49 results on '"Helaers R"'
Search Results
2. 32P Tumor-agnostic plasma assay for circulating tumor DNA predicts outcome in recurrent and/or metastatic squamous cell carcinoma of the head and neck treated with a PD-1 inhibitor
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Honoré, N., primary, Van Der Elst, A., additional, Dietz, A., additional, Van Marcke de Lummen, C., additional, Helaers, R., additional, Mendola, A., additional, Dahou, H., additional, Marbaix, E., additional, Poncin, R., additional, Seront, E., additional, Schmitz, S., additional, Limaye, N., additional, Galot, R., additional, and Machiels, J-P., additional
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- 2023
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3. [OP.6B.03] KIF1B AND NF1 ARE THE MOST FREQUENTLY MUTATED GENES IN PARAGANGLIOMAS AND PHEOCHROMOCYTOMAS TUMOURS FROM A BELGIAN MULTICENTRIC COHORT
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Evenepoel, L., Helaers, R., Vroonen, L., Aydin, S., Hamoir, M., Maiter, D., Vikkula, M., and Persu, A.
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- 2017
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4. P-24 Circulating tumor DNA as a marker of Minimal Residual Disease in squamous cell carcinoma of the head and neck: an agnostic approach
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Honoré, N., primary, Galot, R., additional, van Marcke, C., additional, Helaers, R., additional, Mendola, A., additional, Limaye, N., additional, and Machiels, J-P., additional
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- 2021
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5. 858O Minimal residual disease (MRD) diagnosed by a plasma tumor-agnostic circulating tumor DNA (ctDNA) assay after curative therapy in locally advanced (LA) squamous cell carcinoma of the head and neck (SCCHN) predicts disease relapse and survival
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Honoré, N., Van Marcke de Lummen, C., Galot, R., Helaers, R., van Maanen, A., Ambroise, J., Mendola, A., Dahou, H., Marbaix, E., van Eeckhout, P., Longton, E., Magremanne, M., Schmitz, S., Limaye, N., and Machiels, J-P.
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- 2023
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6. Liquid biopsy for mutational profiling of locoregional recurrent and/or metastatic squamous cell carcinoma of the head and neck
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Galot, R., primary, Van Marcke de Lummen, C., additional, Helaers, R., additional, Mendola, A., additional, Goebbels, R.-M., additional, Caignet, X., additional, Ambroise, J., additional, Wittouck, K., additional, Vikkula, M., additional, Limaye, N., additional, and Machiels, J.-P., additional
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- 2019
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7. DiGeST: Distributed Computing for Scalable Gene and Variant Ranking with Hadoop/Spark
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Helaers R, Guillaume Smits, Marc Abramowicz, Gianluca Bontempi, Tom Lenaerts, Yann-Aël Le Borgne, Electronics and Informatics, Informatics and Applied Informatics, and Artificial Intelligence
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Clinical genomics ,Ranking ,Computer science ,Distributed computing ,Scalability ,Spark (mathematics) ,1000 Genomes Project ,Genome ,Gene ,Exome ,DNA sequencing ,Genetic association ,Genotype frequency - Abstract
BackgroundThe advent of next-generation sequencing technologies has opened new avenues for clinical genomics research. In particular, as sequencing costs continue to decrease, an ever-growing number of clinical genomics institutes now rely on DNA sequencing studies at varying scales - genome, exome, mendeliome - for uncovering disease-associated variants or genes, in both rare and non-rare diseases.A common methodology for identifying such variants or genes is to rely on genetic association studies (GAS), that test whether allele or genotype frequencies differ between two groups of individuals, usually diseased subjects and healthy controls. Current bioinformatics tools for performing GAS are designed to run on standalone machines, and do not scale well with the increasing size of study designs and the search for multi-locus genetic associations. More efficient distributed and scalable data analysis solutions are needed to address this challenge.ResultsWe developed a Big Data solution stack for distributing computations in genetic association studies, that address both single and multi-locus associations. The proposed stack, called DiGeST (Distributed Gene/variant Scoring Tool) is divided in two main components: a Hadoop/Spark high-performance computing back-end for efficient data storage and distributed computing, and a Web front-end providing users with a rich set of options to filter, compare and explore exome data from different sample populations. Using exome data from the 1000 Genomes Project, we show that our distributed implementation smoothly scales with computing resources. We make the resulting software stack Open-Source, and provide virtualisation scripts to run the complete environment both on standalone machine or Hadoop-based cluster.ConclusionsHadoop/Spark provides a powerful and well-suited distributed computing framework for genetic association studies. Our work illustrates the flexibility, ease of use and scalability of the framework, and more generally advocates for its wider adoption in bioinformatics pipelines.
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- 2017
8. Splice-site mutations in VEGFC cause loss of function and Nonne-Milroy-like primary lymphedema
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Fastré, E., primary, Lanteigne, L-E., additional, Helaers, R., additional, Giacalone, G., additional, Revencu, N., additional, Dionyssiou, D., additional, Demiri, E., additional, Brouillard, P., additional, and Vikkula, M., additional
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- 2018
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9. Blue Rubber Bleb Nevus (BRBN) Syndrome Is Caused by Somatic TEK (TIE2) Mutations.
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Soblet, J., Kangas, J., Nätynki, M., Mendola, A., Helaers, R., Uebelhoer, M., Kaakinen, M., Cordisco, M., Dompmartin, A., Enjolras, O., Holden, S., Irvine, A.D., Kangesu, L., Léauté-Labrèze, C., Lanoel, L., Lokmic, Z., Maas, S., McAleer, M.A., Penington, A., Rieu, P.N.M.A., Syed, S., Vleuten, C.J.M. van der, Watson, R., Fishman, S.J., Mulliken, J.B., Eklund, L., Limaye, N., Boon, L.M., Vikkula, M., Soblet, J., Kangas, J., Nätynki, M., Mendola, A., Helaers, R., Uebelhoer, M., Kaakinen, M., Cordisco, M., Dompmartin, A., Enjolras, O., Holden, S., Irvine, A.D., Kangesu, L., Léauté-Labrèze, C., Lanoel, L., Lokmic, Z., Maas, S., McAleer, M.A., Penington, A., Rieu, P.N.M.A., Syed, S., Vleuten, C.J.M. van der, Watson, R., Fishman, S.J., Mulliken, J.B., Eklund, L., Limaye, N., Boon, L.M., and Vikkula, M.
- Abstract
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- Published
- 2016
10. 1157P - Liquid biopsy for mutational profiling of locoregional recurrent and/or metastatic squamous cell carcinoma of the head and neck
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Galot, R., Van Marcke de Lummen, C., Helaers, R., Mendola, A., Goebbels, R.-M., Caignet, X., Ambroise, J., Wittouck, K., Vikkula, M., Limaye, N., and Machiels, J.-P.
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- 2019
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11. Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles
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Tzika A.C. Helaers R. Schramm G. & M. C. Milinkovitch
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animal structures - Abstract
Background Reptiles are largely under represented in comparative genomics despite the fact that they are substantially more diverse in many respects than mammals. Given the high divergence of reptiles from classical model species next generation sequencing of their transcriptomes is an approach of choice for gene identification and annotation. Results Here we use 454 technology to sequence the brain transcriptome of four divergent reptilian and one reference avian species: the Nile crocodile the corn snake the bearded dragon the red eared turtle and the chicken. Using an in house pipeline for recursive similarity searches of >3000000 reads against multiple databases from 7 reference vertebrates we compile a reptilian comparative transcriptomics dataset with homology assignment for 20000 to 31000 transcripts per species and a cumulated non redundant sequence length of 248.6 Mbases. Our approach identifies the majority (87) of chicken brain transcripts and about 50 of de novo assembled reptilian transcripts. In addition to 57502 microsatellite loci we identify thousands of SNP and indel polymorphisms for population genetic and linkage analyses. We also build very large multiple alignments for Sauropsida and mammals (two million residues per species) and perform extensive phylogenetic analyses suggesting that turtles are not basal living reptiles but are rather associated with Archosaurians hence potentially answering a long standing question in the phylogeny of Amniotes. Conclusions The reptilian transcriptome (freely available at http://www.reptilian transcriptomes.org webcite) should prove a useful new resource as reptiles are becoming important new models for comparative genomics ecology and evolutionary developmental genetics.
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- 2011
12. gViz, a novel tool for the visualization of co-expression networks
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Depiereux Sophie, Pierre Michael, De Meulder Bertrand, Bareke Eric, Helaers Raphaël, Habra Naji, and Depiereux Eric
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Medicine ,Biology (General) ,QH301-705.5 ,Science (General) ,Q1-390 - Abstract
Abstract Background The quantity of microarray data available on the Internet has grown dramatically over the past years and now represents millions of Euros worth of underused information. One way to use this data is through co-expression analysis. To avoid a certain amount of bias, such data must often be analyzed at the genome scale, for example by network representation. The identification of co-expression networks is an important means to unravel gene to gene interactions and the underlying functional relationship between them. However, it is very difficult to explore and analyze a network of such dimensions. Several programs (Cytoscape, yEd) have already been developed for network analysis; however, to our knowledge, there are no available GraphML compatible programs. Findings We designed and developed gViz, a GraphML network visualization and exploration tool. gViz is built on clustering coefficient-based algorithms and is a novel tool to visualize and manipulate networks of co-expression interactions among a selection of probesets (each representing a single gene or transcript), based on a set of microarray co-expression data stored as an adjacency matrix. Conclusions We present here gViz, a software tool designed to visualize and explore large GraphML networks, combining network theory, biological annotation data, microarray data analysis and advanced graphical features.
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- 2011
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13. MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics
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Milinkovitch Michel C and Helaers Raphaël
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities. Results Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers. Conclusions The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org.
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- 2010
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14. Somatic Loss-of-Function PIK3R1 and Activating Non-hotspot PIK3CA Mutations Associated with Capillary Malformation with Dilated Veins (CMDV).
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De Bortoli M, Queisser A, Pham VC, Dompmartin A, Helaers R, Boutry S, Claus C, De Roo AK, Hammer F, Brouillard P, Abdelilah-Seyfried S, Boon LM, and Vikkula M
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- Humans, Animals, Male, Female, Adult, Loss of Function Mutation, Middle Aged, Endothelial Cells metabolism, Endothelial Cells pathology, Signal Transduction genetics, Veins abnormalities, Veins pathology, High-Throughput Nucleotide Sequencing, Child, Adolescent, Aged, Class I Phosphatidylinositol 3-Kinases genetics, Zebrafish genetics, Capillaries abnormalities, Capillaries pathology, Class Ia Phosphatidylinositol 3-Kinase genetics, Vascular Malformations genetics, Vascular Malformations pathology
- Abstract
Common capillary malformations are red vascular skin lesions, most commonly associated with somatic activating GNAQ or GNA11 mutations. We focused on capillary malformations lacking such a mutation to identify previously unreported genetic causes. We used targeted next-generation sequencing on 82 lesions. Bioinformatic analysis allowed the identification of 9 somatic pathogenic variants in PIK3R1 and PIK3CA, encoding for the regulatory and catalytic subunits of phosphoinositide 3-kinase, respectively. Recharacterization of these lesions unraveled a common phenotype: a pale capillary malformation associated with visible dilated veins. Primary endothelial cells from 2 PIK3R1-mutated lesions were isolated, and PI3k-Akt-mTOR and RAS-RAF-MAPK signaling were assessed by western blot. This unveiled an abnormal increase in Akt phosphorylation, effectively reduced by PI3K pathway inhibitors, such as mTOR, Akt, and PIK3CA inhibitors. The effects of mutant PIK3R1 were further studied using zebrafish embryos. Endothelium-specific expression of PIK3R1 mutants resulted in abnormal development of the posterior capillary-venous plexus. In summary, capillary malformation associated with visible dilated veins emerges as a clinical entity associated with somatic pathogenic variants in PIK3R1 or PIK3CA (nonhotspot). Our findings suggest that the activated Akt signaling can be effectively reversed by PI3K pathway inhibitors. In addition, the proposed zebrafish model holds promise as a valuable tool for future drug screening aimed at developing patient-tailored treatments., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2024
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15. A New Tool to Identify Pediatric Patients with Atypical Diabetes Associated with Gene Polymorphisms.
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Welsch S, Harvengt A, Gallo P, Martin M, Beckers D, Mouraux T, Seret N, Lebrethon MC, Helaers R, Brouillard P, Vikkula M, and Lysy PA
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- Humans, Child, Male, Female, Adolescent, Polymorphism, Genetic, Child, Preschool, Diagnosis, Differential, Glycated Hemoglobin analysis, Cohort Studies, Insulin, Diabetes Mellitus, Type 2 genetics, Diabetes Mellitus, Type 2 diagnosis, Diabetes Mellitus, Type 1 genetics, Diabetes Mellitus, Type 1 diagnosis
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Backgruound: Recent diabetes subclassifications have improved the differentiation between patients with type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus despite several overlapping features, yet without considering genetic forms of diabetes. We sought to facilitate the identification of monogenic diabetes by creating a new tool that we validated in a pediatric maturity-onset diabetes of the young (MODY) cohort., Methods: We first created the DIAgnose MOnogenic DIAbetes (DIAMODIA) criteria based on the pre-existing, but incomplete, MODY calculator. This new score is composed of four strong and five weak criteria, with patients having to display at least one weak and one strong criterion., Results: The effectiveness of the DIAMODIA criteria was evaluated in two patient cohorts, the first consisting of patients with confirmed MODY diabetes (n=34) and the second of patients with T1DM (n=390). These DIAMODIA criteria successfully detected 100% of MODY patients. Multiple correspondence analysis performed on the MODY and T1DM cohorts enabled us to differentiate MODY patients from T1DM. The three most relevant variables to distinguish a MODY from T1DM profile were: lower insulin-dose adjusted A1c score ≤9, glycemic target-adjusted A1c score ≤4.5, and absence of three anti-islet cell autoantibodies., Conclusion: We validated the DIAMODIA criteria, as it effectively identified all monogenic diabetes patients (MODY cohort) and succeeded to differentiate T1DM from MODY patients. The creation of this new and effective tool is likely to facilitate the characterization and therapeutic management of patients with atypical diabetes, and promptly referring them for genetic testing which would markedly improve clinical care and counseling, as well.
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- 2024
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16. Epilepsy with faint capillary malformation or reticulated telangiectasia associated with mosaic AKT3 pathogenic variants.
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De Bortoli M, Ivars M, Revencu N, Nassogne MC, Lavarino C, Paco S, Lammens M, Renders A, Dumitriu D, Helaers R, Boon LM, Baselga E, and Vikkula M
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- Female, Humans, Infant, Newborn, Male, Genetic Association Studies, Genetic Predisposition to Disease, Mosaicism, Mutation genetics, Phenotype, Adolescent, Capillaries abnormalities, Capillaries pathology, Epilepsy genetics, Epilepsy pathology, Proto-Oncogene Proteins c-akt genetics, Telangiectasis genetics, Telangiectasis pathology, Telangiectasis diagnosis, Vascular Malformations genetics, Vascular Malformations pathology, Vascular Malformations diagnosis, Vascular Malformations complications
- Abstract
Capillary malformations (CMs) are the most common type of vascular anomalies, affecting around 0.3% of newborns. They are usually caused by somatic pathogenic variants in GNAQ or GNA11. PIK3CA and PIK3R1, part of the phosphoinositide 3-kinase-protein kinase B-mammalian target of rapamycin pathway, are mutated in fainter CMs such as diffuse CM with overgrowth and megalencephaly CM. In this study, we present two young patients with a CM-like phenotype associated with cerebral anomalies and severe epilepsy. Pathogenic variants in PIK3CA and PIK3R1, as well as GNAQ and GNA11, were absent in affected cutaneous tissue biopsies. Instead, we identified two somatic pathogenic variants in the AKT3 gene. Subsequent analysis of the DNA obtained from surgically resected brain tissue of one of the two patients confirmed the presence of the AKT3 variant. Focal cortical dysplasia was also detected in this patient. Genetic analysis thus facilitated workup to reach a precise diagnosis for these patients, associating the vascular anomaly with the neurological symptoms. This study underscores the importance of searching for additional signs and symptoms to guide the diagnostic workup, especially in cases with atypical vascular malformations. In addition, it strongly emphasizes the significance of genotype-phenotype correlation studies in guiding clinicians' informed decision-making regarding patient care., (© 2024 The Authors. American Journal of Medical Genetics Part A published by Wiley Periodicals LLC.)
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- 2024
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17. Tumour-agnostic plasma assay for circulating tumour DNA predicts outcome in recurrent and/or metastatic squamous cell carcinoma of the head and neck treated with a PD-1 inhibitor.
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Honoré N, van der Elst A, Dietz A, van Marcke C, Helaers R, Mendola A, Dahou H, Marbaix E, Poncin R, Seront E, Schmitz S, Limaye N, Galot R, and Machiels JP
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- Humans, Squamous Cell Carcinoma of Head and Neck drug therapy, Squamous Cell Carcinoma of Head and Neck genetics, Immune Checkpoint Inhibitors therapeutic use, Neoplasm Recurrence, Local drug therapy, Neoplasm Recurrence, Local genetics, Neoplasm Recurrence, Local pathology, Circulating Tumor DNA genetics, Head and Neck Neoplasms drug therapy, Head and Neck Neoplasms genetics, Papillomavirus Infections, Carcinoma, Squamous Cell drug therapy, Carcinoma, Squamous Cell genetics, Carcinoma, Squamous Cell secondary
- Abstract
Background: Only 15-20% of recurrent and/or metastatic squamous cell carcinoma of the head and neck (R/M SCCHN) patients derive long-term benefit from nivolumab or pembrolizumab. We developed a circulating tumour DNA (ctDNA) tumour-agnostic assay aimed at the early prediction of single agent programmed cell death 1 (PD1) inhibitor efficacy in R/M SCCHN., Patients and Methods: Our tumour-agnostic assay included 37 genes frequently mutated in R/M SCCHN and two HPV16 genes. Primary endpoint was the concordance between ctDNA kinetics (ΔctDNA) and the best overall response according to Response Evaluation Criteria in Solid Tumors version 1.1. ΔctDNA was defined as the difference in mean variant allele frequency (VAF) between the on-treatment sample harvested 6-10 weeks (FU1) after PD1 inhibitor initiation and the pre-treatment plasma sample (ΔctDNA = mean FU1 VAF - mean pre-treatment VAF)., Results: ctDNA was detected in 35/44 (80%) of the pre-treatment plasma samples. The concordance between ΔctDNA and imaging response was observed in 74%. Median progression-free survival was 8.6 months in the favourable ΔctDNA group and 2.5 months in the unfavourable ΔctDNA group (p = 0.057). Median overall survival (OS) was 18.1 and 8.2 months in the favourable and unfavourable ΔctDNA groups, respectively (p = 0.13). In patients with PD-L1 expressing SCCHN (Combined Positive Score ≥1), OS was significantly better in patients with favourable ΔctDNA compared with patients with unfavourable ΔctDNA: median OS was 41.5 and 8.4 months (p = 0.033), respectively., Conclusions: Tumour-agnostic ctDNA analysis for human papillomavirus (HPV)-negative and HPV-positive R/M SCCHN is feasible. ctDNA kinetics show promising results in predicting the efficacy of PD1 inhibitors in R/M SCCHN., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)
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- 2023
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18. Ureteropelvic junction obstruction with primary lymphoedema associated with CELSR1 variants.
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Alpaslan M, Mestré-Godin S, Lay A, Giacalone G, Helaers R, Adham S, Kovacsik H, Guillemard S, Mercier E, Boon L, Revencu N, Brouillard P, Quere I, and Vikkula M
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- Female, Humans, Male, Cadherins genetics, Cadherins metabolism, Chromosome Deletion, Chromosome Disorders genetics, Lymphedema genetics
- Abstract
Background: Primary lymphoedema (PL) is a chronic, debilitating disease caused by developmental and functional defects of the lymphatic system. It is marked by an accumulation of interstitial fluid, fat and tissue fibrosis. There is no cure. More than 50 genes and genetic loci have been linked to PL. We sought to study systematically cell polarity signalling protein Cadherin Epidermal Growth Factor Laminin G Seven-pass G-type Receptor 1 ( CELSR1 ) variants linked to PL., Methods: We investigated 742 index patients from our PL cohort using exome sequencing., Results: We identified nine variants predicted to cause CELSR1 loss of function. Four of them were tested for nonsense-mediated mRNA decay, but none was observed. Most of the truncated CELSR1 proteins would lack the transmembrane domain, if produced. The affected individuals had puberty/late-onset PL on lower extremities. The variants had a statistically significant difference in penetrance between female patients (87%) and male patients (20%). Eight variant carriers had a kidney anomaly, mostly in the form of ureteropelvic junction obstruction, which has not been associated with CELSR1 before. CELSR1 is located in the 22q13.3 deletion locus of the Phelan-McDermid syndrome. As variable renal defects are often seen in patients with the Phelan-McDermid syndrome, CELSR1 may be the long-sought gene for the renal defects., Conclusion: PL associated with a renal anomaly suggests a CELSR1 -related cause., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2023
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19. Molecular investigation in individuals with orofacial clefts and microphthalmia-anophthalmia-coloboma spectrum.
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Atique Tacla M, de Mello Copelli M, Pairet E, Monlleó IL, Ribeiro EM, Lustosa Mendes E, Helaers R, Vieira TP, Vikkula M, and Gil-da-Silva-Lopes VL
- Abstract
This study describes genomic findings among individuals with both orofacial clefts (OC) and microphthalmia/anophthalmia/coloboma (MAC) recorded in the Brazilian Database on Craniofacial Anomalies (BDCA). Chromosomal microarray analysis (CMA) and Whole Exome Sequencing (WES) were performed in 17 individuals with OC-MAC. Clinical interpretation of molecular findings was based on data available at the BDCA and on re-examination. No copy number variants (CNVs) classified as likely pathogenic or pathogenic were detected by CMA. WES allowed a conclusive diagnosis in six individuals (35.29%), two of them with variants in the CHD7 gene, and the others with variants in the TFAP2A, POMT1, PTPN11, and TP63 genes with the following syndromes: CHARGE, CHD7-spectrum, Branchiooculofacial, POMT1-spectrum, LEOPARD, and ADULT. Variants of uncertain significance (VUS) possibly associated to the phenotypes were found in six other individuals. Among the individuals with VUSes, three individuals presented variants in genes associated to defects of cilia structure and/or function, including DYNC2H1, KIAA0586, WDR34, INTU, RPGRIP1L, KIF7, and LMNA. These results show that WES was the most effective molecular approach for OC-MAC in this cohort. This study also reinforces the genetic heterogeneity of OC-MAC, and the importance of genes related to ciliopathies in this phenotype., (© 2023. The Author(s), under exclusive licence to European Society of Human Genetics.)
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- 2023
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20. Rare variant association on unrelated individuals in case-control studies using aggregation tests: existing methods and current limitations.
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Boutry S, Helaers R, Lenaerts T, and Vikkula M
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- Humans, Phenotype, Case-Control Studies, Models, Genetic, Genome-Wide Association Study, Genetic Variation
- Abstract
Over the past years, progress made in next-generation sequencing technologies and bioinformatics have sparked a surge in association studies. Especially, genome-wide association studies (GWASs) have demonstrated their effectiveness in identifying disease associations with common genetic variants. Yet, rare variants can contribute to additional disease risk or trait heterogeneity. Because GWASs are underpowered for detecting association with such variants, numerous statistical methods have been recently proposed. Aggregation tests collapse multiple rare variants within a genetic region (e.g. gene, gene set, genomic loci) to test for association. An increasing number of studies using such methods successfully identified trait-associated rare variants and led to a better understanding of the underlying disease mechanism. In this review, we compare existing aggregation tests, their statistical features and scope of application, splitting them into the five classical classes: burden, adaptive burden, variance-component, omnibus and other. Finally, we describe some limitations of current aggregation tests, highlighting potential direction for further investigations., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
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- 2023
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21. Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data.
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Boutry S, Helaers R, Lenaerts T, and Vikkula M
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- Computer Simulation, Genetic Association Studies, Genomics, Models, Genetic, High-Throughput Nucleotide Sequencing, Genetic Variation, Genome-Wide Association Study
- Abstract
The development of high-throughput next-generation sequencing technologies and large-scale genetic association studies produced numerous advances in the biostatistics field. Various aggregation tests, i.e. statistical methods that analyze associations of a trait with multiple markers within a genomic region, have produced a variety of novel discoveries. Notwithstanding their usefulness, there is no single test that fits all needs, each suffering from specific drawbacks. Selecting the right aggregation test, while considering an unknown underlying genetic model of the disease, remains an important challenge. Here we propose a new ensemble method, called Excalibur, based on an optimal combination of 36 aggregation tests created after an in-depth study of the limitations of each test and their impact on the quality of result. Our findings demonstrate the ability of our method to control type I error and illustrate that it offers the best average power across all scenarios. The proposed method allows for novel advances in Whole Exome/Genome sequencing association studies, able to handle a wide range of association models, providing researchers with an optimal aggregation analysis for the genetic regions of interest., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Boutry et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2023
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22. SATB2 -Associated Syndrome Due to a c.715C>T:p(Arg239*) Variant in Adulthood: Natural History and Literature Review.
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Copelli MM, Pairet E, Atique-Tacla M, Vieira TP, Appenzeller S, Helaers R, Vikkula M, and Gil-da-Silva-Lopes VL
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- Male, Humans, Phenotype, Syndrome, Genetic Association Studies, Transcription Factors genetics, Matrix Attachment Region Binding Proteins genetics, Intellectual Disability genetics
- Abstract
SATB2 -associated syndrome (SAS) is a rare condition, and it is characterized by severe developmental delay/intellectual disability, especially severe speech delay/or absence, craniofacial abnormalities, and behavioral problems. Most of the published reports are limited to children, with little information about the natural history of the disease and the possible novel signs and symptoms or behavioral changes in adulthood. We describe the management and follow-up of a 25-year-old male with SAS due to a de novo heterozygous nonsense variant SATB2 :c.715C>T:p.(Arg239*) identified by whole-exome sequencing and review the literature. The case herein described contributes to a better characterization of the natural history of this genetic condition and in addition to the genotype-phenotype correlation of the SATB2 :c.715C>T:p.(Arg239*) variant in SAS, highlights some particularities of its management.
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- 2023
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23. Transcriptional drifts associated with environmental changes in endothelial cells.
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Afshar Y, Ma F, Quach A, Jeong A, Sunshine HL, Freitas V, Jami-Alahmadi Y, Helaers R, Li X, Pellegrini M, Wohlschlegel JA, Romanoski CE, Vikkula M, and Iruela-Arispe ML
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- Humans, Endothelium, Cells, Cultured, Coculture Techniques, Endothelial Cells metabolism, Gene Expression Profiling
- Abstract
Environmental cues, such as physical forces and heterotypic cell interactions play a critical role in cell function, yet their collective contributions to transcriptional changes are unclear. Focusing on human endothelial cells, we performed broad individual sample analysis to identify transcriptional drifts associated with environmental changes that were independent of genetic background. Global gene expression profiling by RNA sequencing and protein expression by liquid chromatography-mass spectrometry directed proteomics distinguished endothelial cells in vivo from genetically matched culture (in vitro) samples. Over 43% of the transcriptome was significantly changed by the in vitro environment. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes. Inclusion of heterotypic interactions by co-culture of endothelial cells with smooth muscle cells normalized approximately 9% of the original in vivo signature. We also identified novel flow dependent genes, as well as genes that necessitate heterotypic cell interactions to mimic the in vivo transcriptome. Our findings highlight specific genes and pathways that rely on contextual information for adequate expression from those that are agnostic of such environmental cues., Competing Interests: YA, FM, AQ, AJ, HS, VF, YJ, RH, XL, MP, JW, CR, MV, MI No competing interests declared, (© 2023, Afshar et al.)
- Published
- 2023
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24. Pathogenic variants in MDFIC cause recessive central conducting lymphatic anomaly with lymphedema.
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Byrne AB, Brouillard P, Sutton DL, Kazenwadel J, Montazaribarforoushi S, Secker GA, Oszmiana A, Babic M, Betterman KL, Brautigan PJ, White M, Piltz SG, Thomas PQ, Hahn CN, Rath M, Felbor U, Korenke GC, Smith CL, Wood KH, Sheppard SE, Adams DM, Kariminejad A, Helaers R, Boon LM, Revencu N, Moore L, Barnett C, Haan E, Arts P, Vikkula M, Scott HS, and Harvey NL
- Subjects
- Animals, Endothelial Cells, Female, Humans, Hydrops Fetalis genetics, Hydrops Fetalis metabolism, Mice, Pregnancy, Chylothorax genetics, Chylothorax metabolism, Lymphatic Vessels pathology, Lymphedema genetics, Lymphedema metabolism, Myogenic Regulatory Factors genetics
- Abstract
Central conducting lymphatic anomaly (CCLA), characterized by the dysfunction of core collecting lymphatic vessels including the thoracic duct and cisterna chyli, and presenting as chylothorax, pleural effusions, chylous ascites, and lymphedema, is a severe disorder often resulting in fetal or perinatal demise. Although pathogenic variants in RAS/mitogen activated protein kinase (MAPK) signaling pathway components have been documented in some patients with CCLA, the genetic etiology of the disorder remains uncharacterized in most cases. Here, we identified biallelic pathogenic variants in MDFIC , encoding the MyoD family inhibitor domain containing protein, in seven individuals with CCLA from six independent families. Clinical manifestations of affected fetuses and children included nonimmune hydrops fetalis (NIHF), pleural and pericardial effusions, and lymphedema. Generation of a mouse model of human MDFIC truncation variants revealed that homozygous mutant mice died perinatally exhibiting chylothorax. The lymphatic vasculature of homozygous Mdfic mutant mice was profoundly mispatterned and exhibited major defects in lymphatic vessel valve development. Mechanistically, we determined that MDFIC controls collective cell migration, an important early event during the formation of lymphatic vessel valves, by regulating integrin β
1 activation and the interaction between lymphatic endothelial cells and their surrounding extracellular matrix. Our work identifies MDFIC variants underlying human lymphatic disease and reveals a crucial, previously unrecognized role for MDFIC in the lymphatic vasculature. Ultimately, understanding the genetic and mechanistic basis of CCLA will facilitate the development and implementation of new therapeutic approaches to effectively treat this complex disease.- Published
- 2022
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25. How to choose the right real-time RT-PCR primer sets for the SARS-CoV-2 genome detection?
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Anantharajah A, Helaers R, Defour JP, Olive N, Kabera F, Croonen L, Deldime F, Vaerman JL, Barbée C, Bodéus M, Scohy A, Verroken A, Rodriguez-Villalobos H, and Kabamba-Mukadi B
- Subjects
- COVID-19 diagnosis, COVID-19 virology, COVID-19 Nucleic Acid Testing, Coronavirus genetics, Humans, RNA, Viral genetics, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, SARS-CoV-2 genetics, Sensitivity and Specificity, Sequence Alignment, Viral Load, Viral Proteins genetics, DNA Primers genetics, Genome, Viral genetics, SARS-CoV-2 isolation & purification
- Abstract
Objectives: The SARS-CoV-2 pandemic has created an unprecedented need for rapid large-scale diagnostic testing to prompt clinical and public health interventions. Currently, several quantitative reverse-transcription polymerase chain reaction (RT-qPCR) assays recommended by the World Health Organization are being used by clinical and public health laboratories and typically target regions of the RNA-dependent RNA polymerase (RdRp), envelope (E) and nucleocapsid (N) coding region. However, it is currently unclear if results from different tests are comparable. This study aimed to clarify the clinical performances of the primer/probe sets designed by US CDC and Charité/Berlin to help clinical laboratories in assay selection for SARS-CoV-2 routine detection., Methods: We compared the clinical performances of the recommended primer/probe sets using one hundred nasopharyngeal swab specimens from patients who were clinically diagnosed with COVID-19. An additional 30 "pre-intervention screening" samples from patients who were not suspected of COVID-19 were also included in this study. We also performed sequence alignment between 31064 European SARS-CoV-2 and variants of concern genomes and the recommended primer/probe sets., Results: The present study demonstrates substantial differences in SARS-CoV-2 RNA detection sensitivity among the primer/probe sets recommended by the World Health Organization especially for low-level viral loads. The alignment of thousands of SARS-CoV-2 sequences reveals that the genetic diversity remains relatively low at the primer/probe binding sites. However, multiple nucleotide mismatches might contribute to false negatives., Conclusion: An understanding of the limitations depending on the targeted genes and primer/probe sets may influence the selection of molecular detection assays by clinical laboratories., (Copyright © 2021 Elsevier B.V. All rights reserved.)
- Published
- 2021
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26. KRAS-driven model of Gorham-Stout disease effectively treated with trametinib.
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Homayun-Sepehr N, McCarter AL, Helaers R, Galant C, Boon LM, Brouillard P, Vikkula M, and Dellinger MT
- Subjects
- Acrylonitrile analogs & derivatives, Acrylonitrile pharmacology, Aniline Compounds pharmacology, Animals, Disease Models, Animal, Gain of Function Mutation, High-Throughput Nucleotide Sequencing methods, Humans, Lymphangiogenesis genetics, Mice, Signal Transduction, Tertiary Lymphoid Structures genetics, Tertiary Lymphoid Structures pathology, Bone and Bones pathology, Lymphatic Vessels abnormalities, Lymphatic Vessels pathology, Osteolysis, Essential genetics, Osteolysis, Essential pathology, Proto-Oncogene Proteins p21(ras) genetics, Pyridones pharmacology, Pyrimidinones pharmacology
- Abstract
Gorham-Stout disease (GSD) is a sporadically occurring lymphatic disorder. Patients with GSD develop ectopic lymphatics in bone, gradually lose bone, and can have life-threatening complications, such as chylothorax. The etiology of GSD is poorly understood, and current treatments for this disease are inadequate for most patients. To explore the pathogenesis of GSD, we performed targeted high-throughput sequencing with samples from a patient with GSD and identified an activating somatic mutation in KRAS (p.G12V). To characterize the effect of hyperactive KRAS signaling on lymphatic development, we expressed an active form of KRAS (p.G12D) in murine lymphatics (iLECKras mice). We found that iLECKras mice developed lymphatics in bone, which is a hallmark of GSD. We also found that lymphatic valve development and maintenance was altered in iLECKras mice. Because most iLECKras mice developed chylothorax and died before they had significant bone disease, we analyzed the effect of trametinib (an FDA-approved MEK1/2 inhibitor) on lymphatic valve regression in iLECKras mice. Notably, we found that trametinib suppressed this phenotype in iLECKras mice. Together, our results demonstrate that somatic activating mutations in KRAS can be associated with GSD and reveal that hyperactive KRAS signaling stimulates the formation of lymphatics in bone and impairs the development of lymphatic valves. These findings provide insight into the pathogenesis of GSD and suggest that trametinib could be an effective treatment for GSD.
- Published
- 2021
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27. Non-hotspot PIK3CA mutations are more frequent in CLOVES than in common or combined lymphatic malformations.
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Brouillard P, Schlögel MJ, Homayun Sepehr N, Helaers R, Queisser A, Fastré E, Boutry S, Schmitz S, Clapuyt P, Hammer F, Dompmartin A, Weitz-Tuoretmaa A, Laranne J, Pasquesoone L, Vilain C, Boon LM, and Vikkula M
- Subjects
- Class I Phosphatidylinositol 3-Kinases genetics, Endothelial Cells, Humans, Mutation, Klippel-Trenaunay-Weber Syndrome, Lipoma, Lymphatic Abnormalities, Vascular Malformations
- Abstract
Background: Theragnostic management, treatment according to precise pathological molecular targets, requests to unravel patients' genotypes. We used targeted next-generation sequencing (NGS) or digital droplet polymerase chain reaction (ddPCR) to screen for somatic PIK3CA mutations on DNA extracted from resected lesional tissue or lymphatic endothelial cells (LECs) isolated from lesions. Our cohort (n = 143) was composed of unrelated patients suffering from a common lymphatic malformation (LM), a combined lymphatic malformation [lymphatico-venous malformation (LVM), capillaro-lymphatic malformation (CLM), capillaro-lymphatico-venous malformation (CLVM)], or a syndrome [CLVM with hypertrophy (Klippel-Trenaunay-Weber syndrome, KTS), congenital lipomatous overgrowth-vascular malformations-epidermal nevi -syndrome (CLOVES), unclassified PIK3CA-related overgrowth syndrome (PROS) or unclassified vascular (lymphatic) anomaly syndrome (UVA)]., Results: We identified a somatic PIK3CA mutation in resected lesions of 108 out of 143 patients (75.5%). The frequency of the variant allele ranged from 0.54 to 25.33% in tissues, and up to 47% in isolated endothelial cells. We detected a statistically significant difference in the distribution of mutations between patients with common and combined LM compared to the syndromes, but not with KTS. Moreover, the variant allele frequency was higher in the syndromes., Conclusions: Most patients with an common or combined lymphatic malformation with or without overgrowth harbour a somatic PIK3CA mutation. However, in about a quarter of patients, no such mutation was detected, suggesting the existence of (an)other cause(s). We detected a hotspot mutation more frequently in common and combined LMs compared to syndromic cases (CLOVES and PROS). Diagnostic genotyping should thus not be limited to PIK3CA hotspot mutations. Moreover, the higher mutant allele frequency in syndromes suggests a wider distribution in patients' tissues, facilitating detection. Clinical trials have demonstrated efficacy of Sirolimus and Alpelisib in treating patients with an LM or PROS. Genotyping might lead to an increase in efficacy, as treatments could be more targeted, and responses could vary depending on presence and type of PIK3CA-mutation.
- Published
- 2021
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28. Dysregulation of Rho GTPases in orofacial cleft patients-derived primary cells leads to impaired cell migration, a potential cause of cleft/lip palate development.
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El-Sibai M, El Hajj J, Al Haddad M, El Baba N, Al Saneh M, Daoud Khatoun W, Helaers R, Vikkula M, El Atat O, Sabbagh J, Abou Chebel N, and Ghassibe-Sabbagh M
- Subjects
- Adolescent, Cell Adhesion drug effects, Cell Polarity drug effects, Cell Proliferation drug effects, Cells, Cultured, Cleft Lip genetics, Cleft Palate genetics, Collagen pharmacology, Female, Humans, Phenotype, Exome Sequencing, cdc42 GTP-Binding Protein metabolism, rhoA GTP-Binding Protein metabolism, Cell Movement drug effects, Cleft Lip enzymology, Cleft Lip pathology, Cleft Palate enzymology, Cleft Palate pathology, rho GTP-Binding Proteins metabolism
- Abstract
Cleft lip and/or palate are a split in the lip, the palate or both. This results from the inability of lip buds and palatal shelves to properly migrate and assemble during embryogenesis. By extracting primary cells from a cleft patient, we aimed at offering a better understanding of the signaling mechanisms and interacting molecules involved in the lip and palate formation and fusion. With Rho GTPases being indirectly associated with cleft occurrence, we investigated the role of the latter in both. First, whole exome sequencing was conducted in a patient with cleft lip and palate. Primary fibroblastic cells originating from the upper right gingiva region were extracted and distinct cellular populations from two individuals were obtained: a control with no cleft phenotype and a patient with a cleft lip and palate. The genetic data showed three candidate variables in ARHGEF18, EPDR1, and CUL7. Next, the molecular data showed no significant change in proliferation rates between healthy patient cells and CL/P patient cells. However, CL/P patient cells showed decreased migration, increased adhesion and presented with a more elongated phenotype. Additionally, RhoA activity was upregulated in these cells, whereas Cdc42 activity was downregulated, resulting in loss of polarity. Our results are suggestive of a possible correlation between a dysregulation of Rho GTPases and the observed phenotype of cleft lip and palate patient cells. This insight into the intramolecular aspect of this disorder helps link the genetic defect with the observed phenotype and offers a possible mechanism by which CL/P occurs., (Copyright © 2021 Elsevier B.V. All rights reserved.)
- Published
- 2021
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29. Analysing ambiguities in trypanosomatids taxonomy by barcoding.
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Boucinha C, Caetano AR, Santos HL, Helaers R, Vikkula M, Branquinha MH, Dos Santos ALS, Grellier P, Morelli KA, and d'Avila-Levy CM
- Subjects
- Phylogeny, Biodiversity, DNA Barcoding, Taxonomic, Trypanosomatina classification, Trypanosomatina genetics
- Abstract
Background: Biodiversity screens and phylogenetic studies are dependent on reliable DNA sequences in public databases. Biological collections possess vouchered specimens with a traceable history. Therefore, DNA sequencing of samples available at institutional collections can greatly contribute to taxonomy, and studies on evolution and biodiversity., Methods: We sequenced part of the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) and the SSU rRNA (V7/V8) genes from 102 trypanosomatid cultures, which are available on request at www.colprot.fiocruz.br., Objective: The main objective of this work was to use phylogenetic inferences, using the obtained DNA sequences and those from representatives of all Trypanosomatidae genera, to generate phylogenetic trees that can simplify new isolates screenings., Findings: A DNA sequence is provided for the first time for several isolates, the phylogenetic analysis allowed the classification or reclassification of several specimens, identification of candidates for new genera and species, as well as the taxonomic validation of several deposits., Main Conclusions: This survey aimed at presenting a list of validated species and their associated DNA sequences combined with a short historical overview of each isolate, which can support taxonomic and biodiversity research and promote culture collections.
- Published
- 2020
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30. Liquid biopsy for mutational profiling of locoregional recurrent and/or metastatic head and neck squamous cell carcinoma.
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Galot R, van Marcke C, Helaers R, Mendola A, Goebbels RM, Caignet X, Ambroise J, Wittouck K, Vikkula M, Limaye N, and Machiels JH
- Subjects
- Female, Humans, Male, Neoplasm Metastasis, Neoplasm Recurrence, Local, High-Throughput Nucleotide Sequencing methods, Liquid Biopsy methods, Squamous Cell Carcinoma of Head and Neck surgery
- Abstract
Objectives: The molecular landscape of head and neck squamous cell carcinoma (HNSCC) harbors potentially actionable genomic alterations. We aimed to study the utility of liquid biopsy to (i) characterize the mutational landscape of recurrent/metastatic HNSCC using a comprehensive gene panel and (ii) estimate the concordance between DNA mutations identified from circulating tumor DNA (ctDNA) and matched tumor tissues., Materials and Methods: Targeted next-generation sequencing (NGS) was performed on cell-free DNA (cfDNA) of 39 patients with locoregional recurrent (n = 19) and/or metastatic (n = 20) HNSCC. Tumor biopsy (n = 18) was sequenced using the same technique., Results: ctDNA was detected in 51% of patients (20/39) with a higher probability of detection in metastatic than locoregional recurrent disease (70% versus 30%, p = 0.025). 81% and 58% of the tissue tumor variants were not detected in plasma when considering all patients and only metastatic patients with detectable ctDNA, respectively. In a multivariate analysis, the likelihood of detecting the tissue tumor variant in plasma was related to metastatic status (p = 0.012), tumor variant allele frequency (p < 0.001) and ctDNA quantity (p < 0.001). 26% of the variants were detected only in liquid and not in the solid biopsy. Three patients without an available tumor sample had plasma containing three different potentially actionable PIK3CA mutations., Conclusion: CtDNA detection and characterization using targeted NGS is feasible in metastatic HNSCC. Liquid biopsies do not reflect the complete mutation profile of the tumor but have the potential to identify actionable mutations when tumor biopsies are not available as well as variants not found in matched tumor tissue., Competing Interests: Declaration of Competing Interest None declared., (Copyright © 2020 Elsevier Ltd. All rights reserved.)
- Published
- 2020
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31. Tumor sequencing is useful to refine the analysis of germline variants in unexplained high-risk breast cancer families.
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Van Marcke C, Helaers R, De Leener A, Merhi A, Schoonjans CA, Ambroise J, Galant C, Delrée P, Rothé F, Bar I, Khoury E, Brouillard P, Canon JL, Vuylsteke P, Machiels JP, Berlière M, Limaye N, Vikkula M, and Duhoux FP
- Subjects
- Adult, Aged, DNA Copy Number Variations, Female, Genetic Predisposition to Disease, Humans, Middle Aged, Neoplasm Grading, Risk Factors, BRCA1 Protein genetics, BRCA2 Protein genetics, Breast Neoplasms diagnosis, Breast Neoplasms genetics, Genetic Testing methods, Germ-Line Mutation, Exome Sequencing methods
- Abstract
Background: Multigene panels are routinely used to assess for predisposing germline mutations in families at high breast cancer risk. The number of variants of unknown significance thereby identified increases with the number of sequenced genes. We aimed to determine whether tumor sequencing can help refine the analysis of germline variants based on second somatic genetic events in the same gene., Methods: Whole-exome sequencing (WES) was performed on whole blood DNA from 70 unrelated breast cancer patients referred for genetic testing and without a BRCA1, BRCA2, TP53, or CHEK2 mutation. Rare variants were retained in a list of 735 genes. WES was performed on matched tumor DNA to identify somatic second hits (copy number alterations (CNAs) or mutations) in the same genes. Distinct methods (among which immunohistochemistry, mutational signatures, homologous recombination deficiency, and tumor mutation burden analyses) were used to further study the role of the variants in tumor development, as appropriate., Results: Sixty-eight patients (97%) carried at least one germline variant (4.7 ± 2.0 variants per patient). Of the 329 variants, 55 (17%) presented a second hit in paired tumor tissue. Of these, 53 were CNAs, resulting in tumor enrichment (28 variants) or depletion (25 variants) of the germline variant. Eleven patients received variant disclosure, with clinical measures for five of them. Seven variants in breast cancer-predisposing genes were considered not implicated in oncogenesis. One patient presented significant tumor enrichment of a germline variant in the oncogene ERBB2, in vitro expression of which caused downstream signaling pathway activation., Conclusion: Tumor sequencing is a powerful approach to refine variant interpretation in cancer-predisposing genes in high-risk breast cancer patients. In this series, the strategy provided clinically relevant information for 11 out of 70 patients (16%), adapted to the considered gene and the familial clinical phenotype.
- Published
- 2020
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32. First Draft Genome of the Trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore Technology and Illumina Sequencing.
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d'Avila-Levy CM, Bearzatto B, Ambroise J, Helaers R, Butenko A, Yurchenko V, Morelli KA, Santos HLC, Brouillard P, Grellier P, Gala JL, and Vikkula M
- Abstract
Here, we present first draft genome sequence of the trypanosomatid Herpetomonas muscarum ingenoplastis . This parasite was isolated repeatedly in the black blowfly, Phormia regina , and it forms a phylogenetically distinct clade in the Trypanosomatidae family., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
- Published
- 2020
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33. RASA1 mosaic mutations in patients with capillary malformation-arteriovenous malformation.
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Revencu N, Fastre E, Ravoet M, Helaers R, Brouillard P, Bisdorff-Bresson A, Chung CWT, Gerard M, Dvorakova V, Irvine AD, Boon LM, and Vikkula M
- Subjects
- Arteriovenous Malformations diagnosis, Arteriovenous Malformations metabolism, Capillaries metabolism, DNA Mutational Analysis, High-Throughput Nucleotide Sequencing, Humans, Port-Wine Stain diagnosis, Port-Wine Stain metabolism, Arteriovenous Malformations genetics, Capillaries abnormalities, Mosaicism, Mutation, Port-Wine Stain genetics, p120 GTPase Activating Protein genetics
- Abstract
Background: Capillary malformation-arteriovenous malformation is an autosomal dominant disorder, characterised by capillary malformations and increased risk of fast-flow vascular malformations, caused by loss-of-function mutations in the RASA1 or EPHB4 genes. Around 25% of the patients do not seem to carry a germline mutation in either one of these two genes. Even if other genes could be involved, some individuals may have mutations in the known genes that escaped detection by less sensitive techniques. We tested the hypothesis that mosaic mutations could explain some of previously negative cases., Methods: DNA was extracted from peripheral blood lymphocytes, saliva or vascular malformation tissues from four patients. RASA1 and EPHB4 coding regions and exon/intron boundaries were analysed by targeted custom gene panel sequencing. A second panel and/or Sanger sequencing were used to confirm the identified mutations., Results: Four distinct mosaic RASA1 mutations, with an allele frequency ranging from 3% to 25%, were identified in four index patients with classical capillary malformation-arteriovenous malformation phenotype. Three mutations were known, one was novel. In one patient, a somatic second hit was also identified. One index case had three affected children, illustrating that the mosaicism was also present in the germline., Conclusion: This study shows that RASA1 mosaic mutations can cause capillary malformation-arteriovenous malformation. Thus, highly sensitive sequencing techniques should be considered as diagnostic tools, especially for patients with no family history. Even low-level mosaicism can cause the classical phenotype and increased risk for offspring. In addition, our study further supports the second-hit pathophysiological mechanism to explain the multifocality of vascular lesions in this disorder., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2020
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34. Likely Pathogenic Variants in One Third of Non-Syndromic Discontinuous Cleft Lip and Palate Patients.
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Demeer B, Revencu N, Helaers R, Gbaguidi C, Dakpe S, François G, Devauchelle B, Bayet B, and Vikkula M
- Subjects
- Child, Cleft Lip pathology, Cleft Palate pathology, Discs Large Homolog 1 Protein genetics, Female, Genetic Testing methods, Humans, Male, Receptor, Fibroblast Growth Factor, Type 1 genetics, Exome Sequencing methods, Cleft Lip genetics, Cleft Palate genetics, Mutation
- Abstract
Oral clefts are composed of cleft of the lip, cleft of the lip and palate, or cleft of the palate, and they are associated with a wide range of expression and severity. When cleft of the palate is associated with cleft of the lip with preservation of the primary palate, it defines an atypical phenotype called discontinuous cleft. Although this phenotype may represent 5% of clefts of the lip and/or palate (CLP), it is rarely specifically referred to and its pathophysiology is unknown. We conducted whole exome sequencing (WES) and apply a candidate gene approach to non-syndromic discontinuous CLP individuals in order to identify genes and deleterious variants that could underlie this phenotype. We discovered loss-of-function variants in two out of the seven individuals, implicating FGFR1 and DLG1 genes, which represents almost one third of this cohort. Whole exome sequencing of clinically well-defined subgroups of CLP, such as discontinuous cleft, is a relevant approach to study CLP etiopathogenesis. It could facilitate more accurate clinical, epidemiological and fundamental research, ultimately resulting in better diagnosis and care of CLP patients. Non-syndromic discontinuous cleft lip and palate seems to have a strong genetic basis.
- Published
- 2019
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35. SLC13A3 variants cause acute reversible leukoencephalopathy and α-ketoglutarate accumulation.
- Author
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Dewulf JP, Wiame E, Dorboz I, Elmaleh-Bergès M, Imbard A, Dumitriu D, Rak M, Bourillon A, Helaers R, Malla A, Renaldo F, Boespflug-Tanguy O, Vincent MF, Benoist JF, Wevers RA, Schlessinger A, Van Schaftingen E, Nassogne MC, and Schiff M
- Subjects
- Adolescent, Aspartic Acid cerebrospinal fluid, Aspartic Acid metabolism, Child, Preschool, Female, HEK293 Cells, Humans, Ketoglutaric Acids cerebrospinal fluid, Ketoglutaric Acids urine, Leukoencephalopathies metabolism, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Male, Mutation, Missense, Pedigree, Respiratory Tract Infections, Succinic Acid metabolism, Symporters metabolism, Tonsillitis, Exome Sequencing, Aspartic Acid analogs & derivatives, Ketoglutaric Acids metabolism, Leukoencephalopathies genetics, Symporters genetics
- Abstract
Objective: SLC13A3 encodes the plasma membrane Na
+ /dicarboxylate cotransporter 3, which imports inside the cell 4 to 6 carbon dicarboxylates as well as N-acetylaspartate (NAA). SLC13A3 is mainly expressed in kidney, in astrocytes, and in the choroid plexus. We describe two unrelated patients presenting with acute, reversible (and recurrent in one) neurological deterioration during a febrile illness. Both patients exhibited a reversible leukoencephalopathy and a urinary excretion of α-ketoglutarate (αKG) that was markedly increased and persisted over time. In one patient, increased concentrations of cerebrospinal fluid NAA and dicarboxylates (including αKG) were observed. Extensive workup was unsuccessful, and a genetic cause was suspected., Methods: Whole exome sequencing (WES) was performed. Our teams were connected through GeneMatcher., Results: WES analysis revealed variants in SLC13A3. A homozygous missense mutation (p.Ala254Asp) was found in the first patient. The second patient was heterozygous for another missense mutation (p.Gly548Ser) and an intronic mutation affecting splicing as demonstrated by reverse transcriptase polymerase chain reaction performed in muscle tissue (c.1016 + 3A > G). Mutations and segregation were confirmed by Sanger sequencing. Functional studies performed on HEK293T cells transiently transfected with wild-type and mutant SLC13A3 indicated that the missense mutations caused a marked reduction in the capacity to transport αKG, succinate, and NAA., Interpretation: SLC13A3 deficiency causes acute and reversible leukoencephalopathy with marked accumulation of αKG. Urine organic acids (especially αKG and NAA) and SLC13A3 mutations should be screened in patients presenting with unexplained reversible leukoencephalopathy, for which SLC13A3 deficiency is a novel differential diagnosis. ANN NEUROL 2019;85:385-395., (© 2019 American Neurological Association.)- Published
- 2019
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36. Unmasking familial CPX by WES and identification of novel clinical signs.
- Author
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Demeer B, Revencu N, Helaers R, Devauchelle B, François G, Bayet B, and Vikkula M
- Subjects
- Adolescent, Adult, CHARGE Syndrome diagnosis, CHARGE Syndrome genetics, Child, Child, Preschool, Female, Genes, X-Linked, Humans, Male, Mutation, Pedigree, Polymorphism, Single Nucleotide, Young Adult, Ankyloglossia diagnosis, Ankyloglossia genetics, Genetic Predisposition to Disease, Genome-Wide Association Study, Phenotype, Exome Sequencing
- Abstract
Mutations in the T-Box transcription factor gene TBX22 are found in X-linked Cleft Palate with or without Ankyloglossia syndrome (CPX syndrome). In addition to X-linked inheritance, ankyloglossia, present in the majority of CPX patients, is an important diagnostic marker, but it is frequently missed or unreported, as it is a "minor" feature. Other described anomalies include cleft lip, micro and/or hypodontia, and features of CHARGE syndrome. We conducted whole exome sequencing (WES) on 22 individuals from 17 "a priori" non-syndromic cleft lip and/or cleft palate (CL/P) families. We filtered the data for heterozygous pathogenic variants within a set of predefined candidate genes. Two canonical splice-site mutations were found in TBX22. Detailed re-phenotyping of the two probands and their families unravelled orofacial features previously not associated with the CPX phenotypic spectrum: choanal atresia, Pierre-Robin sequence, and overgrowths on the posterior edge of the hard palate, on each side of the palatal midline. This study emphasizes the importance of WES analysis in familial CLP cases, combined with deep (reverse) phenotyping in "a priori" non-syndromic clefts., (© 2018 Wiley Periodicals, Inc.)
- Published
- 2018
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37. Whole exome sequencing identifies mutations in 10% of patients with familial non-syndromic cleft lip and/or palate in genes mutated in well-known syndromes.
- Author
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Basha M, Demeer B, Revencu N, Helaers R, Theys S, Bou Saba S, Boute O, Devauchelle B, Francois G, Bayet B, and Vikkula M
- Subjects
- Abnormalities, Multiple diagnosis, Abnormalities, Multiple physiopathology, Adult, Brain physiopathology, Child, Preschool, Cleft Lip diagnosis, Cleft Lip physiopathology, Cleft Palate diagnosis, Cleft Palate physiopathology, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Mutation genetics, Pedigree, Polymorphism, Single Nucleotide genetics, Exome Sequencing methods, Young Adult, Abnormalities, Multiple genetics, Brain abnormalities, Cleft Lip genetics, Cleft Palate genetics, DNA-Binding Proteins genetics, Low Density Lipoprotein Receptor-Related Protein-6 genetics, T-Box Domain Proteins genetics, Transcription Factors genetics, Tumor Suppressor Proteins genetics
- Abstract
Background: Oral clefts, that is, clefts of the lip and/or cleft palate (CL/P), are the most common craniofacial birth defects with an approximate incidence of ~1/700. To date, physicians stratify patients with oral clefts into either syndromic CL/P (syCL/P) or non-syndromic CL/P (nsCL/P) depending on whether the CL/P is associated with another anomaly or not. In general, patients with syCL/P follow Mendelian inheritance, while those with nsCL/P have a complex aetiology and, as such, do not adhere to Mendelian inheritance. Genome-wide association studies have identified approximately 30 risk loci for nsCL/P, which could explain a small fraction of heritability., Methods: To identify variants causing nsCL/P, we conducted whole exome sequencing on 84 individuals with nsCL/P, drawn from multiplex families (n=46)., Results: We identified rare damaging variants in four genes known to be mutated in syCL/P: TP63 (one family), TBX1 (one family), LRP6 (one family) and GRHL3 (two families), and clinical reassessment confirmed the isolated nature of their CL/P., Conclusion: These data demonstrate that patients with CL/P without cardinal signs of a syndrome may still carry a mutation in a gene linked to syCL/P. Rare coding and non-coding variants in syCL/P genes could in part explain the controversial question of 'missing heritability' for nsCL/P. Therefore, gene panels designed for diagnostic testing of syCL/P should be used for patients with nsCL/P, especially when there is at least third-degree family history. This would allow a more precise management, follow-up and genetic counselling. Moreover, stratified cohorts would allow hunting for genetic modifiers., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)
- Published
- 2018
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38. Loss of ADAMTS3 activity causes Hennekam lymphangiectasia-lymphedema syndrome 3.
- Author
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Brouillard P, Dupont L, Helaers R, Coulie R, Tiller GE, Peeden J, Colige A, and Vikkula M
- Subjects
- ADAMTS Proteins metabolism, Adult, Alleles, Amino Acid Sequence, Amino Acid Substitution, Child, Conserved Sequence, Craniofacial Abnormalities metabolism, Endothelial Cells metabolism, Female, HEK293 Cells, Humans, Lymphangiectasis, Intestinal metabolism, Lymphedema metabolism, Male, Mutation, Missense, Pedigree, Procollagen N-Endopeptidase metabolism, Vascular Endothelial Growth Factor C genetics, Vascular Endothelial Growth Factor C metabolism, Vascular Endothelial Growth Factor Receptor-3 genetics, Vascular Endothelial Growth Factor Receptor-3 metabolism, ADAMTS Proteins deficiency, ADAMTS Proteins genetics, Craniofacial Abnormalities genetics, Lymphangiectasis, Intestinal genetics, Lymphedema genetics, Procollagen N-Endopeptidase deficiency, Procollagen N-Endopeptidase genetics
- Abstract
Primary lymphedema is due to developmental and/or functional defects in the lymphatic system. It may affect any part of the body, with predominance for the lower extremities. Twenty-seven genes have already been linked to primary lymphedema, either isolated, or as part of a syndrome. The proteins that they encode are involved in VEGFR3 receptor signaling. They account for about one third of all primary lymphedema cases, underscoring the existence of additional genetic factors. We used whole-exome sequencing to investigate the underlying cause in a non-consanguineous family with two children affected by lymphedema, lymphangiectasia and distinct facial features. We discovered bi-allelic missense mutations in ADAMTS3. Both were predicted to be highly damaging. These amino acid substitutions affect well-conserved residues in the prodomain and in the peptidase domain of ADAMTS3. In vitro, the mutant proteins were abnormally processed and sequestered within cells, which abolished proteolytic activation of pro-VEGFC. VEGFC processing is also affected by CCBE1 mutations that cause the Hennekam lymphangiectasia-lymphedema syndrome syndrome type1. Our data identifies ADAMTS3 as a novel gene that can be mutated in individuals affected by the Hennekam syndrome. These patients have distinctive facial features similar to those with mutations in CCBE1. Our results corroborate the recent in vitro and murine data that suggest a close functional interaction between ADAMTS3 and CCBE1 in triggering VEGFR3 signaling, a cornerstone for the differentiation and function of lymphatic endothelial cells., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2017
- Full Text
- View/download PDF
39. Germline Loss-of-Function Mutations in EPHB4 Cause a Second Form of Capillary Malformation-Arteriovenous Malformation (CM-AVM2) Deregulating RAS-MAPK Signaling.
- Author
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Amyere M, Revencu N, Helaers R, Pairet E, Baselga E, Cordisco M, Chung W, Dubois J, Lacour JP, Martorell L, Mazereeuw-Hautier J, Pyeritz RE, Amor DJ, Bisdorff A, Blei F, Bombei H, Dompmartin A, Brooks D, Dupont J, González-Enseñat MA, Frieden I, Gérard M, Kvarnung M, Hanson-Kahn AK, Hudgins L, Léauté-Labrèze C, McCuaig C, Metry D, Parent P, Paul C, Petit F, Phan A, Quere I, Salhi A, Turner A, Vabres P, Vicente A, Wargon O, Watanabe S, Weibel L, Wilson A, Willing M, Mulliken JB, Boon LM, and Vikkula M
- Subjects
- Databases, Genetic, Female, Genome-Wide Association Study methods, Humans, Male, Pedigree, Arteriovenous Malformations diagnosis, Arteriovenous Malformations genetics, Capillaries abnormalities, Germ-Line Mutation genetics, MAP Kinase Signaling System physiology, Port-Wine Stain diagnosis, Port-Wine Stain genetics, Receptor, EphB4 genetics, p120 GTPase Activating Protein genetics
- Abstract
Background: Most arteriovenous malformations (AVMs) are localized and occur sporadically. However, they also can be multifocal in autosomal-dominant disorders, such as hereditary hemorrhagic telangiectasia and capillary malformation (CM)-AVM. Previously, we identified RASA1 mutations in 50% of patients with CM-AVM. Herein we studied non-RASA1 patients to further elucidate the pathogenicity of CMs and AVMs., Methods: We conducted a genome-wide linkage study on a CM-AVM family. Whole-exome sequencing was also performed on 9 unrelated CM-AVM families. We identified a candidate gene and screened it in a large series of patients. The influence of several missense variants on protein function was also studied in vitro., Results: We found evidence for linkage in 2 loci. Whole-exome sequencing data unraveled 4 distinct damaging variants in EPHB4 in 5 families that cosegregated with CM-AVM. Overall, screening of EPHB4 detected 47 distinct mutations in 54 index patients: 27 led to a premature stop codon or splice-site alteration, suggesting loss of function. The other 20 are nonsynonymous variants that result in amino acid substitutions. In vitro expression of several mutations confirmed loss of function of EPHB4. The clinical features included multifocal CMs, telangiectasias, and AVMs., Conclusions: We found EPHB4 mutations in patients with multifocal CMs associated with AVMs. The phenotype, CM-AVM2, mimics RASA1 -related CM-AVM1 and also hereditary hemorrhagic telangiectasia. RASA1 -encoded p120RASGAP is a direct effector of EPHB4. Our data highlight the pathogenetic importance of this interaction and indicts EPHB4-RAS-ERK signaling pathway as a major cause for AVMs., (© 2017 American Heart Association, Inc.)
- Published
- 2017
- Full Text
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40. KIF1B and NF1 are the most frequently mutated genes in paraganglioma and pheochromocytoma tumors.
- Author
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Evenepoel L, Helaers R, Vroonen L, Aydin S, Hamoir M, Maiter D, Vikkula M, and Persu A
- Subjects
- Adult, Female, High-Throughput Nucleotide Sequencing, Humans, Male, Middle Aged, Mutation, Adrenal Gland Neoplasms genetics, Kinesins genetics, Neurofibromin 1 genetics, Paraganglioma genetics, Pheochromocytoma genetics
- Published
- 2017
- Full Text
- View/download PDF
41. PDGFRB gain-of-function mutations in sporadic infantile myofibromatosis.
- Author
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Arts FA, Sciot R, Brichard B, Renard M, de Rocca Serra A, Dachy G, Noël LA, Velghe AI, Galant C, Debiec-Rychter M, Van Damme A, Vikkula M, Helaers R, Limaye N, Poirel HA, and Demoulin JB
- Subjects
- Child, Child, Preschool, Female, Humans, Infant, Infant, Newborn, Male, Myofibromatosis genetics, Myofibromatosis metabolism, Receptor, Platelet-Derived Growth Factor beta metabolism, Receptor, TIE-2 genetics, Mutation, Myofibromatosis congenital, Receptor, Platelet-Derived Growth Factor beta genetics
- Abstract
Infantile myofibromatosis is one of the most prevalent soft tissue tumors of infancy and childhood. Multifocal nodules with visceral lesions are associated with a poor prognosis. A few familial cases have been linked to mutations in various genes including PDGFRB. In this study, we sequenced PDGFRB, which encodes a receptor tyrosine kinase, in 16 cases of myofibromatosis or solitary myofibroma. Mutations in the coding sequence of PDGFRB were identified in 6 out of 8 patients with the sporadic multicentric form of the disease and in 1 out of 8 patients with isolated myofibroma. Two patients had the same mutation in multiple separated lesions. By contrast, a third patient had three different PDGFRB mutations in the three nodules analyzed. Mutations were located in the transmembrane, juxtamembrane and kinase domains of the receptor. We showed that these mutations activated receptor signaling in the absence of ligand and transformed fibroblasts. In one case, a weakly-activating germline variant was associated with a stronger somatic mutation, suggesting a two-hit model for familial myofibromatosis. Furthermore, the mutant receptors were sensitive to the tyrosine kinase inhibitor imatinib, except D850V, which was inhibited by dasatinib and ponatinib, suggesting a targeted therapy for severe myofibromatosis. In conclusion, we identified gain-of-function PDGFRB mutations in the majority of multifocal infantile myofibromatosis cases, shedding light on the mechanism of disease development, which is reminiscent of multifocal venous malformations induced by TIE2 mutations. Our results provide a genetic test to facilitate diagnosis, and preclinical data for development of molecular therapies., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2017
- Full Text
- View/download PDF
42. Blue Rubber Bleb Nevus (BRBN) Syndrome Is Caused by Somatic TEK (TIE2) Mutations.
- Author
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Soblet J, Kangas J, Nätynki M, Mendola A, Helaers R, Uebelhoer M, Kaakinen M, Cordisco M, Dompmartin A, Enjolras O, Holden S, Irvine AD, Kangesu L, Léauté-Labrèze C, Lanoel A, Lokmic Z, Maas S, McAleer MA, Penington A, Rieu P, Syed S, van der Vleuten C, Watson R, Fishman SJ, Mulliken JB, Eklund L, Limaye N, Boon LM, and Vikkula M
- Subjects
- Belgium, Cohort Studies, Female, Gastrointestinal Neoplasms diagnosis, Humans, Incidence, Male, Nevus, Blue diagnosis, Rare Diseases, Skin Neoplasms diagnosis, Vascular Malformations diagnosis, Gastrointestinal Neoplasms genetics, Genetic Predisposition to Disease epidemiology, Mutation, Nevus, Blue genetics, Receptor, TIE-2 genetics, Skin Neoplasms genetics, Vascular Malformations genetics
- Abstract
Blue rubber bleb nevus syndrome (Bean syndrome) is a rare, severe disorder of unknown cause, characterized by numerous cutaneous and internal venous malformations; gastrointestinal lesions are pathognomonic. We discovered somatic mutations in TEK, the gene encoding TIE2, in 15 of 17 individuals with blue rubber bleb nevus syndrome. Somatic mutations were also identified in five of six individuals with sporadically occurring multifocal venous malformations. In contrast to common unifocal venous malformation, which is most often caused by the somatic L914F TIE2 mutation, multifocal forms are predominantly caused by double (cis) mutations, that is, two somatic mutations on the same allele of the gene. Mutations are identical in all lesions from a given individual. T1105N-T1106P is recurrent in blue rubber bleb nevus, whereas Y897C-R915C is recurrent in sporadically occurring multifocal venous malformation: both cause ligand-independent activation of TIE2, and increase survival, invasion, and colony formation when expressed in human umbilical vein endothelial cells., (Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2017
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- View/download PDF
43. Somatic Activating PIK3CA Mutations Cause Venous Malformation.
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Limaye N, Kangas J, Mendola A, Godfraind C, Schlögel MJ, Helaers R, Eklund L, Boon LM, and Vikkula M
- Subjects
- Alleles, Class I Phosphatidylinositol 3-Kinases, Gene Expression Regulation, Gene Frequency, Genetic Association Studies, High-Throughput Nucleotide Sequencing, Human Umbilical Vein Endothelial Cells drug effects, Human Umbilical Vein Endothelial Cells enzymology, Human Umbilical Vein Endothelial Cells pathology, Humans, Neovascularization, Pathologic enzymology, Neovascularization, Pathologic pathology, Phosphatidylinositol 3-Kinases metabolism, Phosphoinositide-3 Kinase Inhibitors, Protein Kinase Inhibitors pharmacology, Receptor, TIE-2 antagonists & inhibitors, Receptor, TIE-2 genetics, Receptor, TIE-2 metabolism, Signal Transduction, Thiazoles pharmacology, Transfection, Vascular Malformations enzymology, Vascular Malformations pathology, Veins enzymology, Veins pathology, Mutation, Neovascularization, Pathologic genetics, Phosphatidylinositol 3-Kinases genetics, Vascular Malformations genetics
- Abstract
Somatic mutations in TEK, the gene encoding endothelial cell tyrosine kinase receptor TIE2, cause more than half of sporadically occurring unifocal venous malformations (VMs). Here, we report that somatic mutations in PIK3CA, the gene encoding the catalytic p110α subunit of PI3K, cause 54% (27 out of 50) of VMs with no detected TEK mutation. The hotspot mutations c.1624G>A, c.1633G>A, and c.3140A>G (p.Glu542Lys, p.Glu545Lys, and p.His1047Arg), frequent in PIK3CA-associated cancers, overgrowth syndromes, and lymphatic malformation (LM), account for >92% of individuals who carry mutations. Like VM-causative mutations in TEK, the PIK3CA mutations cause chronic activation of AKT, dysregulation of certain important angiogenic factors, and abnormal endothelial cell morphology when expressed in human umbilical vein endothelial cells (HUVECs). The p110α-specific inhibitor BYL719 restores all abnormal phenotypes tested, in PIK3CA- as well as TEK-mutant HUVECs, demonstrating that they operate via the same pathogenic pathways. Nevertheless, significant genotype-phenotype correlations in lesion localization and histology are observed between individuals with mutations in PIK3CA versus TEK, pointing to gene-specific effects., (Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2015
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44. Meta-Analysis of Microarray Data of Rainbow Trout Fry Gonad Differentiation Modulated by Ethynylestradiol.
- Author
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Depiereux S, Le Gac F, De Meulder B, Pierre M, Helaers R, Guiguen Y, Kestemont P, and Depiereux E
- Subjects
- Animals, Sex Differentiation genetics, Ethinyl Estradiol pharmacology, Gonads drug effects, Gonads growth & development, Oligonucleotide Array Sequence Analysis methods, Oncorhynchus mykiss genetics, Oncorhynchus mykiss growth & development, Sex Differentiation drug effects
- Abstract
Sex differentiation in fish is a highly labile process easily reversed by the use of exogenous hormonal treatment and has led to environmental concerns since low doses of estrogenic molecules can adversely impact fish reproduction. The goal of this study was to identify pathways altered by treatment with ethynylestradiol (EE2) in developing fish and to find new target genes to be tested further for their possible role in male-to-female sex transdifferentiation. To this end, we have successfully adapted a previously developed bioinformatics workflow to a meta-analysis of two datasets studying sex reversal following exposure to EE2 in juvenile rainbow trout. The meta-analysis consisted of retrieving the intersection of the top gene lists generated for both datasets, performed at different levels of stringency. The intersecting gene lists, enriched in true positive differentially expressed genes (DEGs), were subjected to over-representation analysis (ORA) which allowed identifying several statistically significant enriched pathways altered by EE2 treatment and several new candidate pathways, such as progesterone-mediated oocyte maturation and PPAR signalling. Moreover, several relevant key genes potentially implicated in the early transdifferentiation process were selected. Altogether, the results show that EE2 has a great effect on gene expression in juvenile rainbow trout. The feminization process seems to result from the altered transcription of genes implicated in normal female gonad differentiation, resulting in expression similar to that observed in normal females (i.e. the repression of key testicular markers cyp17a1, cyp11b, tbx1), as well as from other genes (including transcription factors) that respond specifically to the EE2 treatment. The results also showed that the bioinformatics workflow can be applied to different types of microarray platforms and could be generalized to (eco)toxicogenomics studies for environmental risk assessment purposes.
- Published
- 2015
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45. gViz, a novel tool for the visualization of co-expression networks.
- Author
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Helaers R, Bareke E, De Meulder B, Pierre M, Depiereux S, Habra N, and Depiereux E
- Abstract
Background: The quantity of microarray data available on the Internet has grown dramatically over the past years and now represents millions of Euros worth of underused information. One way to use this data is through co-expression analysis. To avoid a certain amount of bias, such data must often be analyzed at the genome scale, for example by network representation. The identification of co-expression networks is an important means to unravel gene to gene interactions and the underlying functional relationship between them. However, it is very difficult to explore and analyze a network of such dimensions. Several programs (Cytoscape, yEd) have already been developed for network analysis; however, to our knowledge, there are no available GraphML compatible programs., Findings: We designed and developed gViz, a GraphML network visualization and exploration tool. gViz is built on clustering coefficient-based algorithms and is a novel tool to visualize and manipulate networks of co-expression interactions among a selection of probesets (each representing a single gene or transcript), based on a set of microarray co-expression data stored as an adjacency matrix., Conclusions: We present here gViz, a software tool designed to visualize and explore large GraphML networks, combining network theory, biological annotation data, microarray data analysis and advanced graphical features.
- Published
- 2011
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46. MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.
- Author
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Helaers R and Milinkovitch MC
- Subjects
- Artificial Intelligence, Internet, Likelihood Functions, Software, Algorithms, Computational Biology methods, Phylogeny
- Abstract
Background: The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities., Results: Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers., Conclusions: The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org.
- Published
- 2010
- Full Text
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47. 2x genomes--depth does matter.
- Author
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Milinkovitch MC, Helaers R, Depiereux E, Tzika AC, and Gabaldón T
- Subjects
- Animals, Cats, Databases, Genetic, Dogs, Fishes genetics, Gene Duplication, Genome, Guinea Pigs, Humans, Insecta genetics, Mice, Models, Genetic, Primates genetics, Rabbits, Rats, Rodentia genetics, Sequence Analysis, DNA, Comparative Genomic Hybridization, Evolution, Molecular, Phylogeny
- Abstract
Background: Given the availability of full genome sequences, mapping gene gains, duplications, and losses during evolution should theoretically be straightforward. However, this endeavor suffers from overemphasis on detecting conserved genome features, which in turn has led to sequencing multiple eutherian genomes with low coverage rather than fewer genomes with high-coverage and more even distribution in the phylogeny. Although limitations associated with analysis of low coverage genomes are recognized, they have not been quantified., Results: Here, using recently developed comparative genomic application systems, we evaluate the impact of low-coverage genomes on inferences pertaining to gene gains and losses when analyzing eukaryote genome evolution through gene duplication. We demonstrate that, when performing inference of genome content evolution, low-coverage genomes generate not only a massive number of false gene losses, but also striking artifacts in gene duplication inference, especially at the most recent common ancestor of low-coverage genomes. We show that the artifactual gains are caused by the low coverage of genome sequence per se rather than by the increased taxon sampling in a biased portion of the species tree., Conclusions: We argue that it will remain difficult to differentiate artifacts from true changes in modes and tempo of genome evolution until there is better homogeneity in both taxon sampling and high-coverage sequencing. This is important for broadening the utility of full genome data to the community of evolutionary biologists, whose interests go well beyond widely conserved physiologies and developmental patterns as they seek to understand the generative mechanisms underlying biological diversity.
- Published
- 2010
- Full Text
- View/download PDF
48. Historical constraints on vertebrate genome evolution.
- Author
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Milinkovitch MC, Helaers R, and Tzika AC
- Abstract
Recent analyses indicated that genes with larger effect of knockout or mutation and with larger probability to revert to single copy after whole genome duplication are expressed earlier in development. Here, we further investigate whether tissue specificity of gene expression is constrained by the age of origin of the corresponding genes. We use 38 metazoan genomes and a comparative genomic application system to integrate inference of gene duplication with expression data from 17,503 human genes into a strictly phylogenetic framework. We show that the number of anatomical systems in which genes are expressed decreases steadily with decreased age of the genes' first appearance in the phylogeny: the oldest genes are expressed, on average, in twice as many anatomical systems than the genes gained recently in evolution. These results are robust to different sources of expression data, to different levels of the anatomical system hierarchy, and to the use of gene families rather than duplication events. Finally, we show that the rate of increase in gene tissue specificity correlates with the relative rate of increase in the maximum number of cell types in the corresponding taxa. Although subfunctionalization and increase in cell type number throughout evolution could constitute, respectively, the proximal and ultimate causes of this correlation, the two phenomena are intermingled. Our analyses identify a striking historical constraint in gene expression: the number of cell types in existence at the time of a gene appearance (through duplication or de novo origination) tends to determine its level of tissue specificity for tens or hundreds of millions of years.
- Published
- 2009
- Full Text
- View/download PDF
49. MANTIS: a phylogenetic framework for multi-species genome comparisons.
- Author
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Tzika AC, Helaers R, Van de Peer Y, and Milinkovitch MC
- Subjects
- Base Sequence, Computer Graphics, Molecular Sequence Data, Sequence Alignment methods, Chromosome Mapping methods, Database Management Systems, Databases, Genetic, Phylogeny, Sequence Analysis, DNA methods, Software, User-Computer Interface
- Abstract
Motivation: Practitioners of comparative genomics face huge analytical challenges as whole genome sequences and functional/expression data accumulate. Furthermore, the field would greatly benefit from a better integration of this wealth of data with evolutionary concepts., Results: Here, we present MANTIS, a relational database for the analysis of (i) gains and losses of genes on specific branches of the metazoan phylogeny, (ii) reconstructed genome content of ancestral species and (iii) over- or under-representation of functions/processes and tissue specificity of gained, duplicated and lost genes. MANTIS estimates the most likely positions of gene losses on the true phylogeny using a maximum-likelihood function. A user-friendly interface and an extensive query system allow to investigate questions pertaining to gene identity, phylogenetic mapping and function/expression parameters., Availability: MANTIS is freely available at http://www.mantisdb.org and constitutes the missing link between multi-species genome comparisons and functional analyses.
- Published
- 2008
- Full Text
- View/download PDF
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