1
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Baens M, Stirparo R, Lampi Y, Verbeke D, Vandepoel R, Cools J, Marynen P, de Bock CE, Bornschein S. Malt1 self-cleavage is critical for regulatory T cell homeostasis and anti-tumor immunity in mice. Eur J Immunol 2018; 48:1728-1738. [PMID: 30025160 PMCID: PMC6220888 DOI: 10.1002/eji.201847597] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/04/2018] [Accepted: 07/13/2018] [Indexed: 12/31/2022]
Abstract
Mucosa-associated lymphoid tissue 1 (Malt1) regulates immune cell function by mediating the activation of nuclear factor κB (NF-κB) signaling through both its adaptor and proteolytic function. Malt1 is also a target of its own protease activity and this self-cleavage further contributes to NF-κB activity. Until now, the functional distinction between Malt1 self-cleavage and its general protease function in regulating NF-κB signaling and immune activation remained unclear. Here we demonstrate, using a new mouse model, the importance of Malt1 self-cleavage in regulating expression of NF-κB target genes and subsequent T cell activation. Significantly, we further establish that Treg homeostasis is critically linked to Malt1 function via a Treg intrinsic and extrinsic mechanism. TCR-mediated Malt1 proteolytic activity and self-cleavage was found to drive Il2 expression in conventional CD4+ T cells, thereby regulating Il2 availability for Treg homeostasis. Remarkably, the loss of Malt1-mediated self-cleavage alone was sufficient to cause a significant Treg deficit resulting in increased anti-tumor immune reactivity without associated autoimmunity complications. These results establish for the first time that inhibition of MALT1 proteolytic activity could be a viable therapeutic strategy to augment anti-tumor immunity.
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Affiliation(s)
- Mathijs Baens
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Cistim Leuven vzwLeuvenBelgium
| | - Rocco Stirparo
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | - Youlia Lampi
- Switch LaboratoryVIBLeuvenBelgium
- KU Leuven Department for Cellular and MolecularLeuvenBelgium
| | - Delphine Verbeke
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | - Roel Vandepoel
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | - Jan Cools
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | | | - Charles E. de Bock
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | - Simon Bornschein
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
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2
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van de Werken HJG, Haan JC, Feodorova Y, Bijos D, Weuts A, Theunis K, Holwerda SJB, Meuleman W, Pagie L, Thanisch K, Kumar P, Leonhardt H, Marynen P, van Steensel B, Voet T, de Laat W, Solovei I, Joffe B. Small chromosomal regions position themselves autonomously according to their chromatin class. Genome Res 2017; 27:922-933. [PMID: 28341771 PMCID: PMC5453326 DOI: 10.1101/gr.213751.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/22/2017] [Indexed: 11/24/2022]
Abstract
The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes.
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Affiliation(s)
- Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute & Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands.,Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Josien C Haan
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Dominika Bijos
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - An Weuts
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Koen Theunis
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Sjoerd J B Holwerda
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Wouter Meuleman
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Parveen Kumar
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Boris Joffe
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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3
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Vermeesch JR, Melotte C, Froyen G, Van Vooren S, Dutta B, Maas N, Vermeulen S, Menten B, Speleman F, De Moor B, Van Hummelen P, Marynen P, Fryns JP, Devriendt K. Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2016; 53:413-22. [PMID: 15750031 DOI: 10.1369/jhc.4a6436.2005] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Array CGH (comparative genomic hybridization) enables the identification of chromosomal copy number changes. The availability of clone sets covering the human genome opens the possibility for the widespread use of array CGH for both research and diagnostic purposes. In this manuscript we report on the parameters that were critical for successful implementation of the technology, assess quality criteria, and discuss the potential benefits and pitfalls of the technology for improved pre- and postnatal constitutional genetic diagnosis. We propose to name the genome-wide array CGH “molecular karyotyping,” in analogy with conventional karyotyping that uses staining methods to visualize chromosomes.
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4
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Fieremans N, Van Esch H, Holvoet M, Van Goethem G, Devriendt K, Rosello M, Mayo S, Martinez F, Jhangiani S, Muzny DM, Gibbs RA, Lupski JR, Vermeesch JR, Marynen P, Froyen G. Identification of Intellectual Disability Genes in Female Patients with a Skewed X-Inactivation Pattern. Hum Mutat 2016; 37:804-11. [PMID: 27159028 DOI: 10.1002/humu.23012] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 12/30/2022]
Abstract
Intellectual disability (ID) is a heterogeneous disorder with an unknown molecular etiology in many cases. Previously, X-linked ID (XLID) studies focused on males because of the hemizygous state of their X chromosome. Carrier females are generally unaffected because of the presence of a second normal allele, or inactivation of the mutant X chromosome in most of their cells (skewing). However, in female ID patients, we hypothesized that the presence of skewing of X-inactivation would be an indicator for an X chromosomal ID cause. We analyzed the X-inactivation patterns of 288 females with ID, and found that 22 (7.6%) had extreme skewing (>90%), which is significantly higher than observed in the general population (3.6%; P = 0.029). Whole-exome sequencing of 19 females with extreme skewing revealed causal variants in six females in the XLID genes DDX3X, NHS, WDR45, MECP2, and SMC1A. Interestingly, variants in genes escaping X-inactivation presumably cause both XLID and skewing of X-inactivation in three of these patients. Moreover, variants likely accounting for skewing only were detected in MED12, HDAC8, and TAF9B. All tested candidate causative variants were de novo events. Hence, extreme skewing is a good indicator for the presence of X-linked variants in female patients.
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Affiliation(s)
- Nathalie Fieremans
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium.,Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Maureen Holvoet
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Gert Van Goethem
- Het GielsBos, Gierle, Belgium and Department of Neurology, University Hospital of Antwerp (UZA), Antwerp, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Monica Rosello
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Sonia Mayo
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Francisco Martinez
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas
| | - Joris R Vermeesch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium
| | - Guy Froyen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium
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5
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Callaerts-Vegh Z, Ahmed T, Vermaercke B, Marynen P, Balschun D, Froyen G, D'Hooge R. Nxf7 deficiency impairs social exploration and spatio-cognitive abilities as well as hippocampal synaptic plasticity in mice. Front Behav Neurosci 2015. [PMID: 26217206 PMCID: PMC4498129 DOI: 10.3389/fnbeh.2015.00179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nuclear RNA export factors (NXF) are conserved in all metazoans and are deemed essential for shuttling RNA across the nuclear envelope and other post-transcriptional processes (such as mRNA metabolism, storage and stability). Disruption of human NXF5 has been implicated in intellectual and psychosocial disabilities. In the present report, we use recently described Nxf7 knockout (KO) mice as an experimental model to analyze in detail the behavioral consequences of clinical NXF5 deficiency. We examined male Nxf7 KO mice using an extended cognitive and behavioral test battery, and recorded extracellular field potentials in the hippocampal CA1 region. We observed various cognitive and behavioral changes including alterations in social exploration, impaired spatial learning and spatio-cognitive abilities. We also defined a new experimental paradigm to discriminate search strategies in Morris water maze and showed significant differences between Nxf7 KO and control animals. Furthermore, while we observed no difference in a nose poke suppression in an conditioned emotional response (CER) protocol, Nxf7 KO mice were impaired in discriminating between differentially reinforced cues in an auditory fear conditioning protocol. This distinct neurocognitive phenotype was accompanied by impaired hippocampal Long-term potentiation (LTP), while long-term depression (LTD) was not affected by Nxf7 deficiency. Our data demonstrate that disruption of murine Nxf7 leads to behavioral phenotypes that may relate to the intellectual and social deficits in patients with NXF5 deficiency.
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Affiliation(s)
| | - Tariq Ahmed
- Laboratory of Biological Psychology, University of Leuven, KU Leuven Leuven, Belgium
| | - Ben Vermaercke
- Laboratory of Biological Psychology, University of Leuven, KU Leuven Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, University of Leuven and VIB Center for the Biology of Disease Leuven, Belgium
| | - Detlef Balschun
- Laboratory of Biological Psychology, University of Leuven, KU Leuven Leuven, Belgium
| | - Guy Froyen
- Human Genome Laboratory, University of Leuven and VIB Center for the Biology of Disease Leuven, Belgium
| | - Rudi D'Hooge
- Laboratory of Biological Psychology, University of Leuven, KU Leuven Leuven, Belgium
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6
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Baens M, Bonsignore L, Somers R, Vanderheydt C, Weeks SD, Gunnarsson J, Nilsson E, Roth RG, Thome M, Marynen P. MALT1 auto-proteolysis is essential for NF-κB-dependent gene transcription in activated lymphocytes. PLoS One 2014; 9:e103774. [PMID: 25105596 PMCID: PMC4126661 DOI: 10.1371/journal.pone.0103774] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 07/03/2014] [Indexed: 11/30/2022] Open
Abstract
Mucosa-associated lymphoid tissue 1 (MALT1) controls antigen receptor–mediated signalling to nuclear factor κB (NF-κB) through both its adaptor and protease function. Upon antigen stimulation, MALT1 forms a complex with BCL10 and CARMA1, which is essential for initial IκBα phosphorylation and NF-κB nuclear translocation. Parallel induction of MALT1 protease activity serves to inactivate negative regulators of NF-κB signalling, such as A20 and RELB. Here we demonstrate a key role for auto-proteolytic MALT1 cleavage in B- and T-cell receptor signalling. MALT1 cleavage occurred after Arginine 149, between the N-terminal death domain and the first immunoglobulin-like region, and did not affect its proteolytic activity. Jurkat T cells expressing an un-cleavable MALT1-R149A mutant showed unaltered initial IκBα phosphorylation and normal nuclear accumulation of NF-κB subunits. Nevertheless, MALT1 cleavage was required for optimal activation of NF-κB reporter genes and expression of the NF-κB targets IL-2 and CSF2. Transcriptome analysis confirmed that MALT1 cleavage after R149 was required to induce NF-κB transcriptional activity in Jurkat T cells. Collectively, these data demonstrate that auto-proteolytic MALT1 cleavage controls antigen receptor-induced expression of NF-κB target genes downstream of nuclear NF-κB accumulation.
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Affiliation(s)
- Mathijs Baens
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Center for Human Genetics, KU Leuven, Leuven, Belgium
- * E-mail:
| | - Luca Bonsignore
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Riet Somers
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Charlotte Vanderheydt
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Stephen D. Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jenny Gunnarsson
- Reagent and Assay Development, Discovery Sciences, Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Ewa Nilsson
- Reagent and Assay Development, Discovery Sciences, Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Robert G. Roth
- Reagent and Assay Development, Discovery Sciences, Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Margot Thome
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Peter Marynen
- Human Genome Laboratory, Center for Human Genetics, KU Leuven, Leuven, Belgium
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7
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Fieremans N, Bauters M, Belet S, Verbeeck J, Jansen AC, Seneca S, Roelens F, De Baere E, Marynen P, Froyen G. De novo MECP2 duplications in two females with intellectual disability and unfavorable complete skewed X-inactivation. Hum Genet 2014; 133:1359-67. [DOI: 10.1007/s00439-014-1469-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/09/2014] [Indexed: 12/11/2022]
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8
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Bauters M, Frints SG, Van Esch H, Spruijt L, Baldewijns MM, de Die-Smulders CEM, Fryns JP, Marynen P, Froyen G. Evidence for increased SOX3 dosage as a risk factor for X-linked hypopituitarism and neural tube defects. Am J Med Genet A 2014; 164A:1947-52. [PMID: 24737742 DOI: 10.1002/ajmg.a.36580] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/24/2014] [Indexed: 11/09/2022]
Abstract
Genomic duplications of varying lengths at Xq26-q27 involving SOX3 have been described in families with X-linked hypopituitarism. Using array-CGH we detected a 1.1 Mb microduplication at Xq27 in a large family with three males suffering from X-linked hypopituitarism. The duplication was mapped from 138.7 to 139.8 Mb, harboring only two annotated genes, SOX3 and ATP11C, and was shown to be a direct tandem copy number gain. Unexpectedly, the microduplication did not fully segregate with the disease in this family suggesting that SOX3 duplications have variable penetrance for X-linked hypopituitarism. In the same family, a female fetus presenting with a neural tube defect was also shown to carry the SOX3 copy number gain. Since we also demonstrated increased SOX3 mRNA levels in amnion cells derived from an unrelated t(X;22)(q27;q11) female fetus with spina bifida, we propose that increased levels of SOX3 could be a risk factor for neural tube defects.
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Affiliation(s)
- Marijke Bauters
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium; Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
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9
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Vandewalle J, Langen M, Zschaetzsch M, Nijhof B, Kramer JM, Brems H, Bauters M, Lauwers E, Srahna M, Marynen P, Verstreken P, Schenck A, Hassan BA, Froyen G. Ubiquitin ligase HUWE1 regulates axon branching through the Wnt/β-catenin pathway in a Drosophila model for intellectual disability. PLoS One 2013; 8:e81791. [PMID: 24303071 PMCID: PMC3841167 DOI: 10.1371/journal.pone.0081791] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/26/2013] [Indexed: 12/11/2022] Open
Abstract
We recently reported that duplication of the E3 ubiquitin ligase HUWE1 results in intellectual disability (ID) in male patients. However, the underlying molecular mechanism remains unknown. We used Drosophila melanogaster as a model to investigate the effect of increased HUWE1 levels on the developing nervous system. Similar to the observed levels in patients we overexpressed the HUWE1 mRNA about 2-fold in the fly. The development of the mushroom body and neuromuscular junctions were not altered, and basal neurotransmission was unaffected. These data are in agreement with normal learning and memory in the courtship conditioning paradigm. However, a disturbed branching phenotype at the axon terminals of the dorsal cluster neurons (DCN) was detected. Interestingly, overexpression of HUWE1 was found to decrease the protein levels of dishevelled (dsh) by 50%. As dsh as well as Fz2 mutant flies showed the same disturbed DCN branching phenotype, and the constitutive active homolog of β-catenin, armadillo, could partially rescue this phenotype, our data strongly suggest that increased dosage of HUWE1 compromises the Wnt/β-catenin pathway possibly by enhancing the degradation of dsh.
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Affiliation(s)
- Joke Vandewalle
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marion Langen
- Laboratory of Neurogenetics, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Marlen Zschaetzsch
- Laboratory of Neurogenetics, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Bonnie Nijhof
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour & Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jamie M. Kramer
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour & Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hilde Brems
- Laboratory for Neurofibromatosis Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marijke Bauters
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Elsa Lauwers
- Laboratory of Neuronal Communication, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Mohammed Srahna
- Laboratory of Neurogenetics, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Patrik Verstreken
- Laboratory of Neuronal Communication, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Annette Schenck
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour & Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bassem A. Hassan
- Laboratory of Neurogenetics, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
- * E-mail: (GF); (BAH)
| | - Guy Froyen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
- * E-mail: (GF); (BAH)
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10
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Vandewalle J, Bauters M, Van Esch H, Belet S, Verbeeck J, Fieremans N, Holvoet M, Vento J, Spreiz A, Kotzot D, Haberlandt E, Rosenfeld J, Andrieux J, Delobel B, Dehouck MB, Devriendt K, Fryns JP, Marynen P, Goldstein A, Froyen G. The mitochondrial solute carrier SLC25A5 at Xq24 is a novel candidate gene for non-syndromic intellectual disability. Hum Genet 2013; 132:1177-85. [PMID: 23783460 DOI: 10.1007/s00439-013-1322-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 05/30/2013] [Indexed: 11/28/2022]
Abstract
Loss-of-function mutations in several different neuronal pathways have been related to intellectual disability (ID). Such mutations often are found on the X chromosome in males since they result in functional null alleles. So far, microdeletions at Xq24 reported in males always have been associated with a syndromic form of ID due to the loss of UBE2A. Here, we report on overlapping microdeletions at Xq24 that do not include UBE2A or affect its expression, in patients with non-syndromic ID plus some additional features from three unrelated families. The smallest region of overlap, confirmed by junction sequencing, harbors two members of the mitochondrial solute carrier family 25, SLC25A5 and SLC25A43. However, identification of an intragenic microdeletion including SLC25A43 but not SLC25A5 in a healthy boy excluded a role for SLC25A43 in cognition. Therefore, our findings point to SLC25A5 as a novel gene for non-syndromic ID. This highly conserved gene is expressed ubiquitously with high levels in cortex and hippocampus, and a presumed role in mitochondrial exchange of ADP/ATP. Our data indicate that SLC25A5 is involved in memory formation or establishment, which could add mitochondrial processes to the wide array of pathways that regulate normal cognitive functions.
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Affiliation(s)
- Joke Vandewalle
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
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11
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Vanmarsenille L, Verbeeck J, Belet S, Roebroek AJ, Van de Putte T, Nevelsteen J, Callaerts-Vegh Z, D’Hooge R, Marynen P, Froyen G. Generation and characterization of an Nxf7 knockout mouse to study NXF5 deficiency in a patient with intellectual disability. PLoS One 2013; 8:e64144. [PMID: 23675524 PMCID: PMC3652825 DOI: 10.1371/journal.pone.0064144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/09/2013] [Indexed: 12/11/2022] Open
Abstract
Members of the Nuclear eXport Factor (NXF) family are involved in the export of mRNA from the nucleus to the cytoplasm, or hypothesized to play a role in transport of cytoplasmic mRNA. We previously reported on the loss of NXF5 in a male patient with a syndromic form of intellectual disability. To study the functional role of NXF5 we identified the mouse counterpart. Based on synteny, mouse Nxf2 is the ortholog of human NXF5. However, we provide several lines of evidence that mouse Nxf7 is the actual functional equivalent of NXF5. Both Nxf7 and NXF5 are predominantly expressed in the brain, show cytoplasmic localization, and present as granules in neuronal dendrites suggesting a role in cytoplasmic mRNA metabolism in neurons. Nxf7 was primarily detected in the pyramidal cells of the hippocampus and in layer V of the cortex. Similar to human NXF2, mouse Nxf2 is highly expressed in testis and shows a nuclear localization. Interestingly, these findings point to a different evolutionary path for both NXF genes in human and mouse. We thus generated and validated Nxf7 knockout mice, which were fertile and did not present any gross anatomical or morphological abnormalities. Expression profiling in the hippocampus and the cortex did not reveal significant changes between wild-type and Nxf7 knockout mice. However, impaired spatial memory was observed in these KO mice when evaluated in the Morris water maze test. In conclusion, our findings provide strong evidence that mouse Nxf7 is the functional counterpart of human NXF5, which might play a critical role in mRNA metabolism in the brain.
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Affiliation(s)
- Lieselot Vanmarsenille
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jelle Verbeeck
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stefanie Belet
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Anton J. Roebroek
- Experimental Mouse Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tom Van de Putte
- Laboratory of Molecular Biology (Celgen), Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joke Nevelsteen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Rudi D’Hooge
- Laboratory of Biological Psychology, KU Leuven, Leuven, Belgium
- Leuven Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Guy Froyen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
- * E-mail:
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12
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Weuts A, Voet T, Verbeeck J, Lambrechts N, Wirix E, Schoonjans L, Danloy S, Marynen P, Froyen G. Telomere length homeostasis and telomere position effect on a linear human artificial chromosome are dictated by the genetic background. Nucleic Acids Res 2012; 40:11477-89. [PMID: 23066103 PMCID: PMC3526267 DOI: 10.1093/nar/gks926] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Telomere position effect (TPE) is the influence of telomeres on subtelomeric epigenetic marks and gene expression. Previous studies suggested that TPE depends on genetic background. As these analyses were performed on different chromosomes, cell types and species, it remains unclear whether TPE represents a chromosome—rather than genetic background-specific regulation. We describe the development of a Linear Human Artificial Chromosome (L-HAC) as a new tool for telomere studies. The L-HAC was generated through the Cre-loxP-mediated addition of telomere ends to an existing circular HAC (C-HAC). As it can be transferred to genetically distinct cell lines and animal models the L-HAC enables the study of TPE in an unprecedented manner. The HAC was relocated to four telomerase-positive cell lines via microcell-mediated chromosome transfer and subsequently to mice via blastocyst injection of L-HAC+-ES-cells. We could show consistent genetic background-dependent adaptation of telomere length and telomere-associated de novo subtelomeric DNA methylation in mouse ES-R1 cells as well as in mice. Expression of the subtelomeric neomycin gene was inversely correlated with telomere length and subtelomeric methylation. We thus provide a new tool for functional telomere studies and provide strong evidence that telomere length, subtelomeric chromatin marks and expression of subtelomeric genes are genetic background dependent.
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Affiliation(s)
- An Weuts
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
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13
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Froyen G, Belet S, Martinez F, Santos-Rebouças C, Declercq M, Verbeeck J, Donckers L, Berland S, Mayo S, Rosello M, Pimentel M, Fintelman-Rodrigues N, Hovland R, Rodrigues dos Santos S, Raymond F, Bose T, Corbett M, Sheffield L, van Ravenswaaij-Arts C, Dijkhuizen T, Coutton C, Satre V, Siu V, Marynen P. Copy-number gains of HUWE1 due to replication- and recombination-based rearrangements. Am J Hum Genet 2012; 91:252-64. [PMID: 22840365 DOI: 10.1016/j.ajhg.2012.06.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 05/21/2012] [Accepted: 06/21/2012] [Indexed: 12/20/2022] Open
Abstract
We previously reported on nonrecurrent overlapping duplications at Xp11.22 in individuals with nonsyndromic intellectual disability (ID) harboring HSD17B10, HUWE1, and the microRNAs miR-98 and let-7f-2 in the smallest region of overlap. Here, we describe six additional individuals with nonsyndromic ID and overlapping microduplications that segregate in the families. High-resolution mapping of the 12 copy-number gains reduced the minimal duplicated region to the HUWE1 locus only. Consequently, increased mRNA levels were detected for HUWE1, but not HSD17B10. Marker and SNP analysis, together with identification of two de novo events, suggested a paternally derived intrachromosomal duplication event. In four independent families, we report on a polymorphic 70 kb recurrent copy-number gain, which harbors part of HUWE1 (exon 28 to 3' untranslated region), including miR-98 and let-7f-2. Our findings thus demonstrate that HUWE1 is the only remaining dosage-sensitive gene associated with the ID phenotype. Junction and in silico analysis of breakpoint regions demonstrated simple microhomology-mediated rearrangements suggestive of replication-based duplication events. Intriguingly, in a single family, the duplication was generated through nonallelic homologous recombination (NAHR) with the use of HUWE1-flanking imperfect low-copy repeats, which drive this infrequent NAHR event. The recurrent partial HUWE1 copy-number gain was also generated through NAHR, but here, the homologous sequences used were identified as TcMAR-Tigger DNA elements, a template that has not yet been reported for NAHR. In summary, we showed that an increased dosage of HUWE1 causes nonsyndromic ID and demonstrated that the Xp11.22 region is prone to recombination- and replication-based rearrangements.
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14
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Dewaele B, Floris G, Finalet-Ferreiro J, Fletcher CD, Coindre JM, Guillou L, Hogendoorn PCW, Wozniak A, Vanspauwen V, Schöffski P, Marynen P, Vandenberghe P, Sciot R, Debiec-Rychter M. Coactivated platelet-derived growth factor receptor {alpha} and epidermal growth factor receptor are potential therapeutic targets in intimal sarcoma. Cancer Res 2010; 70:7304-14. [PMID: 20685895 DOI: 10.1158/0008-5472.can-10-1543] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Intimal sarcoma (IS) is a rare, malignant, and aggressive tumor that shows a relentless course with a concomitant low survival rate and for which no effective treatment is available. In this study, 21 cases of large arterial blood vessel IS were analyzed by immunohistochemistry and fluorescence in situ hybridization and selectively by karyotyping, array comparative genomic hybridization, sequencing, phospho-kinase antibody arrays, and Western immunoblotting in search for novel diagnostic markers and potential molecular therapeutic targets. Ex vivo immunoassays were applied to test the sensitivity of IS primary tumor cells to the receptor tyrosine kinase (RTK) inhibitors imatinib and dasatinib. We showed that amplification of platelet-derived growth factor receptor α (PDGFRA) is a common finding in IS, which should be considered as a molecular hallmark of this entity. This amplification is consistently associated with PDGFRA activation. Furthermore, the tumors reveal persistent activation of the epidermal growth factor receptor (EGFR), concurrent to PDGFRA activation. Activated PDGFRA and EGFR frequently coexist with amplification and overexpression of the MDM2 oncogene. Ex vivo immunoassays on primary IS cells from one case showed the potency of dasatinib to inhibit PDGFRA and downstream signaling pathways. Our findings provide a rationale for investigating therapies that target PDGFRA, EGFR, or MDM2 in IS. Given the clonal heterogeneity of this tumor type and the potential cross-talk between the PDGFRA and EGFR signaling pathways, targeting multiple RTKs and aberrant downstream effectors might be required to improve the therapeutic outcome for patients with this disease.
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Affiliation(s)
- Barbara Dewaele
- Department of Human Genetics, University of Leuven, Herestraat 49, B-3000 Leuven, Belgium
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15
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Van Roosbroeck K, Cools J, Dierickx D, Thomas J, Vandenberghe P, Stul M, Delabie J, De Wolf-Peeters C, Marynen P, Wlodarska I. ALK-positive large B-cell lymphomas with cryptic SEC31A-ALK and NPM1-ALK fusions. Haematologica 2010; 95:509-13. [PMID: 20207848 DOI: 10.3324/haematol.2009.014761] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We report 2 ALK-positive large B-cell lymphoma cases showing granular cytoplasmic and cytoplasmic/nuclear ALK immunostaining in which cryptic ALK rearrangements were identified by fluorescent in situ hybridization and molecular analysis. In the first case, the ALK-involving t(2;3)(p23;q27) masked the cryptic SEC31A-ALK fusion generated by an insertion of the 5' end of SEC31A (4q21) upstream of the 3' end of ALK. This rearrangement was associated with loss of the 5' end of ALK and duplication of SEC31A-ALK on der(20). In the second case with complex rearrangements of both chromosomes 2, a submicroscopic NPM1-ALK fusion created by insertion of the 3' end of ALK into the NPM1 locus was evidenced. Further studies of SEC31A-ALK showed that this variant fusion transforms IL3-dependent Ba/F3 cells to growth factor independence, and that the ALK inhibitor TAE-684 reduces cell proliferation and kinase activity of SEC31A-ALK and its downstream effectors ERK1/2, AKT, STAT3 and STAT5.
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Affiliation(s)
- Katrien Van Roosbroeck
- Center for Human Genetics, K.U. Leuven, Gasthuisberg, Herestraat 49, Box 602, B-3000 Leuven, Belgium
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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Affiliation(s)
- Xavier Sagaert
- Section of Morphology and Molecular Pathology, Department of Pathology, Katholieke Universiteit Leuven, Leuven, Belgium.
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17
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Froyen G, Govaerts K, Van Esch H, Verbeeck J, Tuomi ML, Heikkilä H, Torniainen S, Devriendt K, Fryns JP, Marynen P, Järvelä I, Ala-Mello S. Novel PORCN mutations in focal dermal hypoplasia. Clin Genet 2009; 76:535-43. [PMID: 19863546 DOI: 10.1111/j.1399-0004.2009.01248.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Focal dermal hypoplasia (FDH), Goltz or Goltz-Gorlin syndrome, is an X-linked dominant multisystem disorder characterized primarily by involvement of the skin, skeletal system and eyes. We screened for mutations in the PORCN gene in eight patients of Belgian and Finnish origin with firm clinical suspicion of FDH. First, we performed quantitative PCR (qPCR) analysis to define the copy number at this locus. Next, we sequenced the coding regions and flanking intronic sequences of the PORCN gene. Three de novo mutations were identified in our patients with FDH: a 150-kb deletion removing six genes including PORCN, as defined by qPCR and X-array-CGH, and two heterozygous missense mutations; c.992T>G (p.L331R) in exon 11 and c.1094G>A (p.R365Q) in exon 13 of the gene. Both point mutations changed highly conserved amino acids and were not found in 300 control X chromosomes. The three patients in whom mutations were identified all present with characteristic dermal findings together with limb manifestations, which were not seen in our mutation-negative patients. The clinical characteristics of our patients with PORCN mutations were compared with the previously reported mutation-positive cases. In this report, we summarize the literature on PORCN mutations and associated phenotypes.
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Affiliation(s)
- G Froyen
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, VIB, 3000 Leuven, Belgium.
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18
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Van Loo P, Tousseyn T, Vanhentenrijk V, Dierickx D, Malecka A, Vanden Bempt I, Verhoef G, Delabie J, Marynen P, Matthys P, De Wolf-Peeters C. T-cell/histiocyte-rich large B-cell lymphoma shows transcriptional features suggestive of a tolerogenic host immune response. Haematologica 2009; 95:440-8. [PMID: 19797726 DOI: 10.3324/haematol.2009.009647] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Gene expression profiling has successfully identified the prognostic significance of the host response in lymphomas. The aggressive T-cell/histiocyte-rich large B-cell lymphoma and the indolent nodular lymphocyte-predominant Hodgkin's lymphoma are both characterized by a paucity of tumor cells embedded in an overwhelming background. The tumor cells of both lymphomas share several characteristics, while the cellular composition of their microenvironment is clearly different. DESIGN AND METHODS We collected 33 cases of T-cell/histiocyte-rich large B-cell lymphoma and 56 cases of nodular lymphocyte-predominant Hodgkin's lymphoma and performed microarray gene expression profiling on ten cases of each lymphoma, to obtain a better understanding of the lymphoma host response. By quantitative reverse transcriptase polymerase chain reaction we verified that these 20 selected cases were representative of the entire population of T-cell/histiocyte-rich large B-cell and nodular lymphocyte-predominant Hodgkin's lymphomas. RESULTS We observed that the microenvironment in nodular lymphocyte-predominant Hodgkin's lymphoma is molecularly very similar to a lymph node characterized by follicular hyperplasia, while the microenvironment in T-cell/histiocyte-rich large B-cell lymphoma is clearly different. The T-cell/histiocyte-rich large B-cell lymphoma signature is hallmarked by up-regulation of CCL8, interferon-gamma, indoleamine 2,3 dioxygenase, VSIG4 and Toll-like receptors. These features may be responsible for the recruitment and activation of T cells, macrophages and dendritic cells, characterizing the stromal component of this lymphoma, and may point towards innate immunity and a tumor tolerogenic immune response in T-cell/histiocyte-rich large B-cell lymphoma. CONCLUSIONS The gene expression profile of T-cell/histiocyte-rich large B-cell lymphoma, in comparison with that of nodular lymphocyte-predominant Hodgkin's lymphoma, shows features suggestive of a distinct tolerogenic host immune response that may play a key role in the aggressive behavior of this lymphoma, and that may serve as a potential target for future therapy.
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Affiliation(s)
- Peter Van Loo
- Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium
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Düwel M, Welteke V, Oeckinghaus A, Baens M, Kloo B, Ferch U, Darnay BG, Ruland J, Marynen P, Krappmann D. A20 negatively regulates T cell receptor signaling to NF-kappaB by cleaving Malt1 ubiquitin chains. J Immunol 2009; 182:7718-28. [PMID: 19494296 DOI: 10.4049/jimmunol.0803313] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The Carma1-Bcl10-Malt1 signaling module bridges TCR signaling to the canonical IkappaB kinase (IKK)/NF-kappaB pathway. Covalent attachment of regulatory ubiquitin chains to Malt1 paracaspase directs TCR signaling to IKK activation. Further, the ubiquitin-editing enzyme A20 was recently suggested to suppress T cell activation, but molecular targets for A20 remain elusive. In this paper, we show that A20 regulates the strength and duration of the IKK/NF-kappaB response upon TCR/CD28 costimulation. By catalyzing the removal of K63-linked ubiquitin chains from Malt1, A20 prevents sustained interaction between ubiquitinated Malt1 and the IKK complex and thus serves as a negative regulator of inducible IKK activity. Upon T cell stimulation, A20 is rapidly removed and paracaspase activity of Malt1 has been suggested to cleave A20. Using antagonistic peptides or reconstitution of Malt1(-/-) T cells, we show that Malt1 paracaspase activity is required for A20 cleavage and optimal IL-2 production, but dispensable for initial IKK/NF-kappaB signaling in CD4(+) T cells. However, proteasomal inhibition impairs A20 degradation and impedes TCR/CD28-induced IKK activation. Taken together, A20 functions as a Malt1 deubiquitinating enzyme and proteasomal degradation and de novo synthesis of A20 contributes to balance TCR/CD28-induced IKK/NF-kappaB signaling.
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Affiliation(s)
- Michael Düwel
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Toxicology, Neuherberg, Germany
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21
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Bauters M, Weuts A, Vandewalle J, Nevelsteen J, Marynen P, Van Esch H, Froyen G. Detection and validation of copy number variation in X-linked mental retardation. Cytogenet Genome Res 2009; 123:44-53. [PMID: 19287138 DOI: 10.1159/000184691] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2008] [Indexed: 11/19/2022] Open
Abstract
Studies to identify the genetic defects associated with X-linked mental retardation (XLMR) in males have revealed tens of genes important for normal brain development and cognitive functioning in men. Despite extensive efforts in breakpoint cloning of chromosomal rearrangements and mutation screening of candidate genes on the X chromosome, still many XLMR families and sporadic cases remain unsolved. It is now clear that submicroscopic copy number changes on the X chromosome can explain about 5% of these idiopathic cases. Interestingly, beside gene deletions, an increase in gene dosage due to genomic duplications seems to contribute to causality more often than expected. Since larger duplications on the X chromosome are tolerated compared to deletions, they often harbour more than one gene hampering the identification of the causal gene. In contrast to copy number variations (CNVs) on autosomes, most disease-associated CNVs on the X chromosome in males are inherited from their mothers who normally do not present with any clinical symptoms due to non-random X inactivation. Here, we review the different methods applied to study copy number alterations on the X chromosome in patients with cognitive impairment, discuss those CNVs that are associated with disease and elaborate on the genes and mechanisms involved. At the end, we will resume in vivo assays to study the relation of CNVs on the X chromosome and mental disability.
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Affiliation(s)
- M Bauters
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, VIB Leuven, Belgium
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22
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Lehnert S, Van Loo P, Thilakarathne PJ, Marynen P, Verbeke G, Schuit FC. Evidence for co-evolution between human microRNAs and Alu-repeats. PLoS One 2009; 4:e4456. [PMID: 19209240 PMCID: PMC2637760 DOI: 10.1371/journal.pone.0004456] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 12/16/2008] [Indexed: 12/26/2022] Open
Abstract
This paper connects Alu repeats, the most abundant repetitive elements in the human genome and microRNAs, small RNAs that alter gene expression at the post-transcriptional level. Base-pair complementarity could be demonstrated between the seed sequence of a subset of human microRNAs and Alu repeats that are integrated parallel (sense) in mRNAs. The most common target site coincides with the evolutionary most conserved part of Alu. A primate-specific gene cluster on chromosome 19 encodes the majority of miRNAs that target the most conserved sense Alu site. The individual miRNA genes within this cluster are flanked by an Alu-LINE signature, which has been duplicated with the clustered miRNA genes. Gene duplication events in this locus are supported by comparing repeat length variations of the LINE elements within the cluster with those in the rest of the chromosome. Thus, a dual relationship exists between an evolutionary young miRNA cluster and their Alu targets that may have evolved in the same time window. One hypothesis for this dual relationship is that these miRNAs could protect against too high rates of duplicative transposition, which would destroy the genome.
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Affiliation(s)
- Stefan Lehnert
- Gene Expression Unit, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Peter Van Loo
- Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Bioinformatics group, Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Peter Marynen
- Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Geert Verbeke
- Biostatistical Centre, U. Z. Sint-Rafaël, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Frans C. Schuit
- Gene Expression Unit, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
- * E-mail:
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23
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Bousquet M, Quelen C, Rosati R, Mansat-De Mas V, La Starza R, Bastard C, Lippert E, Talmant P, Lafage-Pochitaloff M, Leroux D, Gervais C, Viguié F, Lai JL, Terre C, Beverlo B, Sambani C, Hagemeijer A, Marynen P, Delsol G, Dastugue N, Mecucci C, Brousset P. Myeloid cell differentiation arrest by miR-125b-1 in myelodysplastic syndrome and acute myeloid leukemia with the t(2;11)(p21;q23) translocation. ACTA ACUST UNITED AC 2008; 205:2499-506. [PMID: 18936236 PMCID: PMC2571925 DOI: 10.1084/jem.20080285] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most chromosomal translocations in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) involve oncogenes that are either up-regulated or form part of new chimeric genes. The t(2;11)(p21;q23) translocation has been cloned in 19 cases of MDS and AML. In addition to this, we have shown that this translocation is associated with a strong up-regulation of miR-125b (from 6- to 90-fold). In vitro experiments revealed that miR-125b was able to interfere with primary human CD34+ cell differentiation, and also inhibited terminal (monocytic and granulocytic) differentiation in HL60 and NB4 leukemic cell lines. Therefore, miR-125b up-regulation may represent a new mechanism of myeloid cell transformation, and myeloid neoplasms carrying the t(2;11) translocation define a new clinicopathological entity.
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Affiliation(s)
- Marina Bousquet
- Institut National de Santé et de Recherche Médicale, U563, Centre de Physiopathologie de Toulouse-Purpan, 31300 Toulouse, France
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Dewaele B, Wasag B, Cools J, Sciot R, Prenen H, Vandenberghe P, Wozniak A, Schöffski P, Marynen P, Debiec-Rychter M. Activity of dasatinib, a dual SRC/ABL kinase inhibitor, and IPI-504, a heat shock protein 90 inhibitor, against gastrointestinal stromal tumor-associated PDGFRAD842V mutation. Clin Cancer Res 2008; 14:5749-58. [PMID: 18794084 DOI: 10.1158/1078-0432.ccr-08-0533] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
PURPOSE Activating mutations in platelet-derived growth factor receptor-alpha (PDGFRA) have been reported in approximately 5% to 10% of patients with gastrointestinal stromal tumors (GIST). Imatinib efficiently inhibits the juxtamembrane PDGFRA mutations, whereas many tyrosine kinase domain activation loop PDGFRA mutations confer primary resistance to imatinib. In this study, we compared the efficacy of second-line tyrosine kinase inhibitors such as dasatinib, sorafenib, and nilotinib against two GIST-related PDGFRA mutants, PDGFRA(D842V) and PDGFRA(DeltaDIM842-844). In addition, we sought to investigate the inhibitory effect of the heat shock protein 90 inhibitor, IPI-504, on these mutants. EXPERIMENTAL DESIGN Primary imatinib-resistant tumor cells and cell lines expressing imatinib-resistant PDGFRA(D842V) or imatinib-sensitive PDGFRA(DeltaDIM842-844) mutants were treated with different concentrations of dasatinib, sorafenib, nilotinib, and IPI-504. The effect of treatment on proliferation, survival, and signaling was determined. RESULTS All inhibitors tested exhibited a high efficacy toward the PDGFRA(DeltaDIM842-844) mutant. In contrast, ex vivo and in vitro assays revealed that only dasatinib potently inhibited the PDGFRA(D842V) isoform with an IC(50) value of 62 nmol/L. Sorafenib and nilotinib were significantly less efficacious against this mutation, inhibiting the PDGFRA kinase activity at >1,000 and >5,000 nmol/L, and suppressing the proliferation of the cells expressing the PDGFRA(D842V) mutant with an IC(50) value of 239 and 1,310 nmol/L, respectively. IPI-504 treatment potently inhibited PDGFRA kinase activity by inducing the degradation of PDGFRA(D842V) and PDGFRA(DeltaDIM842-844) at 256 and 182 nmol/L, respectively. CONCLUSIONS Treatment with dasatinib or the heat shock protein 90 inhibitor IPI-504 may provide a therapeutic alternative for GIST patients whose tumors carry the imatinib-resistant PDGFRA(D842V) mutant isoform.
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Affiliation(s)
- Barbara Dewaele
- Department of Human Genetics, K.U. Leuven, and VIB Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium
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De Roock W, Janssens M, Biesmans B, Jacobs B, De Schutter J, Humblet Y, Peeters M, Van Cutsem E, Marynen P, Tejpar S. 98 POSTER DUSP4 expression level in colorectal primaries predicts overall survival benefit in Kras wild-type and Kras mutant colorectal cancer after treatment with cetuximab for metastatic disease. EJC Suppl 2008. [DOI: 10.1016/s1359-6349(08)72030-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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26
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De Keersmaecker K, Rocnik JL, Bernad R, Lee BH, Leeman D, Gielen O, Verachtert H, Folens C, Munck S, Marynen P, Fornerod M, Gilliland DG, Cools J. Kinase activation and transformation by NUP214-ABL1 is dependent on the context of the nuclear pore. Mol Cell 2008; 31:134-42. [PMID: 18614052 DOI: 10.1016/j.molcel.2008.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 03/20/2008] [Accepted: 05/02/2008] [Indexed: 11/24/2022]
Abstract
Genetic alterations causing constitutive tyrosine kinase activation are observed in a broad spectrum of cancers. Thus far, these mutant kinases have been localized to the plasma membrane or cytoplasm, where they engage proliferation and survival pathways. We report that the NUP214-ABL1 fusion is unique among these because of its requisite localization to the nuclear pore complex for its transforming potential. We show that NUP214-ABL1 displays attenuated transforming capacity as compared to BCR-ABL1 and that NUP214-ABL1 preferentially transforms T cells, which is in agreement with its unique occurrence in T cell acute lymphoblastic leukemia. Furthermore, NUP214-ABL1 differs from BCR-ABL1 in subcellular localization, initiation of kinase activity, and signaling and lacks phosphorylation on its activation loop. In addition to delineating an unusual mechanism for kinase activation, this study provides new insights into the spectrum of chromosomal translocations involving nucleoporins by indicating that the nuclear pore context itself may play a central role in transformation.
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Affiliation(s)
- Kim De Keersmaecker
- Department of Molecular and Developmental Genetics, VIB, K.U. Leuven, Leuven 3000, Belgium
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Lahortiga I, Akin C, Cools J, Wilson TM, Mentens N, Arthur DC, Maric I, Noel P, Kocabas C, Marynen P, Lessin LS, Wlodarska I, Robyn J, Metcalfe DD. Activity of imatinib in systemic mastocytosis with chronic basophilic leukemia and a PRKG2-PDGFRB fusion. Haematologica 2008; 93:49-56. [PMID: 18166785 DOI: 10.3324/haematol.11836] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Translocations involving region 5q31-32 (PDGFRB) have been reported in a variety of myeloproliferative diseases and are often associated with significant peripheral eosinophilia. We report an unusual case of a patient presenting with peripheral basophilia and systemic mastocytosis in whom cytogenetic analysis revealed a t(4;5)(q21.1;q31.3). DESIGN AND METHODS We used molecular analyses to determine the role of PDGFRB in this case. The patient was treated with imatinib. RESULTS Fluorescence in situ hybridization (FISH) documented a breakpoint in PDGFRB. In agreement with this, the patient responded very well to imatinib with resolution of clinical symptoms, basophilia, and mast cell disease. Molecular analyses revealed that PDGFRB, encoding an imatinib-sensitive tyrosine kinase, was fused to PRKG2. The fusion gene incorporates the first two exons of PRKG2 fused to the truncated exon 12 of PDGFRB, resulting in the disruption of its juxtamembrane domain. Functional studies confirmed that the activity and transforming properties of PRKG2-PDGFRbeta were dependent on the disruption of the auto-inhibitory juxtamembrane domain. CONCLUSIONS Our results identify a second case of the PRKG2-PDGFRB fusion and confirm the unusual PDGFRB breakpoint associated with this fusion. This work also illustrates the use of imatinib for the treatment of specific cases of systemic mastocytosis.
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Affiliation(s)
- Idoya Lahortiga
- Human Genome Laboratory, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium
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Frints SGM, Lenzner S, Bauters M, Jensen LR, Van Esch H, des Portes V, Moog U, Macville MVE, van Roozendaal K, Schrander-Stumpel CTRM, Tzschach A, Marynen P, Fryns JP, Hamel B, van Bokhoven H, Chelly J, Beldjord C, Turner G, Gecz J, Moraine C, Raynaud M, Ropers HH, Froyen G, Kuss AW. MCT8 mutation analysis and identification of the first female with Allan–Herndon–Dudley syndrome due to loss of MCT8 expression. Eur J Hum Genet 2008; 16:1029-37. [DOI: 10.1038/ejhg.2008.66] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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29
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Van Loo P, Aerts S, Thienpont B, De Moor B, Moreau Y, Marynen P. ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Genome Biol 2008; 9:R66. [PMID: 18394174 PMCID: PMC2643937 DOI: 10.1186/gb-2008-9-4-r66] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2007] [Revised: 03/07/2008] [Accepted: 04/07/2008] [Indexed: 12/23/2022] Open
Abstract
ModuleMiner detects cis-regulatory modules in a set of co-expressed genes in tissue-specific microarray clusters and in embryonic development datasets. We present ModuleMiner, a novel algorithm for computationally detecting cis-regulatory modules (CRMs) in a set of co-expressed genes. ModuleMiner outperforms other methods for CRM detection on benchmark data, and successfully detects CRMs in tissue-specific microarray clusters and in embryonic development gene sets. Interestingly, CRM predictions for differentiated tissues exhibit strong enrichment close to the transcription start site, whereas CRM predictions for embryonic development gene sets are depleted in this region.
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Affiliation(s)
- Peter Van Loo
- Department of Molecular and Developmental Genetics, VIB, Herestraat 49, B-3000 Leuven, Belgium.
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30
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Bauters M, Van Esch H, Friez MJ, Boespflug-Tanguy O, Zenker M, Vianna-Morgante AM, Rosenberg C, Ignatius J, Raynaud M, Hollanders K, Govaerts K, Vandenreijt K, Niel F, Blanc P, Stevenson RE, Fryns JP, Marynen P, Schwartz CE, Froyen G. Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair. Genome Res 2008; 18:847-58. [PMID: 18385275 DOI: 10.1101/gr.075903.107] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Recurrent submicroscopic genomic copy number changes are the result of nonallelic homologous recombination (NAHR). Nonrecurrent aberrations, however, can result from different nonexclusive recombination-repair mechanisms. We previously described small microduplications at Xq28 containing MECP2 in four male patients with a severe neurological phenotype. Here, we report on the fine-mapping and breakpoint analysis of 16 unique microduplications. The size of the overlapping copy number changes varies between 0.3 and 2.3 Mb, and FISH analysis on three patients demonstrated a tandem orientation. Although eight of the 32 breakpoint regions coincide with low-copy repeats, none of the duplications are the result of NAHR. Bioinformatics analysis of the breakpoint regions demonstrated a 2.5-fold higher frequency of Alu interspersed repeats as compared with control regions, as well as a very high GC content (53%). Unexpectedly, we obtained the junction in only one patient by long-range PCR, which revealed nonhomologous end joining as the mechanism. Breakpoint analysis in two other patients by inverse PCR and subsequent array comparative genomic hybridization analysis demonstrated the presence of a second duplicated region more telomeric at Xq28, of which one copy was inserted in between the duplicated MECP2 regions. These data suggest a two-step mechanism in which part of Xq28 is first inserted near the MECP2 locus, followed by breakage-induced replication with strand invasion of the normal sister chromatid. Our results indicate that the mechanism by which copy number changes occur in regions with a complex genomic architecture can yield complex rearrangements.
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Affiliation(s)
- Marijke Bauters
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, VIB, B-3000 Leuven, Belgium
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31
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De Keersmaecker K, Lahortiga I, Mentens N, Folens C, Van Neste L, Bekaert S, Vandenberghe P, Odero MD, Marynen P, Cools J. In vitro validation of -secretase inhibitors alone or in combination with other anti-cancer drugs for the treatment of T-cell acute lymphoblastic leukemia. Haematologica 2008; 93:533-42. [DOI: 10.3324/haematol.11894] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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32
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Froyen G, Corbett M, Vandewalle J, Jarvela I, Lawrence O, Meldrum C, Bauters M, Govaerts K, Vandeleur L, Van Esch H, Chelly J, Sanlaville D, van Bokhoven H, Ropers HH, Laumonnier F, Ranieri E, Schwartz CE, Abidi F, Tarpey PS, Futreal PA, Whibley A, Raymond FL, Stratton MR, Fryns JP, Scott R, Peippo M, Sipponen M, Partington M, Mowat D, Field M, Hackett A, Marynen P, Turner G, Gécz J. Submicroscopic duplications of the hydroxysteroid dehydrogenase HSD17B10 and the E3 ubiquitin ligase HUWE1 are associated with mental retardation. Am J Hum Genet 2008; 82:432-43. [PMID: 18252223 DOI: 10.1016/j.ajhg.2007.11.002] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Revised: 10/17/2007] [Accepted: 11/01/2007] [Indexed: 11/16/2022] Open
Abstract
Submicroscopic copy-number imbalances contribute significantly to the genetic etiology of human disease. Here, we report a novel microduplication hot spot at Xp11.22 identified in six unrelated families with predominantly nonsyndromic XLMR. All duplications segregate with the disease, including the large families MRX17 and MRX31. The minimal, commonly duplicated region contains three genes: RIBC1, HSD17B10, and HUWE1. RIBC1 could be excluded on the basis of its absence of expression in the brain and because it escapes X inactivation in females. For the other genes, expression array and quantitative PCR analysis in patient cell lines compared to controls showed a significant upregulation of HSD17B10 and HUWE1 as well as several important genes in their molecular pathways. Loss-of-function mutations of HSD17B10 have previously been associated with progressive neurological disease and XLMR. The E3 ubiquitin ligase HUWE1 has been implicated in TP53-associated regulation of the neuronal cell cycle. Here, we also report segregating sequence changes of highly conserved residues in HUWE1 in three XLMR families; these changes are possibly associated with the phenotype. Our findings demonstrate that an increased gene dosage of HSD17B10, HUWE1, or both contribute to the etiology of XLMR and suggest that point mutations in HUWE1 are associated with this disease too.
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Affiliation(s)
- Guy Froyen
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, VIB, B-3000 Leuven, Belgium.
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Froyen G, Van Esch H, Bauters M, Hollanders K, Frints SGM, Vermeesch JR, Devriendt K, Fryns JP, Marynen P. Detection of genomic copy number changes in patients with idiopathic mental retardation by high-resolution X-array-CGH: important role for increased gene dosage of XLMR genes. Hum Mutat 2007; 28:1034-42. [PMID: 17546640 DOI: 10.1002/humu.20564] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A tiling X-chromosome-specific genomic array with a theoretical resolution of 80 kb was developed to screen patients with idiopathic mental retardation (MR) for submicroscopic copy number differences. Four patients with aberrations previously detected at lower resolution were first analyzed. This facilitated delineation of the location and extent of the aberration at high resolution and subsequently, more precise genotype-phenotype analyses. A cohort of 108 patients was screened, 57 of which were suspected of X-linked mental retardation (XLMR), 26 were probands of brother pairs, and 25 were sporadic cases. A total of 15 copy number changes in 14 patients (13%) were detected, which included two deletions and 13 duplications ranging from 0.1 to 2.7 Mb. The aberrations are associated with the phenotype in five patients (4.6%), based on the following criteria: de novo aberration; involvement of a known or candidate X-linked nonsyndromic(syndromic) MR (MRX(S)) gene; segregation with the disease in the family; absence in control individuals; and skewed X-inactivation in carrier females. These include deletions that contain the MRX(S) genes CDKL5, OPHN1, and CASK, and duplications harboring CDKL5, NXF5, MECP2, and GDI1. In addition, seven imbalances were apparent novel polymorphic regions because they do not fulfill the proposed criteria. Taken together, our data strongly suggest that not only deletions but also duplications on the X chromosome contribute to the phenotype more often than expected, supporting the increased gene dosage mechanism for deregulation of normal cognitive development.
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Affiliation(s)
- Guy Froyen
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, VIB, Leuven, Belgium.
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Brems H, Chmara M, Sahbatou M, Denayer E, Taniguchi K, Kato R, Somers R, Messiaen L, De Schepper S, Fryns JP, Cools J, Marynen P, Thomas G, Yoshimura A, Legius E. Germline loss-of-function mutations in SPRED1 cause a neurofibromatosis 1-like phenotype. Nat Genet 2007; 39:1120-6. [PMID: 17704776 DOI: 10.1038/ng2113] [Citation(s) in RCA: 283] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 07/05/2007] [Indexed: 02/07/2023]
Abstract
We report germline loss-of-function mutations in SPRED1 in a newly identified autosomal dominant human disorder. SPRED1 is a member of the SPROUTY/SPRED family of proteins that act as negative regulators of RAS->RAF interaction and mitogen-activated protein kinase (MAPK) signaling. The clinical features of the reported disorder resemble those of neurofibromatosis type 1 and consist of multiple café-au-lait spots, axillary freckling and macrocephaly. Melanocytes from a café-au-lait spot showed, in addition to the germline SPRED1 mutation, an acquired somatic mutation in the wild-type SPRED1 allele, indicating that complete SPRED1 inactivation is needed to generate a café-au-lait spot in this syndrome. This disorder is yet another member of the recently characterized group of phenotypically overlapping syndromes caused by mutations in the genes encoding key components of the RAS-MAPK pathway. To our knowledge, this is the first report of mutations in the SPRY (SPROUTY)/SPRED family of genes in human disease.
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Affiliation(s)
- Hilde Brems
- Department of Human Genetics, Catholic University Leuven, 3000 Leuven, Belgium
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Abstract
BACKGROUND The tissue-specific pattern of tissue factor (TF) expression suggests that it plays a major role in the hemostatic protection of specific organs, such as the heart and lung. In support of this notion, we found that mice expressing very low levels of TF exhibit hemostatic defects in the heart and lung. Hemosiderosis and fibrosis are observed in the hearts of all low TF mice as early as 3 months of age. In contrast, TF(+/-) mice expressing approximately 50% of wild-type levels of TF had no detectable hemostatic defects. OBJECTIVE AND METHODS The objective of this study was to determine the threshold of TF that is required to maintain hemostasis under normal and pathologic conditions, and to investigate the specific role of cardiac myocyte TF in heart hemostasis using mice with altered levels of TF expression in cardiac myocytes. RESULTS First, we found that mice with 20% of wild-type levels of TF activity in their hearts had hemosiderosis and fibrosis by 6 months of age. Secondly, mice with a selective deletion of the TF gene in cardiac myocytes had a mild hemostatic defect under normal conditions but exhibited a significant increase in hemosiderosis and fibrosis after challenge with isoproterenol. Finally, we showed that cardiac myocyte-specific overexpression of TF abolished hemosiderin deposition and fibrosis in the hearts of low TF mice. CONCLUSIONS Taken together, our results indicate that TF expression by cardiac myocytes is important to maintain heart hemostasis under normal and pathologic conditions.
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Affiliation(s)
- R Pawlinski
- Department of Immunology, The Scripps Research Institute, La Jolla, CA, USA
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36
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Crescenzi B, La Starza R, Nozzoli C, Ciolli S, Matteucci C, Romoli S, Rigacci L, Gorello P, Bosi A, Martelli MF, Marynen P, Mecucci C. Molecular cytogenetic findings in a four-way t(1;12;5;12)(p36;p13;q33;q24) underlying the ETV6-PDGFRB fusion gene in chronic myelomonocytic leukemia. ACTA ACUST UNITED AC 2007; 176:67-71. [PMID: 17574967 DOI: 10.1016/j.cancergencyto.2007.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 03/04/2007] [Accepted: 03/09/2007] [Indexed: 10/23/2022]
Abstract
Fluorescence in situ hybridization (FISH) and reverse-transcription polymerase chain reaction (RT-PCR) detected the ETV6-PDGFRB fusion in a patient with chronic myelomonocytic leukemia characterized by bone marrow and peripheral blood eosinophilia and a four-way t(1;12;5;12)(p36;p13;q33;q24) on bone marrow cells. The patient consequently underwent imatinib mesylate therapy and achieved hematologic, FISH, and molecular remission. The FICTION technique (fluorescence immunophenotyping and interphase cytogenetics as a tool for the investigation of neoplasms) demonstrated that eosinophils and CD13(+) and CD14(+) cells belong to the neoplastic clone bearing the ETV6-PDGFRB rearrangement. Molecular cytogenetics is the most reliable approach to detect the involvement of promiscuous genes, such as PDGFRB, and to properly classify genetic entities for which targeted therapies are available. Assessment of cell lineages harboring the genomic lesion may contribute in the understanding of leukemogenic pathways.
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MESH Headings
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 12
- Chromosomes, Human, Pair 5
- Humans
- In Situ Hybridization, Fluorescence
- Karyotyping
- Leukemia, Myelomonocytic, Chronic/genetics
- Male
- Middle Aged
- Oncogene Proteins, Fusion/genetics
- Translocation, Genetic
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Affiliation(s)
- Barbara Crescenzi
- Department of Hematology, University of Perugia, IBiT Foundation (Fondazione IRCCS Biotecnologie nel Trapianto), via Brunamonti 51, 06122 Perugia, Italy
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37
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Pospisilova H, Baens M, Michaux L, Stul M, Van Hummelen P, Van Loo P, Vermeesch J, Jarosova M, Zemanova Z, Michalova K, Van den Berghe I, Alexander HD, Hagemeijer A, Vandenberghe P, Cools J, De Wolf-Peeters C, Marynen P, Wlodarska I. Interstitial del(14)(q) involving IGH: a novel recurrent aberration in B-NHL. Leukemia 2007; 21:2079-83. [PMID: 17525729 DOI: 10.1038/sj.leu.2404739] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Lahortiga I, De Keersmaecker K, Van Vlierberghe P, Graux C, Cauwelier B, Lambert F, Mentens N, Beverloo HB, Pieters R, Speleman F, Odero MD, Bauters M, Froyen G, Marynen P, Vandenberghe P, Wlodarska I, Meijerink JPP, Cools J. Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia. Nat Genet 2007; 39:593-5. [PMID: 17435759 DOI: 10.1038/ng2025] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 03/14/2007] [Indexed: 12/28/2022]
Abstract
We identified a duplication of the MYB oncogene in 8.4% of individuals with T cell acute lymphoblastic leukemia (T-ALL) and in five T-ALL cell lines. The duplication is associated with a threefold increase in MYB expression, and knockdown of MYB expression initiates T cell differentiation. Our results identify duplication of MYB as an oncogenic event and suggest that MYB could be a therapeutic target in human T-ALL.
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Affiliation(s)
- Idoya Lahortiga
- Human Genome Laboratory, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
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Lierman E, Lahortiga I, Van Miegroet H, Mentens N, Marynen P, Cools J. The ability of sorafenib to inhibit oncogenic PDGFRbeta and FLT3 mutants and overcome resistance to other small molecule inhibitors. Haematologica 2007; 92:27-34. [PMID: 17229632 DOI: 10.3324/haematol.10692] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Activated tyrosine kinases are implicated in the pathogenesis of chronic and acute leukemia, and represent attractive targets for therapy. Sorafenib (BAY43-9006, Nexavar) is a small molecule B-RAF inhibitor that is used for the treatment of renal cell carcinoma, and has been shown to have activity against receptor tyrosine kinases from the platelet-derived growth factor receptor (PDGFR) and vascular endothelial growth factor receptor (VEGFR) families. We investigated the efficacy of sorafenib at inhibiting mutants of the receptor tyrosine kinases PDGFRbeta, KIT, and FLT3, which are implicated in the pathogenesis of myeloid malignancies. DESIGN AND METHODS We tested the effect of sorafenib on the proliferation of hematopoietic cells transformed by ETV6-PDGFRbeta, FLT3 with an internal tandem duplication or D835Y point mutation, and the KIT(D816V) mutant. The direct effect of sorafenib on the activity of these kinases and their downstream signaling was tested using phospho-specific antibodies. RESULTS We show that sorafenib is a potent inhibitor of ETV6-PDGFRbeta and FLT3 mutants, including some of the mutants that confer resistance to PKC412 and other FLT3 inhibitors. Sorafenib induced a cell cycle block and apoptosis in the acute myeloid leukemia cell lines MV4-11 and MOLM-13, both expressing FLT3 with an internal tandem duplication, whereas no effect was observed on four other acute myeloid leukemia cell lines. The imatinib-resistant KIT(D816V) mutant, associated with systemic mastocytosis, was found to be resistant to sorafenib. INTERPRETATION AND CONCLUSIONS These results warrant further clinical studies of sorafenib for the treatment of myeloid malignancies expressing activated forms of PDGFRbeta and FLT3.
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Affiliation(s)
- Els Lierman
- Department of Molecular and Developmental Genetics, Flanders Interuniversity Institute for Biotechnology (VIB), University of Leuven, Leuven, Belgium
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Froyen G, Bauters M, Boyle J, Van Esch H, Govaerts K, van Bokhoven H, Ropers HH, Moraine C, Chelly J, Fryns JP, Marynen P, Gecz J, Turner G. Loss of SLC38A5 and FTSJ1 at Xp11.23 in three brothers with non-syndromic mental retardation due to a microdeletion in an unstable genomic region. Hum Genet 2007; 121:539-47. [PMID: 17333282 DOI: 10.1007/s00439-007-0343-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Accepted: 02/07/2007] [Indexed: 12/26/2022]
Abstract
Using high resolution X chromosome array-CGH we identified an interstitial microdeletion at Xp11.23 in three brothers with moderate to severe mental retardation (MR) without dysmorphic features. The extent of the deletion was subsequently delineated to about 50 kb by regular PCR and included only the SLC38A5 and FTSJ1 genes. The loss of the FTSJ1 MR gene in males is expected to result in the observed phenotype but the contribution of the deletion of the solute carrier SLC38A5 gene is less clear. Their mother also carries the deletion and completely inactivates the aberrant X chromosome. Interestingly, the distal breakpoint is situated within a 200 kb SSX repeat region that appears to stimulate recombination since subtle copy number changes often occur at this location and it is frequently involved in translocations in tumours. Since this apparent SSX unstable structure is flanked proximally by FTSJ1 and PQBP1, subtle deletions or duplications at this location would be expected to cause MR, as in our family. So far, we have screened a cohort of 300 patients but did not find additional aberrations at the FTSJ1 locus indicating that the frequency is likely to be low.
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Affiliation(s)
- Guy Froyen
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, VIB, Leuven, Belgium.
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41
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La Starza R, Rosati R, Roti G, Gorello P, Bardi A, Crescenzi B, Pierini V, Calabrese O, Baens M, Folens C, Cools J, Marynen P, Martelli MF, Mecucci C, Cuneo A. A new NDE1/PDGFRB fusion transcript underlying chronic myelomonocytic leukaemia in Noonan Syndrome. Leukemia 2007; 21:830-3. [PMID: 17301821 DOI: 10.1038/sj.leu.2404541] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
MESH Headings
- Adult
- Base Sequence
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 5
- Female
- Gene Fusion
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myelomonocytic, Chronic/genetics
- Noonan Syndrome/genetics
- Receptor, Platelet-Derived Growth Factor beta/genetics
- Site-Specific DNA-Methyltransferase (Adenine-Specific)/genetics
- Transcription, Genetic
- Translocation, Genetic
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42
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Noels H, van Loo G, Hagens S, Broeckx V, Beyaert R, Marynen P, Baens M. A Novel TRAF6 binding site in MALT1 defines distinct mechanisms of NF-kappaB activation by API2middle dotMALT1 fusions. J Biol Chem 2007; 282:10180-9. [PMID: 17287209 DOI: 10.1074/jbc.m611038200] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The recurrent translocation t(11;18)(q21;q21) associated with mucosa-associated lymphoid tissue (MALT) lymphoma results in the expression of an API2.MALT1 fusion protein that constitutively activates NF-kappaB. The first baculovirus IAP repeat (BIR) domain of API2 and the C terminus of MALT1, which contains its caspase-like domain, are present in all reported fusion variants and interact with TRAF2 and TRAF6, respectively, suggesting their contribution to NF-kappaB signaling by API2.MALT1. Also, the involvement of BCL10 has been suggested via binding to BIR1 of API2 and via its interaction with the immunoglobulin domains of MALT1, present in half of the fusion variants. However, conflicting reports exist concerning their roles in API2.MALT1-induced NF-kappaB signaling. In this report, streptavidin pulldowns of biotinylated API2.MALT1 fusion variants showed that none of the fusion variants interacted with endogenous BCL10; its role in NF-kappaB signaling by API2.MALT1 was further questioned by RNA interference experiments. In contrast, TRAF6 was essential for NF-kappaB activation by all fusion variants, and we identified a novel TRAF6 binding site in the second immunoglobulin domain of MALT1, which enhanced NF-kappaB activation when present in the fusion protein. Furthermore, inclusion of both immunoglobulin domains in API2.MALT1 further enhanced NF-kappaB signaling via intramolecular TRAF6 activation. Finally, binding of TRAF2 to BIR1 contributed to NF-kappaB activation by API2.MALT1, although additional mechanisms involving BIR1-mediated raft association are also important. Taken together, these data reveal distinct mechanisms of NF-kappaB activation by the different API2.MALT1 fusion variants with an essential role for TRAF6.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- B-Cell CLL-Lymphoma 10 Protein
- Binding Sites/genetics
- Caspases/genetics
- Caspases/metabolism
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 18/genetics
- G Protein-Coupled Inwardly-Rectifying Potassium Channels/genetics
- G Protein-Coupled Inwardly-Rectifying Potassium Channels/metabolism
- Humans
- Jurkat Cells
- Lymphoma, B-Cell, Marginal Zone/genetics
- Lymphoma, B-Cell, Marginal Zone/metabolism
- Mucosa-Associated Lymphoid Tissue Lymphoma Translocation 1 Protein
- NF-kappa B/genetics
- NF-kappa B/metabolism
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oncogene Proteins, Fusion
- Protein Binding/genetics
- Protein Structure, Tertiary/genetics
- Signal Transduction
- TNF Receptor-Associated Factor 2/genetics
- TNF Receptor-Associated Factor 2/metabolism
- TNF Receptor-Associated Factor 6/genetics
- TNF Receptor-Associated Factor 6/metabolism
- Translocation, Genetic/genetics
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Affiliation(s)
- Heidi Noels
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, Flanders Institute for Biotechnology VIB, B-3000 Leuven, Belgium
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43
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Crescenzi B, Chase A, Starza RL, Beacci D, Rosti V, Gallì A, Specchia G, Martelli MF, Vandenberghe P, Cools J, Jones AV, Cross NCP, Marynen P, Mecucci C. FIP1L1-PDGFRA in chronic eosinophilic leukemia and BCR-ABL1 in chronic myeloid leukemia affect different leukemic cells. Leukemia 2007; 21:397-402. [PMID: 17215855 DOI: 10.1038/sj.leu.2404510] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We investigated genetically affected leukemic cells in FIP1L1-PDGFRA+ chronic eosinophilic leukemia (CEL) and in BCR-ABL1+ chronic myeloid leukemia (CML), two myeloproliferative disorders responsive to imatinib. Fluorescence in situ hybridization specific for BCR-ABL1 and for FIP1L1-PDGFRA was combined with cytomorphology or with lineage-restricted monoclonal antibodies and applied in CML and CEL, respectively. In CEL the amount of FIP1L1-PDGFRA+ cells among CD34+ and CD133+ cells, B and T lymphocytes, and megakaryocytes were within normal ranges. Positivity was found in eosinophils, granulo-monocytes and varying percentages of erythrocytes. In vitro assays with imatinib showed reduced survival of peripheral blood mononuclear cells but no reduction in colony-forming unit growth medium (CFU-GM) growth. In CML the BCR-ABL1 fusion gene was detected in CD34+/CD133+ cells, granulo-monocytes, eosinophils, erythrocytes, megakaryocytes and B-lymphocytes. Growth of both peripheral blood mononuclear cells and CFU-GM was inhibited by imatinib. This study provided evidence for marked differences in the leukemic masses which are targeted by imatinib in CEL or CML, as harboring FIP1L1-PDGFRA or BCR-ABL1.
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MESH Headings
- AC133 Antigen
- Antigens, CD/analysis
- Antigens, CD34/analysis
- Antineoplastic Agents/therapeutic use
- Benzamides
- Cell Lineage
- Chronic Disease
- Clone Cells/enzymology
- Drug Resistance
- Eosinophils/enzymology
- Erythrocytes/enzymology
- Fusion Proteins, bcr-abl/analysis
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Glycophorins/analysis
- Glycoproteins/analysis
- Granulocytes/enzymology
- Hematopoietic Stem Cells/enzymology
- Humans
- Hypereosinophilic Syndrome/drug therapy
- Hypereosinophilic Syndrome/enzymology
- Hypereosinophilic Syndrome/genetics
- Hypereosinophilic Syndrome/pathology
- Imatinib Mesylate
- Immunophenotyping
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Lymphocyte Subsets/enzymology
- Megakaryocytes/enzymology
- Monocytes/enzymology
- Myeloid Cells/enzymology
- Neoplastic Stem Cells/enzymology
- Oncogene Proteins, Fusion/analysis
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Peptides/analysis
- Piperazines/therapeutic use
- Protein Kinase Inhibitors/therapeutic use
- Pyrimidines/therapeutic use
- Receptor, Platelet-Derived Growth Factor alpha/analysis
- Receptor, Platelet-Derived Growth Factor alpha/antagonists & inhibitors
- Tumor Stem Cell Assay
- X Chromosome Inactivation
- mRNA Cleavage and Polyadenylation Factors/analysis
- mRNA Cleavage and Polyadenylation Factors/antagonists & inhibitors
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Affiliation(s)
- B Crescenzi
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
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44
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Baens M, Noels H, Broeckx V, Hagens S, Fevery S, Billiau AD, Vankelecom H, Marynen P. The dark side of EGFP: defective polyubiquitination. PLoS One 2006; 1:e54. [PMID: 17183684 PMCID: PMC1762387 DOI: 10.1371/journal.pone.0000054] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Accepted: 10/25/2006] [Indexed: 02/03/2023] Open
Abstract
Enhanced Green Fluorescent Protein (EGFP) is the most commonly used live cell reporter despite a number of conflicting reports that it can affect cell physiology. Thus far, the precise mechanism of GFP-associated defects remained unclear. Here we demonstrate that EGFP and EGFP fusion proteins inhibit polyubiquitination, a posttranslational modification that controls a wide variety of cellular processes, like activation of kinase signalling or protein degradation by the proteasome. As a consequence, the NF-kappaB and JNK signalling pathways are less responsive to activation, and the stability of the p53 tumour suppressor is enhanced in cell lines and in vivo. In view of the emerging role of polyubiquitination in the regulation of numerous cellular processes, the use of EGFP as a live cell reporter should be carefully considered.
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Affiliation(s)
- Mathijs Baens
- Applied Human Genomics, Center for Human Genetics, Molecular Genetics-Flanders Interuniversity Institute for Biotechnology (VIB), University of Leuven, Belgium.
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45
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de Raedt T, Cools J, Debiec-Rychter M, Brems H, Mentens N, Sciot R, Himpens J, de Wever I, Schöffski P, Marynen P, Legius E. Intestinal neurofibromatosis is a subtype of familial GIST and results from a dominant activating mutation in PDGFRA. Gastroenterology 2006; 131:1907-12. [PMID: 17087943 DOI: 10.1053/j.gastro.2006.07.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Accepted: 06/08/2006] [Indexed: 01/25/2023]
Abstract
BACKGROUND & AIMS Intestinal neurofibromatosis (Online Mendelian inheritance in Man database number 162220) is an alternate form of neurofibromatosis. Patients present with neurofibromas limited to the intestine in the absence of any other typical features of NF1 and NF2. At present, the molecular basis of intestinal neurofibromatosis remains elusive. The aim of the present study was to find the gene responsible for intestinal neurofibromatosis and to characterize functionally the mutation. METHODS Three candidate genes (NF1, KIT, and PDGFRA) were screened for mutations in 3 sisters diagnosed with intestinal neurofibromatosis. Five tumors were available for pathologic examination. Activation (phosphorylation) of PDGFRalpha was subsequently tested by Western blot analysis on a transfected 293T and Ba/F3 cell line. RESULTS We found an inherited mutation (Y555C) in the juxtamembrane domain of PDGFRA in the affected individuals. The Y555C mutation leads to autophosphorylation and thus activation of PDGFRalpha. These observations confirm that PDGFRalpha(Y555C) is an oncogenic kinase. The clinical phenotype in the reported family resembles the syndrome of familial gastrointestinal stromal tumors (familial GIST). Somatic activating mutations in KIT and PDGFRA are frequent in sporadic GISTs, and mutations in both genes have also been described in familial GISTs. The tumors in the reported family are morphologically identical to intestinal neurofibromas, but, immunohistochemically, they do not express S100 or any of the known GIST markers. CONCLUSIONS The inherited PDGFRA mutation in the reported family shows that intestinal neurofibromatosis is allelic to familial GIST caused by PDGRA mutations. We therefore propose that these tumors be classified as familial KIT-negative gastrointestinal stromal tumors.
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Affiliation(s)
- Thomas de Raedt
- Department of Human Genetics, Catholic University of Leuven, Leuven, Belgium
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46
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Sagaert X, Theys T, De Wolf-Peeters C, Marynen P, Baens M. Splenic marginal zone lymphoma-like features in API2-MALT1 transgenic mice that are exposed to antigenic stimulation. Haematologica 2006; 91:1693-6. [PMID: 17145608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Recently, we described a transgenic mouse model to analyze the effect of the API2-MALT1 fusion-protein in vivo. Our results showed that the expression of API2-MALT1 is not sufficient to induce the development of lymphoma masses. Here, we demonstrate that immunization with Freund's complete adjuvant led to the loss of compartmentalization of the splenic white pulp in API2-MALT1 transgenic mice, resulting in a splenic marginal zone lymphoma-like lymphoid hyperplasia of a peculiar B-cell subset that disappeared as soon as the antigenic stimulation faded away. These data indicate an effect of API2-MALT1 expression on the normal immune response.
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Affiliation(s)
- Xavier Sagaert
- Department of Morphology and Molecular Pathology, University of Leuven, Leuven, Belgium.
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47
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Raedt TD, Stephens M, Heyns I, Brems H, Thijs D, Messiaen L, Stephens K, Lazaro C, Wimmer K, Kehrer-Sawatzki H, Vidaud D, Kluwe L, Marynen P, Legius E. Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion. Nat Genet 2006; 38:1419-23. [PMID: 17115058 DOI: 10.1038/ng1920] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 10/16/2006] [Indexed: 11/08/2022]
Abstract
Several large-scale studies of human genetic variation have provided insights into processes such as recombination that have shaped human diversity. However, regions such as low-copy repeats (LCRs) have proven difficult to characterize, hindering efforts to understand the processes operating in these regions. We present a detailed study of genetic variation and underlying recombination processes in two copies of an LCR (NF1REPa and NF1REPc) on chromosome 17 involved in the generation of NF1 microdeletions and in a third copy (REP19) on chromosome 19 from which the others originated over 6.7 million years ago. We find evidence for shared hotspots of recombination among the LCRs. REP19 seems to contain hotspots in the same place as the nonallelic recombination hotspots in NF1REPa and NF1REPc. This apparent conservation of patterns of recombination hotspots in moderately diverged paralogous regions contrasts with recent evidence that these patterns are not conserved in less-diverged orthologous regions of chimpanzees.
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Affiliation(s)
- Thomas De Raedt
- Department of Human Genetics, Catholic University Leuven, Leuven, Belgium
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48
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Prenen H, Dewaele B, Cools J, Mentens N, Stefan C, Sciot R, Schöffski P, Marynen P, van Oosterom A, Debiec-Rychter M. 563 POSTER In vitro activity of the multi-targeted kinase inhibitor sorafenib (BAY43-9006) against gastrointestinal stromal tumor (GIST) mutants refractory to imatinib mesylate. EJC Suppl 2006. [DOI: 10.1016/s1359-6349(06)70568-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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49
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La Starza R, Aventin A, Matteucci C, Crescenzi B, Romoli S, Testoni N, Pierini V, Ciolli S, Sambani C, Locasciulli A, Di Bona E, Lafage-Pochitaloff M, Martelli MF, Marynen P, Mecucci C. Genomic gain at 6p21: a new cryptic molecular rearrangement in secondary myelodysplastic syndrome and acute myeloid leukemia. Leukemia 2006; 20:958-64. [PMID: 16617324 DOI: 10.1038/sj.leu.2404208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence in situ hybridization and comparative genomic hybridization characterized 6p rearrangements in eight primary and in 10 secondary myeloid disorders (including one patient with Fanconi anemia) and found different molecular lesions in each group. In primary disorders, 6p abnormalities, isolated in six patients, were highly heterogeneous with different breakpoints along the 6p arm. Reciprocal translocations were found in seven. In the 10 patients with secondary acute myeloid leukemia/myelodysplastic syndrome (AML/MDS), the short arm of chromosome 6 was involved in unbalanced translocations in 7. The other three patients showed full or partial trisomy of the 6p arm, that is, i(6)(p10) (one patient) and dup(6)(p) (two patients). In 5/7 patients with unbalanced translocations, DNA sequences were overrepresented at band 6p21 as either cryptic duplications (three patients) or cryptic low-copy gains (two patients). In the eight patients with cytogenetic or cryptic 6p gains, we identified a common overrepresented region extending for 5-6 megabases from the TNF gene to the ETV-7 gene. 6p abnormalities were isolated karyotype changes in four patients. Consequently, in secondary AML/MDS, we hypothesize that 6p gains are major pathogenetic events arising from acquired and/or congenital genomic instability.
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Affiliation(s)
- R La Starza
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
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50
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Prenen H, Cools J, Mentens N, Folens C, Sciot R, Schöffski P, Van Oosterom A, Marynen P, Debiec-Rychter M. Efficacy of the kinase inhibitor SU11248 against gastrointestinal stromal tumor mutants refractory to imatinib mesylate. Clin Cancer Res 2006; 12:2622-7. [PMID: 16638875 DOI: 10.1158/1078-0432.ccr-05-2275] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE The majority of gastrointestinal stromal tumors harbor mutations in the receptor tyrosine kinases KIT or platelet-derived growth factor receptor A (PDGFRA), and respond to treatment with the tyrosine kinase inhibitor imatinib. Some tumors, however, show primary resistance to imatinib treatment, and most others become resistant during treatment. The most common mechanism of imatinib resistance involves specific mutations in the kinase domains of KIT or PDGFRA. We tested the activity of SU11248, an orally active small-molecule tyrosine kinase inhibitor, to inhibit important imatinib-resistant KIT and PDGFRA mutants. EXPERIMENTAL DESIGN Primary imatinib-resistant tumor cells and cell lines expressing clinically identified imatinib-resistant KIT-V654A, KIT-T670I, or PDGFRA-D842V mutant isoforms were evaluated for sensitivity to SU11248 by Western immunoblotting and proliferation assays. Three patients with the KIT-V654A mutation were treated with SU11248. RESULTS Based on ex vivo assays, SU11248 potently inhibits KIT kinase activity of V654A and T670I mutants and suppresses proliferation of the cells expressing these mutations. Sensitivity of KIT-V654A and KIT-T670I mutants to SU11248 was confirmed using cell lines expressing these mutants. In contrast, SU11248 did not potently inhibit the PDGFRA-D842V mutant. In agreement with these results, two of the three imatinib-resistant patients with the KIT-V654A mutation responded to SU11248 treatment. CONCLUSIONS These studies suggest that SU11248 may be a useful therapeutic agent to treat gastrointestinal stromal tumors harboring the imatinib-resistant KIT-V654A or KIT-T670I mutations, but it has no effect on the activity of the PDGFRA-D842V mutant. Specific kinase inhibitors should be designed to inhibit the constitutive activating PDGFRA mutation at codon 842.
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Affiliation(s)
- Hans Prenen
- Departments of General Medical Oncology and Human Genetics, Flanders Interuniversity Institute for Biotechnology (VIB), Leuven, Belgium
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