Publications by authors named "Nadine Van Roy"

96 Publications

A challenging diagnosis of a nonsecretor plasma cell dyscrasia with pleomorphic plasmablastic morphology.

Clin Case Rep 2020 Dec 18;8(12):3070-3074. Epub 2020 Sep 18.

Department of Laboratory Medicine Ghent University Hospital Ghent Belgium.

This report highlights the importance of integrating clinical, radiological, genetic, and pathological laboratory findings to make a correct diagnosis especially with challenging and rare entities.
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http://dx.doi.org/10.1002/ccr3.3260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7752493PMC
December 2020

Age Dependency of the Prognostic Impact of Tumor Genomics in Localized Resectable -Nonamplified Neuroblastomas. Report From the SIOPEN Biology Group on the LNESG Trials and a COG Validation Group.

J Clin Oncol 2020 11 9;38(31):3685-3697. Epub 2020 Sep 9.

Children's Cancer Research Institute, St Anna Kinderkrebsforschung, Vienna, Austria.

Purpose: For localized, resectable neuroblastoma without amplification, surgery only is recommended even if incomplete. However, it is not known whether the genomic background of these tumors may influence outcome.

Patients And Methods: Diagnostic samples were obtained from 317 tumors, International Neuroblastoma Staging System stages 1/2A/2B, from 3 cohorts: Localized Neuroblastoma European Study Group I/II and Children's Oncology Group. Genomic data were analyzed using multi- and pangenomic techniques and fluorescence in-situ hybridization in 2 age groups (cutoff age, 18 months) and were quality controlled by the International Society of Pediatric Oncology European Neuroblastoma (SIOPEN) Biology Group.

Results: Patients with stage 1 tumors had an excellent outcome (5-year event-free survival [EFS] ± standard deviation [SD], 95% ± 2%; 5-year overall survival [OS], 99% ± 1%). In contrast, patients with stage 2 tumors had a reduced EFS in both age groups (5-year EFS ± SD, 84% ± 3% in patients < 18 months of age and 75% ± 7% in patients ≥ 18 months of age). However, OS was significantly decreased only in the latter group (5-year OS ± SD in < 18months and ≥ 18months, 96% ± 2% and 81% ± 7%, respectively; = .001). In < 18months, relapses occurred independent of segmental chromosome aberrations (SCAs); only 1p loss decreased EFS (5-year EFS ± SD in patients 1p loss and no 1p loss, 62% ± 13% and 87% ± 3%, respectively; = .019) but not OS (5-year OS ± SD, 92% ± 8% and 97% ± 2%, respectively). In patients ≥ 18 months, only SCAs led to relapse and death, with 11q loss as the strongest marker (11q loss and no 11q loss: 5-year EFS ± SD, 48% ± 16% and 85% ± 7%, = .033; 5-year OS ± SD, 46% ± 22% and 92% ± 6%, = .038).

Conclusion: Genomic aberrations of resectable non-amplified stage 2 neuroblastomas have a distinct age-dependent prognostic impact. Chromosome 1p loss is a risk factor for relapse but not for diminished OS in patients < 18 months, SCAs (especially 11q loss) are risk factors for reduced EFS and OS in those > 18months. In older patients with SCA, a randomized trial of postoperative chemotherapy compared with observation alone may be indicated.
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http://dx.doi.org/10.1200/JCO.18.02132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605396PMC
November 2020

Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study.

Epigenetics 2021 Jan-Feb;16(2):196-208. Epub 2020 Jul 14.

Department of Biomolecular Medicine, Ghent University , Ghent, Belgium.

In the clinical management of paediatric solid tumours, histological examination of tumour tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumour is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumour samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of paediatric tumours using cell-free reduced representation bisulphite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumour type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free DNA. We demonstrate that the majority of misclassifications were associated with sample quality and not with the extent of disease. Our approach has the potential to help tackle some of the remaining diagnostic challenges in paediatric oncology in a cost-effective and minimally invasive manner.
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http://dx.doi.org/10.1080/15592294.2020.1790950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889189PMC
July 2020

Correction to: The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: as review.

Eur J Pediatr 2020 09;179(9):1497-1498

Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.

In the original version of this article, a reader pointed out that there was a mistake in the phrasing in a paragraph. This could potentially be harmful to children. The authors agree to change the wording. "vitreous fluid" will be changed to "aqueous humor".
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http://dx.doi.org/10.1007/s00431-020-03692-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645481PMC
September 2020

Targeting cytokine- and therapy-induced PIM1 activation in preclinical models of T-cell acute lymphoblastic leukemia and lymphoma.

Blood 2020 05;135(19):1685-1695

Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.

T-cell acute lymphoblastic leukemia (T-ALL) and T-cell acute lymphoblastic lymphoma (T-LBL) are aggressive hematological malignancies that are currently treated with high-dose chemotherapy. Over the last several years, the search toward novel and less-toxic therapeutic strategies for T-ALL/T-LBL patients has largely focused on the identification of cell-intrinsic properties of the tumor cell. However, non-cell-autonomous activation of specific oncogenic pathways might also offer opportunities that could be exploited at the therapeutic level. In line with this, we here show that endogenous interleukin 7 (IL7) can increase the expression of the oncogenic kinase proviral integration site for Moloney-murine leukemia 1 (PIM1) in CD127+ T-ALL/T-LBL, thereby rendering these tumor cells sensitive to in vivo PIM inhibition. In addition, using different CD127+ T-ALL/T-LBL xenograft models, we also reveal that residual tumor cells, which remain present after short-term in vivo chemotherapy, display consistent upregulation of PIM1 as compared with bulk nontreated tumor cells. Notably, this effect was transient as increased PIM1 levels were not observed in reestablished disease after abrogation of the initial chemotherapy. Furthermore, we uncover that this phenomenon is, at least in part, mediated by the ability of glucocorticoids to cause transcriptional upregulation of IL7RA in T-ALL/T-LBL patient-derived xenograft (PDX) cells, ultimately resulting in non-cell-autonomous PIM1 upregulation by endogenous IL7. Finally, we confirm in vivo that chemotherapy in combination with a pan-PIM inhibitor can improve leukemia survival in a PDX model of CD127+ T-ALL. Altogether, our work reveals that IL7 and glucocorticoids coordinately drive aberrant activation of PIM1 and suggests that IL7-responsive CD127+ T-ALL and T-LBL patients could benefit from PIM inhibition during induction chemotherapy.
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http://dx.doi.org/10.1182/blood.2019003880DOI Listing
May 2020

The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: a review.

Eur J Pediatr 2020 Feb 3;179(2):191-202. Epub 2020 Jan 3.

Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.

Cell-free DNA profiling using patient blood is emerging as a non-invasive complementary technique for cancer genomic characterization. Since these liquid biopsies will soon be integrated into clinical trial protocols for pediatric cancer treatment, clinicians should be informed about potential applications and advantages but also weaknesses and potential pitfalls. Small retrospective studies comparing genetic alterations detected in liquid biopsies with tumor biopsies for pediatric solid tumor types are encouraging. Molecular detection of tumor markers in cell-free DNA could be used for earlier therapy response monitoring and residual disease detection as well as enabling detection of pathognomonic and therapeutically relevant genomic alterations.Conclusion: Existing analyses of liquid biopsies from children with solid tumors increasingly suggest a potential relevance for molecular diagnostics, prognostic assessment, and therapeutic decision-making. Gaps remain in the types of tumors studied and value of detection methods applied. Here we review the current stand of liquid biopsy studies for pediatric solid tumors with a dedicated focus on cell-free DNA analysis. There is legitimate hope that integrating fully validated liquid biopsy-based innovations into the standard of care will advance patient monitoring and personalized treatment of children battling solid cancers.What is Known:• Liquid biopsies are finding their way into routine oncological screening, diagnosis, and disease monitoring in adult cancer types fast.• The most widely adopted source for liquid biopsies is blood although other easily accessible body fluids, such as saliva, pleural effusions, urine, or cerebrospinal fluid (CSF) can also serve as sources for liquid biopsiesWhat is New:• Retrospective proof-of-concept studies in small cohorts illustrate that liquid biopsies in pediatric solid tumors yield tremendous potential to be used in diagnostics, for therapy response monitoring and in residual disease detection.• Liquid biopsy diagnostics could tackle some long-standing issues in the pediatric oncology field; they can enable accurate genetic diagnostics in previously unbiopsied tumor types like renal tumors or brain stem tumors leading to better treatment strategies.
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http://dx.doi.org/10.1007/s00431-019-03545-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6971142PMC
February 2020

Detection of Copy Number Alterations by Shallow Whole-Genome Sequencing of Formalin-Fixed, Paraffin-Embedded Tumor Tissue.

Arch Pathol Lab Med 2019 Dec 17. Epub 2019 Dec 17.

From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy).

Context.—: In routine clinical practice, tumor tissue is stored in formalin-fixed, paraffin-embedded blocks. However, the use of formalin-fixed, paraffin-embedded tissue for genome analysis is challenged by poorer DNA quality and quantity. Although several studies have reported genome-wide massive parallel sequencing applied on formalin-fixed, paraffin-embedded samples for mutation analysis, copy number analysis is not yet commonly performed.

Objective.—: To evaluate the use of formalin-fixed, paraffin-embedded tissue for copy number alteration detection using shallow whole-genome sequencing, more generally referred to as copy number variation sequencing.

Design.—: We selected samples from 21 patients, covering a range of different tumor entities. The performance of copy number detection was compared across 3 setups: array comparative genomic hybridization in combination with fresh material; copy number variation sequencing on fresh material; and copy number variation sequencing on formalin-fixed, paraffin-embedded material.

Results.—: Very similar copy number profiles between paired samples were obtained. Although formalin-fixed, paraffin-embedded profiles often displayed more noise, detected copy numbers seemed equally reliable if the tumor fraction was at least 20%.

Conclusions.—: Copy number variation sequencing of formalin-fixed, paraffin-embedded material represents a trustworthy method. It is very likely that copy number variation sequencing of routinely obtained biopsy material will become important for individual patient care and research. Moreover, the basic technology needed for copy number variation sequencing is present in most molecular diagnostics laboratories.
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http://dx.doi.org/10.5858/arpa.2019-0010-OADOI Listing
December 2019

Noonan syndrome-associated myeloproliferative disorder with somatically acquired monosomy 7: impact on clinical decision making.

Br J Haematol 2019 11 15;187(4):E83-E86. Epub 2019 Oct 15.

Division of Paediatric Haematology-Oncology and Stem Cell Transplantation, Department of Paediatrics, Ghent University Hospital, Ghent, Belgium.

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http://dx.doi.org/10.1111/bjh.16191DOI Listing
November 2019

Pinpointing a potential role for CLEC12B in cancer predisposition through familial exome sequencing.

Pediatr Blood Cancer 2019 02 23;66(2):e27513. Epub 2018 Oct 23.

Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium.

Predisposition to cancer is only partly understood, and thus, the contribution of still undiscovered cancer predisposing variants necessitates further research. In search of such variants, we performed exome sequencing on the germline DNA of a family with two children affected by ganglioneuroma and neuroblastoma. Applying stringent selection criteria, we identified a potential deleterious, missense mutation in CLEC12B, coding for a lectin C-type receptor that is predicted to regulate immune function. Although further screening in a larger population and functional characterization is needed, we propose CLEC12B as a candidate cancer predisposition gene.
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http://dx.doi.org/10.1002/pbc.27513DOI Listing
February 2019

Correction: MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences.

Leukemia 2018 10;32(10):2304

Department of Biology, University of Bari "Aldo Moro", Bari, Italy.

In the original version of this Article, the affiliation details for Giovanni Martinelli were incorrectly given as 'Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy' and it should have been given as 'Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy and not Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy.'Furthermore, the original version of this Article contained an error in the spelling of the authors Alberto L'Abbate and Pietro D'Addabbo, an acute accent was used instead of an apostrophe for these authors names.These errors have now been corrected in both the PDF and HTML versions of the Article.
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http://dx.doi.org/10.1038/s41375-018-0177-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608236PMC
October 2018

A case of chronic eosinophilic leukemia with secondary transformation to acute myeloid leukemia.

Leuk Res Rep 2018 9;9:45-47. Epub 2018 Apr 9.

Department of Hematology, Ghent University Hospital, Ghent, Belgium.

The natural history of primary eosinophilia remains highly variable and is characterized by underlying disease heterogeneity. Chronic eosinophilic leukemia, not otherwise specified (CEL-NOS) is a rare and aggressive disease characterized by non-specific cytogenetic abnormalities or elevated blasts, with high risk of transformation to acute leukemia. We describe a case of CEL-NOS with two hierarchically related non-specific cytogenetic rearrangements, associated with an mutation and followed by evolution to secondary AML. mutations are not previously described in CEL-NOS.
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http://dx.doi.org/10.1016/j.lrr.2018.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993353PMC
April 2018

The long non-coding RNA landscape in juvenile myelomonocytic leukemia.

Haematologica 2018 11 1;103(11):e501-e504. Epub 2018 Jun 1.

Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Belgium.

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http://dx.doi.org/10.3324/haematol.2018.189977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278979PMC
November 2018

MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences.

Leukemia 2018 10 22;32(10):2152-2166. Epub 2018 Feb 22.

Department of Biology, University of Bari "Aldo Moro", Bari, Italy.

Double minutes (dmin), homogeneously staining regions, and ring chromosomes are vehicles of gene amplification in cancer. The underlying mechanism leading to their formation as well as their structure and function in acute myeloid leukemia (AML) remain mysterious. We combined a range of high-resolution genomic methods to investigate the architecture and expression pattern of amplicons involving chromosome band 8q24 in 23 cases of AML (AML-amp). This revealed that different MYC-dmin architectures can coexist within the same leukemic cell population, indicating a step-wise evolution rather than a single event origin, such as through chromothripsis. This was supported also by the analysis of the chromothripsis criteria, that poorly matched the model in our samples. Furthermore, we found that dmin could evolve toward ring chromosomes stabilized by neocentromeres. Surprisingly, amplified genes (mainly PVT1) frequently participated in fusion transcripts lacking a corresponding DNA template. We also detected a significant overexpression of the circular RNA of PVT1 (circPVT1) in AML-amp cases versus AML with a normal karyotype. Our results show that 8q24 amplicons in AML are surprisingly plastic DNA structures with an unexpected association to novel fusion transcripts and circular RNAs.
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http://dx.doi.org/10.1038/s41375-018-0033-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6170393PMC
October 2018

"Atypical" Pleomorphic Lipomatous Tumor: A Clinicopathologic, Immunohistochemical and Molecular Study of 21 Cases, Emphasizing its Relationship to Atypical Spindle Cell Lipomatous Tumor and Suggesting a Morphologic Spectrum (Atypical Spindle Cell/Pleomorphic Lipomatous Tumor).

Am J Surg Pathol 2017 Nov;41(11):1443-1455

*Department of Pathology ¶Center for Medical Genetics, Ghent University Hospital †CRIG, Cancer Research Institute Ghent, Ghent University, Ghent, Belgium ‡Dermatopathology Bodensee, Friedrichshafen, Germany §Department of Pathology, Diakonessenhuis, Utrecht ∥MRC-Holland, Amsterdam #Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.

The classification of the until recently poorly explored group of atypical adipocytic neoplasms with spindle cell features, for which recently the term atypical spindle cell lipomatous tumor (ASLT) has been proposed, remains challenging. Recent studies have proposed ASLT as a unique entity with (in at least a significant subset of cases) a specific genetic background, namely deletions/losses of 13q14, including RB1 and its flanking genes RCBTB2, DLEU1, and ITM2B. Similar genetic aberrations have been reported in pleomorphic liposarcomas (PLSs). This prompted us to investigate a series of 21 low-grade adipocytic neoplasms with a pleomorphic lipoma-like appearance, but with atypical morphologic features (including atypical spindle cells, pleomorphic [multinucleated] cells, pleomorphic lipoblasts and poor circumscription), for which we propose the term "atypical" pleomorphic lipomatous tumor (APLT). Five cases of PLS were also included in this study. We used multiplex ligation-dependent probe amplification to evaluate genetic changes of 13q14. In addition, array-based comparative genomic hybridization was performed on 4 APLTs and all PLSs. Multiplex ligation-dependent probe amplification showed consistent loss of RB1 and its flanking gene RCBTB2 in all cases of APLT. This genetic alteration was also present in all PLSs, suggesting genetic overlap, in addition to morphologic overlap, with APLTs. However, array-based comparative genomic hybridization demonstrated more complex genetic alterations with more losses and gains in PLSs compared with APLTs. APLTs arose in the subcutis (67%) more frequently than in the deep (subfascial) soft tissues (33%). With a median follow-up of 42 months, recurrences were documented in 2 of 12 APLTs for which a long follow-up was available. Herein, we also demonstrate that APLTs share obvious overlapping morphologic, immunohistochemical, genetic and clinical characteristics with the recently defined ASLT, suggesting that they are related lesions that form a spectrum (atypical spindle cell/pleomorphic lipomatous tumor).
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http://dx.doi.org/10.1097/PAS.0000000000000936DOI Listing
November 2017

Shallow Whole Genome Sequencing on Circulating Cell-Free DNA Allows Reliable Noninvasive Copy-Number Profiling in Neuroblastoma Patients.

Clin Cancer Res 2017 Oct 14;23(20):6305-6314. Epub 2017 Jul 14.

Center for Medical Genetics, Ghent University, Ghent, Belgium.

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. In 37 patients with NB, cfDNA analysis using shallow whole genome sequencing (sWGS) was compared with arrayCGH analysis of primary tumor tissue. 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 and amplification and deletion could be readily detected with sWGS using a low input of cfDNA. 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. .
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http://dx.doi.org/10.1158/1078-0432.CCR-17-0675DOI Listing
October 2017

Thermodynamic framework to assess low abundance DNA mutation detection by hybridization.

PLoS One 2017 25;12(5):e0177384. Epub 2017 May 25.

Flemish Institute for Technological Research, VITO, Mol, Belgium.

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177384PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444680PMC
September 2017

EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research.

Authors:
Jan Van Deun Pieter Mestdagh Patrizia Agostinis Özden Akay Sushma Anand Jasper Anckaert Zoraida Andreu Martinez Tine Baetens Els Beghein Laurence Bertier Geert Berx Janneke Boere Stephanie Boukouris Michel Bremer Dominik Buschmann James B Byrd Clara Casert Lesley Cheng Anna Cmoch Delphine Daveloose Eva De Smedt Seyma Demirsoy Victoria Depoorter Bert Dhondt Tom A P Driedonks Aleksandra Dudek Abdou Elsharawy Ilaria Floris Andrew D Foers Kathrin Gärtner Abhishek D Garg Edward Geeurickx Jan Gettemans Farzaneh Ghazavi Bernd Giebel Tom Groot Kormelink Grace Hancock Hetty Helsmoortel Andrew F Hill Vincent Hyenne Hina Kalra David Kim Joanna Kowal Sandra Kraemer Petra Leidinger Carina Leonelli Yaxuan Liang Lien Lippens Shu Liu Alessandra Lo Cicero Shaun Martin Suresh Mathivanan Prabhu Mathiyalagan Támas Matusek Gloria Milani Marta Monguió-Tortajada Liselot M Mus Dillon C Muth Andrea Németh Esther N M Nolte-'t Hoen Lorraine O'Driscoll Roberta Palmulli Michael W Pfaffl Bjarke Primdal-Bengtson Erminia Romano Quentin Rousseau Susmita Sahoo Natalia Sampaio Monisha Samuel Benjamin Scicluna Bieke Soen Anneleen Steels Johannes V Swinnen Maarit Takatalo Safia Thaminy Clotilde Théry Joeri Tulkens Isabel Van Audenhove Susanne van der Grein Alan Van Goethem Martijn J van Herwijnen Guillaume Van Niel Nadine Van Roy Alexander R Van Vliet Niels Vandamme Suzanne Vanhauwaert Glenn Vergauwen Frederik Verweij Annelynn Wallaert Marca Wauben Kenneth W Witwer Marijke I Zonneveld Olivier De Wever Jo Vandesompele An Hendrix

Nat Methods 2017 02;14(3):228-232

Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.

We argue that the field of extracellular vesicle (EV) biology needs more transparent reporting to facilitate interpretation and replication of experiments. To achieve this, we describe EV-TRACK, a crowdsourcing knowledgebase (http://evtrack.org) that centralizes EV biology and methodology with the goal of stimulating authors, reviewers, editors and funders to put experimental guidelines into practice.
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http://dx.doi.org/10.1038/nmeth.4185DOI Listing
February 2017

Tandem repeats of Allium fistulosum associated with major chromosomal landmarks.

Mol Genet Genomics 2017 Apr 1;292(2):453-464. Epub 2017 Feb 1.

Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia.

Tandem repeats are often associated with important chromosomal landmarks, such as centromeres, telomeres, subtelomeric, and other heterochromatic regions, and can be good candidates for molecular cytogenetic markers. Tandem repeats present in many plant species demonstrate dramatic differences in unit length, proportion in the genome, and chromosomal organization. Members of genus Allium with their large genomes represent a challenging task for current genetics. Using the next generation sequencing data, molecular, and cytogenetic methods, we discovered two tandemly organized repeats in the Allium fistulosum genome (2n = 2C = 16), HAT58 and CAT36. Together, these repeats comprise 0.25% of the bunching onion genome with 160,000 copies/1 C of HAT58 and 93,000 copies/1 C of CAT36. Fluorescent in situ hybridization (FISH) and C-banding showed that HAT58 and CAT36 associated with the interstitial and pericentromeric heterochromatin of the A. fistulosum chromosomes 5, 6, 7, and 8. FISH with HAT58 and CAT36 performed on A. cepa (2n = 2C = 16) and A. wakegi (2n = 2C = 16), a natural allodiploid hybrid between A. fistulosum and A. cepa, revealed that these repeats are species specific and produced specific hybridization patterns only on A. fistulosum chromosomes. Thus, the markers can be used in interspecific breeding programs for monitoring of alien genetic material. We applied Non-denaturing FISH that allowed detection of the repeat bearing chromosomes within 3 h. A polymorphism of the HAT58 chromosome location was observed. This finding suggests that the rapid evolution of the HAT58 repeat is still ongoing.
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http://dx.doi.org/10.1007/s00438-016-1286-9DOI Listing
April 2017

Towards a FISH-based karyotype of L. (Rosaceae).

Comp Cytogenet 2016 4;10(4):543-554. Epub 2016 Nov 4.

Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 49, 127550, Moscow, Russia; Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 3, 127550, Moscow, Russia.

The genus Linnaeus, 1753 has important economic value in ornamental sector and many breeding activities are going on supported by molecular studies. However, the cytogenetic studies of rose species are scarce and mainly focused on chromosome counting and chromosome morphology-based karyotyping. Due to the small size of the chromosomes and a high frequency of polyploidy in the genus, karyotyping is very challenging for rose species and requires FISH-based cytogenetic markers to be applied. Therefore, in this work the aim is to establish a FISH-based karyotype for (Crépin, 1888), a rose species with several benefits for advanced molecular cytogenetic studies of genus (Kirov et al. 2015a). It is shown that FISH signals from 5S, 45S and an -type telomeric repeat are distributed on five (1, 2, 4, 5 and 7) of seven chromosome pairs. In addition, it is demonstrated that the interstitial telomeric repeat sequences (ITR) are located in the centromeric regions of four chromosome pairs. Using low hybridization stringency for ITR visualization, we showed that the number of ITR signals increases four times (1-4 signals). This study is the first to propose a FISH-based karyotype for the reliable identification of chromosomes. The possible origin of ITR loci is discussed.
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http://dx.doi.org/10.3897/CompCytogen.v10i4.9536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240508PMC
November 2016

Unique long non-coding RNA expression signature in ETV6/RUNX1-driven B-cell precursor acute lymphoblastic leukemia.

Oncotarget 2016 11;7(45):73769-73780

Center for Medical Genetics, Department of Paediatrics and Genetics, Ghent University Hospital, Ghent, Belgium.

Overwhelming evidence indicates that long non-coding RNAs have essential roles in tumorigenesis. Nevertheless, their role in the molecular pathogenesis of pediatric B-cell precursor acute lymphoblastic leukemia has not been extensively explored. Here, we conducted a comprehensive analysis of the long non-coding RNA transcriptome in ETV6/RUNX1-positive BCP-ALL, one of the most frequent subtypes of pediatric leukemia. First, we used primary leukemia patient samples to identify an ETV6/RUNX1 specific expression signature consisting of 596 lncRNA transcripts. Next, integration of this lncRNA signature with RNA sequencing of BCP-ALL cell lines and lncRNA profiling of an in vitro model system of ETV6/RUNX1 knockdown, revealed that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 are truly regulated by the oncogenic fusion protein. Moreover, sustained inactivation of lnc-RTN4R-1 and lnc-NKX2-3-1 in ETV6/RUNX1 positive cells caused profound changes in gene expression. All together, our study defined a unique lncRNA expression signature associated with ETV6/RUNX1-positive BCP-ALL and identified lnc-RTN4R-1 and lnc-NKX2-3-1 as lncRNAs that might be functionally implicated in the biology of this prevalent subtype of human leukemia.
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http://dx.doi.org/10.18632/oncotarget.12063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5342012PMC
November 2016

Monosomy 22 and partial loss of INI1 expression in a biphasic synovial sarcoma with an Ewing sarcoma-like poorly differentiated component: Report of a case.

Pathol Res Pract 2016 Jul 13;212(7):658-64. Epub 2016 Apr 13.

Department of Pathology, Ghent University and Ghent University Hospital, Ghent, Belgium.

Poorly differentiated synovial sarcoma (PDSS) is a less common subtype of synovial sarcoma (SS) associated with a poor prognosis. We present a case of a SS with a poorly differentiated component that resembles Ewing sarcoma (ES). Initial immunohistochemical staining revealed a characteristic and strong expression of transducin-like enhancer of split 1 (TLE1) and weak to absent expression of integrase integrator 1 (INI1) staining. Stainings for keratin and epithelial membrane antigen (EMA) were negative in the tumoral lesion. Fluorescence In Situ Hybridization (FISH) analysis showed a rearrangement of the synaptotagmin (SYT) gene, confirming the diagnosis of SS. FISH analysis for the EWS RNA-binding protein 1 (EWSR1) gene revealed monoallelic loss of EWSR1. This finding was confirmed by an array comparative genomic hybridization (aCGH), showing complete loss of chromosome 22. Based on literature review, showing only a handful of cases of cytogenetically studied SS with loss of chromosome 22, this is probably a rare event in SS. Therefore, we assume that monoallelic loss of chromosome 22 cannot fully elaborate the underlying mechanism of the INI1 staining pattern in all SS, but it could account for the weak to absent INI1 staining in at least some cases.
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http://dx.doi.org/10.1016/j.prp.2016.04.003DOI Listing
July 2016

LIN28B overexpression defines a novel fetal-like subgroup of juvenile myelomonocytic leukemia.

Blood 2016 Mar 28;127(9):1163-72. Epub 2015 Dec 28.

Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium;

Juvenile myelomonocytic leukemia (JMML) is a rare and aggressive stem cell disease of early childhood. RAS activation constitutes the core component of oncogenic signaling. In addition, leukemic blasts in one-fourth of JMML patients present with monosomy 7, and more than half of patients show elevated age-adjusted fetal hemoglobin (HbF) levels. Hematopoietic stem cell transplantation is the current standard of care and results in an event-free survival rate of 50% to 60%, indicating that novel molecular-driven therapeutic options are urgently needed. Using gene expression profiling in a series of 82 patient samples, we aimed at understanding the molecular biology behind JMML and identified a previously unrecognized molecular subgroup characterized by high LIN28B expression. LIN28B overexpression was significantly correlated with higher HbF levels, whereas patients with monosomy 7 seldom showed enhanced LIN28B expression. This finding gives a biological explanation of why patients with monosomy 7 are rarely diagnosed with high age-adjusted HbF levels. In addition, this new fetal-like JMML subgroup presented with reduced levels of most members of the let-7 microRNA family and showed characteristic overexpression of genes involved in fetal hematopoiesis and stem cell self-renewal. Lastly, high LIN28B expression was associated with poor clinical outcome in our JMML patient series but was not independent from other prognostic factors such as age and age-adjusted HbF levels. In conclusion, we identified elevated LIN28B expression as a hallmark of a novel fetal-like subgroup in JMML.
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http://dx.doi.org/10.1182/blood-2015-09-667808DOI Listing
March 2016

Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma.

Oncotarget 2016 Jan;7(2):1960-72

Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium.

Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in CCDC177, NXPH1, lnc-MRPL3-2, lnc-TREX1-1 and one on a region from chromosome 8 with no further annotation) predict event-free survival and 4 additional assays (located in SPRED3, TNFAIP2, NPM2 and CYYR1) also predict overall survival. Furthermore, a robust 58-marker methylation signature predicting overall and event-free survival was established. In conclusion, this study encompasses the largest DNA methylation biomarker study in neuroblastoma so far. We identified and independently validated several novel prognostic biomarkers, as well as a prognostic 58-marker methylation signature.
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http://dx.doi.org/10.18632/oncotarget.6477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811509PMC
January 2016

Focus on 16p13.3 Locus in Colon Cancer.

PLoS One 2015 29;10(7):e0131421. Epub 2015 Jul 29.

Department of Gastroenterology-Digestive Oncology, Ghent University Hospital, Ghent, Belgium.

Background: With one million new cases of colorectal cancer (CRC) diagnosed annually in the world, CRC is the third most commonly diagnosed cancer in the Western world. Patients with stage I-III CRC can be cured with surgery but are at risk for recurrence. Colorectal cancer is characterized by the presence of chromosomal deletions and gains. Large genomic profiling studies have however not been conducted in this disease. The number of a specific genetic aberration in a tumour sample could correlate with recurrence-free survival or overall survival, possibly leading to its use as biomarker for therapeutic decisions. At this point there are not sufficient markers for prediction of disease recurrence in colorectal cancer, which can be used in the clinic to discriminate between stage II patients who will benefit from adjuvant chemotherapy. For instance, the benefit of adjuvant chemotherapy has been most clearly demonstrated in stage III disease with an approximately 30 percent relative reduction in the risk of disease recurrence. The benefits of adjuvant chemotherapy in stage II disease are less certain, the risk for relapse is much smaller in the overall group and the specific patients at risk are hard to identify.

Materials And Methods: In this study, array-comparative genomic hybridization analysis (array-CGH) was applied to study high-resolution DNA copy number alterations in 93 colon carcinoma samples. These genomic data were combined with parameters like KRAS mutation status, microsatellite status and clinicopathological characteristics.

Results: Both large and small chromosomal losses and gains were identified in our sample cohort. Recurrent gains were found for chromosome 1q, 7, 8q, 13 and 20 and losses were mostly found for 1p, 4, 8p, 14, 15, 17p, 18, 21 and 22. Data analysis demonstrated that loss of chromosome 4 is linked to a worse prognosis in our patients series. Besides these alterations, two interesting small regions of overlap were identified, which could be associated with disease recurrence. Gain of the 16p13.3 locus (including the RNA binding protein, fox-1 homolog gene, RBFOX1) was linked with a worse recurrence-free survival in our patient cohort. On the other hand, loss of RBFOX1 was only found in patients without disease recurrence. Most interestingly, above mentioned characteristics were also found in stage II patients, for whom there is a high medical need for the identification of new prognostic biomarkers.

Conclusions: In conclusion, copy number variation of the 16p13.3 locus seems to be an important parameter for prediction of disease recurrence in colon cancer.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131421PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519182PMC
April 2016

The challenging differential diagnosis of skin tumours with a rhabdoid phenotype: not all tumours with rhabdoid phenotype belong to the group of SMARCB1-deficient tumours.

Histopathology 2016 Mar 17;68(4):608-12. Epub 2015 Sep 17.

Department of Pathology, Ghent University Hospital, Ghent, Belgium.

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http://dx.doi.org/10.1111/his.12790DOI Listing
March 2016

Heterogeneous cytogenetic subgroups and outcomes in childhood acute megakaryoblastic leukemia: a retrospective international study.

Blood 2015 Sep 27;126(13):1575-84. Epub 2015 Jul 27.

St. Jude Children's Research Hospital, Memphis, TN;

Comprehensive clinical studies of patients with acute megakaryoblastic leukemia (AMKL) are lacking. We performed an international retrospective study on 490 patients (age ≤18 years) with non-Down syndrome de novo AMKL diagnosed from 1989 to 2009. Patients with AMKL (median age 1.53 years) comprised 7.8% of pediatric AML. Five-year event-free (EFS) and overall survival (OS) were 43.7% ± 2.7% and 49.0% ± 2.7%, respectively. Patients diagnosed in 2000 to 2009 were treated with higher cytarabine doses and had better EFS (P = .037) and OS (P = .003) than those diagnosed in 1989 to 1999. Transplantation in first remission did not improve survival. Cytogenetic data were available for 372 (75.9%) patients: hypodiploid (n = 18, 4.8%), normal karyotype (n = 49, 13.2%), pseudodiploid (n = 119, 32.0%), 47 to 50 chromosomes (n = 142, 38.2%), and >50 chromosomes (n = 44, 11.8%). Chromosome gain occurred in 195 of 372 (52.4%) patients: +21 (n = 106, 28.5%), +19 (n = 93, 25.0%), +8 (n = 77, 20.7%). Losses occurred in 65 patients (17.5%): -7 (n = 13, 3.5%). Common structural chromosomal aberrations were t(1;22)(p13;q13) (n = 51, 13.7%) and 11q23 rearrangements (n = 38, 10.2%); t(9;11)(p22;q23) occurred in 21 patients. On the basis of frequency and prognosis, AMKL can be classified to 3 risk groups: good risk-7p abnormalities; poor risk-normal karyotypes, -7, 9p abnormalities including t(9;11)(p22;q23)/MLL-MLLT3, -13/13q-, and -15; and intermediate risk-others including t(1;22)(p13;q13)/OTT-MAL (RBM15-MKL1) and 11q23/MLL except t(9;11). Risk-based innovative therapy is needed to improve patient outcomes.
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http://dx.doi.org/10.1182/blood-2015-02-629204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582334PMC
September 2015

CD200/BTLA deletions in pediatric precursor B-cell acute lymphoblastic leukemia treated according to the EORTC-CLG 58951 protocol.

Haematologica 2015 Oct 2;100(10):1311-9. Epub 2015 Jul 2.

Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Belgium

DNA copy number analysis has been instrumental for the identification of genetic alterations in B-cell precursor acute lymphoblastic leukemia. Notably, some of these genetic defects have been associated with poor treatment outcome and might be relevant for future risk stratification. In this study, we characterized recurrent deletions of CD200 and BTLA genes, mediated by recombination-activating genes, and used breakpoint-specific polymerase chain reaction assay to screen a cohort of 1154 cases of B-cell precursor acute lymphoblastic leukemia uniformly treated according to the EORTC-CLG 58951 protocol. CD200/BTLA deletions were identified in 56 of the patients (4.8%) and were associated with an inferior 8-year event free survival in this treatment protocol [70.2% ± 1.2% for patients with deletions versus 83.5% ± 6.4% for non-deleted cases (hazard ratio 2.02; 95% confidence interval 1.23-3.32; P=0.005)]. Genetically, CD200/BTLA deletions were strongly associated with ETV6-RUNX1-positive leukemias (P<0.0001), but were also identified in patients who did not have any genetic abnormality that is currently used for risk stratification. Within the latter population of patients, the presence of CD200/BTLA deletions was associated with inferior event-free survival and overall survival. Moreover, the multivariate Cox model indicated that these deletions had independent prognostic impact on event-free survival when adjusting for conventional risk criteria. All together, these findings further underscore the rationale for copy number profiling as an important tool for risk stratification in human B-cell precursor acute lymphoblastic leukemia. This trial was registered at www.ClinicalTrials.gov as #NCT00003728.
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http://dx.doi.org/10.3324/haematol.2015.126953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4591763PMC
October 2015