241 results on '"Franki Speleman"'
Search Results
2. Long noncoding RNA expression profiling in cancer: Challenges and opportunities
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Hetty Helsmoortel, Karen Verboom, Pieter Mestdagh, Jo Vandesompele, Lucia Lorenzi, Anneleen Decock, Franki Speleman, Francisco Avila Cobos, Steve Lefever, Pieter-Jan Volders, and Celine Everaert
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Cancer Research ,RNA ,Computational biology ,Biology ,Non-coding RNA ,Long non-coding RNA ,Chromatin ,Gene expression profiling ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Neoplasms ,030220 oncology & carcinogenesis ,Gene expression ,Biomarkers, Tumor ,Genetics ,Animals ,Humans ,Transcriptome profiling ,RNA, Long Noncoding - Abstract
In recent years, technological advances in transcriptome profiling revealed that the repertoire of human RNA molecules is more diverse and extended than originally thought. This diversity and complexity mainly derive from a large ensemble of noncoding RNAs. Because of their key roles in cellular processes important for normal development and physiology, disruption of noncoding RNA expression is intrinsically linked to human disease, including cancer. Therefore, studying the noncoding portion of the transcriptome offers the prospect of identifying novel therapeutic and diagnostic targets. Although evidence of the relevance of noncoding RNAs in cancer is accumulating, we still face many challenges when it comes to accurately profiling their expression levels. Some of these challenges are inherent to the technologies employed, whereas others are associated with characteristics of the noncoding RNAs themselves. In this review, we discuss the challenges related to long noncoding RNA expression profiling, highlight how cancer long noncoding RNAs provide new opportunities for cancer diagnosis and treatment, and reflect on future developments.
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- 2019
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3. A g316a polymorphism in the ornithine decarboxylase gene promoter modulates mycn‐driven childhood neuroblastoma
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Rogier Versteeg, Gian Paolo Tonini, Gudrun Schleiermacher, Amanda J. Russell, Angelika Eggert, Murray D. Norris, Jaydutt Bhalshankar, Michael D. Hogarty, Tom Van Maerken, Glenn M. Marshall, Mark J. Cowley, Kwun M. Fong, Lesley J. Ashton, John M. Maris, Sharon J. Diskin, Michelle Haber, Jayne Murray, Michelle J. Henderson, Stefania Purgato, Raymond L. Stallings, Jan Koster, Paolo Pigini, Ali Rihani, Zalman Vaksman, Jo Vandesompele, Wendy B. London, Rosa Noguera, Emanuele Valli, Laura D. Gamble, Franki Speleman, Federico M. Giorgi, Giovanni Perini, Giorgio Milazzo, Simone Di Giacomo, David S. Ziegler, Oncogenomics, CCA - Cancer biology and immunology, Gamble L.D., Purgato S., Henderson M.J., Di Giacomo S., Russell A.J., Pigini P., Murray J., Valli E., Milazzo G., Giorgi F.M., Cowley M., Ashton L.J., Bhalshankar J., Schleiermacher G., Rihani A., Van Maerken T., Vandesompele J., Speleman F., Versteeg R., Koster J., Eggert A., Noguera R., Stallings R.L., Tonini G.P., Fong K., Vaksman Z., Diskin S.J., Maris J.M., London W.B., Marshall G.M., Ziegler D.S., Hogarty M.D., Perini G., Norris M.D., and Haber M.
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0301 basic medicine ,Cancer Research ,SNP ,Single-nucleotide polymorphism ,Biology ,lcsh:RC254-282 ,Article ,Ornithine decarboxylase ,03 medical and health sciences ,neuroblastoma ,Neuroblastoma ,0302 clinical medicine ,Genotype ,MYCN ,Medicine and Health Sciences ,Transcriptional regulation ,medicine ,ODC1 ,neoplasms ,Wild type ,Promoter ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Molecular biology ,030104 developmental biology ,Oncology ,030220 oncology & carcinogenesis ,Childhood Neuroblastoma - Abstract
Simple Summary Neuroblastoma is a devasting childhood cancer in which multiple copies (amplification) of the cancer-causing gene MYCN strongly predict poor outcome. Neuroblastomas are reliant on high levels of cellular components called polyamines for their growth and malignant behavior, and the gene regulating polyamine synthesis is called ODC1. ODC1 is often coamplified with MYCN, and in fact is regulated by MYCN, and like MYCN is prognostic of poor outcome. Here we studied a naturally occurring genetic variant or polymorphism that occurs in the ODC1 gene, and used gene editing to demonstrate the functional importance of this variant in terms of ODC1 levels and growth of neuroblastoma cells. We showed that this variant impacts the ability of MYCN to regulate ODC1, and that it also influences outcome in neuroblastoma, with the rarer variant associated with a better survival. This study addresses the important topic of genetic polymorphisms in cancer. Ornithine decarboxylase (ODC1), a critical regulatory enzyme in polyamine biosynthesis, is a direct transcriptional target of MYCN, amplification of which is a powerful marker of aggressive neuroblastoma. A single nucleotide polymorphism (SNP), G316A, within the first intron of ODC1, results in genotypes wildtype GG, and variants AG/AA. CRISPR-cas9 technology was used to investigate the effects of AG clones from wildtype MYCN-amplified SK-N-BE(2)-C cells and the effect of the SNP on MYCN binding, and promoter activity was investigated using EMSA and luciferase assays. AG clones exhibited decreased ODC1 expression, growth rates, and histone acetylation and increased sensitivity to ODC1 inhibition. MYCN was a stronger transcriptional regulator of the ODC1 promoter containing the G allele, and preferentially bound the G allele over the A. Two neuroblastoma cohorts were used to investigate the clinical impact of the SNP. In the study cohort, the minor AA genotype was associated with improved survival, while poor prognosis was associated with the GG genotype and AG/GG genotypes in MYCN-amplified and non-amplified patients, respectively. These effects were lost in the GWAS cohort. We have demonstrated that the ODC1 G316A polymorphism has functional significance in neuroblastoma and is subject to allele-specific regulation by the MYCN oncoprotein.
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- 2021
4. RRM2 is a target for synthetic lethal interactions with replication stress checkpoint addiction in high-risk neuroblastoma
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Steven Goossens, Aline Eggermont, J. Van Laere, C. Van Neste, E De Smet, Amber Louwagie, F. Devloed, Volodimir Olexiouk, M. Rishfi, Matthias Fischer, Laurentijn Tilleman, Sven Eyckerman, Emmy Dolman, Vanessa Vermeirssen, Pauline Depuydt, Lisa Depestel, B. De Wilde, Liselot Mus, Bieke Decaesteker, Franki Speleman, Kaat Durinck, Louis Delhaye, K. M. Keller, F. Van Nieuwerburgh, Julie Morscio, W Van Loocke, Christoph Bartenhagen, Dieter Deforce, Ellen Sanders, Jan J. Molenaar, Stephen S. Roberts, Siebe Loontiens, Carolina de Carvalho Nunes, and P. Van Vlierberghe
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Transcriptome ,Prexasertib ,Downregulation and upregulation ,Somatic cell ,Neuroblastoma ,Cancer research ,medicine ,Copy-number variation ,Tumor initiation ,Biology ,medicine.disease ,Gene - Abstract
SummaryNeuroblastoma is a pediatric tumor originating from the sympathetic nervous system responsible for 10-15 percent of all childhood cancer deaths. Half of all neuroblastoma patients present with high-risk disease at diagnosis. Despite intensive multi-modal therapies nearly 50 percent of high-risk cases relapse and die of their disease. In contrast to the overall paucity of mutations, high-risk neuroblastoma nearly invariably present with recurrent somatic segmental chromosome copy number variants. For several focal aberrations (e.g. MYCN and LIN28B amplification), the direct role in tumor formation has been established. However, for recurrent aberrations, such as chromosome 2p and 17q gains, the identification of genes contributing to tumor initiation or progression has been challenging due to the scarcity of small segmental gains or amplifications. In this study, we identified and functionally evaluated the ribonucleotide reductase regulatory subunit 2 (RRM2) as a top-ranked 2p putative co-driver and therapeutic target in high-risk neuroblastoma enforcing replicative stress resistance. In vitro knock down and pharmacological RRM2 inhibition highlight RRM2 dependency in neuroblastoma cells, further supported by the finding that co-overexpression of RRM2 in a dβh-MYCN transgenic zebrafish line increased tumor penetrance with 80% and accelerated tumor formation. Given the critical role of RRM2 in replication fork progression and regulation of RRM2 through ATR/CHK1 signaling, we tested combined RRM2 and ATR/CHK1 small molecule inhibition with triapine and BAY1895344/prexasertib respectively, and observed strong synergism, in particular for combined RRM2 and CHK1 inhibition. Transcriptome analysis following combinatorial drugging revealed HEXIM1 as one of the strongest upregulated genes. Using programmable DNA binding of dCas9 with a promiscuous biotin ligase, RRM2 promotor bound proteins were identified including HEXIM1 and NurRD complex members, supporting a cooperative role for HEXIM1 upregulation together with CHK1 inhibition in further attenuating RRM2 expression levels. We evaluated the impact of combined RRM2/CHK1 inhibition in vivo, with treatment of a murine xenograft model showing rapid and complete tumor regression, without tumor regrowth upon treatment arrest. In conclusion, we identified RRM2 as a novel dependency gene in neuroblastoma and promising target for synergistic drug combinations with small compounds targeting DNA checkpoint regulators.
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- 2020
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5. Comprehensive benchmarking of single cell RNA sequencing technologies for characterizing cellular perturbation
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Nurten Yigit, Olivier Thas, Jasper Anckaert, Karen Verboom, Kaat Durinck, Jo Vandesompele, Yvan Saeys, Niels Vandamme, Franki Speleman, Dries Rombaut, and Alemu Takele Assefa
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Neuroblastoma cell ,medicine.anatomical_structure ,Cellular heterogeneity ,Cell ,medicine ,RNA ,Transcriptional response ,Computational biology ,Biology ,Tissue composition ,Gene ,Transcriptome Sequencing - Abstract
Technological advances in transcriptome sequencing of single cells continues to provide an unprecedented view on tissue composition and cellular heterogeneity. While several studies have compared different single cell RNA-seq methods with respect to data quality and their ability to distinguish cell subpopulations, none of these studies investigated the heterogeneity of the cellular transcriptional response upon a chemical perturbation. In this study, we evaluated the transcriptional response of NGP neuroblastoma cells upon nutlin-3 treatment using the C1, ddSeq and Chromium single cell systems. These devices and library preparation methods are representative for the wide variety of platforms, ranging from microfluid chips to droplet-based systems and from full transcript sequencing to 3-prime end sequencing. In parallel, we used bulk RNA-seq for molecular characterization of the transcriptional response. Two complementary metrics to evaluate performance were applied: the first is the number and identity of differentially expressed genes as defined in consensus by two statistical models, and the second is the enrichment analysis of biological signals. Where relevant, to make the data more comparable, we downsampled sequencing library size, selected cell subpopulations based on specific RNA abundance features, or created pseudobulk samples. While the C1 detects the highest number of genes per cell and better resembles bulk RNA-seq, the Chromium identifies most differentially expressed genes, albeit still substantially fewer than bulk RNA-seq. Gene set enrichment analyses reveals that detection of a limited set of the most abundant genes in single cell RNA-seq experiments is sufficient for molecular phenotyping. Finally, single cell RNA-seq reveals a heterogeneous response of NGP neuroblastoma cells upon nutlin-3 treatment, revealing putative late-responder or resistant cells, both undetected in bulk RNA-seq experiments.
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- 2020
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6. Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development
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Pieter-Jan Volders, Marieke Lavaert, Kaat Durinck, Anne-Catherine Dolens, Bart Vandekerckhove, Pieter Van Vlierberghe, Tessa Kerre, Karin Weening, Pieter Mestdagh, Juliette Roels, Franki Speleman, Joni Van der Meulen, Jo Vandesompele, Katleen De Preter, Imke Velghe, Jelle De Medts, Tom Taghon, Katrien De Mulder, and Georges Leclercq
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Receptors, Antigen, T-Cell, alpha-beta ,BCL11B ,T cell ,Context (language use) ,Thymus Gland ,Biology ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Immunity ,microRNA ,Genetics ,medicine ,Humans ,Cell Lineage ,Receptor, Notch1 ,Molecular Biology ,Gene ,030304 developmental biology ,0303 health sciences ,Messenger RNA ,Mechanism (biology) ,Tumor Suppressor Proteins ,Cell Differentiation ,Receptors, Antigen, T-Cell, gamma-delta ,Articles ,Cell biology ,Repressor Proteins ,medicine.anatomical_structure ,030217 neurology & neurosurgery ,Signal Transduction - Abstract
γδ and αβ T cells have unique roles in immunity and both originate in the thymus from T‐lineage committed precursors through distinct but unclear mechanisms. Here, we show that Notch1 activation is more stringently required for human γδ development compared to αβ‐lineage differentiation and performed paired mRNA and miRNA profiling across 11 discrete developmental stages of human T cell development in an effort to identify the potential Notch1 downstream mechanism. Our data suggest that the miR‐17–92 cluster is a Notch1 target in immature thymocytes and that miR‐17 can restrict BCL11B expression in these Notch‐dependent T cell precursors. We show that enforced miR‐17 expression promotes human γδ T cell development and, consistently, that BCL11B is absolutely required for αβ but less for γδ T cell development. This study suggests that human γδ T cell development is mediated by a stage‐specific Notch‐driven negative feedback loop through which miR‐17 temporally restricts BCL11B expression and provides functional insights into the developmental role of the disease‐associated genes BCL11B and the miR‐17–92 cluster in a human context.
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- 2020
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7. Large-scale circular RNA deregulation in T-ALL: Unlocking unique ectopic expression of molecular subtypes
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Giuseppe Germano, Pieter Van Vlierberghe, Enrico Gaffo, Anna Dal Molin, Stefania Bortoluzzi, Kaat Durinck, Juliette Roels, Franki Speleman, Geertruij te Kronnie, Maria Teresa Siddi, Stéphanie Gachet, Tom Taghon, Matthias De Decker, Valentina Serafin, Alessia Buratin, and Maddalena Paganin
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0301 basic medicine ,LMO2 ,Lymphoid Neoplasia ,RNA ,Hematology ,RNA, Circular ,Biology ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Cell biology ,Cell Line ,Ectopic Gene Expression ,03 medical and health sciences ,MicroRNAs ,030104 developmental biology ,0302 clinical medicine ,Circular RNA ,030220 oncology & carcinogenesis ,microRNA ,Gene silencing ,Humans ,Ectopic expression ,Gene ,TAL1 - Abstract
Circular RNAs (circRNAs) are stable RNA molecules that can drive cancer through interactions with microRNAs and proteins and by the expression of circRNA encoded peptides. The aim of the study was to define the circRNA landscape and potential impact in T-cell acute lymphoblastic leukemia (T-ALL). Analysis by CirComPara of RNA-sequencing data from 25 T-ALL patients, immature, HOXA overexpressing, TLX1, TLX3, TAL1, or LMO2 rearranged, and from thymocyte populations of human healthy donors disclosed 68 554 circRNAs. Study of the top 3447 highly expressed circRNAs identified 944 circRNAs with significant differential expression between malignant T cells and normal counterparts, with most circRNAs displaying increased expression in T-ALL. Next, we defined subtype-specific circRNA signatures in molecular genetic subgroups of human T-ALL. In particular, circZNF609, circPSEN1, circKPNA5, and circCEP70 were upregulated in immature, circTASP1, circZBTB44, and circBACH1 in TLX3, circHACD1, and circSTAM in HOXA, circCAMSAP1 in TLX1, and circCASC15 in TAL-LMO. Backsplice sequences of 14 circRNAs ectopically expressed in T-ALL were confirmed, and overexpression of circRNAs in T-ALL with specific oncogenic lesions was substantiated by quantification in a panel of 13 human cell lines. An oncogenic role of circZNF609 in T-ALL was indicated by decreased cell viability upon silencing in vitro. Furthermore, functional predictions identified circRNA-microRNA gene axes informing modes of circRNA impact in molecular subtypes of human T-ALL.
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- 2020
8. TBX2 is a neuroblastoma core regulatory circuitry component enhancing MYCN/FOXM1 reactivation of DREAM targets
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Dieter Deforce, Dries Rombaut, Karen Verboom, Jan J. Molenaar, Suzanne Vanhauwaert, Pieter Mestdagh, Johan van Nes, G Schleiermacher, Bieke Decaesteker, Johannes H. Schulte, Filip Van Nieuwerburgh, Franki Speleman, Christophe Van Neste, Rogier Versteeg, Jolien De Wyn, Carl Herrmann, Katleen De Preter, Geertrui Denecker, Moritz Gartlgruber, Kaat Durinck, Daniel Dreidax, Pauline Depuydt, Fanny De Vloed, Valentina Boeva, Wouter Van Loocke, Waleed M. Kholosy, Frank Westermann, Bianca Koopmans, Emmy Dolman, Anke H. W. Essing, Carolina de Carvalho Nunes, Siebe Loontiens, Anton G. Henssen, Oncogenomics, CCA - Cancer biology and immunology, and Human Genetics
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0301 basic medicine ,Cancer Research ,General Physics and Astronomy ,Phenylenediamines ,BET-BROMODOMAIN INHIBITION ,Epigenesis, Genetic ,Histones ,Neuroblastoma ,MYCN ,Panobinostat ,Medicine and Health Sciences ,Transcriptional regulation ,TUMOR-SUPPRESSOR ,lcsh:Science ,Epigenomics ,Regulation of gene expression ,Gene knockdown ,N-Myc Proto-Oncogene Protein ,Multidisciplinary ,Brain Neoplasms ,Kv Channel-Interacting Proteins ,Azepines ,CANCER ,Cyclin-Dependent Kinases ,Gene Expression Regulation, Neoplastic ,Organoids ,TRANSCRIPTION FACTORS ,Signal Transduction ,EXPRESSION ,SEQUENCING DATA ,DNA Copy Number Variations ,Cell Survival ,Science ,Antineoplastic Agents ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Cell Line, Tumor ,medicine ,Humans ,Transcription factor ,neoplasms ,CHROMOSOME ARM 17Q ,SET ENRICHMENT ANALYSIS ,HEK 293 cells ,Forkhead Box Protein M1 ,Biology and Life Sciences ,General Chemistry ,Triazoles ,medicine.disease ,GENE ,Repressor Proteins ,030104 developmental biology ,HEK293 Cells ,Pyrimidines ,Cancer research ,FOXM1 ,lcsh:Q ,Tumor Suppressor Protein p53 ,T-Box Domain Proteins ,Cyclin-Dependent Kinase-Activating Kinase - Abstract
Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on 17q marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that TBX2 is a constituent of the recently established core regulatory circuitry in neuroblastoma with features of a cell identity transcription factor, driving proliferation through activation of p21-DREAM repressed FOXM1 target genes. Combined MYCN/TBX2 knockdown enforces cell growth arrest suggesting that TBX2 enhances MYCN sustained activation of FOXM1 targets. Targeting transcriptional addiction by combined CDK7 and BET bromodomain inhibition shows synergistic effects on cell viability with strong repressive effects on CRC gene expression and p53 pathway response as well as several genes implicated in transcriptional regulation. In conclusion, we provide insight into the role of the TBX2 CRC gene in transcriptional dependency of neuroblastoma cells warranting clinical trials using BET and CDK7 inhibitors., In high-risk neuroblastoma cases, gains in chromosome 17q are common. Here, the authors investigate the epigenomics and transcriptomics of neuroblastoma, identifying TBX2 as a core regulatory circuitry component enhancing the reactivation of DREAM targets by MYCN/FOXM1.
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- 2018
9. A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing
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Francisco Avila Cobos, Pieter-Jan Volders, Pieter Van Vlierberghe, Kaat Durinck, Emmanuelle Clappier, Charles E. de Bock, Zeynep Kalender Atak, Tom Taghon, Jo Vandesompele, Jan Cools, Jean Soulier, Karen Verboom, Franki Speleman, Simon Bornschein, Stein Aerts, Wouter Van Loocke, and Bieke Decaesteker
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0301 basic medicine ,T-Lymphocytes ,Disease ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,law.invention ,long non-coding RNAs ,Randomized controlled trial ,law ,Medicine and Health Sciences ,THERAPEUTIC RESPONSE ,Medicine ,RNA sequencing ,Azepines ,Hematology ,Gene Expression Regulation, Neoplastic ,Adult Acute Lymphoblastic Leukemia ,RNA Interference ,RNA, Long Noncoding ,CGVHD ,CLINICAL-TRIALS ,medicine.medical_specialty ,Randomization ,MEDLINE ,ACUTE GVHD ,DIAGNOSIS ,Odds ,03 medical and health sciences ,super-enhancer ,Cell Line, Tumor ,Proto-Oncogene Proteins ,Internal medicine ,Humans ,Pediatric Acute Lymphoblastic Leukemia ,Online Only Articles ,Homeodomain Proteins ,NIH CRITERIA ,Sequence Analysis, RNA ,business.industry ,Gene Expression Profiling ,Biology and Life Sciences ,Odds ratio ,CONSENSUS DEVELOPMENT PROJECT ,Triazoles ,Transplantation ,Clinical trial ,030104 developmental biology ,MARROW ,WORKING GROUP-REPORT ,Poly A ,business - Abstract
Graft-versus-host disease (GvHD) assessment has been shown to be a challenge for healthcare professionals, leading to the development of the eGVHD App (www.uzleuven.be/egvhd). In this study, we formally evaluated the accuracy of using the App compared to traditional assessment methods to assess GvHD. Our national multicenter randomized controlled trial involved seven Belgian transplantation centers and 78 healthcare professionals selected using a 2-stage convenience sampling approach between January and April 2017. Using a 1:1 randomization stratified by profession, healthcare professionals were assigned to use either the App ("APP") or their usual GvHD assessment aids ("No APP") to assess the diagnosis and severity score of 10 expert-validated clinical vignettes. Our main outcome measure was the difference in accuracy for GvHD severity scoring between both groups. The odds of being correct were 6.14 (95% CI: 2.83-13.34) and 6.29 (95% CI: 4.32-9.15) times higher in favor of the "APP" group for diagnosis and scoring, respectively (P
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- 2018
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10. Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription-qPCR data in mice
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Pieter Van Vlierberghe, Irina Lambertz, Ali Rihani, Steven Goossens, Niels Vandamme, Bieke Decaesteker, Andy Willaert, Marjolijn Renard, Marine Vanhomwegen, Jolien Van Laere, Jody J. Haigh, Geert Berx, Suzanne Vanhauwaert, Jo Vandesompele, and Franki Speleman
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Male ,0301 basic medicine ,Normalization (statistics) ,Cardiovascular Abnormalities ,lcsh:Medicine ,Mice, Transgenic ,Computational biology ,Biology ,Skin Diseases ,Article ,Mice ,Neuroblastoma ,03 medical and health sciences ,Reference genes ,Gene expression ,Medicine and Health Sciences ,Animals ,Humans ,REAL-TIME PCR ,lcsh:Science ,Gene ,Zebrafish ,IN-VIVO ,Repetitive Sequences, Nucleic Acid ,GENE-EXPRESSION ,Multidisciplinary ,Reverse Transcriptase Polymerase Chain Reaction ,lcsh:R ,RNA ,Biology and Life Sciences ,Reference Standards ,biology.organism_classification ,Reverse transcriptase ,MARFAN-SYNDROME ,Mice, Inbred C57BL ,MODEL ,Disease Models, Animal ,030104 developmental biology ,Real-time polymerase chain reaction ,DIFFERENTIATION ,Leukemia, Prolymphocytic, T-Cell ,Female ,lcsh:Q - Abstract
Reverse transcription quantitative PCR (RT-qPCR) is the gold standard method for gene expression analysis on mRNA level. To remove experimental variation, expression levels of the gene of interest are typically normalized to the expression level of stably expressed endogenous reference genes. Identifying suitable reference genes and determining the optimal number of reference genes should precede each quantification study. Popular reference genes are not necessarily stably expressed in the examined conditions, possibly leading to inaccurate results. Stably and universally expressed repetitive elements (ERE) have previously been shown to be an excellent alternative for normalization using classic reference genes in human and zebrafish samples. Here, we confirm that in mouse tissues, EREs are broadly applicable reference targets for RT-qPCR normalization, provided that the RNA samples undergo a thorough DNase treatment. We identified Orr1a0, Rltr2aiap, and Rltr13a3 as the most stably expressed mouse EREs across six different experimental conditions. Therefore, we propose this set of ERE reference targets as good candidates for normalization of RT-qPCR data in a plethora of conditions. The identification of widely applicable stable mouse RT-qPCR reference targets for normalization has great potential to facilitate future murine gene expression studies and improve the validity of RT-qPCR data.
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- 2018
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11. Cell of origin dictates aggression and stem cell number in acute lymphoblastic leukemia
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Franki Speleman, Elaine G. Garcia, Sara P. Garcia, David M. Langenau, Sowmya Iyer, Siebe Loontiens, and Ruslan I. Sadreyev
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0301 basic medicine ,Cancer Research ,T-Lymphocytes ,Lymphoblastic Leukemia ,Cell of origin ,Biology ,Article ,Animals, Genetically Modified ,03 medical and health sciences ,Transgenic zebrafish ,Tumor Cells, Cultured ,medicine ,Animals ,Humans ,Cell Lineage ,Zebrafish ,B-Lymphocytes ,Aggression ,Hematology ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,Clone Cells ,030104 developmental biology ,Oncology ,Neoplastic Stem Cells ,Cancer research ,medicine.symptom ,Stem cell - Published
- 2018
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12. Epigenetic regulation of neuroblastoma development
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Franki Speleman and Kaat Durinck
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0301 basic medicine ,Histology ,Carcinogenesis ,Biology ,medicine.disease_cause ,Chromatin remodeling ,Epigenesis, Genetic ,Pathology and Forensic Medicine ,Neuroblastoma ,03 medical and health sciences ,medicine ,Animals ,Humans ,Histone code ,Epigenetics ,DNA, Neoplasm ,Cell Biology ,Epigenome ,DNA Methylation ,Chromatin ,030104 developmental biology ,DNA methylation ,RNA, Long Noncoding ,Neuroscience ,Epigenetic therapy - Abstract
In recent years, technological advances have enabled a detailed landscaping of the epigenome and the mechanisms of epigenetic regulation that drive normal cell function, development and cancer. Rather than merely a structural entity to support genome compaction, we now look at chromatin as a very dynamic and essential constellation that is actively participating in the tight orchestration of transcriptional regulation as well as DNA replication and repair. The unique feature of chromatin flexibility enabling fast switches towards more or less restricted epigenetic cellular states is, not surprisingly, intimately connected to cancer development and treatment resistance, and the central role of epigenetic alterations in cancer is illustrated by the finding that up to 50% of all mutations across cancer entities affect proteins controlling the chromatin status. We summarize recent insights into epigenetic rewiring underlying neuroblastoma (NB) tumor formation ranging from changes in DNA methylation patterns and mutations in epigenetic regulators to global effects on transcriptional regulatory circuits that involve key players in NB oncogenesis. Insights into the disruption of the homeostatic epigenetic balance contributing to developmental arrest of sympathetic progenitor cells and subsequent NB oncogenesis are rapidly growing and will be exploited towards the development of novel therapeutic strategies to increase current survival rates of patients with high-risk NB.
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- 2018
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13. Abstract 2481: Time-resolved transcriptome analysis of murine TH-MYCN driven neuroblastoma identifies MEIS2 as early initiating factor and novel core gene regulatory circuitry constituent
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Glenn M. Marshall, A. Thomas Look, Katleen De Preter, Kaat Durinck, Pieter-Jan Volders, Anneleen Beckers, Daniel R. Carter, Belamy B. Cheung, Mark W. Zimmerman, Carolina de Carvalho Nunes, Bieke Decaesteker, Christophe Van Neste, Adam D. Durbin, Franki Speleman, Wouter Van Loocke, Nina Weichert-Leahey, and Jolien Dewyn
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Transcriptome ,Cancer Research ,Oncology ,Neuroblastoma ,medicine ,Computational biology ,Biology ,medicine.disease ,neoplasms ,Core gene - Abstract
Introduction: Neuroblastoma (NB) is a pediatric malignancy arising from peripheral neuronal sympathoblasts and exhibiting remarkable clinical and genetic heterogeneity. Patients older than 18 months have a poor prognosis with tumors presenting with highly recurrent segmental copy number alterations and MYCN amplification in half of these high-risk cases. The mechanism by which MYCN contributes to the development of neuroblastoma is unresolved and direct targeting of this key oncogene is not currently possible. Experimental Procedures: Our discovery efforts focused on identifying cooperating interactors and vulnerabilities in the MYCN regulatory network. MYCN-driven NBs can be modeled in mice with morphologic and genomic features that recapitulate human MYCN amplified NBs. Thus, this model serves as a valid tool for cross-species genomic analysis. Using this model, we performed a time-resolved analysis of the dynamic transcriptional changes of protein coding genes during murine TH-MYCN driven neuroblastoma development, focusing on timepoints representing tumor initiation and early tumor growth. We triangulated expression changes of key genes with publicly available exome-wide CRISPR-cas9 knockout analyses on a panel of human neuroblastoma cell lines and patient survival data. This unique data resource uncovered the relevance of MEIS2 as putative early cooperating initiating factor for neuroblastoma. Analysis of the genome-wide binding profile of MEIS2 in MYCN-amplified NB cell lines showed a striking overlap with enhancer-driven gene expression in regions of open chromatin, providing evidence that MEIS2 is a novel member of the adrenergic neuroblastoma core-regulatory circuitry. CRISPR-Cas9 mediated deletion of MEIS2 in animal models suppresses establishment of neuroblastoma tumors, indicating its putative requirement for tumor initiation. MEIS2, as a member of the CRC binds to several master regulators of gene expression, including the FOXM1 locus. Summary and conclusion: In conclusion, we present an in-depth characterization of the dynamic transcriptome profiles of TH-MYCN driven murine premalignant and established tumors and integrate with both primary human neuroblastoma tumor expression data, epigenetic and functional genomics data to identify and validate candidate cooperating dependencies suitable for targeting as a precision medicine approach in neuroblastoma. Citation Format: Kaat Durinck, Mark Zimmerman, Nina Weichert-Leahey, Jolien Dewyn, Wouter Van Loocke, Carolina Nunes, Anneleen Beckers, Bieke Decaesteker, Pieter-Jan Volders, Christophe Van Neste, Belamy Cheung, Daniel Carter, Thomas A. Look, Glenn Marshall, Katleen De Preter, Adam Durbin, Franki Speleman. Time-resolved transcriptome analysis of murine TH-MYCN driven neuroblastoma identifies MEIS2 as early initiating factor and novel core gene regulatory circuitry constituent [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2481.
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- 2021
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14. Shallow Whole Genome Sequencing on Circulating Cell-Free DNA Allows Reliable Noninvasive Copy-Number Profiling in Neuroblastoma Patients
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Marleen Renard, Jo Van Dorpe, Nadine Van Roy, Genevieve Laureys, Katleen De Preter, Franki Speleman, Bram De Wilde, Tom Sante, Björn Menten, Tim Lammens, Charlotte Vandeputte, Malaïka Van Der Linden, and Annelies Dheedene
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0301 basic medicine ,Cancer Research ,DNA Copy Number Variations ,Genes, myc ,Biology ,Circulating Tumor DNA ,Neuroblastoma ,03 medical and health sciences ,0302 clinical medicine ,Biomarkers, Tumor ,medicine ,Humans ,Neoplasm Metastasis ,Liquid biopsy ,Gene ,ATRX ,Neoplasm Staging ,Whole genome sequencing ,Comparative Genomic Hybridization ,Whole Genome Sequencing ,Liquid Biopsy ,Infant ,medicine.disease ,Molecular biology ,Primary tumor ,Circulating Cell-Free DNA ,030104 developmental biology ,Oncology ,Child, Preschool ,030220 oncology & carcinogenesis ,Cancer research ,Comparative genomic hybridization - Abstract
Purpose: Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and by the presence of typical copy-number alterations (CNAs). Given the strong association of these CNA profiles with prognosis, analysis of the CNA profile at diagnosis is mandatory. Therefore, we tested whether the analysis of circulating cell-free DNA (cfDNA) present in plasma samples of patients with NB could offer a valuable alternative to primary tumor DNA for CNA profiling. Experimental Design: In 37 patients with NB, cfDNA analysis using shallow whole genome sequencing (sWGS) was compared with arrayCGH analysis of primary tumor tissue. Results: Comparison of CNA profiles on cfDNA showed highly concordant patterns, particularly in high-stage patients. Numerical chromosome imbalances as well as large and focal structural aberrations including MYCN and LIN28B amplification and ATRX deletion could be readily detected with sWGS using a low input of cfDNA. Conclusions: In conclusion, sWGS analysis on cfDNA offers a cost-effective, noninvasive, rapid, robust and sensitive alternative for tumor DNA copy-number profiling in most patients with NB. Clin Cancer Res; 23(20); 6305–14. ©2017 AACR.
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- 2017
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15. Comprehensive miRNA expression profiling in human T-cell acute lymphoblastic leukemia by small RNA-sequencing
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Wouter Van Loocke, Tom Taghon, Annelynn Wallaert, Franki Speleman, Lucie Hernandez, and Pieter Van Vlierberghe
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0301 basic medicine ,Gene isoform ,Small RNA ,MICRORNAS ,T-Lymphocytes ,Science ,ONCOGENE ,Biology ,Article ,PATHWAY ,03 medical and health sciences ,REPERTOIRE ,IsomiR ,microRNA ,Gene expression ,Medicine and Health Sciences ,Humans ,Gene silencing ,TUMOR-SUPPRESSOR ,GENE-EXPRESSION ,Genetics ,ADENYLATION ,Multidisciplinary ,COMPLEXITY ,Sequence Analysis, RNA ,Gene Expression Profiling ,RNA ,Biology and Life Sciences ,SIGNATURES DEFINE ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,Gene expression profiling ,MicroRNAs ,030104 developmental biology ,Medicine ,GENERATION - Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease that can be classified into different molecular genetic subtypes according to their mRNA gene expression profile. In this study, we applied RNA sequencing to investigate the full spectrum of miRNA expression in primary T-ALL patient samples, T-ALL leukemia cell lines and healthy donor thymocytes. Notably, this analysis revealed that genetic subtypes of human T-ALL also display unique miRNA expression signatures, which are largely conserved in human T-ALL cell lines with corresponding genetic background. Furthermore, small RNA-sequencing also unraveled the variety of isoforms that are expressed for each miRNA in T-ALL and showed that a significant number of miRNAs are actually represented by an alternative isomiR. Finally, comparison of CD34+ and CD4+CD8+ healthy donor thymocytes and T-ALL miRNA profiles allowed identifying several novel miRNAs with putative oncogenic or tumor suppressor functions in T-ALL. Altogether, this study provides a comprehensive overview of miRNA expression in normal and malignant T-cells and sets the stage for functional evaluation of novel miRNAs in T-ALL disease biology.
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- 2017
16. Long non-coding RNAs in leukemia
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Franki Speleman, Pieter Van Vlierberghe, Annelynn Wallaert, Kaat Durinck, and Tim Lammens
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0301 basic medicine ,Chronic lymphocytic leukemia ,Disease ,Biology ,Bioinformatics ,Neoplasm genetics ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,Regulation of gene expression ,Leukemia ,Gene Expression Regulation, Leukemic ,RNA ,Hematology ,Chromatin Assembly and Disassembly ,Prognosis ,medicine.disease ,Cell Transformation, Neoplastic ,030104 developmental biology ,Drug Resistance, Neoplasm ,030220 oncology & carcinogenesis ,Biomarker (medicine) ,RNA, Long Noncoding ,Biomarkers ,Signal Transduction - Abstract
Over the last years, long non-coding RNAs (lncRNAs) have emerged as putative regulators of malignant hematopoietic development. Here, we review recent literature on the involvement of lncRNAs in leukemia, including their role in driving or sustaining disease and their potential impact on diagnosis, classification, and prognosis.Leukemogenesis is a complex process resulting from the accumulation of multiple genetic alterations. Over the last years, advances in high-throughput sequencing and transcriptome profiling have enabled the identification of lncRNAs involved in leukemia development. lncRNAs are able to distinguish different subtypes of human leukemia and several reports have identified specific patterns of lncRNA expression associated with clinical patient characteristics. Although functional studies on the actual role of these lncRNAs during transformation remain scarce, emerging evidence suggests that complex interactions between coding and non-coding transcript are truly involved in leukemia development.Introduction of lncRNAs as an additional layer of complexity in human leukemia might provide new molecular genetic insights in the biology of this disease and could create unique opportunities for the identification of novel drug targets and diagnostic or prognostic biomarkers.
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- 2017
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17. Glutathione biosynthesis is upregulated at the initiation of MYCN-driven neuroblastoma tumorigenesis
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Glenn M. Marshall, Marina Pajic, Murray D. Norris, Eric Sekyere, Katleen De Preter, Belamy B. Cheung, Rani E. George, Daniel R. Carter, Michelle Haber, Selina K. Sutton, Anneleen Beckers, Jamie I. Fletcher, Jayne Murray, and Franki Speleman
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0301 basic medicine ,Cancer Research ,Carcinogenesis ,Mice, Transgenic ,Tumor initiation ,Biology ,PKM2 ,medicine.disease_cause ,N-Myc Proto-Oncogene Protein ,Mice ,Neuroblastoma ,03 medical and health sciences ,chemistry.chemical_compound ,Peripheral Nervous System Neoplasms ,Genetics ,medicine ,Animals ,Humans ,Buthionine sulfoximine ,neoplasms ,Ganglia, Sympathetic ,Articles ,General Medicine ,Glutathione ,medicine.disease ,Molecular biology ,Biosynthetic Pathways ,Disease Models, Animal ,030104 developmental biology ,Oncology ,chemistry ,Metabolome ,Cancer research ,Molecular Medicine ,N-Myc - Abstract
The MYCN gene is amplified and overexpressed in a large proportion of high stage neuroblastoma patients and has been identified as a key driver of tumorigenesis. However, the mechanism by which MYCN promotes tumor initiation is poorly understood. Here we conducted metabolic profiling of pre‐malignant sympathetic ganglia and tumors derived from the TH‐MYCN mouse model of neuroblastoma, compared to non‐malignant ganglia from wildtype littermates. We found that metabolites involved in the biosynthesis of glutathione, the most abundant cellular antioxidant, were the most significantly upregulated metabolic pathway at tumor initiation, and progressively increased to meet the demands of tumorigenesis. A corresponding increase in the expression of genes involved in ribosomal biogenesis suggested that MYCN‐driven transactivation of the protein biosynthetic machinery generated the necessary substrates to drive glutathione biosynthesis. Pre‐malignant sympathetic ganglia from TH‐MYCN mice had higher antioxidant capacity and required glutathione upregulation for cell survival, when compared to wildtype ganglia. Moreover, in vivo administration of inhibitors of glutathione biosynthesis significantly delayed tumorigenesis when administered prophylactically and potentiated the anticancer activity of cytotoxic chemotherapy against established tumors. Together these results identify enhanced glutathione biosynthesis as a selective metabolic adaptation required for initiation of MYCN‐driven neuroblastoma, and suggest that glutathione‐targeted agents may be used as a potential preventative strategy, or as an adjuvant to existing chemotherapies in established disease.
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- 2016
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18. PRL3 enhances T cell acute lymphoblastic leukemia growth through suppressing T cell signaling pathways and apoptosis
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Jessica S. Blackburn, D Do, Mariana L. Oliveira, P. Van Vlierberghe, Sara P. Garcia, C Yan, João T. Barata, Filip Matthijssens, Tom Taghon, J R Allen, W Van Loocke, David M. Langenau, Franki Speleman, Elaine G. Garcia, Sowmya Iyer, A Veloso, R Morris, Siebe Loontiens, Alejandro Gutierrez, Karin M. McCarthy, N Iftimia, Wilhelm Haas, and Dalton C. Brunson
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0301 basic medicine ,Cancer Research ,VAV1 ,T cell ,T-Lymphocytes ,Phosphatase ,Apoptosis ,Protein tyrosine phosphatase ,Mice, SCID ,Biology ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Mice, Inbred NOD ,medicine ,Biomarkers, Tumor ,Tumor Cells, Cultured ,Animals ,Humans ,Zebrafish ,Cell Proliferation ,Hematology ,medicine.disease ,Prognosis ,Xenograft Model Antitumor Assays ,Neoplasm Proteins ,Gene Expression Regulation, Neoplastic ,Leukemia ,030104 developmental biology ,medicine.anatomical_structure ,Oncology ,030220 oncology & carcinogenesis ,Cancer research ,Phosphorylation ,Female ,Signal transduction ,Protein Tyrosine Phosphatases ,Tyrosine kinase - Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of thymocytes and is largely driven by the NOTCH/MYC pathway. Yet, additional oncogenic drivers are required for transformation. Here, we identify protein tyrosine phosphatase type 4 A3 (PRL3) as a collaborating oncogenic driver in T-ALL. PRL3 is expressed in a large fraction of primary human T-ALLs and is commonly co-amplified with MYC. PRL3 also synergized with MYC to initiate early-onset ALL in transgenic zebrafish and was required for human T-ALL growth and maintenance. Mass-spectrometry phosphoproteomic analysis and mechanistic studies uncovered that PRL3 suppresses downstream T-cell phosphorylation signaling pathways, including those modulated by VAV1, and subsequently suppresses apoptosis in leukemia cells. Taken together, our studies have identified new roles for PRL3 as a collaborating oncogenic driver in human T-ALL and suggest that therapeutic targeting of the PRL3 phosphatase will likely be a useful treatment strategy for T-ALL.
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- 2020
19. In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors
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Suzanne Vanhauwaert, Katleen De Preter, Franki Speleman, Pieter Mestdagh, Jo Vandesompele, Kaat Durinck, Geertrui Denecker, Bieke Decaesteker, Carina Leonelli, Christophe Van Neste, Karen Sermon, Sara De Brouwer, Basic (bio-) Medical Sciences, and Reproduction and Genetics
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0301 basic medicine ,MICRORNAS ,Genes, myc ,lcsh:Medicine ,Mice ,Neuroblastoma ,TARGETING MYCN ,BINDING ,Gene expression ,Medicine and Health Sciences ,TRANSCRIPTION ,lcsh:Science ,GENE-EXPRESSION ,Multidisciplinary ,Cell Cycle ,Prognosis ,CANCER ,Publisher Correction ,Neoplastic Stem Cells ,Stem cell ,STEM-CELLS ,Signal Transduction ,In silico ,B-MYB ,DNA-DAMAGE RESPONSE ,Antineoplastic Agents ,Mice, Transgenic ,Biology ,Article ,03 medical and health sciences ,microRNA ,medicine ,Animals ,Humans ,Computer Simulation ,neoplasms ,Gene ,Embryonic Stem Cells ,LANDSCAPE ,lcsh:R ,Forkhead Box Protein M1 ,Biology and Life Sciences ,medicine.disease ,Embryonic stem cell ,030104 developmental biology ,general ,Drug Design ,Cancer research ,FOXM1 ,lcsh:Q ,DNA Damage - Abstract
Chemotherapy resistance is responsible for high mortality rates in neuroblastoma. MYCN, an oncogenic driver in neuroblastoma, controls pluripotency genes including LIN28B. We hypothesized that enhanced embryonic stem cell (ESC) gene regulatory programs could mark tumors with high pluripotency capacity and subsequently increased risk for therapy failure. An ESC miRNA signature was established based on publicly available data. In addition, an ESC mRNA signature was generated including the 500 protein coding genes with the highest positive expression correlation with the ESC miRNA signature score in 200 neuroblastomas. High ESC m(i)RNA expression signature scores were significantly correlated with poor neuroblastoma patient outcome specifically in the subgroup of MYCN amplified tumors and stage 4 nonamplified tumors. Further data-mining identified FOXM1, as the major predicted driver of this ESC signature, controlling a large set of genes implicated in cell cycle control and DNA damage response. Of further interest, re-analysis of published data showed that MYCN transcriptionally activates FOXM1 in neuroblastoma cells. In conclusion, a novel ESC m(i)RNA signature stratifies neuroblastomas with poor prognosis, enabling the identification of therapy-resistant tumors. The finding that this signature is strongly FOXM1 driven, warrants for drug design targeted at FOXM1 or key components controlling this pathway.
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- 2018
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20. Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes
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Kaat Durinck, Charlotte Gistelinck, Jo Vandesompele, Lisa Depestel, Suzanne Vanhauwaert, Siebe Loontiens, Karen Verboom, Givani Dewyn, Andy Willaert, Filip Matthijssens, Franki Speleman, and Wouter Van Loocke
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EXPRESSION ,0106 biological sciences ,Quality Control ,FACS sorting ,Lysis ,lcsh:QH426-470 ,lcsh:Biotechnology ,Cell Count ,Biology ,01 natural sciences ,Transcriptome ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,Gene expression ,Lysis buffer ,Genetics ,Animals ,Zebrafish ,030304 developmental biology ,0303 health sciences ,Sequence Analysis, RNA ,Methodology Article ,Biology and Life Sciences ,RNA ,RNA sequencing ,Flow Cytometry ,Cell biology ,MODEL ,GENOME ,genomic DNA ,lcsh:Genetics ,RNA isolation ,RNA extraction ,DNA microarray ,Poly A ,010606 plant biology & botany ,Biotechnology - Abstract
Background Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield are key determinant factors for accurate expression profiling. Limited cell number and FACS induced cellular stress make RNA isolation of sorted zebrafish cells a delicate process. We aimed to optimize a workflow to extract sufficient amounts of high-quality RNA from a limited number of FACS sorted cells from Tg(fli1a:GFP) zebrafish embryos, which can be used for accurate gene expression analysis. Results We evaluated two suitable RNA isolation kits (the RNAqueous micro and the RNeasy plus micro kit) and determined that sorting cells directly into lysis buffer is a critical step for success. For low cell numbers, this ensures direct cell lysis, protects RNA from degradation and results in a higher RNA quality and yield. We showed that this works well up to 0.5× dilution of the lysis buffer with sorted cells. In our sort settings, this corresponded to 30,000 and 75,000 cells for the RNAqueous micro kit and RNeasy plus micro kit respectively. Sorting more cells dilutes the lysis buffer too much and requires the use of a collection buffer. We also demonstrated that an additional genomic DNA removal step after RNA isolation is required to completely clear the RNA from any contaminating genomic DNA. For cDNA synthesis and library preparation, we combined SmartSeq v4 full length cDNA library amplification, Nextera XT tagmentation and sample barcoding. Using this workflow, we were able to generate highly reproducible RNA sequencing results. Conclusions The presented optimized workflow enables to generate high quality RNA and allows accurate transcriptome profiling of small populations of sorted zebrafish cells. Electronic supplementary material The online version of this article (10.1186/s12864-019-5608-2) contains supplementary material, which is available to authorized users.
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- 2018
21. Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients
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Rogier Versteeg, Wendy B. London, Valérie Combaret, Jan Koster, Rosa Noguera, Gudrun Schleiermacher, Toby Dylan Hocking, Julie R. Park, Matthias Fischer, Edward F. Attiyeh, Michael D. Hogarty, Genevieve Laureys, Katleen De Preter, Miki Ohira, Pauline Depuydt, Ruth Ladenstein, Franki Speleman, Gian Paolo Tonini, Jessica Theissen, Peter F. Ambros, Raffaella Defferrari, Shahab Asgharzadeh, Akira Nakagawara, Valentina Boeva, Luigi Varesio, Ulrike Pötschger, Barbara Hero, Inge M. Ambros, John M. Maris, Eve Lapouble, Robrecht Cannoodt, Katia Mazzocco, Dominique Valteau-Couanet, Susan G. Kreissman, Meredith S. Irwin, Oncogenomics, and CCA - Imaging and biomarkers
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0301 basic medicine ,Oncology ,Cancer Research ,Somatic cell ,Neuroblastoma ,0302 clinical medicine ,Gene duplication ,Medicine and Health Sciences ,High risk neuroblastoma ,N-Myc Proto-Oncogene Protein ,ABNORMALITIES ,Intensive treatment ,Genomics ,Articles ,Prognosis ,3. Good health ,Child, Preschool ,030220 oncology & carcinogenesis ,Chromosomes, Human, Pair 6 ,Chromosome Deletion ,INTEGRATION ,medicine.medical_specialty ,DNA Copy Number Variations ,CLASSIFICATION ,03 medical and health sciences ,AGE ,Internal medicine ,STRATIFICATION ,Clinical heterogeneity ,Biomarkers, Tumor ,medicine ,Humans ,Genetic Predisposition to Disease ,Copy number aberration ,neoplasms ,Genetic Association Studies ,Neoplasm Staging ,ACCUMULATION ,business.industry ,OUTCOME PREDICTION ,Gene Amplification ,Infant ,Biology and Life Sciences ,DNA ,medicine.disease ,DELINEATION ,030104 developmental biology ,COPY NUMBER ,Outcome prediction ,business - Abstract
Background Neuroblastoma is characterized by substantial clinical heterogeneity. Despite intensive treatment, the survival rates of high-risk neuroblastoma patients are still disappointingly low. Somatic chromosomal copy number aberrations have been shown to be associated with patient outcome, particularly in low- and intermediate-risk neuroblastoma patients. To improve outcome prediction in high-risk neuroblastoma, we aimed to design a prognostic classification method based on copy number aberrations. Methods In an international collaboration, normalized high-resolution DNA copy number data (arrayCGH and SNP arrays) from 556 high-risk neuroblastomas obtained at diagnosis were collected from nine collaborative groups and segmented using the same method. We applied logistic and Cox proportional hazard regression to identify genomic aberrations associated with poor outcome. Results In this study, we identified two types of copy number aberrations that are associated with extremely poor outcome. Distal 6q losses were detected in 5.9% of patients and were associated with a 10-year survival probability of only 3.4% (95% confidence interval [CI] = 0.5% to 23.3%, two-sided P = .002). Amplifications of regions not encompassing the MYCN locus were detected in 18.1% of patients and were associated with a 10-year survival probability of only 5.8% (95% CI = 1.5% to 22.2%, two-sided P < .001). Conclusions Using a unique large copy number data set of high-risk neuroblastoma cases, we identified a small subset of high-risk neuroblastoma patients with extremely low survival probability that might be eligible for inclusion in clinical trials of new therapeutics. The amplicons may also nominate alternative treatments that target the amplified genes.
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- 2018
22. PS920 PHF6 LOSS DRIVES IL7R ONCOGENE ADDICTION IN TLX1 DRIVEN T-ALL
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Franki Speleman, Tom Taghon, P. Van Vlierberghe, Givani Dewyn, David M. Langenau, João T. Barata, Suzanne Vanhauwaert, Mariana L. Oliveira, Kaat Durinck, Lisa Depestel, Jan Cools, Siebe Loontiens, and C E de Bock
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Cancer research ,Hematology ,Interleukin-7 receptor ,Oncogene Addiction ,Psychology - Published
- 2019
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23. Network Modeling of microRNA-mRNA Interactions in Neuroblastoma Tumorigenesis Identifies miR-204 as a Direct Inhibitor of MYCN
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Michelle Haber, Chelsea Mayoh, Franki Speleman, Glenn M. Marshall, Katleen De Preter, Amit Lalwani, Murray D. Norris, Tzong-Tyng Hung, Chi Yan Ooi, Belamy B. Cheung, Daniel R. Carter, Sara De Brouwer, Zsuzsanna Nagy, Tao Liu, Anneleen Beckers, Bing Liu, and Bieke Decaesteker
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0301 basic medicine ,Male ,Cancer Research ,Carcinogenesis ,Gene regulatory network ,Datasets as Topic ,Mice, Nude ,Mice, Transgenic ,Biology ,medicine.disease_cause ,law.invention ,03 medical and health sciences ,Mice ,Neuroblastoma ,law ,Peripheral Nervous System Neoplasms ,Cell Line, Tumor ,microRNA ,medicine ,Animals ,Humans ,Gene Regulatory Networks ,Genes, Tumor Suppressor ,RNA, Messenger ,Promoter Regions, Genetic ,neoplasms ,Cell Proliferation ,Regulation of gene expression ,N-Myc Proto-Oncogene Protein ,Oncogenes ,medicine.disease ,Pediatric cancer ,Xenograft Model Antitumor Assays ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,030104 developmental biology ,Oncology ,Cancer research ,Suppressor ,Female ,N-Myc - Abstract
Neuroblastoma is a pediatric cancer of the sympathetic nervous system where MYCN amplification is a key indicator of poor prognosis. However, mechanisms by which MYCN promotes neuroblastoma tumorigenesis are not fully understood. In this study, we analyzed global miRNA and mRNA expression profiles of tissues at different stages of tumorigenesis from TH-MYCN transgenic mice, a model of MYCN-driven neuroblastoma. On the basis of a Bayesian learning network model in which we compared pretumor ganglia from TH-MYCN+/+ mice to age-matched wild-type controls, we devised a predicted miRNA–mRNA interaction network. Among the miRNA–mRNA interactions operating during human neuroblastoma tumorigenesis, we identified miR-204 as a tumor suppressor miRNA that inhibited a subnetwork of oncogenes strongly associated with MYCN-amplified neuroblastoma and poor patient outcome. MYCN bound to the miR-204 promoter and repressed miR-204 transcription. Conversely, miR-204 directly bound MYCN mRNA and repressed MYCN expression. miR-204 overexpression significantly inhibited neuroblastoma cell proliferation in vitro and tumorigenesis in vivo. Together, these findings identify novel tumorigenic miRNA gene networks and miR-204 as a tumor suppressor that regulates MYCN expression in neuroblastoma tumorigenesis. Significance: Network modeling of miRNA–mRNA regulatory interactions in a mouse model of neuroblastoma identifies miR-204 as a tumor suppressor and negative regulator of MYCN. Cancer Res; 78(12); 3122–34. ©2018 AACR.
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- 2017
24. T-ALL and thymocytes: a message of noncoding RNAs
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Tom Taghon, Pieter Van Vlierberghe, Annelynn Wallaert, Franki Speleman, and Kaat Durinck
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0301 basic medicine ,Cancer Research ,RNA, Untranslated ,Carcinogenesis ,T cell ,Review ,Biology ,medicine.disease_cause ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,lcsh:RC254-282 ,Microprocessor complex ,03 medical and health sciences ,hemic and lymphatic diseases ,microRNA ,Medicine and Health Sciences ,medicine ,Animals ,Humans ,TUMOR-SUPPRESSOR ,COMPETING ENDOGENOUS RNA ,Molecular Biology ,Gene ,ACUTE LYMPHOBLASTIC-LEUKEMIA ,GENE-EXPRESSION ,CELL DEVELOPMENT ,Genetics ,Thymocytes ,Competing endogenous RNA ,Cell growth ,lcsh:RC633-647.5 ,Lymphopoiesis ,Biology and Life Sciences ,SIGNATURES DEFINE ,MicroRNA ,MICROPROCESSOR COMPLEX ,Hematology ,lcsh:Diseases of the blood and blood-forming organs ,MIRNA EXPRESSION ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,MICRORNA BIOGENESIS ,Long non-coding RNA ,LncRNA ,GLUCOCORTICOID-RECEPTOR ,030104 developmental biology ,medicine.anatomical_structure ,Oncology ,T-ALL - Abstract
In the last decade, the role for noncoding RNAs in disease was clearly established, starting with microRNAs and later expanded towards long noncoding RNAs. This was also the case for T cell acute lymphoblastic leukemia, which is a malignant blood disorder arising from oncogenic events during normal T cell development in the thymus. By studying the transcriptomic profile of protein-coding genes, several oncogenic events leading to T cell acute lymphoblastic leukemia (T-ALL) could be identified. In recent years, it became apparent that several of these oncogenes function via microRNAs and long noncoding RNAs. In this review, we give a detailed overview of the studies that describe the noncoding RNAome in T-ALL oncogenesis and normal T cell development.
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- 2017
25. Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome
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Geertrui Denecker, Candy Kumps, Kaat Durinck, Robrecht Cannoodt, Katleen De Preter, Shana Claeys, and Franki Speleman
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0301 basic medicine ,REACTOME PATHWAY KNOWLEDGEBASE ,HYPOXIA-INDUCIBLE ADRENOMEDULLIN ,medicine.drug_class ,CELL LUNG-CANCER ,Inflammation ,UP-REGULATION ,Transcriptome ,03 medical and health sciences ,neuroblastoma ,0302 clinical medicine ,Breast cancer ,Downregulation and upregulation ,Neuroblastoma ,hemic and lymphatic diseases ,HEPATOCELLULAR-CARCINOMA ,medicine ,Medicine and Health Sciences ,BREAST-CANCER ,ALK signaling ,FUNCTIONAL VALIDATION ,IN-VIVO ,dynamic ,business.industry ,Sunitinib ,MYCN AMPLIFICATION ,Biology and Life Sciences ,medicine.disease ,ALK inhibitor ,030104 developmental biology ,Oncology ,ALK ,030220 oncology & carcinogenesis ,Hepatocellular carcinoma ,Cancer research ,ALK inhibition ,medicine.symptom ,business ,RESISTANCE ,Research Paper ,medicine.drug - Abstract
// Shana Claeys 1, 2 , Geertrui Denecker 1, 2 , Robrecht Cannoodt 1, 2, 3, 4, 5 , Candy Kumps 1, 6 , Kaat Durinck 1, 2 , Frank Speleman 1, 2 and Katleen De Preter 1, 2 1 Center for Medical Genetics, Ghent University, Ghent, Belgium 2 Cancer Research Institute Ghent, Ghent University, Ghent, Belgium 3 Bioinformatics Institute Ghent From Nucleotides to Networks, Ghent, Belgium 4 Data Mining and Modelling for Biomedicine group, VIB Inflammation Research Center, Ghent, Belgium 5 Department of Respiratory Medicine, Ghent University, Ghent, Belgium 6 Department of Uro-Gynaecology, Ghent University Hospital, Ghent, Belgium Correspondence to: Katleen De Preter, email: Katleen.DePreter@UGent.be Keywords: neuroblastoma; ALK; ALK inhibition; ALK signaling; dynamic Received: July 28, 2017 Accepted: October 17, 2017 Published: November 06, 2017 ABSTRACT Background: Neuroblastoma is an aggressive childhood malignancy of the sympathetic nervous system. Despite multi-modal therapy, survival of high-risk patients remains disappointingly low, underscoring the need for novel treatment strategies. The discovery of ALK activating mutations opened the way to precision treatment in a subset of these patients. Previously, we investigated the transcriptional effects of pharmacological ALK inhibition on neuroblastoma cell lines, six hours after TAE684 administration, resulting in the 77-gene ALK signature, which was shown to gradually decrease from 120 minutes after TAE684 treatment, to gain deeper insight into the molecular effects of oncogenic ALK signaling. Aim: Here, we further dissected the transcriptional dynamic profiles of neuroblastoma cells upon TAE684 treatment in a detailed timeframe of ten minutes up to six hours after inhibition, in order to identify additional early targets for combination treatment. Results: We observed an unexpected initial upregulation of positively regulated MYCN target genes following subsequent downregulation of overall MYCN activity. In addition, we identified adrenomedullin (ADM), previously shown to be implicated in sunitinib resistance, as the earliest response gene upon ALK inhibition. Conclusions: We describe the early and late effects of ALK inhibitor TAE684 treatment on the neuroblastoma transcriptome. The observed unexpected upregulation of ADM warrants further investigation in relation to putative ALK resistance in neuroblastoma patients currently undergoing ALK inhibitor treatment.
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- 2017
26. Targeting tachykinin receptors in neuroblastoma
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Andrea Odersky, Anton G. Henssen, Kathy Astrahanseff, Katleen De Preter, Annabell Szymansky, Angelika Eggert, Marleen Seiler, Simon Schäfers, Joachim Struck, Andreas Bergmann, Alexander Schramm, Johannes H. Schulte, Franki Speleman, Kristina Althoff, and Anneleen Beckers
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0301 basic medicine ,Cancer Research ,medicine.medical_treatment ,Medizin ,Drug Evaluation, Preclinical ,Apoptosis ,Substance P ,Pharmacology ,BIOCONDUCTOR ,Targeted therapy ,Mice ,chemistry.chemical_compound ,0302 clinical medicine ,E2F2 Transcription Factor ,Neurokinin-1 Receptor Antagonists ,Medicine and Health Sciences ,Prodrugs ,Molecular Targeted Therapy ,NK-1 ,Aprepitant ,E2F2 ,ANTAGONIST APREPITANT ,aprepitant ,Receptors, Neurokinin-1 ,Flow Cytometry ,targeted therapy ,Tumor Burden ,3. Good health ,NEUROKININ-1 RECEPTOR ,CELL LINES ,APOPTOSIS ,NK1R ,Treatment Outcome ,Oncology ,030220 oncology & carcinogenesis ,GROWTH ,Female ,Signal Transduction ,Research Paper ,medicine.drug ,EXPRESSION ,Cell Survival ,Morpholines ,Mice, Nude ,Antineoplastic Agents ,Enzyme-Linked Immunosorbent Assay ,03 medical and health sciences ,neuroblastoma ,Cell Line, Tumor ,Neuroblastoma ,Tachykinin receptor 1 ,medicine ,Animals ,Humans ,Viability assay ,fosaprepitant ,Cell Proliferation ,business.industry ,Gene Expression Profiling ,Biology and Life Sciences ,PATHWAYS ,medicine.disease ,SUBSTANCE-P ,Xenograft Model Antitumor Assays ,030104 developmental biology ,chemistry ,Tumor Suppressor Protein p53 ,Tachykinin receptor ,business - Abstract
Neuroblastoma is the most common extracranial tumor in children. Despite aggressive multimodal treatment, high-risk neuroblastoma remains a clinical challenge with survival rates below 50%. Adding targeted drugs to first-line therapy regimens is a promising approach to improve survival in these patients. TACR1 activation by substance P has been reported to be mitogenic in cancer cell lines. Tachykinin receptor (TACR1) antagonists are approved for clinical use as an antiemetic remedy since 2003. Tachykinin receptor inhibition has recently been shown to effectively reduce growth of several tumor types. Here, we report that neuroblastoma cell lines express TACR1, and that targeting TACR1 activity significantly reduced cell viability and induced apoptosis in neuroblastoma cell lines. Gene expression profiling revealed that TACR1 inhibition repressed E2F2 and induced TP53 signaling. Treating mice harboring established neuroblastoma xenograft tumors with Aprepitant also significantly reduced tumor burden. Thus, we provide evidence that the targeted inhibition of tachykinin receptor signaling shows therapeutic efficacy in preclinical models for high-risk neuroblastoma.
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- 2017
27. Epigenetics in T-cell acute lymphoblastic leukemia
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Franki Speleman, Pieter Van Vlierberghe, Joni Van der Meulen, Inge Van de Walle, Bruce Poppe, Sofie Peirs, and Tom Taghon
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Epigenetic regulation of neurogenesis ,Carcinogenesis ,T-Lymphocytes ,medicine.medical_treatment ,T cell ,Immunology ,Hematopoietic stem cell transplantation ,Biology ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Epigenesis, Genetic ,Histones ,medicine ,Animals ,Humans ,Immunology and Allergy ,Cell Lineage ,Epigenetics ,Cancer epigenetics ,Progenitor cell ,Cell Differentiation ,DNA Methylation ,medicine.anatomical_structure ,DNA methylation ,Cancer research ,Bone marrow ,Protein Processing, Post-Translational - Abstract
Normal T-cell development is a strictly regulated process in which hematopoietic progenitor cells migrate from the bone marrow to the thymus and differentiate from early T-cell progenitors toward mature and functional T cells. During this maturation process, cooperation between a variety of oncogenes and tumor suppressors can drive immature thymocytes into uncontrolled clonal expansion and cause T-cell acute lymphoblastic leukemia (T-ALL). Despite improved insights in T-ALL disease biology and comprehensive characterization of its genetic landscape, clinical care remained largely similar over the past decades and still consists of high-dose multi-agent chemotherapy potentially followed by hematopoietic stem cell transplantation. Even with such aggressive treatment regimens, which are often associated with considerable side effects, clinical outcome is still extremely poor in a significant subset of T-ALL patients as a result of therapy resistance or hematological relapses. Recent genetic studies have identified recurrent somatic alterations in genes involved in DNA methylation and post-translational histone modifications in T-ALL, suggesting that epigenetic homeostasis is critically required in restraining tumor development in the T-cell lineage. In this review, we provide an overview of the epigenetic regulators that could be implicated in T-ALL disease biology and speculate how the epigenetic landscape of T-ALL could trigger the development of epigenetic-based therapies to further improve the treatment of human T-ALL.
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- 2014
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28. The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia
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Suzanne Vanhauwaert, Pieter-Jan Volders, Pieter Rondou, Jo Vandesompele, Tom Taghon, Annelynn Wallaert, Bruce Poppe, Jan Cools, Pieter Van Vlierberghe, Ellen Geerdens, Inge Van de Walle, Yves Benoit, Franki Speleman, Kaat Durinck, Pieter Mestdagh, Nadine Van Roy, Wouter Van Loocke, and Jean Soulier
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Chromatin Immunoprecipitation ,Blotting, Western ,Notch signaling pathway ,Biology ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Real-Time Polymerase Chain Reaction ,medicine.disease_cause ,Cohort Studies ,Transcriptome ,hemic and lymphatic diseases ,Gene expression ,Biomarkers, Tumor ,medicine ,Humans ,RNA, Messenger ,Enzyme Inhibitors ,Receptor, Notch1 ,Cells, Cultured ,B cell ,Oligonucleotide Array Sequence Analysis ,Mutation ,Thymocytes ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Articles ,Hematology ,Prognosis ,Long non-coding RNA ,Cell Transformation, Neoplastic ,medicine.anatomical_structure ,Case-Control Studies ,Cancer research ,RNA, Long Noncoding ,Amyloid Precursor Protein Secretases ,Carcinogenesis ,CD8 ,Follow-Up Studies ,Signal Transduction - Abstract
Genetic studies in T-cell acute lymphoblastic leukemia have uncovered a remarkable complexity of oncogenic and loss-of-function mutations. Amongst this plethora of genetic changes, NOTCH1 activating mutations stand out as the most frequently occurring genetic defect, identified in more than 50% of T-cell acute lymphoblastic leukemias, supporting a role as an essential driver for this gene in T-cell acute lymphoblastic leukemia oncogenesis. In this study, we aimed to establish a comprehensive compendium of the long non-coding RNA transcriptome under control of Notch signaling. For this purpose, we measured the transcriptional response of all protein coding genes and long non-coding RNAs upon pharmacological Notch inhibition in the human T-cell acute lymphoblastic leukemia cell line CUTLL1 using RNA-sequencing. Similar Notch dependent profiles were established for normal human CD34(+) thymic T-cell progenitors exposed to Notch signaling activity in vivo. In addition, we generated long non-coding RNA expression profiles (array data) from ex vivo isolated Notch active CD34(+) and Notch inactive CD4(+)CD8(+) thymocytes and from a primary cohort of 15 T-cell acute lymphoblastic leukemia patients with known NOTCH1 mutation status. Integration of these expression datasets with publicly available Notch1 ChIP-sequencing data resulted in the identification of long non-coding RNAs directly regulated by Notch activity in normal and malignant T cells. Given the central role of Notch in T-cell acute lymphoblastic leukemia oncogenesis, these data pave the way for the development of novel therapeutic strategies that target hyperactive Notch signaling in human T-cell acute lymphoblastic leukemia.
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- 2014
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29. A nanobody modulates the p53 transcriptional program without perturbing its functional architecture
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Steven De Gieter, Olivier Zwaenepoel, Kaat Durinck, Jan Gettemans, Franki Speleman, Remy Loris, Adriaan Verhelle, Jonas Bethuyne, Gholamreza Hassanzadeh-Ghassabeh, Abel Garcia-Pino, Cellular and Molecular Immunology, Structural Biology Brussels, Department of Bio-engineering Sciences, and Ultrastructure
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Models, Molecular ,Transcriptional Activation ,Immunoprecipitation ,STRUCTURAL BIOLOGY ,CELL-LINES ,Biology ,Cell Line ,Transactivation ,PROTEIN-PROTEIN INTERACTIONS ,Structural Biology ,molecular biophysics ,Genetics ,Transcriptional regulation ,Humans ,CORE DOMAIN ,WILD-TYPE ,small angle X-ray scatter ,Promoter Regions, Genetic ,Transcription factor ,IN-VIVO ,MUTANT P53 ,X-ray crystallography ,P53 ,Wild type ,Biology and Life Sciences ,DNA-binding domain ,Sciences bio-médicales et agricoles ,Single-Domain Antibodies ,Molecular biology ,Chromatin ,Cell biology ,TUMOR SUPPRESSION ,Protein Structure, Tertiary ,DNA-BINDING DOMAIN ,PIFITHRIN-ALPHA ,Tumor Suppressor Protein p53 ,transcription regulation ,Chromatin immunoprecipitation - Abstract
The p53 transcription factor plays an important role in genome integrity. To perform this task, p53 regulates the transcription of genes promoting various cellular outcomes including cell cycle arrest, apoptosis or senescence. The precise regulation of this activity remains elusive as numerous mechanisms, e.g. posttranslational modifications of p53 and (non-)covalent p53 binding partners, influence the p53 transcriptional program. We developed a novel, non-invasive tool to manipulate endogenous p53. Nanobodies (Nb), raised against the DNA-binding domain of p53, allow us to distinctively target both wild type and mutant p53 with great specificity. Nb3 preferentially binds 'structural' mutant p53, i.e. R175H and R282W, while a second but distinct nanobody, Nb139, binds both mutant and wild type p53. The co-crystal structure of the p53 DNA-binding domain in complex with Nb139 (1.9 Å resolution) reveals that Nb139 binds opposite the DNA-binding surface. Furthermore, we demonstrate that Nb139 does not disturb the functional architecture of the p53 DNA-binding domain using conformation-specific p53 antibody immunoprecipitations, glutaraldehyde crosslinking assays and chromatin immunoprecipitation. Functionally, the binding of Nb139 to p53 allows us to perturb the transactivation of p53 target genes. We propose that reduced recruitment of transcriptional co-activators or modulation of selected post-transcriptional modifications account for these observations., info:eu-repo/semantics/published
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- 2014
30. miR-542-3p exerts tumor suppressive functions in neuroblastoma by downregulating Survivin
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Kwanghee Baek, Matthias Epple, Johannes H. Schulte, Sven Lindner, Sena Yoon, Shirley K. Knauer, Sarah Karczewski, A Bohrer, Jan J. Molenaar, Alexander Schramm, Anneleen Beckers, Franki Speleman, Angelika Eggert, Pieter Mestdagh, Kristina Althoff, Andrea Odersky, Diana Kozlova, and Jo Vandesompele
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Cancer Research ,Oncogene ,Cell growth ,Cancer ,Biology ,medicine.disease ,N-Myc Proto-Oncogene Protein ,Molecular biology ,Oncology ,Neuroblastoma ,microRNA ,Survivin ,medicine ,Cancer research ,Ectopic expression ,neoplasms - Abstract
MicroRNAs (miRNAs) are deregulated in a variety of human cancers, including neuroblastoma, the most common extracranial tumor of childhood. We previously reported a signature of 42 miRNAs to be highly predictive of neuroblastoma outcome. One miRNA in this signature, miR-542, was downregulated in tumors from patients with adverse outcome. Reanalysis of quantitative PCR and next-generation sequencing transcript data revealed that miR-542-5p as well as miR-542-3p expression is inversely correlated with poor prognosis in neuroblastoma patients. We, therefore, analyzed the function of miR-542 in neuroblastoma tumor biology. Ectopic expression of miR-542-3p in neuroblastoma cell lines reduced cell viability and proliferation, induced apoptosis and downregulated Survivin. Survivin expression was also inversely correlated with miR-542-3p expression in primary neuroblastomas. Reporter assays confirmed that miR-542-3p directly targeted Survivin. Downregulating Survivin using siRNA copied the phenotype of miR-542-3p expression in neuroblastoma cell lines, while cDNA-mediated ectopic expression of Survivin partially rescued the phenotype induced by miR-542-3p expression. Treating nude mice bearing neuroblastoma xenografts with miR-542-3p-loaded nanoparticles repressed Survivin expression, decreased cell proliferation and induced apoptosis in the respective xenograft tumors. We conclude that miR-542-3p exerts its tumor suppressive function in neuroblastoma, at least in part, by targeting Survivin. Expression of miR-542-3p could be a promising therapeutic strategy for treating aggressive neuroblastoma.
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- 2014
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31. The epigenetic landscape of T-cell acute lymphoblastic leukemia
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Pieter Van Vlierberghe, Franki Speleman, Joni Van der Meulen, and Nadine Van Roy
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Genome, Human ,Genetic heterogeneity ,Cell Differentiation ,Oncogenes ,Cell Biology ,Disease ,Epigenome ,DNA Methylation ,Biology ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Bioinformatics ,medicine.disease ,Biochemistry ,Genome ,Epigenesis, Genetic ,Histones ,Leukemia ,DNA methylation ,Polycomb-group proteins ,medicine ,Humans ,Genes, Tumor Suppressor ,Epigenetics - Abstract
The genetic landscape of T-ALL has been very actively explored during the past decades. This leads to an overwhelming body of exciting novel findings providing insight into (1) the genetic heterogeneity of the disease with marked genetic subsets, (2) the mechanisms by which aberrant T-cell development drive leukemogenesis and (3) emerging opportunities for novel therapeutic interventions. Of further interest, recent genome wide sequencing studies identified proteins that actively participate in the regulation of the T-cell epigenome as novel oncogenes and tumor suppressor genes in T-ALL. The identification of these perturbed molecular epigenetic events in the pathogenesis of T-ALL will contribute to the further exploration of novel therapies in this cancer type. As some epigenetic therapies have recently been approved for a number of hematological neoplasms, one could speculate that targeted therapies against epigenetic regulators might offer good prospects for T-ALL treatment in the near future. In this review, we summarize the epigenetic discoveries made in T-ALL hitherto and discuss possible new venues for epigenetic therapeutic intervention in this aggressive subtype of human leukemia. This article is part of a Directed Issue entitled: Rare Cancers.
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- 2014
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32. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer
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Gunnar Rätsch, John A. Porco, Jonathan H. Schatz, Chunying Zhao, Elisa de Stanchina, Kamini Singh, Christina M. Rodrigo, Viraj Sanghvi, Julie Teruya-Feldstein, Man Jiang, Jerry Pelletier, Michelle A. Kelliher, Franki Speleman, Philipp Drewe, Andrew Wolfe, Justine E. Roderick, Joni Van der Meulen, Pieter Rondou, Vinagolu K. Rajasekhar, Konstantinos J. Mavrakis, Hans-Guido Wendel, and Yi Zhong
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Transcription, Genetic ,Biology ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Article ,Epigenesis, Genetic ,Mice ,03 medical and health sciences ,0302 clinical medicine ,DHX36 ,Transcription (biology) ,Cell Line, Tumor ,Animals ,Humans ,Nucleotide Motifs ,Post-transcriptional regulation ,030304 developmental biology ,Oncogene Proteins ,Genetics ,0303 health sciences ,Multidisciplinary ,Base Sequence ,RNA ,Non-coding RNA ,Antineoplastic Agents, Phytogenic ,RNA Helicase A ,Triterpenes ,3. Good health ,Cell biology ,G-Quadruplexes ,Mice, Inbred C57BL ,RNA silencing ,Protein Biosynthesis ,030220 oncology & carcinogenesis ,eIF4A ,Eukaryotic Initiation Factor-4A ,Female ,5' Untranslated Regions ,Ribosomes ,Transcription Factors - Abstract
The translational control of oncoprotein expression is implicated in many cancers. Here we report an eIF4A RNA helicase-dependent mechanism of translational control that contributes to oncogenesis and underlies the anticancer effects of silvestrol and related compounds. For example, eIF4A promotes T-cell acute lymphoblastic leukaemia development in vivo and is required for leukaemia maintenance. Accordingly, inhibition of eIF4A with silvestrol has powerful therapeutic effects against murine and human leukaemic cells in vitro and in vivo. We use transcriptome-scale ribosome footprinting to identify the hallmarks of eIF4A-dependent transcripts. These include 5′ untranslated region (UTR) sequences such as the 12-nucleotide guanine quartet (CGG)4 motif that can form RNA G-quadruplex structures. Notably, among the most eIF4A-dependent and silvestrol-sensitive transcripts are a number of oncogenes, superenhancer-associated transcription factors, and epigenetic regulators. Hence, the 5′ UTRs of select cancer genes harbour a targetable requirement for the eIF4A RNA helicase. The translation of many messenger RNAs that encode important oncogenes and transcription factors depends on the eIF4A RNA helicase to resolve G-quadruplex structures, implying eIF4A inhibition as an effective cancer therapy. The expression of some oncoproteins is regulated at the translational level. Hans-Guido Wendel and colleagues show that a subset of oncoprotein- and transcription factor-encoding mRNAs that are dependent on the translation initiation factor eIF4A contain a G-quadruplex-forming structure in their 5′ untranslated regions. These findings explain why silvestrol, a plant-derived anticancer agent that targets eIF4A-dependent translation, is not generally toxic but can be well tolerated except in cancer cells which are dependent on the activities of these proteins. In a separate study in this issue, Stephan Vagner and colleagues show that inhibition of eIF4F cooperates with BRAF inhibitors in reducing the growth of melanomas linked to BRAF mutations.
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- 2014
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33. Lack of association betweenMDM2promoter SNP309 and clinical outcome in patients with neuroblastoma
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Johannes H. Schulte, Bram De Wilde, Simona Coco, Raymond L. Stallings, Fjoralba Zeka, Angelika Eggert, Ali Rihani, Jo Vandesompele, Tom Van Maerken, Rosa Noguera, Franki Speleman, Genevieve Laureys, Rogier Versteeg, Koen Norga, and Gian Paolo Tonini
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biology ,business.industry ,Mdm2 snp309 ,Promoter ,Single-nucleotide polymorphism ,Hematology ,medicine.disease ,enzymes and coenzymes (carbohydrates) ,Oncology ,Neuroblastoma ,Pediatrics, Perinatology and Child Health ,Genotype ,biology.protein ,Cancer research ,Medicine ,Mdm2 ,In patient ,business ,neoplasms ,Genotyping - Abstract
While a polymorphism located within the promoter region of the MDM2 proto-oncogene, SNP309 (T > G), has previously been associated with increased risk and aggressiveness of neuroblastoma and other tumor entities, a protective effect has also been reported in certain other cancers. In this study, we evaluated the association of MDM2 SNP309 with outcome in 496 patients with neuroblastoma and its effect on MDM2 expression. No significant difference in overall or event-free survival was observed among patients with neuroblastoma with or without MDM2 SNP309. The presence of SNP309 does not affect MDM2 expression in neuroblastoma. Pediatr Blood Cancer 2014; 61:1867–1870. © 2014 Wiley Periodicals, Inc.
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- 2014
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34. ABT-199 mediated inhibition of BCL-2 as a novel therapeutic strategy in T-cell acute lymphoblastic leukemia
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Filip Matthijssens, Franki Speleman, Sofie Peirs, Jules P.P. Meijerink, Steven Goossens, Delphine Briot, Charles E. de Bock, Tom Taghon, Sandrine Degryse, Bruce Poppe, Yves Benoit, Kirsten Canté-Barrett, Terence H. Rabbitts, Tim Lammens, Emmanuelle Clappier, Jean Soulier, Pieter Van Vlierberghe, Barbara De Moerloose, Inge Van de Walle, Jan Cools, Katia Ruggero, and Pediatrics
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Cell Survival ,medicine.medical_treatment ,T cell ,Blotting, Western ,Immunology ,Antineoplastic Agents ,Mice, SCID ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Biochemistry ,Jurkat cells ,Inhibitory Concentration 50 ,Jurkat Cells ,Mice, Inbred NOD ,In vivo ,Cell Line, Tumor ,Antineoplastic Combined Chemotherapy Protocols ,Tumor Cells, Cultured ,medicine ,Animals ,Humans ,Doxorubicin ,Child ,Cells, Cultured ,Oligonucleotide Array Sequence Analysis ,Sulfonamides ,Chemotherapy ,Gene Expression Regulation, Leukemic ,Reverse Transcriptase Polymerase Chain Reaction ,business.industry ,Gene Expression Profiling ,Cancer ,Drug Synergism ,Cell Biology ,Hematology ,Bridged Bicyclo Compounds, Heterocyclic ,medicine.disease ,Survival Analysis ,Xenograft Model Antitumor Assays ,Lymphoma ,HEK293 Cells ,medicine.anatomical_structure ,Proto-Oncogene Proteins c-bcl-2 ,Cancer research ,business ,TAL1 ,medicine.drug - Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a high-risk subtype of acute lymphoblastic leukemia (ALL) with gradually improved survival through introduction of intensified chemotherapy. However, therapy-resistant or refractory T-ALL remains a major clinical challenge. Here, we evaluated B-cell lymphoma (BCL)-2 inhibition by the BH3 mimetic ABT-199 as a new therapeutic strategy in human T-ALL. The T-ALL cell line LOUCY, which shows a transcriptional program related to immature T-ALL, exhibited high in vitro and in vivo sensitivity for ABT-199 in correspondence with high levels of BCL-2. In addition, ABT-199 showed synergistic therapeutic effects with different chemotherapeutic agents including doxorubicin, l-asparaginase, and dexamethasone. Furthermore, in vitro analysis of primary patient samples indicated that some immature, TLX3- or HOXA-positive primary T-ALLs are highly sensitive to BCL-2 inhibition, whereas TAL1 driven tumors mostly showed poor ABT-199 responses. Because BCL-2 shows high expression in early T-cell precursors and gradually decreases during normal T-cell differentiation, differences in ABT-199 sensitivity could partially be mediated by distinct stages of differentiation arrest between different molecular genetic subtypes of human T-ALL. In conclusion, our study highlights BCL-2 as an attractive molecular target in specific subtypes of human T-ALL that could be exploited by ABT-199.
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- 2014
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35. Abstract 3696: PHF6loss drives IL7R oncogene addiction in TLX1 driven T-ALL
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Charles E. de Bock, Givani Dewyn, Jan Cools, João T. Barata, Kaat Durinck, Lisa Depestel, Pieter Van Vlierberghe, David M. Langenau, Tom Taghon, Franki Speleman, Suzanne Vanhauwaert, Siebe Loontiens, and Mariana L Oliveira
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Regulation of gene expression ,Cancer Research ,Gene knockdown ,Oncogene ,Lymphoblast ,Biology ,Oncogene Addiction ,medicine.disease ,biology.organism_classification ,Leukemia ,Oncology ,medicine ,Cancer research ,Interleukin-7 receptor ,Zebrafish - Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease. The PHF6 gene is frequently targeted by loss-of-function mutations or deletions, with the highest prevalence in TLX1 or TLX3 rearranged T-ALLs. To gain insights into the putative function of PHF6 as a tumor suppressor in the T-cell lineage, we investigated the effects of PHF6 knock down during normal and malignant thymocytes. Notably, we observed broad effects on the investigated transcriptomes suggesting an important role for PHF6 in gene regulation. Furthermore, IL7R was identified as a common transcriptional target that was significantly upregulated upon PHF6 knockdown in both normal and malignant T cells. IL7R encodes a cytokine receptor critically involved in normal thymic development and which also acts as a bona fide oncogene in subset of primary T-ALLs. Thus, loss of PHF6 might further boost oncogenic addiction of leukemic T-cell lymphoblast to IL7-induced JAK-STAT signaling. To further explore the role of PHF6 inactivation in TLX1 driven leukemogenesis in vivo, we performed zebrafish modeling. For this, we generated a stable tg(rag2:TLX1, rag2:GFP) overexpressing as well as a phf6 knock out zebrafish line. These lines were crossed and offspring was monitored for T-ALL formation. Interestingly, three fish out of a cohort of 80 animals developed leukemia between 10 to 18 months of age. These leukemias originated from the thymus, spreaded throughout the whole body and were transplantable. Thus far, no leukemia was detected in PHF6 mutated or TLX1 overexpressing only zebrafish. Leukemic cells obtained from tumors that developed in the PHF6null TLX1rag2-TLX1/GFP animals were subjected to RNA-, ATAC- and H3K27ac ChIP-sequencing to assess the epigenetic status of the IL7R locus. In addition, exome-, and CNV-sequencing was performed to identify somatic lesions that cooperated loss of Phf6 during TLX1 driven T-cell transformation in zebrafish. Furthermore, additional injections of TLX1 in combination with an activating IL7R mutant into phf6 mutant zebrafish are currently ongoing to monitor additional effects on accelerated tumor formation. In conclusion, our data suggest that loss of PHF6 drives TLX1 mediated leukemogenesis, at least in part, by increasing surface IL7R expression. Therefore, we believe that increased addiction to oncogenic JAK-STAT signaling may render PHF6 mutant leukemic cells more sensitive to JAK inhibitors, a notion that we are currently investigating in our TLX1/PHF6 and TLX1/PHF6/IL7R zebrafish models. Citation Format: Siebe Loontiens, Kaat Durinck, Suzanne Vanhauwaert, Lisa Depestel, Mariana L. Oliveira, Givani Dewyn, Charles De Bock, João T. Barata, David Langenau, Jan Cools, Tom Taghon, Pieter Van Vlierberghe, Frank Speleman. PHF6loss drives IL7R oncogene addiction in TLX1 driven T-ALL [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3696.
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- 2019
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36. Hyperdiploidy with 58-66 chromosomes in childhood B-acute lymphoblastic leukemia is highly curable: 58951 CLG-EORTC results
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Nicolas Sirvent, Martine Munzer, Carine Gervais, Manuel R. Teixeira, Pierre Heimann, Matthias Karrasch, Yves Bertrand, Brigitte Nelken, Isabelle Luquet, Patrick Boutard, Marie Pierre Pagès, Karima Yakouben, Hélène Cavé, Franki Speleman, Sandrine Girard, Marie Agnès Collonge, Patrick Lutz, Anne Uyttebroeck, Yves Benoit, Geneviève Plat, Alice Ferster, Marleen Bakkus, Stefan Suciu, Pierre Rohrlich, Nicole Dastugue, and Hematology
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Male ,Oncology ,medicine.medical_specialty ,Pediatrics ,Adolescent ,Lymphoblastic Leukemia ,Immunology ,Biochemistry ,Chromosomes ,Polyploidy ,Genetic Heterogeneity ,Precursor B-Cell Lymphoblastic Leukemia-Lymphoma ,hemic and lymphatic diseases ,Internal medicine ,Humans ,Medicine ,In patient ,Favorable outcome ,Age of Onset ,Child ,Chromosome Aberrations ,Clinical Trials as Topic ,business.industry ,Remission Induction ,Infant, Newborn ,B-ALL ,Infant ,Childhood B Acute Lymphoblastic Leukemia ,hyperdiploidy ,Cell Biology ,Hematology ,Diploidy ,Minimal residual disease ,Child, Preschool ,Karyotyping ,Female ,Hyperdiploidy ,business ,Follow-Up Studies - Abstract
The aim of our study was to analyze the factors contributing to heterogeneity of prognosis in patients with hyperdiploidy50 chromosomes (HD50), a group of B-cell precursor acute lymphoblastic leukemia with favorable outcome. The 541 HD50 patients registered prospectively in the 58951 European Organisation for Research and Treatment of Cancer (EORTC) Children's Leukemia Group (CLG) trial, identified by karyotype (446 patients) and by DNA index (DI) (490 patients), had a 6-year event-free survival (EFS) of 89.0% (standard error [SE] = 1.5%) and a 6-year overall survival (OS) of 95.9% (SE = 0.9%). The strongest prognostic factor was the modal number of chromosomes (MNC): the 6-year EFS of 51-53, 54-57, and 58-66 MNC groups were 80%, 89%, and 99%, respectively (P.0001). Ploidy assessed by DI was also a favorable factor: the higher the DI, the better the outcome. The 6-year EFS of the 3 subgroups of DI1.16/≥1.16-1.24/≥1.24 were 83%, 90%, and 95%, respectively (P = .009). All usual combinations of trisomies (chromosomes 4, 10, 17, 18) were significant favorable factors but had lower EFS when MNC was lower than 58. In multivariate analysis, MNC remained the strongest factor. Consequently, the best indicator for excellent outcome was ploidy assessed by karyotype because patients with 58-66 chromosomes stood every chance of being cured (OS of 100% at 6-year follow-up) with less-intensive therapy. This trial was registered at www.clinicaltrials.gov as #NCT00003728. Registered: http://www.eortc.org/, http://clinicaltrials.gov/show/NCT00003728.
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- 2013
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37. Novel TAL1 targets beyond protein-coding genes: identification of TAL1-regulated microRNAs in T-cell acute lymphoblastic leukemia
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Franki Speleman, Maté Ongenaert, João T. Barata, Nádia C. Correia, Kaat Durinck, Francisco J. Enguita, Pieter Rondou, and Ana Paula Leite
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Cancer Research ,T-Cell Acute Lymphocytic Leukemia Protein 1 ,T cell ,Biology ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,03 medical and health sciences ,0302 clinical medicine ,Cell Line, Tumor ,Proto-Oncogene Proteins ,hemic and lymphatic diseases ,microRNA ,Basic Helix-Loop-Helix Transcription Factors ,medicine ,Humans ,Gene ,030304 developmental biology ,Regulation of gene expression ,Genetics ,0303 health sciences ,hemic and immune systems ,Hematology ,3. Good health ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,medicine.anatomical_structure ,Oncology ,Cell culture ,030220 oncology & carcinogenesis ,Cancer research ,Identification (biology) ,TAL1 - Abstract
Novel TAL1 targets beyond protein-coding genes: identification of TAL1-regulated microRNAs in T-cell acute lymphoblastic leukemia
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- 2013
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38. RT-qPCR gene expression analysis in zebrafish
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Paul Coucke, Suzanne Vanhauwaert, Jo Vandesompele, Franki Speleman, A De Paepe, Andy Willaert, and Steve Lefever
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0301 basic medicine ,Regulation of gene expression ,biology ,fungi ,food and beverages ,Computational biology ,biology.organism_classification ,Bioinformatics ,Gene expression profiling ,03 medical and health sciences ,030104 developmental biology ,Real-time polymerase chain reaction ,Complementary DNA ,Gene expression ,Sample collection ,Zebrafish ,Gene - Abstract
Gene expression analysis is increasingly important in many fields of biological research. Understanding patterns of expressed genes is assumed to provide insight into complex regulatory networks and can lead to the identification of genes relevant to specific biological processes, including disease. Among different techniques, reverse transcription quantitative polymerase chain reaction (RT-qPCR) is currently regarded as the gold standard for targeted quantification of RNA gene expression, especially because of its high sensitivity, specificity, accuracy, and precision, and also because of its practical simplicity and processing speed. However, different critical factors can influence the outcome of RT-qPCR studies, including isolation of RNA, reverse transcription to cDNA, and data analysis. These factors need to be addressed in order to obtain biologically meaningful results. In this chapter, we describe how RT-qPCR can be used in a reliable way to successfully study differential gene expression in zebrafish. Hereby, we especially focus on how expressed repetitive elements can be employed as reference targets in zebrafish RT-qPCR studies and how they can further improve the quality of the data.
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- 2016
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39. DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
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Jo Vandesompele, Franki Speleman, Maté Ongenaert, Anneleen Decock, and Wim Van Criekinge
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0301 basic medicine ,Statistics and Probability ,Data Descriptor ,Library and Information Sciences ,Biology ,BIOCONDUCTOR PACKAGE ,Education ,Paediatric cancer ,03 medical and health sciences ,Neuroblastoma ,neuroblastoma ,Biomarkers, Tumor ,Medicine and Health Sciences ,Humans ,Methylated DNA immunoprecipitation ,Copy-number variation ,Epigenetics ,Gene ,GENE-EXPRESSION ,Genetics ,DNA methylation ,epigenetics ,REARRANGEMENTS ,Biology and Life Sciences ,CLUSTER ,DNA, Neoplasm ,DNA Fingerprinting ,Computer Science Applications ,Methyl-CpG-binding domain ,READ ALIGNMENT ,INSIGHTS ,030104 developmental biology ,SEQ ,DNA profiling ,CpG site ,DIFFERENTIAL EXPRESSION ANALYSIS ,Next-generation sequencing ,CpG Islands ,methyl-CpG-binding domain (MBD) sequencing ,Statistics, Probability and Uncertainty ,Information Systems - Abstract
Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors by methyl-CpG-binding domain (MBD) sequencing, in order to identify prognostic biomarker candidates. In this data descriptor, we give details on how this data set was generated and which bioinformatics analyses were applied during data processing. Through a series of technical validations, we illustrate that the data are of high quality and that the sequenced fragments represent methylated genomic regions. Furthermore, genes previously described to be methylated in NB are confirmed. As such, these MBD sequencing data are a valuable resource to further study the association of NB risk factors with the NB methylome, and offer the opportunity to integrate methylome data with other -omic data sets on the same tumor samples such as gene copy number and gene expression, also publically available.
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- 2016
40. Segmental chromosomal alterations have prognostic impact in neuroblastoma: a report from the INRG project
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Mosseri, Peter F. Ambros, Gian Paolo Tonini, Edward F. Attiyeh, I.M. Ambros, Tom Monclair, Garrett M. Brodeur, Michelle Haber, Wendy B. London, Rosa Noguera, Javed Khan, Akira Nakagawara, Franki Speleman, Adj Pearson, Katherine K. Matthay, John M. Maris, Susan L. Cohn, Matthias Fischer, and Gudrun Schleiermacher
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Oncology ,Cancer Research ,medicine.medical_specialty ,Pathology ,Biology ,Loss of heterozygosity ,neuroblastoma ,Neuroblastoma ,Internal medicine ,INRG ,medicine ,Humans ,Clinical significance ,genomic profile ,Survival analysis ,Retrospective Studies ,Chromosome Aberrations ,Oncogene Proteins ,N-Myc Proto-Oncogene Protein ,Univariate analysis ,genetic alterations ,Chromosomes, Human, Pair 11 ,Infant ,Nuclear Proteins ,Chromosome ,Genetics and Genomics ,Prognosis ,medicine.disease ,Survival Analysis ,Genetic marker ,Genomic Profile ,Chromosomes, Human, Pair 17 - Abstract
Background: In the INRG dataset, the hypothesis that any segmental chromosomal alteration might be of prognostic impact in neuroblastoma without MYCN amplification (MNA) was tested. Methods: The presence of any segmental chromosomal alteration (chromosome 1p deletion, 11q deletion and/or chromosome 17q gain) defined a segmental genomic profile. Only tumours with a confirmed unaltered status for all three chromosome arms were considered as having no segmental chromosomal alterations. Results: Among the 8800 patients in the INRG database, a genomic type could be attributed for 505 patients without MNA: 397 cases had a segmental genomic type, whereas 108 cases had an absence of any segmental alteration. A segmental genomic type was more frequent in patients >18 months and in stage 4 disease (P
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- 2012
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41. Pharmacological activation of the p53 pathway by nutlin-3 exerts anti-tumoral effects in medulloblastomas
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Michael A. Grotzer, Michel Mittelbronn, Franki Speleman, Lukas C. Heukamp, Katleen De Preter, Alexander Schramm, Theresa Thor, A Künkele, Johannes H. Schulte, Wolfgang Hartmann, Hedwig E. Deubzer, Angelika Eggert, Kristian W. Pajtler, and University of Zurich
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Cancer Research ,Medizin ,Apoptosis ,Piperazines ,Malignant transformation ,Immunoenzyme Techniques ,Mice ,chemistry.chemical_compound ,Cerebellum ,Tumor Cells, Cultured ,1306 Cancer Research ,Gene knockdown ,Cell Cycle ,Imidazoles ,Proto-Oncogene Proteins c-mdm2 ,Nutlin ,Cell cycle ,2728 Neurology (clinical) ,Oncology ,Basic and Translational Investigations ,Mdm2 ,2730 Oncology ,Female ,Signal Transduction ,Cell Survival ,Blotting, Western ,Mice, Nude ,610 Medicine & health ,Biology ,medicine ,Animals ,Humans ,Viability assay ,Cerebellar Neoplasms ,neoplasms ,Cell Proliferation ,Medulloblastoma ,Cell growth ,medicine.disease ,Xenograft Model Antitumor Assays ,Molecular biology ,stomatognathic diseases ,chemistry ,10036 Medical Clinic ,Tissue Array Analysis ,Case-Control Studies ,Mutation ,Cancer research ,biology.protein ,Neurology (clinical) ,Tumor Suppressor Protein p53 - Abstract
Medulloblastomas account for 20% of pediatric brain tumors. With an overall survival of 40%–70%, their treatment is still a challenge. The majority of medulloblastomas lack p53 mutations, but even in cancers retaining wild-type p53, the tumor surveillance function of p53 is inhibited by the oncoprotein MDM2. Deregulation of the MDM2/p53 balance leads to malignant transformation. Here, we analyzed MDM2 mRNA and protein expression in primary medulloblastomas and normal cerebellum and assessed the mutational status of p53 and MDM2 expression in 6 medulloblastoma cell lines. MDM2 expression was elevated in medulloblastomas, compared with cerebellum. Four of 6 medulloblastoma cell lines expressed wild-type p53 and high levels of MDM2. The tumor-promoting p53-MDM2 interaction can be inhibited by the small molecule, nutlin-3, restoring p53 function. Targeting the p53-MDM2 axis using nutlin-3 significantly reduced cell viability and induced either cell cycle arrest or apoptosis and expression of the p53 target gene p21 in these 4 cell lines. In contrast, DAOY and UW-228 cells harboring TP53 mutations were almost unaffected by nutlin-3 treatment. MDM2 knockdown in medulloblastoma cells by siRNA mimicked nutlin-3 treatment, whereas expression of dominant negative p53 abrogated nutlin-3 effects. Oral nutlin-3 treatment of mice with established medulloblastoma xenografts inhibited tumor growth and significantly increased survival. Thus, nutlin-3 reduced medulloblastoma cell viability in vitro and in vivo by re-activating p53 function. We suggest that inhibition of the MDM2-p53 interaction with nutlin-3 is a promising therapeutic option for medulloblastomas with functional p53 that should be further evaluated in clinical trials.
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- 2012
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42. Copy number defects of G1-Cell cycle genes in neuroblastoma are frequent and correlate with high expression of E2F target genes and a poor prognosis
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Katleen De Preter, David Gisselsson, Marli E. Ebus, Rogier Versteeg, Ellen M. Westerhout, Franki Speleman, Iingrid Øra, Jan J. Molenaar, Jan Koster, Huib N. Caron, Peter van Sluis, Cancer Center Amsterdam, Oncogenomics, Amsterdam Public Health, Human Genetics, and Paediatric Oncology
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Cancer Research ,Cyclin A ,Gene Dosage ,Gene Expression ,Neuroblastoma ,Cyclin D1 ,Cyclin-dependent kinase ,Genetics ,Cluster Analysis ,Humans ,RNA, Messenger ,E2F ,Cyclin-Dependent Kinase Inhibitor Proteins ,Cyclin ,Chromosome Aberrations ,biology ,G1 Phase ,Cell cycle ,Prognosis ,Molecular biology ,Cell Cycle Gene ,Cyclin-Dependent Kinases ,E2F Transcription Factors ,Genes, cdc ,biology.protein ,Cancer research ,Comparative genomic hybridization - Abstract
The tightly controlled network of cell cycle genes consists of a core of cyclin dependent kinases (CDKs) that are activated by periodically expressed cyclins. The activity of the cyclin-CDK complexes is regulated by cyclin dependent kinase inhibitors (CDKIs) and multiple signal transduction routes that converge on the cell cycle. Neuroblastoma are pediatric tumors that belong to the group of small round blue cell tumors, characterized by a fast proliferation. Here, we present high throughput analyses of cell cycle regulating genes in neuroblastoma. We analyzed a series of 82 neuroblastomas by comparative genomic hybridization arrays, single nucleotide polymorphism arrays, and Affymetrix expression arrays and analyzed the datasets in parallel with the R2 bioinformatic tool (http://r2.amc.nl). About 30% of the tumors had genomic amplifications, gains, or losses with shortest regions of overlap that suggested implication of a series of G1 cell cycle regulating genes. CCND1 (cyclin D1) and CDK4 were amplified or gained and the chromosomal regions containing the CDKN2 (INK4) group of CDKIs were frequently deleted. Cluster analysis showed that tumors with genomic aberrations in G1 regulating genes over-expressed E2F target genes, which regulate S and G2/M phase progression. These tumors have a poor prognosis. Our findings suggest that pharmacological inhibition of cell cycle genes might bear therapeutic promises for patients with high risk neuroblastoma. (C) 2011 Wiley Periodicals, Inc. (Less)
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- 2011
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43. Neuroblastoma epigenetics: From candidate gene approaches to genome-wide screenings
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Maté Ongenaert, Franki Speleman, Anneleen Decock, and Jo Vandesompele
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Cancer Research ,Candidate gene ,Apoptosis ,Biology ,Proto-Oncogene Mas ,Genome ,N-Myc Proto-Oncogene Protein ,Epigenesis, Genetic ,Histones ,Neuroblastoma ,Humans ,Epigenetics ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Oncogene Proteins ,Regulation of gene expression ,Genome, Human ,Tumor Suppressor Proteins ,Nuclear Proteins ,DNA Methylation ,Chromatin Assembly and Disassembly ,Prognosis ,Chromatin ,Gene Expression Regulation, Neoplastic ,Child, Preschool ,DNA methylation ,Cancer research ,Genome-Wide Association Study - Abstract
Neuroblastoma (NB) is a childhood tumor originating from sympathetic nervous system cells. Although recently new insights into genes involved in NB have emerged, the molecular basis of neuroblastoma development and progression still remains poorly understood. The best-characterized genetic alterations include amplification of the proto-oncogene MYCN, ALK activating mutations or amplification, gain of chromosome arm 17q and losses of 1p, 3p, and 11q. Epigenetic alterations have been described as well: caspase-8 (CASP8) and RAS-association domain family 1 isoform A (RASSF1A) DNA-methylation are important events for the development and progression of neuroblastoma. In total, there are about 75 genes described as epigenetically affected in NB cell lines and/or NB primary samples. These epigenetic alterations were either found using a candidate gene approach or based on the analysis of genome-wide screening techniques. This review gives an extensive overview of all epigenetic changes described in NB as of today, with a main focus on both prognostic use and the potential of genome-wide techniques to find epigenetic prognostic biomarkers in NB. We summarize the key findings so far and the state-of-the-art of the upcoming methods at a unique time frame in the transition towards combined genome wide chromatin immune-precipitation (ChIP) and DNA sequencing techniques.
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- 2011
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44. Isolation of disseminated neuroblastoma cells from bone marrow aspirates for pretreatment risk assessment by array comparative genomic hybridization
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Tim Lammens, Genevieve Laureys, Katleen De Preter, Franki Speleman, Mado Vandewoestyne, Jan Philippé, Dieter Deforce, Candy Kumps, Nadine Van Roy, Katrien Swerts, and Björn Menten
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Comparative Genomic Hybridization ,Cancer Research ,Pathology ,medicine.medical_specialty ,medicine.diagnostic_test ,Magnetic-activated cell sorting ,Laser Capture Microdissection ,Biology ,Flow Cytometry ,medicine.disease ,Primary tumor ,Neuroblastoma ,medicine.anatomical_structure ,Oncology ,Bone Marrow ,Biopsy ,medicine ,Humans ,Bone marrow ,Bone Marrow Neoplasms ,Laser capture microdissection ,Comparative genomic hybridization ,Fluorescence in situ hybridization - Abstract
In neuroblastoma, tumor biopsies are used for prognostic evaluation and risk assessment by molecular genetic analyses such as fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (array CGH). Analysis of primary tumors by array CGH can be hampered by the lack of sufficient tumor cells due to small biopsy size or availability of invaded bone marrow only. Given the importance of accurate assessment of genetic alterations in the diagnostic work-up of patients with neuroblastoma, we evaluated the possibility to analyze bone marrow metastases in patients with disseminated disease. Disseminated neuroblastoma cells were isolated from bone marrow aspirates by using either laser capture microdissection (LCM) or magnetic activated cell sorting (MACS). The array CGH profiles of these isolated metastases were compared to array CGH profiles and/or FISH data of the corresponding primary tumor. Here, we show that the major recurrent DNA copy number alterations detected in primary neuroblastoma tumors (i.e., 1p, 3p and 11q deletion, 17q gain and MYCN amplification) can be detected, with high sensitivity and specificity, in the disseminated neuroblastoma cells isolated from the bone marrow aspirates, using an array platform with high coverage for these regions. Moreover, we demonstrate that for archived material, for example, for retrospective studies, LCM is the method of choice, while for fresh bone marrow aspirates, acquired at the time of diagnosis, MACS is superior.
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- 2011
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45. A cooperative microRNA-tumor suppressor gene network in acute T-cell lymphoblastic leukemia (T-ALL)
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Nicholas B Socci, Franki Speleman, Andrew Wolfe, Eric Delabesse, Yves Benoit, Manu Setty, Xiaoping Liu, Pieter Rondou, Pieter Van Vlierberghe, Joni Van der Meulen, Christina S. Leslie, Aly A. Khan, Peter Vandenberghe, Tom Taghon, Evelien Mets, Konstantinos J. Mavrakis, and Hans-Guido Wendel
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Adult ,Male ,Adolescent ,Tumor suppressor gene ,Blotting, Western ,Fluorescent Antibody Technique ,Apoptosis ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Article ,Immunoenzyme Techniques ,Mice ,Young Adult ,RNA interference ,Cell Line, Tumor ,microRNA ,Biomarkers, Tumor ,Genetics ,medicine ,Animals ,Humans ,Gene silencing ,PTEN ,Gene Regulatory Networks ,Genes, Tumor Suppressor ,RNA, Messenger ,Child ,Luciferases ,Cell Proliferation ,Oligonucleotide Array Sequence Analysis ,Regulation of gene expression ,biology ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Infant ,medicine.disease ,Gene Expression Regulation, Neoplastic ,Survival Rate ,Gene expression profiling ,MicroRNAs ,Leukemia ,Child, Preschool ,biology.protein ,Cancer research ,Female - Abstract
The importance of individual microRNAs (miRNAs) has been established in specific cancers. However, a comprehensive analysis of the contribution of miRNAs to the pathogenesis of any specific cancer is lacking. Here we show that in T-cell acute lymphoblastic leukemia (T-ALL), a small set of miRNAs is responsible for the cooperative suppression of several tumor suppressor genes. Cross-comparison of miRNA expression profiles in human T-ALL with the results of an unbiased miRNA library screen allowed us to identify five miRNAs (miR-19b, miR-20a, miR-26a, miR-92 and miR-223) that are capable of promoting T-ALL development in a mouse model and which account for the majority of miRNA expression in human T-ALL. Moreover, these miRNAs produce overlapping and cooperative effects on tumor suppressor genes implicated in the pathogenesis of T-ALL, including IKAROS (also known as IKZF1), PTEN, BIM, PHF6, NF1 and FBXW7. Thus, a comprehensive and unbiased analysis of miRNA action in T-ALL reveals a striking pattern of miRNA-tumor suppressor gene interactions in this cancer.
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- 2011
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46. Functional Analysis of the p53 Pathway in Neuroblastoma Cells Using the Small-Molecule MDM2 Antagonist Nutlin-3
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Jo Vandesompele, Frank Westermann, Jean-Christophe Marine, Ali Rihani, Daniel Dreidax, Anne De Paepe, Nurten Yigit, Sarah De Clercq, Franki Speleman, and Tom Van Maerken
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Cancer Research ,Nonsense mutation ,Gene mutation ,Biology ,medicine.disease_cause ,Piperazines ,Neuroblastoma ,chemistry.chemical_compound ,Cell Line, Tumor ,medicine ,Humans ,Missense mutation ,Cyclin-Dependent Kinase Inhibitor p16 ,Mutation ,Effector ,Imidazoles ,Proto-Oncogene Proteins c-mdm2 ,Nutlin ,Genes, p53 ,medicine.disease ,Oncology ,chemistry ,Cancer research ,Tumor Suppressor Protein p53 ,Signal transduction ,Signal Transduction - Abstract
Suppression of p53 activity is essential for proliferation and survival of tumor cells. A direct p53-activating compound, nutlin-3, was used in this study, together with p53 mutation analysis, to characterize p53 pathway defects in a set of 34 human neuroblastoma cell lines. We identified 9 cell lines (26%) with a p53 loss-of-function mutation, including 6 missense mutations, 1 nonsense mutation, 1 in-frame deletion, and 1 homozygous deletion of the 3′ end of the p53 gene. Sensitivity to nutlin-3 was highly predictive of absence of p53 mutation. Signaling pathways downstream of p53 were functionally intact in 23 of 25 cell lines with wild-type p53. Knockdown and overexpression experiments revealed a potentiating effect of p14ARF expression on the response of neuroblastoma cells to nutlin-3. Our findings shed light on the spectrum of p53 pathway lesions in neuroblastoma cells, indicate that defects in effector molecules downstream of p53 are remarkably rare in neuroblastoma, and identify p14ARF as a determinant of the outcome of the response to MDM2 inhibition. These insights may prove useful for the clinical translation of evolving strategies aimed at p53 reactivation and for the development of new therapeutic approaches. Mol Cancer Ther; 10(6); 983–93. ©2011 AACR.
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- 2011
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47. PHF6 mutations in adult acute myeloid leukemia
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Jan Cools, Franki Speleman, Iannis Aifantis, Martin S. Tallman, A R Payer, P. Van Vlierberghe, Hugo F. Fernandez, Concepcion Nicolas, Ross L. Levine, Cyrus V. Hedvat, Ari Melnick, Adolfo A. Ferrando, Jawaharlal M. Patel, Omar Abdel-Wahab, Peter Vandenberghe, Elisabeth Paietta, Milagros Balbín, and Camille Lobry
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Adult ,Male ,Cancer Research ,Lineage (genetic) ,Tumor suppressor gene ,Nonsense mutation ,Biology ,medicine.disease_cause ,Article ,Frameshift mutation ,Mice ,hemic and lymphatic diseases ,medicine ,Animals ,Humans ,Genes, Tumor Suppressor ,Myeloid Cells ,Aged ,Genetics ,Sex Characteristics ,Mutation ,Point mutation ,Adult Acute Myeloid Leukemia ,Hematology ,Middle Aged ,Hematopoietic Stem Cells ,medicine.disease ,Repressor Proteins ,Leukemia, Myeloid, Acute ,Leukemia ,Oncology ,Female ,Carrier Proteins - Abstract
Loss of function mutations and deletions encompassing the plant homeodomain finger 6 (PHF6) gene are present in about 20% of T-cell acute lymphoblastic leukemias (ALLs). Here, we report the identification of recurrent mutations in PHF6 in 10/353 adult acute myeloid leukemias (AMLs). Genetic lesions in PHF6 found in AMLs are frameshift and nonsense mutations distributed through the gene or point mutations involving the second plant homeodomain (PHD)-like domain of the protein. As in the case of T-ALL, where PHF6 alterations are found almost exclusively in males, mutations in PHF6 were seven times more prevalent in males than in females with AML. Overall, these results identify PHF6 as a tumor suppressor gene mutated in AML and extend the role of this X-linked tumor suppressor gene in the pathogenesis of hematologic tumors.
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- 2010
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48. NOTCH1 and FBXW7 mutations have a favorable impact on early response to treatment, but not on outcome, in children with T-cell acute lymphoblastic leukemia (T-ALL) treated on EORTC trials 58881 and 58951
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Jacques Otten, Karima Yakouben, Stefan Suciu, Eortc-Clg, L Suarez, Sandra Collette, Patrick Boutard, Emmanuelle Clappier, P Rohrlich, Sandrine Girard, G Brunie, Dominique Plantaz, Franki Speleman, Claude Preudhomme, Nathalie Grardel, Françoise Mazingue, Sophie Kaltenbach, P van Vlierberghe, Yves Benoit, Yves Bertrand, Alain Robert, Hélène Cavé, and Nicole Dastugue
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Oncology ,Cancer Research ,medicine.medical_specialty ,Chemotherapy ,business.industry ,T cell ,Incidence (epidemiology) ,medicine.medical_treatment ,Notch signaling pathway ,Hematology ,Minimal residual disease ,Response to treatment ,Clinical trial ,medicine.anatomical_structure ,hemic and lymphatic diseases ,Internal medicine ,Immunology ,medicine ,business ,Prospective cohort study - Abstract
Risk-adjusted treatment stratification in T-cell acute lymphoblastic leukemias (T-ALLs) is currently based only on early response to chemotherapy. We investigated the prognostic implication of hyperactivation of NOTCH pathway resulting from mutations of NOTCH1 or FBXW7 in children with T-ALL enrolled in EORTC-CLG trials. Overall, 80 out of 134 (60%) patients were NOTCH+ (NOTCH1 and/or FBXW7 mutated). Although clinical presentations were not significantly associated with NOTCH status, NOTCH+ patients showed a better early response to chemotherapy as compared with NOTCH- patients, according to the rate of poor pre-phase 'responders' (25% versus 44%; P=0.02) and the incidence of high minimal residual disease (MRD) levels (11% (7/62) versus 32% (10/31); P=0.01) at completion of induction. However, the outcome of NOTCH+ patients was similar to that of NOTCH- patients, with a 5-year event-free survival (EFS) of 73% and 70% (P=0.82), and 5-year overall survival of 82% and 79% (P=0.62), respectively. In patients with high MRD levels, the 5-year EFS rate was 0% (NOTCH+) versus 42% (NOTCH-), whereas in those with low MRD levels, the outcome was similar: 76% (NOTCH+) versus 78% (NOTCH-). The incidence of isolated central nervous system (CNS) relapses was relatively high in NOTCH1+ patients (8.3%), which could be related to a higher propensity of NOTCH+ leukemic blasts to target the CNS.
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- 2010
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49. Prognostic Impact of Gene Expression–Based Classification for Neuroblastoma
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Frank Berthold, Katharina Schardt, Olivier Delattre, Shahab Asgharzadeh, Andreas Faldum, Frank Westermann, Holger Christiansen, Thorsten Simon, Dilafruz Juraeva, Franki Speleman, Lars Kaderali, Manfred Schwab, Yvonne Kahlert, Gian Paolo Tonini, Smadar Avigad, Marta Piqueras, Joëlle Vermeulen, Alexander Valent, Isabelle Janoueix-Lerosey, Gudrun Schleiermacher, Isaac Yaniv, Paola Scaruffi, Jo Vandesompele, Roland Eils, Boris Decarolis, Barbara Hero, Axel Weber, Rosa Noguera, Patrick Warnat, Benedikt Brors, Matthias Fischer, Jean Bénard, Richard Grundy, Robert C. Seeger, André Oberthuer, and Jessica Theissen
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Adult ,Oncology ,Cancer Research ,medicine.medical_specialty ,Pathology ,Adolescent ,Neuroblastoma ,Text mining ,Internal medicine ,Gene expression ,medicine ,Humans ,Child ,Proportional Hazards Models ,Microarray analysis techniques ,business.industry ,Proportional hazards model ,Gene Expression Profiling ,Hazard ratio ,Infant, Newborn ,Infant ,Cancer ,Prognosis ,medicine.disease ,Gene expression profiling ,Child, Preschool ,business - Abstract
Purpose To evaluate the impact of a predefined gene expression–based classifier for clinical risk estimation and cytotoxic treatment decision making in neuroblastoma patients. Patients and Methods Gene expression profiles of 440 internationally collected neuroblastoma specimens were investigated by microarray analysis, 125 of which were examined prospectively. Patients were classified as either favorable or unfavorable by a 144-gene prediction analysis for microarrays (PAM) classifier established previously on a separate set of 77 patients. PAM classification results were compared with those of current prognostic markers and risk estimation strategies. Results The PAM classifier reliably distinguished patients with contrasting clinical courses (favorable [n = 249] and unfavorable [n = 191]; 5-year event free survival [EFS] 0.84 ± 0.03 v 0.38 ± 0.04; 5-year overall survival [OS] 0.98 ± 0.01 v 0.56 ± 0.05, respectively; both P < .001). Moreover, patients with divergent outcome were robustly discriminated in both German and international cohorts and in prospectively analyzed samples (P ≤ .001 for both EFS and OS for each). In subgroups with clinical low-, intermediate-, and high-risk of death from disease, the PAM predictor significantly separated patients with divergent outcome (low-risk 5-year OS: 1.0 v 0.75 ± 0.10, P < .001; intermediate-risk: 1.0 v 0.82 ± 0.08, P = .042; and high-risk: 0.81 ± 0.08 v 0.43 ± 0.05, P = .001). In multivariate Cox regression models based on both EFS and OS, PAM was a significant independent prognostic marker (EFS: hazard ratio [HR], 3.375; 95% CI, 2.075 to 5.492; P < .001; OS: HR, 11.119, 95% CI, 2.487 to 49.701; P < .001). The highest potential clinical impact of the classifier was observed in patients currently considered as non–high-risk (n = 289; 5-year EFS: 0.87 ± 0.02 v 0.44 ± 0.07; 5-year OS: 1.0 v 0.80 ± 0.06; both P < .001). Conclusion Gene expression–based classification using the 144-gene PAM predictor can contribute to improved treatment stratification of neuroblastoma patients.
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- 2010
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50. Chromosomal and MicroRNA Expression Patterns Reveal Biologically Distinct Subgroups of 11q− Neuroblastoma
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Johannes H. Schulte, Angelika Eggert, Isabella Bray, Jo Vandesompele, Alexander Schramm, Leah Alcock, Franki Speleman, Patrick G. Buckley, Kenneth Bryan, Katleen De Preter, Raymond L. Stallings, and Pieter Mestdagh
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Cancer Research ,Chromosomes, Human, Pair 11 ,Gene Expression Profiling ,Medizin ,Gene Dosage ,Biology ,medicine.disease ,Bioinformatics ,Gene dosage ,Disease-Free Survival ,Gene expression profiling ,MicroRNAs ,Neuroblastoma ,Oncology ,Downregulation and upregulation ,microRNA ,Gene expression ,medicine ,Cancer research ,Humans ,Chromosome Deletion ,Gene ,Comparative genomic hybridization - Abstract
Purpose: The purpose of this study was to further define the biology of the 11q− neuroblastoma tumor subgroup by the integration of array-based comparative genomic hybridization with microRNA (miRNA) expression profiling data to determine if improved patient stratification is possible. Experimental Design: A set of primary neuroblastoma (n = 160), which was broadly representative of all genetic subtypes, was analyzed by array-based comparative genomic hybridization and for the expression of 430 miRNAs. A 15-miRNA expression signature previously shown to be predictive of clinical outcome was used to analyze an independent cohort of 11q− tumors (n = 37). Results: Loss of 4p and gain of 7q occurred at a significantly higher frequency in the 11q− tumors, further defining the genetic characteristics of this subtype. The 11q− tumors could be split into two subgroups using a miRNA expression survival signature that differed significantly in clinical outcome and the overall frequency of large-scale genomic imbalances, with the poor survival subgroup having significantly more imbalances. miRNAs from the expression signature, which were upregulated in unfavorable tumors, were predicted to target downregulated genes from a published mRNA expression classifier of clinical outcome at a higher-than-expected frequency, indicating the miRNAs might contribute to the regulation of genes within the signature. Conclusion: We show that two distinct biological subtypes of neuroblastoma with loss of 11q occur, which differ in their miRNA expression profiles, frequency of segmental imbalances, and clinical outcome. A miRNA expression signature, combined with an analysis of segmental imbalances, provides greater prediction of event-free survival and overall survival outcomes than 11q status by itself, improving patient stratification. Clin Cancer Res; 16(11); 2971–8. ©2010 AACR.
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- 2010
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