)(q21;q21) is of particular interest because it is exclusively documented in MALT lymphomas, mainly with gastrointestinal location. It results in the creation of a fusion protein API2-MALT1 that activates the transcription factor NF-kappaB through enhanced IKK gamma polyubiquitination. Here, we apply the recently developed molecular technique termed comparative expressed sequence hybridization to identify differentially expressed chromosomal regions related to the pathogenesis of gastric MALT lymphomas. By comparing t(11;18)(q21;q21)-positive gastric MALT lymphomas to their t(11;18)(q21;q21)-negative counterparts, we found that the location of the MALT1 break point determines a difference in expression pattern within the t(11;18)(q21;q21)-positive group. Moreover, we could define a gastric MALT lymphoma signature, which most likely comprises the regions and genes with significance in the development of MALT lymphomas, by comparing both t(11;18)(q21;q21)-positive and -negative MALT lymphomas to normal lymphoid tissue. Finally, a significant imprint of the marginal zone signature, established by comparing microdissected, splenic B follicles with and without marginal zone, was evident in the expression profile of MALT lymphoma, further supporting a marginal zone origin for this type of B-cell non-Hodgkin's lymphoma.
Collapse
Affiliation(s)
- Xavier Sagaert
- Section of Morphology and Molecular Pathology, Department of Pathology, Katholieke Universiteit Leuven, Leuven, Belgium.
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Paulsson K, Johansson B. High hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer 2009; 48:637-60. [PMID: 19415723 DOI: 10.1002/gcc.20671] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
High hyperdiploidy (51-67 chromosomes) is the most common cytogenetic abnormality pattern in childhood B-cell precursor acute lymphoblastic leukemia (ALL), occurring in 25-30% of such cases. High hyperdiploid ALL is characterized cytogenetically by a nonrandom gain of chromosomes X, 4, 6, 10, 14, 17, 18, and 21 and clinically by a favorable prognosis. Despite the high frequency of this karyotypic subgroup, many questions remain regarding the epidemiology, etiology, presence of other genetic changes, the time and cell of origin, and the formation and pathogenetic consequences of high hyperdiploidy. However, during the last few years, several studies have addressed some of these important issues, and these, as well as previous reports on high hyperdiploid childhood ALL, are reviewed herein.
Collapse
Affiliation(s)
- Kajsa Paulsson
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden.
| | | |
Collapse
|
14
|
Paulsson K, Horvat A, Strömbeck B, Nilsson F, Heldrup J, Behrendtz M, Forestier E, Andersson A, Fioretos T, Johansson B. Mutations of FLT3, NRAS, KRAS, and PTPN11 are frequent and possibly mutually exclusive in high hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer 2008; 47:26-33. [PMID: 17910045 DOI: 10.1002/gcc.20502] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Although it has been suggested that mutations of the FLT3, NRAS, KRAS, and PTPN11 genes are particularly frequent in high hyperdiploid (>50 chromosomes) pediatric acute lymphoblastic leukemias (ALLs), this has as yet not been confirmed in a large patient cohort. Furthermore, it is unknown whether mutations of these genes coexist in hyperdiploid cases. We performed mutation analyses of FLT3, NRAS, KRAS, and PTPN11 in a consecutive series of 78 high hyperdiploid ALLs. Twenty-six (33%) of the cases harbored a mutation, comprising six activating point mutations and one internal tandem duplication of FLT3 (7/78 cases; 9.0%), eight codon 12, 13, or 61 NRAS mutations (8/78 cases; 10%), five codon 12 or 13 KRAS mutations (5/78 cases, 6.4%), and seven exon 3 or 13 PTPN11 mutations (7/78 cases; 9.0%). No association was seen between the presence of a mutation in FLT3, NRAS, KRAS, or PTPN11 and gender, age, white blood cell count, or relapse, suggesting that they do not confer a negative prognostic impact. Only one case harbored mutations in two different genes, suggesting that mutations of these four genes are generally mutually exclusive. In total, one third of the cases harbored a FLT3, NRAS, KRAS, or PTPN11 mutation, identifying the RTK-RAS signaling pathway as a potential target for novel therapies of high hyperdiploid pediatric ALLs.
Collapse
Affiliation(s)
- Kajsa Paulsson
- Department of Clinical Genetics, University Hospital, Lund, Sweden
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Forestier E, Gauffin F, Andersen MK, Autio K, Borgström G, Golovleva I, Gustafsson B, Heim S, Heinonen K, Heyman M, Hovland R, Johannsson JH, Kerndrup G, Rosenquist R, Schoumans J, Swolin B, Johansson B, Nordgren A. Clinical and cytogenetic features of pediatric dic(9;20)(p13.2;q11.2)-positive B-cell precursor acute lymphoblastic leukemias: A nordic series of 24 cases and review of the literature. Genes Chromosomes Cancer 2008; 47:149-58. [DOI: 10.1002/gcc.20517] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
|
16
|
Ling ZQ, Sugihara H, Tatsuta T, Mukaisho KI, Hattori T. Optimization of comparative expressed sequence hybridization for genome-wide expression profiling at chromosome level. ACTA ACUST UNITED AC 2007; 175:144-53. [PMID: 17556071 DOI: 10.1016/j.cancergencyto.2007.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 02/23/2007] [Accepted: 02/28/2007] [Indexed: 11/28/2022]
Abstract
Comparative expressed sequence hybridization (CESH) has recently been developed for global expression profiling at chromosome level. To improve its specificity and sensitivity, we examined the effects of cDNA amplification and labeling methods on CESH profiles, using a gastric cancer cell line, Kato III, and compared the CESH profiles to cDNA microarray and reverse transcriptase-polymerase chain reaction (RT-PCR) data. CESH results were scarcely affected by the amplification process, either at the RNA level with T7 polymerase or at the cDNA level with degenerate oligonucleotide-primed PCR (DOP-PCR). The labeling method, however, did remarkably affect the CESH results; false positive shifts of the test/reference ratio (T/R) were not detected in self-matched CESH with pre-cDNA labeling and random priming labeling of cDNA but were consistently seen with DOP-PCR labeling in 11 chromosomes. The use of cDNA deriving from mRNA either with pre-cDNA or random priming labeling gave results of higher detection sensitivity for regions of up- or downregulated expression and higher concordance with the microarray and RT-PCR data in the corresponding regions than with conventional CESH. This modification of CESH with random priming labeling was found feasible by its application to Kato III cells with and without 5-aza-2'-deoxycytidine treatment; the regions identified as epigenetically silenced included genes that were reportedly methylated in Kato III.
Collapse
Affiliation(s)
- Zhi-Qiang Ling
- First Department of Pathology, Shiga University of Medical Science, Otsu, 520-2192 Japan
| | | | | | | | | |
Collapse
|
17
|
Paulsson K, Heidenblad M, Mörse H, Borg A, Fioretos T, Johansson B. Identification of cryptic aberrations and characterization of translocation breakpoints using array CGH in high hyperdiploid childhood acute lymphoblastic leukemia. Leukemia 2006; 20:2002-7. [PMID: 16990785 DOI: 10.1038/sj.leu.2404372] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High hyperdiploidy, characterized by non-random trisomies, is the largest cytogenetic subgroup in childhood acute lymphoblastic leukemia (ALL). It is not known whether the gained chromosomes are sufficient for leukemogenesis or if additional genetic aberrations are necessary. However, the suboptimal chromosome morphology of hyperdiploid ALLs makes detection of structural abnormalities difficult if using cytogenetic techniques; alternative methods are, therefore, needed. We performed array comparative genome hybridization (CGH) analyses, with a resolution of 100 kb, of eight cases of high hyperdiploid childhood ALL to characterize structural abnormalities found with G-banding/multicolor fluorescence in situ hybridization (FISH) and to detect novel changes. The non-centromeric breakpoints of four rearrangements, including three translocations and one 1q duplication, were narrowed down to <0.2 Mb. Furthermore, four submicroscopic imbalances involving 0.6-2.7 Mb were detected, comprising two segmental duplications involving 1q22 and 12q24.31 in one case and two hemizygous deletions in 12p13.2-31 - including ETV6 - and in 13q32.3-33.1 in another case. Notably, FISH analysis of the latter revealed an associated reciprocal t(3;13)(q?;32.2-33.1). In conclusion, the array CGH analyses revealed putative leukemia-associated submicroscopic imbalances and rearrangements in 2/8 (25%) hyperdiploid ALLs. The detection and characterization of these additional genetic aberrations will most likely increase our understanding of the pathogenesis of high hyperdiploid childhood ALL.
Collapse
Affiliation(s)
- K Paulsson
- Department of Clinical Genetics, Lund University Hospital, Sweden.
| | | | | | | | | | | |
Collapse
|
18
|
Schubert F, Tausch B, Joos S, Eils R. CGH-Profiler: Data mining based on genomic aberration profiles. BMC Bioinformatics 2005; 6:188. [PMID: 16042799 PMCID: PMC1183191 DOI: 10.1186/1471-2105-6-188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Accepted: 07/25/2005] [Indexed: 01/18/2023] Open
Abstract
Background CGH-Profiler is a program that supports the analysis of genomic aberrations measured by Comparative Genomic Hybridisation (CGH). Comparative genomic hybridisation (CGH) is a well-established, molecular cytogenetic method that allows the detection of chromosomal imbalances in entire genomes. This technique is widely used in routine molecular diagnostics. Typically, chromosomal imbalances are described in a complex syntax based on the International Standard for Cytogenetic Nomenclature (ISCN). This semantic description of chromosomal imbalances hinders a large-scale statistical analysis across different experiments, e.g. for finding aberration patterns associated with a particular disease type or state. Results CGH-Profiler circumvents the semantic ISCN description by importing data from different CGH system vendors and by directly transferring the data into a table format that is readily accessible for subsequent statistical analysis. CGH-profiler comes with different consistency checks, calculates various statistics and automatically assigns a median copy number ratio to each chromosomal band. Import of CGH profiles from different CGH system vendors is already supported; its extension to other systems can be readily achieved through Perl scripts. CGH profiler can also be used to analyse comparative expressed sequence hybridisation (CESH) data. CESH reveals gene expression patterns according to chromosomal locations in a similar manner as CGH detects chromosomal imbalances. Conclusion CGH-Profiler is a useful tool for processing of CGH and CESH data.
Collapse
Affiliation(s)
- Falk Schubert
- Theoretical Bioinformatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Bernhard Tausch
- Theoretical Bioinformatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Current address: Research Group Information Systems and Semantic Web, Institute for Computer Science, University of Koblenz-Landau, Universitätsstraße 1 56070 Koblenz, Germany
| | - Stefan Joos
- Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Roland Eils
- Theoretical Bioinformatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| |
Collapse
|
19
|
Kearney L, Horsley SW. Molecular cytogenetics in haematological malignancy: current technology and future prospects. Chromosoma 2005; 114:286-94. [PMID: 16003502 DOI: 10.1007/s00412-005-0002-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 04/25/2005] [Accepted: 04/25/2005] [Indexed: 01/22/2023]
Abstract
Cytogenetics has played a pivotal role in haematological malignancy, both as an aid to diagnosis and in identifying recurrent chromosomal rearrangements, an essential prerequisite to identifying genes involved in leukaemia and lymphoma pathogenesis. In the late 1980s, a series of technologies based around fluorescence in situ hybridisation (FISH) revolutionised the field. Interphase FISH, multiplex-FISH (M-FISH, SKY) and comparative genomic hybridisation (CGH) have emerged as the most significant of these. More recently, microarray technologies have come to prominence. In the acute leukaemias, the finding of characteristic gene expression signatures corresponding to biological subgroups has heralded gene expression profiling as a possible future alternative to current cytogenetic and morphological methods for diagnosis. In the lymphomas, high-resolution array CGH has successfully identified new regions of deletion and amplification, providing the prospect of disease-specific arrays.
Collapse
Affiliation(s)
- Lyndal Kearney
- Section of Haemato-Oncology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | | |
Collapse
|
20
|
Paulsson K, Mörse H, Fioretos T, Behrendtz M, Strömbeck B, Johansson B. Evidence for a single-step mechanism in the origin of hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer 2005; 44:113-22. [PMID: 15942938 DOI: 10.1002/gcc.20222] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
High hyperdiploidy (>50 chromosomes) in childhood acute lymphoblastic leukemia (ALL) is characterized by nonrandom multiple trisomies and tetrasomies involving in particular chromosomes X, 4, 6, 8, 10, 14, 17, 18, and 21. This characteristic karyotypic pattern, the most common in pediatric ALL, may arise via a tetraploid state with subsequent loss of chromosomes, by sequential gains of chromosomes in consecutive cell divisions, or by simultaneous gain of chromosomes in a single mitosis. These alternatives may be distinguished by investigation of the allelic ratios of loci on the tetrasomic and disomic chromosomes. Previous studies of tetrasomy 21 and of the occurrence of uniparental disomies (UPDs) have suggested that the most likely mechanism is simultaneous gain. However, the other pathways have not been definitely excluded because complete analyses of all disomies and tetrasomies have never been performed. In the present study, we investigated 27 hyperdiploid ALLs by using 58 polymorphic microsatellite markers mapped to 23 of the 24 human chromosomes. Twenty-six tetrasomies were analyzed (involving chromosomes X, 8, 10, 14, 18, and 21), and the frequency of UPDs was determined in 10 cases. In total, 200 chromosomes were studied. Equal allele dosage was observed in 24 of 26 tetrasomies, and only 7 UPDs were found. These data strongly suggest that hyperdiploidy in childhood ALL generally arises by a simultaneous gain of all additional chromosomes in a single abnormal mitosis.
Collapse
Affiliation(s)
- Kajsa Paulsson
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden.
| | | | | | | | | | | |
Collapse
|