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1. CoDE-seq, an augmented whole-exome sequencing, enables the accurate detection of CNVs and mutations in Mendelian obesity and intellectual disability

Author

Louise Montagne, Mehdi Derhourhi, Amélie Piton, Bénédicte Toussaint, Emmanuelle Durand, Emmanuel Vaillant, Dorothée Thuillier, Stefan Gaget, Franck De Graeve, Iandry Rabearivelo, Amélie Lansiaux, Bruno Lenne, Sylvie Sukno, Rachel Desailloud, Miriam Cnop, Ramona Nicolescu, Lior Cohen, Jean-François Zagury, Mélanie Amouyal, Jacques Weill, Jean Muller, Olivier Sand, Bruno Delobel, Philippe Froguel, and Amélie Bonnefond

Subjects
Internal medicine, RC31-1245
Abstract

Objective: The molecular diagnosis of extreme forms of obesity, in which accurate detection of both copy number variations (CNVs) and point mutations, is crucial for an optimal care of the patients and genetic counseling for their families. Whole-exome sequencing (WES) has benefited considerably this molecular diagnosis, but its poor ability to detect CNVs remains a major limitation. We aimed to develop a method (CoDE-seq) enabling the accurate detection of both CNVs and point mutations in one step. Methods: CoDE-seq is based on an augmented WES method, using probes distributed uniformly throughout the genome. CoDE-seq was validated in 40 patients for whom chromosomal DNA microarray was available. CNVs and mutations were assessed in 82 children/young adults with suspected Mendelian obesity and/or intellectual disability and in their parents when available (ntotal = 145). Results: CoDE-seq not only detected all of the 97 CNVs identified by chromosomal DNA microarrays but also found 84 additional CNVs, due to a better resolution. When compared to CoDE-seq and chromosomal DNA microarrays, WES failed to detect 37% and 14% of CNVs, respectively. In the 82 patients, a likely molecular diagnosis was achieved in >30% of the patients. Half of the genetic diagnoses were explained by CNVs while the other half by mutations. Conclusions: CoDE-seq has proven cost-efficient and highly effective as it avoids the sequential genetic screening approaches currently used in clinical practice for the accurate detection of CNVs and point mutations. Keywords: Augmented whole-exome sequencing, Copy number variation, Intellectual disability, Molecular diagnosis, Next-generation sequencing, Obesity

Published
2018
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2. Expression and functional assessment of candidate type 2 diabetes susceptibility genes identify four new genes contributing to human insulin secretion

Author

Fatou K. Ndiaye, Ana Ortalli, Mickaël Canouil, Marlène Huyvaert, Clara Salazar-Cardozo, Cécile Lecoeur, Marie Verbanck, Valérie Pawlowski, Raphaël Boutry, Emmanuelle Durand, Iandry Rabearivelo, Olivier Sand, Lorella Marselli, Julie Kerr-Conte, Vikash Chandra, Raphaël Scharfmann, Odile Poulain-Godefroy, Piero Marchetti, François Pattou, Amar Abderrahmani, Philippe Froguel, and Amélie Bonnefond

Subjects
Internal medicine, RC31-1245
Abstract

Objectives: Genome-wide association studies (GWAS) have identified >100 loci independently contributing to type 2 diabetes (T2D) risk. However, translational implications for precision medicine and for the development of novel treatments have been disappointing, due to poor knowledge of how these loci impact T2D pathophysiology. Here, we aimed to measure the expression of genes located nearby T2D associated signals and to assess their effect on insulin secretion from pancreatic beta cells. Methods: The expression of 104 candidate T2D susceptibility genes was measured in a human multi-tissue panel, through PCR-free expression assay. The effects of the knockdown of beta-cell enriched genes were next investigated on insulin secretion from the human EndoC-βH1 beta-cell line. Finally, we performed RNA-sequencing (RNA-seq) so as to assess the pathways affected by the knockdown of the new genes impacting insulin secretion from EndoC-βH1, and we analyzed the expression of the new genes in mouse models with altered pancreatic beta-cell function. Results: We found that the candidate T2D susceptibility genes' expression is significantly enriched in pancreatic beta cells obtained by laser capture microdissection or sorted by flow cytometry and in EndoC-βH1 cells, but not in insulin sensitive tissues. Furthermore, the knockdown of seven T2D-susceptibility genes (CDKN2A, GCK, HNF4A, KCNK16, SLC30A8, TBC1D4, and TCF19) with already known expression and/or function in beta cells changed insulin secretion, supporting our functional approach. We showed first evidence for a role in insulin secretion of four candidate T2D-susceptibility genes (PRC1, SRR, ZFAND3, and ZFAND6) with no previous knowledge of presence and function in beta cells. RNA-seq in EndoC-βH1 cells with decreased expression of PRC1, SRR, ZFAND6, or ZFAND3 identified specific gene networks related to T2D pathophysiology. Finally, a positive correlation between the expression of Ins2 and the expression of Prc1, Srr, Zfand6, and Zfand3 was found in mouse pancreatic islets with altered beta-cell function. Conclusions: This study showed the ability of post-GWAS functional studies to identify new genes and pathways involved in human pancreatic beta-cell function and in T2D pathophysiology. Keywords: EndoC-βH1, Expression analysis, Genome-wide association study, Insulin secretion, RNAi screening, Type 2 diabetes

Published
2017
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3. KAT2B Is Required for Pancreatic Beta Cell Adaptation to Metabolic Stress by Controlling the Unfolded Protein Response

Author

Nabil Rabhi, Pierre-Damien Denechaud, Xavier Gromada, Sarah Anissa Hannou, Hongbo Zhang, Talha Rashid, Elisabet Salas, Emmanuelle Durand, Olivier Sand, Amélie Bonnefond, Loic Yengo, Carine Chavey, Caroline Bonner, Julie Kerr-Conte, Amar Abderrahmani, Johan Auwerx, Lluis Fajas, Philippe Froguel, and Jean-Sébastien Annicotte

Subjects
Biology (General), QH301-705.5
Abstract

The endoplasmic reticulum (ER) unfolded protein response (UPRer) pathway plays an important role in helping pancreatic β cells to adapt their cellular responses to environmental cues and metabolic stress. Although altered UPRer gene expression appears in rodent and human type 2 diabetic (T2D) islets, the underlying molecular mechanisms remain unknown. We show here that germline and β cell-specific disruption of the lysine acetyltransferase 2B (Kat2b) gene in mice leads to impaired insulin secretion and glucose intolerance. Genome-wide analysis of Kat2b-regulated genes and functional assays reveal a critical role for Kat2b in maintaining UPRer gene expression and subsequent β cell function. Importantly, Kat2b expression is decreased in mouse and human diabetic β cells and correlates with UPRer gene expression in normal human islets. In conclusion, Kat2b is a crucial transcriptional regulator for adaptive β cell function during metabolic stress by controlling UPRer and represents a promising target for T2D prevention and treatment.

Published
2016
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4. What Is the Best NGS Enrichment Method for the Molecular Diagnosis of Monogenic Diabetes and Obesity?

Author

Julien Philippe, Mehdi Derhourhi, Emmanuelle Durand, Emmanuel Vaillant, Aurélie Dechaume, Iandry Rabearivelo, Véronique Dhennin, Martine Vaxillaire, Franck De Graeve, Olivier Sand, Philippe Froguel, and Amélie Bonnefond

Subjects
Medicine, Science
Abstract

Molecular diagnosis of monogenic diabetes and obesity is of paramount importance for both the patient and society, as it can result in personalized medicine associated with a better life and it eventually saves health care spending. Genetic clinical laboratories are currently switching from Sanger sequencing to next-generation sequencing (NGS) approaches but choosing the optimal protocols is not easy. Here, we compared the sequencing coverage of 43 genes involved in monogenic forms of diabetes and obesity, and variant detection rates, resulting from four enrichment methods based on the sonication of DNA (Agilent SureSelect, RainDance technologies), or using enzymes for DNA fragmentation (Illumina Nextera, Agilent HaloPlex). We analyzed coding exons and untranslated regions of the 43 genes involved in monogenic diabetes and obesity. We found that none of the methods achieves yet full sequencing of the gene targets. Nonetheless, the RainDance, SureSelect and HaloPlex enrichment methods led to the best sequencing coverage of the targets; while the Nextera method resulted in the poorest sequencing coverage. Although the sequencing coverage was high, we unexpectedly found that the HaloPlex method missed 20% of variants detected by the three other methods and Nextera missed 10%. The question of which NGS technique for genetic diagnosis yields the highest diagnosis rate is frequently discussed in the literature and the response is still unclear. Here, we showed that the RainDance enrichment method as well as SureSelect, which are both based on the sonication of DNA, resulted in a good sequencing quality and variant detection, while the use of enzymes to fragment DNA (HaloPlex or Nextera) might not be the best strategy to get an accurate sequencing.

Published
2015
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6. Whole-exome sequencing and high throughput genotyping identified KCNJ11 as the thirteenth MODY gene.

Author

Amélie Bonnefond, Julien Philippe, Emmanuelle Durand, Aurélie Dechaume, Marlène Huyvaert, Louise Montagne, Michel Marre, Beverley Balkau, Isabelle Fajardy, Anne Vambergue, Vincent Vatin, Jérôme Delplanque, David Le Guilcher, Franck De Graeve, Cécile Lecoeur, Olivier Sand, Martine Vaxillaire, and Philippe Froguel

Subjects
Medicine, Science
Abstract

BACKGROUND: Maturity-onset of the young (MODY) is a clinically heterogeneous form of diabetes characterized by an autosomal-dominant mode of inheritance, an onset before the age of 25 years, and a primary defect in the pancreatic beta-cell function. Approximately 30% of MODY families remain genetically unexplained (MODY-X). Here, we aimed to use whole-exome sequencing (WES) in a four-generation MODY-X family to identify a new susceptibility gene for MODY. METHODOLOGY: WES (Agilent-SureSelect capture/Illumina-GAIIx sequencing) was performed in three affected and one non-affected relatives in the MODY-X family. We then performed a high-throughput multiplex genotyping (Illumina-GoldenGate assay) of the putative causal mutations in the whole family and in 406 controls. A linkage analysis was also carried out. PRINCIPAL FINDINGS: By focusing on variants of interest (i.e. gains of stop codon, frameshift, non-synonymous and splice-site variants not reported in dbSNP130) present in the three affected relatives and not present in the control, we found 69 mutations. However, as WES was not uniform between samples, a total of 324 mutations had to be assessed in the whole family and in controls. Only one mutation (p.Glu227Lys in KCNJ11) co-segregated with diabetes in the family (with a LOD-score of 3.68). No KCNJ11 mutation was found in 25 other MODY-X unrelated subjects. CONCLUSIONS/SIGNIFICANCE: Beyond neonatal diabetes mellitus (NDM), KCNJ11 is also a MODY gene ('MODY13'), confirming the wide spectrum of diabetes related phenotypes due to mutations in NDM genes (i.e. KCNJ11, ABCC8 and INS). Therefore, the molecular diagnosis of MODY should include KCNJ11 as affected carriers can be ideally treated with oral sulfonylureas.

Published
2012
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7. Clusters of conserved beta cell marker genes for assessment of beta cell phenotype.

Author

Geert A Martens, Lei Jiang, Karine H Hellemans, Geert Stangé, Harry Heimberg, Finn C Nielsen, Olivier Sand, Jacques Van Helden, Leentje Van Lommel, Frans Schuit, Frans K Gorus, and Daniel G Pipeleers

Subjects
Medicine, Science
Abstract

BACKGROUND AND METHODOLOGY: The aim of this study was to establish a gene expression blueprint of pancreatic beta cells conserved from rodents to humans and to evaluate its applicability to assess shifts in the beta cell differentiated state. Genome-wide mRNA expression profiles of isolated beta cells were compared to those of a large panel of other tissue and cell types, and transcripts with beta cell-abundant and -selective expression were identified. Iteration of this analysis in mouse, rat and human tissues generated a panel of conserved beta cell biomarkers. This panel was then used to compare isolated versus laser capture microdissected beta cells, monitor adaptations of the beta cell phenotype to fasting, and retrieve possible conserved transcriptional regulators. PRINCIPAL FINDINGS: A panel of 332 conserved beta cell biomarker genes was found to discriminate both isolated and laser capture microdissected beta cells from all other examined cell types. Of all conserved beta cell-markers, 15% were strongly beta cell-selective and functionally associated to hormone processing, 15% were shared with neuronal cells and associated to regulated synaptic vesicle transport and 30% with immune plus gut mucosal tissues reflecting active protein synthesis. Fasting specifically down-regulated the latter cluster, but preserved the neuronal and strongly beta cell-selective traits, indicating preserved differentiated state. Analysis of consensus binding site enrichment indicated major roles of CREB/ATF and various nutrient- or redox-regulated transcription factors in maintenance of differentiated beta cell phenotype. CONCLUSIONS: Conserved beta cell marker genes contain major gene clusters defined by their beta cell selectivity or by their additional abundance in either neural cells or in immune plus gut mucosal cells. This panel can be used as a template to identify changes in the differentiated state of beta cells.

Published
2011
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8. Molecular diagnosis of neonatal diabetes mellitus using next-generation sequencing of the whole exome.

Author

Amélie Bonnefond, Emmanuelle Durand, Olivier Sand, Franck De Graeve, Sophie Gallina, Kanetee Busiah, Stéphane Lobbens, Albane Simon, Christine Bellanné-Chantelot, Louis Létourneau, Raphael Scharfmann, Jérôme Delplanque, Robert Sladek, Michel Polak, Martine Vaxillaire, and Philippe Froguel

Subjects
Medicine, Science
Abstract

Accurate molecular diagnosis of monogenic non-autoimmune neonatal diabetes mellitus (NDM) is critical for patient care, as patients carrying a mutation in KCNJ11 or ABCC8 can be treated by oral sulfonylurea drugs instead of insulin therapy. This diagnosis is currently based on Sanger sequencing of at least 42 PCR fragments from the KCNJ11, ABCC8, and INS genes. Here, we assessed the feasibility of using the next-generation whole exome sequencing (WES) for the NDM molecular diagnosis.We carried out WES for a patient presenting with permanent NDM, for whom mutations in KCNJ11, ABCC8 and INS and abnormalities in chromosome 6q24 had been previously excluded. A solution hybridization selection was performed to generate WES in 76 bp paired-end reads, by using two channels of the sequencing instrument. WES quality was assessed using a high-resolution oligonucleotide whole-genome genotyping array. From our WES with high-quality reads, we identified a novel non-synonymous mutation in ABCC8 (c.1455G>C/p.Q485H), despite a previous negative sequencing of this gene. This mutation, confirmed by Sanger sequencing, was not present in 348 controls and in the patient's mother, father and young brother, all of whom are normoglycemic.WES identified a novel de novo ABCC8 mutation in a NDM patient. Compared to the current Sanger protocol, WES is a comprehensive, cost-efficient and rapid method to identify mutations in NDM patients. We suggest WES as a near future tool of choice for further molecular diagnosis of NDM cases, negative for chr6q24, KCNJ11 and INS abnormalities.

Published
2010
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9. Fine-tuning enhancer models to predict transcriptional targets across multiple genomes.

Author

Stein Aerts, Jacques van Helden, Olivier Sand, and Bassem A Hassan

Subjects
Medicine, Science
Abstract

Networks of regulatory relations between transcription factors (TF) and their target genes (TG)- implemented through TF binding sites (TFBS)- are key features of biology. An idealized approach to solving such networks consists of starting from a consensus TFBS or a position weight matrix (PWM) to generate a high accuracy list of candidate TGs for biological validation. Developing and evaluating such approaches remains a formidable challenge in regulatory bioinformatics. We perform a benchmark study on 34 Drosophila TFs to assess existing TFBS and cis-regulatory module (CRM) detection methods, with a strong focus on the use of multiple genomes. Particularly, for CRM-modelling we investigate the addition of orthologous sites to a known PWM to construct phyloPWMs and we assess the added value of phylogenentic footprinting to predict contextual motifs around known TFBSs. For CRM-prediction, we compare motif conservation with network-level conservation approaches across multiple genomes. Choosing the optimal training and scoring strategies strongly enhances the performance of TG prediction for more than half of the tested TFs. Finally, we analyse a 35(th) TF, namely Eyeless, and find a significant overlap between predicted TGs and candidate TGs identified by microarray expression studies. In summary we identify several ways to optimize TF-specific TG predictions, some of which can be applied to all TFs, and others that can be applied only to particular TFs. The ability to model known TF-TG relations, together with the use of multiple genomes, results in a significant step forward in solving the architecture of gene regulatory networks.

Published
2007
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10. Making Bioinformatics Training Events and Material More Discoverable Using TeSS, the ELIXIR Training Portal

Author

Finn Bacall, Aitor Apaolaza, Munazah Andrabi, Chris Child, Carole Goble, Olivier Sand, and Alexander Botzki

Subjects
training event, Medical Laboratory Technology, TeSS, bioinformatics training, General Immunology and Microbiology, training catalog, General Neuroscience, Bioschemas annotation, training material, Health Informatics, General Pharmacology, Toxicology and Pharmaceutics, General Biochemistry, Genetics and Molecular Biology
Abstract

Many trainers and organizations are passionate about sharing their training material. Sharing training material has several benefits, such as providing a record of recognition as an author, offering inspiration to other trainers, enabling researchers to discover training resources for their personal learning path, and improving the training resource landscape using data-driven gap analysis from the bioinformatics community. In this article, we present a series of protocols for using the ELIXIR online training registry Training eSupport System (TeSS). TeSS provides a one-stop shop for trainers and trainees to discover online information and content, including training materials, events, and interactive tutorials. For trainees, we provide protocols for registering and logging in and for searching and filtering content. For trainers and organizations, we also show how to manually or automatically register training events and materials. Following these protocols will contribute to promoting training events and add to a growing catalog of materials. This will concomitantly increase the FAIRness of training materials and events. Training registries like TeSS use a scraping mechanism to aggregate training resources from many providers when they have been annotated using Bioschemas specifications. Finally, we describe how to enrich training resources to allow for more efficient sharing of the structured metadata, such as prerequisites, target audience, and learning outcomes using Bioschemas specification. As increasing training events and material are aggregated in TeSS, searching the registry for specific events and materials becomes crucial.

Published
2023
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11. RSAT 2015: Regulatory Sequence Analysis Tools.

Author

Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime Abraham Castro-Mondragón, Jeremy Delerce, Sébastien Jaeger, Christophe Blanchet, Pierre Vincens, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira, Marie Artufel, Lucie Charbonnier-Khamvongsa, Céline Hernandez, Denis Thieffry, Morgane Thomas-Chollier, and Jacques van Helden

Published
2015
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13. The EMBRACE web service collection.

Author

Steve Pettifer, Jon C. Ison, Matús Kalas, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, José María Fernández 0001, Jose Manuel Rodriguez, David G. Pisano, Christophe Blanchet, Mahmut Uludag, Peter M. Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten L. Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B. Clegg, Erik Bongcam-Rudloff, Jean Salzemann, Vincent Breton, Teresa K. Attwood, Graham Cameron, and Gert Vriend

Published
2010
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16. Documenting and defining emergent phenomenology: theoretical foundations for an extensive research strategy

Author

Olivier Sandilands and Daniel M. Ingram

Subjects
meditation, psychedelics, emergence, phenomenology, experience, medicine, Psychology, BF1-990
Abstract

Meditation, psychedelics, and other similar practices or induction methods that can modulate conscious experience, are becoming increasingly popular in clinical and non-clinical settings. The phenomenology associated with such practices or modalities is vast. Many similar effects and experiences are also reported to occur spontaneously. We argue that this experiential range is still not fully described or understood in the contemporary literature, and that there is an ethical mandate to research it more extensively, starting with comprehensive documentation and definition. We review 50 recent clinical or scientific publications to assess the range of phenomena, experiences, effects, after-effects, and impacts associated with a broad variety of psychoactive compounds, meditative practices, and other modalities or events. This results in a large inventory synthesizing the reports of over 30,000 individual subjects. We then critically discuss various terms and concepts that have been used in recent literature to designate all or parts of the range this inventory covers. We make the case that specialized terminologies are needed to ground the nascent research field that is forming around this experiential domain. As a step in this direction, we propose the notion of “emergence” and some of its derivatives, such as “emergent phenomenology,” as possibly foundational candidates.

Published
2024
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17. High Prevalence of Rare Monogenic Forms of Obesity in Obese Guadeloupean Afro-Caribbean Children

Author

Amélie Bonnefond, Franck De Graeve, Laurent Larifla, Philippe Froguel, Véronique Dhennin, Lydia Foucan, Christine Rambhojan, Iandry Rabearivelo, Carl-Thony Michel, Christophe Armand, Emmanuelle Durand, Rachel Billy, Olivier Sand, and Jean-Marc Lacorte

Subjects
Male, 0301 basic medicine, Nonsynonymous substitution, Pediatric Obesity, medicine.medical_specialty, Adolescent, Endocrinology, Diabetes and Metabolism, DNA Mutational Analysis, Clinical Biochemistry, Population, Black People, 030209 endocrinology & metabolism, Context (language use), medicine.disease_cause, Biochemistry, ABCC8, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Endocrinology, SH2B1, Diabetes mellitus, Internal medicine, Prevalence, medicine, Humans, Child, Students, education, Guadeloupe, Genetics, Mutation, education.field_of_study, Schools, biology, business.industry, Biochemistry (medical), High-Throughput Nucleotide Sequencing, medicine.disease, Obesity, 030104 developmental biology, Caribbean Region, biology.protein, Female, business
Abstract

Context The population of Guadeloupe Island exhibits a high prevalence of obesity. Objective We aimed to investigate whether rare genetic mutations in genes involved in monogenic obesity (or diabetes) might be causal in this population of Afro-Caribbean ancestry. Design and setting This was a secondary analysis of a study on obesity conducted in schoolchildren from Guadeloupe in 2013 that aimed to assess changes in children's profiles after a lifestyle intervention program. Through next-generation sequencing, we sequenced coding regions of 59 genes involved in monogenic obesity or diabetes in participants from this study. Participants and interventions A total of 25 obese schoolchildren from Guadeloupe were screened for rare mutations (nonsynonymous, splice-site, or insertion/deletion) in 59 genes. Main outcome measures Correlation between phenotypes and mutations of interest. Results We detected five rare heterozygous mutations in five different children with obesity: MC4R p.Ile301Thr and SIM1 p.Val326Thrfs*43 mutations that were pathogenic; SIM1 p.Ser343Pro and SH2B1 p.Pro90His mutations that were likely pathogenic; and NTRK2 p.Leu140Phe that was of uncertain significance. In parallel, we identified seven carriers of mutations in ABCC8 (p.Lys1521Asn and p.Ala625Val) or KCNJ11 (p.Val13Met and p.Val151Met) that were of uncertain significance. Conclusions We were able to detect pathogenic or likely pathogenic mutations linked to severe obesity in >15% of this population, which is much higher than what we observed in Europeans (∼5%).

Published
2017
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18. Expression and functional assessment of candidate type 2 diabetes susceptibility genes identify four new genes contributing to human insulin secretion

Author

Ana Ortalli, Marlène Huyvaert, Amélie Bonnefond, Lorella Marselli, Piero Marchetti, Marie Verbanck, Fatou K. Ndiaye, Julie Kerr-Conte, Raphaël Scharfmann, Emmanuelle Durand, Philippe Froguel, Amar Abderrahmani, Mickaël Canouil, Olivier Sand, Vikash Chandra, François Pattou, Raphaël Boutry, Valérie Pawlowski, Odile Poulain-Godefroy, C. Lecoeur, Iandry Rabearivelo, and Clara Salazar-Cardozo

Subjects
0301 basic medicine, endocrine system diseases, medicine.medical_treatment, EndoC-βH1, Gene regulatory network, Mice, Obese, EndoC-beta H1, Genome-wide association study, Cell Cycle Proteins, Type 2 diabetes, VARIANTS, Bioinformatics, Expression analysis, PATHWAY, MELLITUS, Mice, Insulin-Secreting Cells, OF-FUNCTION MUTATIONS, Insulin, Gene Regulatory Networks, Genetics, Insulin secretion, 3. Good health, DNA-Binding Proteins, Original Article, Female, ACCURATE, Life Sciences & Biomedicine, lcsh:Internal medicine, Racemases and Epimerases, LINE, Biology, EndoC-βH1, RNAi screening, Molecular Biology, Cell Biology, Cell Line, Endocrinology & Metabolism, 03 medical and health sciences, medicine, Animals, Humans, Secretion, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, lcsh:RC31-1245, Gene, Transcription factor, Genetic association, Adaptor Proteins, Signal Transducing, Science & Technology, nutritional and metabolic diseases, medicine.disease, Mice, Inbred C57BL, 030104 developmental biology, Diabetes Mellitus, Type 2, PANCREATIC BETA-CELLS, GLUCOSE-HOMEOSTASIS, Transcription Factors
Abstract

Objectives Genome-wide association studies (GWAS) have identified >100 loci independently contributing to type 2 diabetes (T2D) risk. However, translational implications for precision medicine and for the development of novel treatments have been disappointing, due to poor knowledge of how these loci impact T2D pathophysiology. Here, we aimed to measure the expression of genes located nearby T2D associated signals and to assess their effect on insulin secretion from pancreatic beta cells. Methods The expression of 104 candidate T2D susceptibility genes was measured in a human multi-tissue panel, through PCR-free expression assay. The effects of the knockdown of beta-cell enriched genes were next investigated on insulin secretion from the human EndoC-βH1 beta-cell line. Finally, we performed RNA-sequencing (RNA-seq) so as to assess the pathways affected by the knockdown of the new genes impacting insulin secretion from EndoC-βH1, and we analyzed the expression of the new genes in mouse models with altered pancreatic beta-cell function. Results We found that the candidate T2D susceptibility genes' expression is significantly enriched in pancreatic beta cells obtained by laser capture microdissection or sorted by flow cytometry and in EndoC-βH1 cells, but not in insulin sensitive tissues. Furthermore, the knockdown of seven T2D-susceptibility genes (CDKN2A, GCK, HNF4A, KCNK16, SLC30A8, TBC1D4, and TCF19) with already known expression and/or function in beta cells changed insulin secretion, supporting our functional approach. We showed first evidence for a role in insulin secretion of four candidate T2D-susceptibility genes (PRC1, SRR, ZFAND3, and ZFAND6) with no previous knowledge of presence and function in beta cells. RNA-seq in EndoC-βH1 cells with decreased expression of PRC1, SRR, ZFAND6, or ZFAND3 identified specific gene networks related to T2D pathophysiology. Finally, a positive correlation between the expression of Ins2 and the expression of Prc1, Srr, Zfand6, and Zfand3 was found in mouse pancreatic islets with altered beta-cell function. Conclusions This study showed the ability of post-GWAS functional studies to identify new genes and pathways involved in human pancreatic beta-cell function and in T2D pathophysiology., Highlights • Expression of genes located nearby T2D associated signals is enriched in β cells. • Knockdown of 7 T2D genes with known role in β cell changes insulin secretion. • Knockdown of 4 T2D genes with unknown role in β cell impairs insulin secretion. • RNA-seq in cells with knockdown of these 4 genes detected T2D-related networks.

Published
2017

20. A Novel Rare Missense Variation of the NOD2 Gene: Evidences of Implication in Crohn’s Disease

Author

Sara Frade-Proud’hon-Clerc, Francis Vasseur, Frédéric Frenois, Olivier Sand, Véronique Dhennin, Philippe Frouguel, Mathurin Fumery, Amélie Bonnefond, Nathalie Guillon-Dellac, Thomas Smol, Corinne Gower-Rousseau, and Emmanuel Vaillant

Subjects
Genetics, Crohn's disease, Variation (linguistics), medicine, Missense mutation, Biology, medicine.disease, Nod2 gene, digestive system diseases
Abstract

The NOD2 gene, involved in innate immune responses to bacterial peptidoglycan, has been found to be strongly associated with Crohn’s Disease, with an Odd Ratio ranging from 3 to 36. Families with 3 or more CD affected patients were related to high frequency of NOD2 gene variations as R702W, G908R, 1007fs and were reported in EPIMAD Registry. However, some rare CD multiplex families were described without identification of common NOD2 linked-to-disease variations. In order to identify new genetic variation(s) with a major effect on Crohn’s disease (CD), whole exome sequencing was performed in available subjects comprising 4 patients on 2 generations affected with Crohn’s disease without R702W and G908R variation, and 3 unaffected related subjects. A new rare and not yet reported missense variation of the NOD2 gene, the N1010K, was detected and co-segregated across affected patients. In silico evaluation and modeling highlighted evidences for a deleterious effect of the N1010K variation regarding CD. Moreover cumulative characterization of N1010K and 1007fs as compound heterozygous state in two more severely CD family members strongly suggesting that the N1010K should be a new risk factor involved in Crohn’s disease genetic susceptibility.

Published
2018
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21. Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd

Author

Mahendra Mariadassou, Laurent X. Nouvel, Fabienne Constant, Diego P. Morgavi, Lucie Rault, Sarah Barbey, Emmanuelle Helloin, Olivier Rué, Sophie Schbath, Frederic Launay, Olivier Sandra, Rachel Lefebvre, Yves Le Loir, Pierre Germon, Christine Citti, and Sergine Even

Subjects
Bovine holobiont, Dairy cow microbiota, Vaginal microbiota, Milk microbiota, Nasal microbiota, Oral microbiota, Veterinary medicine, SF600-1100, Microbiology, QR1-502
Abstract

Abstract Background Host-associated microbes are major determinants of the host phenotypes. In the present study, we used dairy cows with different scores of susceptibility to mastitis with the aim to explore the relationships between microbiota composition and different factors in various body sites throughout lactation as well as the intra- and inter-animal microbial sharing. Results Microbiotas from the mouth, nose, vagina and milk of 45 lactating dairy cows were characterized by metataxonomics at four time points during the first lactation, from 1-week pre-partum to 7 months post-partum. Each site harbored a specific community that changed with time, likely reflecting physiological changes in the transition period and changes in diet and housing. Importantly, we found a significant number of microbes shared among different anatomical sites within each animal. This was between nearby anatomic sites, with up to 32% of the total number of Amplicon Sequence Variants (ASVs) of the oral microbiota shared with the nasal microbiota but also between distant ones (e.g. milk with nasal and vaginal microbiotas). In contrast, the share of microbes between animals was limited (

Published
2023
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22. Genetic variants in LEP , LEPR , and MC4R explain 30% of severe obesity in children from a consanguineous population

Author

Faiza Shabir, Mario Falchi, Jaida Manzoor, Emmanuelle Durand, Amélie Bonnefond, Muhammad Arslan, J. Philippe, Hutokshi Crouch, Taeed A. Butt, Ahsan Waheed Rathore, Sadia Saeed, Muhammad Ali, Hina Ayesha, Philippe Froguel, and Olivier Sand

Subjects
Genetics, Mutation, education.field_of_study, Nutrition and Dietetics, Leptin receptor, Endocrinology, Diabetes and Metabolism, Population, Medicine (miscellaneous), Consanguinity, Biology, medicine.disease_cause, Genetic analysis, Endocrinology, Genetic variation, Genotype, medicine, education, Genotyping, hormones, hormone substitutes, and hormone antagonists
Abstract

Objective Single gene mutations leading to severe obesity have so far been identified in 3-5% cases in European populations. However, prevalence of these pathogenic mutations has not systematically been examined in specific consanguineous populations. Here we describe the incidence of obesity-associated mutations through a step-wise sequence analysis, in a cohort of 73 Pakistani children with severe obesity from consanguineous families. Methods Initially, all subjects were screened for mutations in coding regions of leptin (LEP) and melanocortin 4 receptor (MC4R) genes by direct sequencing. Subjects negative for mutation in these genes were screened using microdroplet PCR enrichment and NGS. Genomic structural variation was assessed by genotyping. Serum leptin, insulin, and cortisol were determined by ELISA. Results Among 73 children with severe obesity (BMI SDS > 3.0), we identified 22 probands and 5 relatives, carrying 10 different loss-of-function homozygous mutations in LEP, leptin receptor (LEPR), and MC4R genes, including 4 novel variants. Hypercortisolemia was significantly emphasized in LEP mutation carriers. Conclusions The prevalence of pathogenic mutations in genes known to directly influence leptin-melanocortin signaling is 30% in our cohort. The results of this study emphasize the desirability of undertaking systematic and in-depth genetic analysis of cases with severe obesity in specific consanguineous populations.

Published
2015
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23. AB0007 Shared genetic predisposition in rheumatoid arthritis–interstitial lung disease and familial pulmonary fibrosis

Author

Serge Amselem, Marie-Christophe Boissier, Catherine Boileau, Benoit Wallaert, Aurélien Justet, Gabriel Thabut, Baptiste Coustet, A Clément, Bruno Crestani, Martin Soubrier, Yannick Allanore, Vincent Cottin, S. Ottaviani, Nadia Nathan, Christelle Ménard, Olivier Sand, Steven Gazal, Hilario Nunes, Lidwine Wemeau-Stervinou, H. Lioté, Isabelle Callebaut, Philippe Dieudé, Pierre-Antoine Juge, Marie-Pierre Debray, P. Richette, R.M. Flipo, Patrick Revy, Dominique Valeyre, Dlm Florence, S. Marchand-Adam, J. Sibilia, T. Schaeverbeke, Aline Frazier, Christophe Richez, Caroline Kannengiesser, Raphael Borie, Claire Dromer, and N. Saidenberg

Subjects
0301 basic medicine, Oncology, medicine.medical_specialty, Pathology, Mutation, business.industry, Interstitial lung disease, Odds ratio, respiratory system, medicine.disease, medicine.disease_cause, respiratory tract diseases, Pathogenesis, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Usual interstitial pneumonia, 030220 oncology & carcinogenesis, Rheumatoid arthritis, Internal medicine, Pulmonary fibrosis, medicine, Genetic predisposition, business
Abstract

Background Despite its high prevalence and mortality, little is known about the pathogenesis of RA–associated interstitial lung disease (RA-ILD). Given that familial pulmonary fibrosis (FPF) and RA–ILD frequently share the usual interstitial pneumonia pattern and common environmental risk factors, we hypothesized that the two diseases may share additional risk factors including FPF-linked genes. Objectives Our aim was to identify coding mutations of FPF-risk genes associated with RA-ILD. Methods We used whole-exome sequencing (WES) followed by restricted analysis of a discrete number of FPF-linked genes and performed a Burden test to assess the excess number of mutations in RA–ILD patients compared to controls. Results Among the 101 RA–ILD patients included, 12 (11.9%) had 13 WESidentified heterozygous mutations in the TERT, RTEL1, PARN or SFTPC coding regions. The burden test, based on 81 RA–ILD patients and 1010 controls of European ancestry, revealed an excess of TERT, RTEL1, PARN or SFTPC mutations for RA–ILD patients (p=9.45’10-4, odds ratio [OR] 3.17 95% CI 1.53 – 6.12). Telomeres were shorter for RA-ILD patients with a TERT, RTEL1 or PARN mutation than controls (p=2.87x10-2). Conclusions Our results support the contribution of FPF-linked genes to RA–ILD susceptibility. Disclosure of Interest None declared

Published
2017
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24. A novel NEUROG3 mutation in neonatal diabetes associated with a neuro-intestinal syndrome

Author

Ayla Güven, Emmanuel Vaillant, Amélie Bonnefond, Franck De Graeve, J. Philippe, Suna Hancili, Philippe Froguel, Olivier Sand, Martine Vaxillaire, Jean-Jacques Robert, Kanetee Busiah, and Michel Polak

Subjects
0301 basic medicine, Proband, Biallelic Mutation, Male, endocrine system, Endocrinology, Diabetes and Metabolism, Nonsense mutation, 030209 endocrinology & metabolism, Nerve Tissue Proteins, Bioinformatics, Diabetes Complications, 03 medical and health sciences, 0302 clinical medicine, Neonatal diabetes mellitus, Malabsorption Syndromes, Diabetes mellitus, Internal Medicine, Basic Helix-Loop-Helix Transcription Factors, Medicine, Humans, Child, Genetics, business.industry, medicine.disease, 030104 developmental biology, Dysplasia, Codon, Nonsense, Child, Preschool, Pediatrics, Perinatology and Child Health, Mutation (genetic algorithm), Female, Age of onset, business
Abstract

Neonatal diabetes mellitus (NDM) is a rare form of non-autoimmune diabetes usually diagnosed in the first 6 months of life. Various genetic defects have been shown to cause NDM with diverse clinical presentations and variable severity. Among transcriptional factor genes associated with isolated or syndromic NDM, a few cases of homozygous mutations in the NEUROG3 gene have been reported, all mutated patients presenting with congenital malabsorptive diarrhea with or without diabetes at a variable age of onset from early life to childhood. Through a targeted next-generation sequencing assay for monogenic diabetes genes, we aimed to search for pathogenic deleterious mutation in a Turkish patient with NDM, severe malabsorptive diarrhea, neurointestinal dysplasia and other atypical features. In this patient, we identified a novel homozygous nonsense mutation (p.Q4*) in NEUROG3. The same biallelic mutation was found in another affected family member. Of note, the study proband presents with abnormalities of the intrahepatic biliary tract, thyroid gland and central nervous system, which has never been reported before in NEUROG3 mutation carriers. Our findings extend the usually described clinical features associated with NEUROG3 deficiency in humans, and question the extent to which a complete lack of NEUROG3 expression may affect pancreas endocrine function in humans.

Published
2017

25. Erratum: Genetic variants in LEP, LEPR, and MC4R explain 30% of severe obesity in children from a consanguineous population

Author

Sadia Saeed, Amelie Bonnefond, Jaida Manzoor, Faiza Shabbir, Hina Ayesha, Julien Philippe, Emmanuelle Durand, Hutokshi Crouch, Olivier Sand, Muhammad Ali, Taeed Butt, Ahsan W. Rathore, Mario Falchi, Muhammad Arslan, and Philippe Froguel

Subjects
Nutrition and Dietetics, Endocrinology, Endocrinology, Diabetes and Metabolism, Medicine (miscellaneous)
Published
2017

26. Shared genetic predisposition in rheumatoid arthritis-interstitial lung disease and familial pulmonary fibrosis

Author

Steven Gazal, Hilario Nunes, Jean Sibilia, Christelle Ménard, Aurélien Justet, Philippe Dieudé, Isabelle Callebaut, Amélie Bonnefond, Martin Soubrier, Patrick Revy, Catherine Boileau, Pierre-Antoine Juge, Thierry Schaeverbeke, Aline Frazier, Nathalie Saidenberg, Sébastien Ottaviani, Nadia Nathan, Bruno Crestani, Christophe Béroud, Baptiste Coustet, Vincent Cottin, Lidwine Wemeau-Stervinou, Jean-Pierre Desvignes, Marie-Christophe Boissier, Florence Dastot-Le Moal, Serge Amselem, Philippe Froguel, Yannick Allanore, Annick Clement, Olivier Sand, Gabriel Thabut, Marie-Pierre Debray, Pascal Richette, Caroline Kannengiesser, Benoit Wallaert, Christophe Richez, Dominique Valeyre, Sylvain Marchand-Adam, Huguette Lioté, Nicolas Leulliot, René-Marc Flipo, Raphael Borie, Claire Dromer, David Salgado, Service de Rhumathologie, Hôpital Bichat - Claude Bernard, Assistance Publique - Hôpitaux de Paris (AP-HP), Université Paris Diderot - Paris 7 (UPD7), Université Sorbonne Paris Cité (USPC), Service de Pneumologie, Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), UMR 1152, Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Génétique, Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), UMR 1149, Centre de Recherches sur l'Inflammation, Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Plateforme de génomique constitutionnelle, Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Pneumologie et Immuno-Allergologie [CHU LIlle], Pole Cardio-vasculaire et pulmonaire [CHU Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Université de Lille, Service de Radiologie, Hospices Civils de Lyon (HCL), UMR 1100, Université Francois Rabelais [Tours], Physiopathologie des maladies génétiques d'expression pédiatrique, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Pierre et Marie Curie - Paris 6 (UPMC), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Rhumatologie, CH Belfort-Montbéliard, UMR 5164, Immuno ConcEpT Lab, Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB), Sorbonne Université (SU), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Ouest]), Muséum national d'Histoire naturelle (MNHN), Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), Université de Lille, Droit et Santé, Institut Européen de Génomique du Diabète - European Genomic Institute for Diabetes - FR 3508 (EGID), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Génétique Médicale et Génomique Fonctionnelle (GMGF), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UMR 1132, Service de Rhumatologie, Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Department of Genomics of Common Diseases, Imperial College London, Service Rhumatologie A, Hôpital Cochin [AP-HP], Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service Imagerie, service de Rhumatologie, Centre Hospitalier Universitaire de Lille (CHU de Lille), Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Service Rhumatologie, Hôpital La Rabta [Tunis], FMTS, CRHI, Laboratoire Immunologie Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA), Fédération Hospitalo-Universitaire OMICARE, Rétrovirus et Pathologie Comparée (RPC), Institut National de la Recherche Agronomique (INRA)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL), Maladie Pulmonaires Rares, Hôpital Louis Pradel [CHU - HCL], UMR U1125 Service rhumatologie, service de rhumatologie, CHU Clermont-Ferrand, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Hôpital Avicenne [AP-HP], service de génétique, Societe Francaise de Rhumatologie, Club Rhumatismes Inflammation, la Chancellerie des Universites de Paris (legs Poix), Sorbonne Paris Cite (FPI-SPC Program), Agence Nationale de la Recherche ANR-10-LABX-46 ANR-10-EQPX-07-01 ANR-14-CE10-0006 ANR-10-INBS-09, France Genomique National Infrastructure, Pfizer, Chugai, Centre de Resources Biologiques Hopital Bichat Paris France, ANR-14-CE10-0006,GENEXGERTEL,Rôles génomiques et extragénomiques de RTEL1(2014), Hôpital Bichat - Claude Bernard, Assistance Publique - Hôpitaux de Paris ( AP-HP ), Université Paris Diderot (Paris 7), Université Sorbonne Paris Cité ( USPC ), Centre Hospitalier Lyon Sud [CHU - HCL] ( CHLS ), Hospices Civils de Lyon ( HCL ) -Hospices Civils de Lyon ( HCL ), Institut National de la Santé et de la Recherche Médicale ( INSERM ), CHU Saint-Etienne, UMR 1137, Fac Sci, Imagine - Institut des maladies génétiques ( IMAGINE - U1163 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Service de Pneumologie et Immuno-Allergologie, Centre Hospitalier Régional Universitaire [Lille] ( CHRU Lille ), Hospices Civils de Lyon ( HCL ), Service de Pneumologie Pédiatrique, Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Trousseau [APHP], Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université Pierre et Marie Curie (Paris 6), Centre National de la Recherche Scientifique ( CNRS ), Université de Bordeaux ( UB ), Sorbonne Universités, Institut de minéralogie, de physique des matériaux et de cosmochimie ( IMPMC ), Muséum National d'Histoire Naturelle ( MNHN ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche pour le Développement ( IRD [France-Ouest] ), Muséum National d’Histoire Naturelle ( MNHN ), Laboratoire de cristallographie et RMN biologiques ( LCRB - UMR 8015 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paris Descartes - Paris 5 ( UPD5 ), Université Droit et Santé (Lille 2) ( UDSL ), European Genomic Institute for Diabetes ( EGID ), Génétique Médicale et Génomique Fonctionnelle ( GMGF ), Aix Marseille Université ( AMU ) -Assistance Publique - Hôpitaux de Marseille ( APHM ) - Hôpital de la Timone [CHU - APHM] ( TIMONE ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Hôpital Lariboisière, Génomique Intégrative et Modélisation des Maladies Métaboliques ( EGID ), Université de Lille-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut Pasteur de Lille, Réseau International des Instituts Pasteur ( RIIP ) -Réseau International des Instituts Pasteur ( RIIP ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre Hospitalier Régional Universitaire [Lille] ( CHRU Lille ), CHU Cochin [AP-HP], Institut Cochin ( UM3 (UMR 8104 / U1016) ), Centre Hospitalier Universitaire de Lille ( CHU de Lille ), Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques, Université Montpellier 1 ( UM1 ) -IFR3-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ), Hôpital La Rabta [Tunis), Université de Strasbourg ( UNISTRA ), Rétrovirus et Pathologie Comparée ( RPC ), Institut National de la Recherche Agronomique ( INRA ) -École pratique des hautes études ( EPHE ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon ( ENVL ), Département Génétique, Institut de l'Elevage, Centre Reference Maladies Respiratoires Rares, Hôpital Armand Trousseau, Assistance Publique - Hôpitaux de Paris ( AP-HP ), Centre Hospitalier Universitaire de Clermont-Ferrand, Unité de Nutrition Humaine - Clermont Auvergne ( UNH ), Université Clermont Auvergne ( UCA ) -Institut national de la recherche agronomique [Auvergne/Rhône-Alpes] ( INRA Auvergne/Rhône-Alpes ), Centre de Recherche en Nutrition Humaine d'Auvergne ( CRNH d'Auvergne ), Hôpital Avicenne, Assistance Publique - Hôpitaux de Paris ( AP-HP ), European Genomic Institute for Diabetes - FR 3508 (EGID), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Centre National de la Recherche Scientifique (CNRS), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE), Institut de l'élevage (IDELE), ProdInra, Archive Ouverte, Centre de référence national pour les maladies respiratoires rares de l’enfant RespiRare [CHU Trousseau], Service de Pneumologie pédiatrique [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de génétique et embryologie médicales [CHU Trousseau], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Trousseau [APHP], Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), European Genomic Institute for Diabetes [Lille] (EGID), Génomique Intégrative et Modélisation des Maladies Métaboliques (EGID), Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE)-Université Claude Bernard Lyon 1 (UCBL), Hôpital Armand Trousseau, Assistance Publique - Hôpitaux de Paris (AP-HP), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Hôpital Avicenne, Assistance Publique - Hôpitaux de Paris (AP-HP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Paris Descartes - Paris 5 (UPD5), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, IFR3, Université Montpellier 1 (UM1)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, Pathology, medicine.disease_cause, Arthritis, Rheumatoid, 0302 clinical medicine, Risk Factors, Pulmonary fibrosis, Exome, Telomerase, Exome sequencing, Mutation, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Interstitial lung disease, Middle Aged, 3. Good health, Europe, Polyarthrite rhumatoïde, maladie pulmonaire, Phenotype, Rheumatoid arthritis, Female, Pulmonary and Respiratory Medicine, Adult, medicine.medical_specialty, Heterozygote, fibrose pulmonaire, 03 medical and health sciences, [ SDV.MHEP ] Life Sciences [q-bio]/Human health and pathology, medicine, Genetic predisposition, Humans, Genetic Predisposition to Disease, respiratory system diseases, Genetic Association Studies, Aged, 030203 arthritis & rheumatology, pulmonary fibrosis, business.industry, Case-control study, DNA Helicases, Sequence Analysis, DNA, medicine.disease, 030228 respiratory system, Case-Control Studies, Immunology, business, Lung Diseases, Interstitial, Software, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Despite its high prevalence and mortality, little is known about the pathogenesis of rheumatoid arthritis-associated interstitial lung disease (RA-ILD). Given that familial pulmonary fibrosis (FPF) and RA-ILD frequently share the usual pattern of interstitial pneumonia and common environmental risk factors, we hypothesised that the two diseases might share additional risk factors, including FPF-linked genes. Our aim was to identify coding mutations of FPF-risk genes associated with RA-ILD.We used whole exome sequencing (WES), followed by restricted analysis of a discrete number of FPF-linked genes and performed a burden test to assess the excess number of mutations in RA-ILD patients compared to controls.Among the 101 RA-ILD patients included, 12 (11.9%) had 13 WES-identified heterozygous mutations in the TERT, RTEL1, PARN or SFTPC coding regions. The burden test, based on 81 RA-ILD patients and 1010 controls of European ancestry, revealed an excess of TERT, RTEL1, PARN or SFTPC mutations in RA-ILD patients (OR 3.17, 95% CI 1.53–6.12; p=9.45×10−4). Telomeres were shorter in RA-ILD patients with a TERT, RTEL1 or PARN mutation than in controls (p=2.87×10−2).Our results support the contribution of FPF-linked genes to RA-ILD susceptibility.

Published
2017
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27. A nonsense loss-of-function mutation in PCSK1 contributes to dominantly inherited human obesity

Author

Philippe Froguel, F. De Graeve, Dorothée Thuillier, J.-P. Delplanque, John W.M. Creemers, Olivier Sand, Pieter Stijnen, Amélie Bonnefond, J. Philippe, G. Gyapay, and David Meyre

Subjects
Male, Genetics, Nutrition and Dietetics, Genotype, Endocrinology, Diabetes and Metabolism, media_common.quotation_subject, Molecular Sequence Data, Nonsense, Medicine (miscellaneous), Biology, White People, Pedigree, Loss of function mutation, Proprotein Convertase 1, Codon, Nonsense, Mutation (genetic algorithm), Humans, Female, Genetic Predisposition to Disease, France, Obesity, media_common, Human obesity
Abstract

Background:A significant proportion of severe familial forms of obesity remain genetically elusive. Taking advantage of our unique cohort of multi-generation obese families, we aimed to assess the contribution of rare mutations in 29 common obesity-associated genes to familial obesity, and to evaluate in these families the putative presence of nine known monogenic forms of obesity.Methods:Through next-generation sequencing, we sequenced the coding regions of 34 genes involved in polygenic and/or monogenic forms of obesity in 201 participants (75 normal weight individuals, 54 overweight individuals and 72 individuals with obesity class I, II or III), from 13 French families. In vitro functional analyses were performed to investigate the mutation PCSK1-p.Arg80* which was identified in a family.Results:A novel heterozygous nonsense variant in PCSK1 (p.Arg80*), encoding a propeptide truncated to less than two exons (out of 14), was found to co-segregate with obesity in a three-generation family. We demonstrated that this mutation inhibits PCSK1 enzyme activity and that this inhibition most likely does not involve a strong physical interaction. Furthermore, both mutations PCSK1-p.Asn180Ser and POMC-p.Phe144Leu, which had previously been reported to be associated with severe obesity, were also identified in this study, but did not co-segregate with obesity. Finally, we did not identify any rare mutations co-segregating with obesity in common obesity susceptibility genes, except for CADM2 and QPCTL, where we found two novel variants (p.Arg81His and p.Leu98Pro, respectively) in three obese individuals.Conclusions:We showed for the first time that a nonsense mutation in PCSK1 was likely to cause dominantly inherited human obesity, due to the inhibiting properties of the propeptide fragment encoded by the null allele. Furthermore, the present family sequencing design challenged the contribution of previously reported mutations to monogenic or at least severe obesity.International Journal of Obesity accepted article preview online, 3 June 2014; doi:10.1038/ijo.2014.96. ispartof: International Journal of Obesity vol:39 issue:2 pages:295-302 ispartof: location:England status: published

Published
2014
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28. Novel LEPR mutations in obese Pakistani children identified by PCR-based enrichment and next generation sequencing

Author

Emmanuelle Durand, Sadia Saeed, Mohsin Arshad, Muhammad Arslan, Taeed A. Butt, Amélie Bonnefond, Philippe Froguel, J. Philippe, Olivier Sand, Mario Falchi, and Jaida Manzoor

Subjects
Sanger sequencing, Genetics, Mutation, education.field_of_study, Nutrition and Dietetics, Splice site mutation, Endocrinology, Diabetes and Metabolism, Leptin, Nonsense mutation, Population, Medicine (miscellaneous), Biology, Gene mutation, medicine.disease_cause, symbols.namesake, Exon, Endocrinology, medicine, symbols, education
Abstract

Objective Mutations in leptin receptor gene (LEPR) result in early onset extreme adiposity. However, their prevalence in different populations is not known. Indeed, LEPR screening by gold standard Sanger sequencing has been limited by its large size and the cost. One-step PCR-based targeted enrichment could be an option for rapid and cost effective molecular diagnosis of monogenic forms of obesity. Methods The study is based on 39 unrelated severely obese Pakistani children, previously shown to be negative for leptin (LEP) and melanocortin 4 receptor (MC4R) gene mutations, from an initial cohort of 62 probands. Patient samples were analyzed by microdroplet PCR-enrichment (RainDance technologies) targeting coding exons of 26 obesity-associated genes combined with next generation sequencing. Hormone levels were analyzed by ELISA. Results The analysis revealed two novel homozygous LEPR mutations, an essential splice site mutation in exon 15 (c.2396-1 G>T), and a nonsense mutation in exon 10 (c.1675 G>A). Both probands had high leptin levels and were phenotypically indistinguishable from age-matched leptin-deficient subjects from the same population. Conclusions The two subjects carrying homozygous LEPR mutations, reported here for the first time in the Pakistani population, constitute 3% of the whole cohort of severely obese children (compared to 17% for LEP and 3% for MC4R).

Published
2013
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29. Nature genetics

Author

Raphaël Boutry, Amar Abderrahmani, Philippe Froguel, Qasim M. Janjua, Sadia Saeed, Waqas I. Khan, Jochen Lang, Muhammad Usman Mirza, Emmanuelle Durand, Franck De Graeve, Taeed A. Butt, Olivier Sand, Jaida Manzoor, Muhammad Ali, G. Queniat, Julien Gaitan, Tuula Rinne, Amélie Bonnefond, Iandry Rabearivelo, Dina A. Schott, Connie T.R.M. Stumpel, Hina Ayesha, Alexandra Milochau, Emmanuel Vaillant, Sadia M. Din, Attiya Haseeb, Filippo Tamanini, Muhammad Arslan, Chimie et Biologie des Membranes et des Nanoobjets (CBMN), École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Polikliniek (9), and Klinische Genetica

Subjects
0301 basic medicine, SUSCEPTIBILITY LOCI, Population, CHILDHOOD, 030209 endocrinology & metabolism, CHILDREN, Genome-wide association study, Biology, Compound heterozygosity, Genetic analysis, Energy homeostasis, EARLY-LIFE, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, 0302 clinical medicine, Genetics, medicine, Sequencing, Clinical genetics, GENOME-WIDE ASSOCIATION, education, Gene, EXENDIN-4, Loss function, 030304 developmental biology, Genetics & Heredity, education.field_of_study, 0303 health sciences, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Science & Technology, Liraglutide, 11 Medical And Health Sciences, [CHIM.MATE]Chemical Sciences/Material chemistry, 06 Biological Sciences, Severe obesity, ADCY3, Early life, BODY-MASS INDEX, INDIVIDUALS, 030104 developmental biology, LIRAGLUTIDE, Susceptibility locus, POPULATIONS, Life Sciences & Biomedicine, Body mass index, 030217 neurology & neurosurgery, Developmental Biology, medicine.drug
Abstract

Study of monogenic forms of obesity has demonstrated the pivotal role of the central leptin–melanocortin pathway in controlling energy balance, appetite and body weight1. The majority of loss-of-function mutations (mostly recessive or co-dominant) have been identified in genes that are directly involved in leptin–melanocortin signaling. These genes, however, only explain obesity in

Published
2018
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30. KAT2B Is Required for Pancreatic Beta Cell Adaptation to Metabolic Stress by Controlling the Unfolded Protein Response

Author

Pierre-Damien Denechaud, Hongbo Zhang, Elisabet Salas, Philippe Froguel, Amar Abderrahmani, Xavier Gromada, Julie Kerr-Conte, Nabil Rabhi, Loic Yengo, Caroline Bonner, Johan Auwerx, Lluis Fajas, Talha Rashid, Amélie Bonnefond, Emmanuelle Durand, Carine Chavey, Olivier Sand, Jean-Sébastien Annicotte, Sarah Anissa Hannou, Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
0301 basic medicine, Male, endocrine system, medicine.medical_specialty, [SDV]Life Sciences [q-bio], Biology, Endoplasmic Reticulum, General Biochemistry, Genetics and Molecular Biology, Germline, Cell Line, 03 medical and health sciences, Mice, Stress, Physiological, Internal medicine, Insulin-Secreting Cells, Gene expression, Glucose Intolerance, Insulin Secretion, Transcriptional regulation, medicine, Animals, Humans, Insulin, p300-CBP Transcription Factors, RNA, Small Interfering, lcsh:QH301-705.5, Gene, ComputingMilieux_MISCELLANEOUS, Mice, Knockout, geography, geography.geographical_feature_category, Endoplasmic reticulum, Islet, Endoplasmic Reticulum Stress, Adaptation, Physiological, Cell biology, Mice, Inbred C57BL, 030104 developmental biology, Endocrinology, lcsh:Biology (General), Unfolded protein response, Unfolded Protein Response, RNA Interference, Beta cell, Signal Transduction, Transcription Factors
Abstract

The endoplasmic reticulum (ER) unfolded protein response (UPR(er)) pathway plays an important role in helping pancreatic β cells to adapt their cellular responses to environmental cues and metabolic stress. Although altered UPR(er) gene expression appears in rodent and human type 2 diabetic (T2D) islets, the underlying molecular mechanisms remain unknown. We show here that germline and β cell-specific disruption of the lysine acetyltransferase 2B (Kat2b) gene in mice leads to impaired insulin secretion and glucose intolerance. Genome-wide analysis of Kat2b-regulated genes and functional assays reveal a critical role for Kat2b in maintaining UPR(er) gene expression and subsequent β cell function. Importantly, Kat2b expression is decreased in mouse and human diabetic β cells and correlates with UPR(er) gene expression in normal human islets. In conclusion, Kat2b is a crucial transcriptional regulator for adaptive β cell function during metabolic stress by controlling UPR(er) and represents a promising target for T2D prevention and treatment.

Published
2015
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31. Genetic variants in LEP, LEPR, and MC4R explain 30% of severe obesity in children from a consanguineous population

Author

Sadia, Saeed, Amélie, Bonnefond, Jaida, Manzoor, Faiza, Shabbir, Hina, Ayesha, Julien, Philippe, Emmanuelle, Durand, Hutokshi, Crouch, Olivier, Sand, Muhammad, Ali, Taeed, Butt, Ahsan W, Rathore, Mario, Falchi, Muhammad, Arslan, and Philippe, Froguel

Subjects
Leptin, Male, Adolescent, Genotype, Infant, Newborn, Genetic Variation, Infant, Obesity, Morbid, Consanguinity, Child, Preschool, Mutation, Humans, Receptor, Melanocortin, Type 4, Receptors, Leptin, Female, Obesity, Child
Abstract

Single gene mutations leading to severe obesity have so far been identified in 3-5% cases in European populations. However, prevalence of these pathogenic mutations has not systematically been examined in specific consanguineous populations. Here we describe the incidence of obesity-associated mutations through a step-wise sequence analysis, in a cohort of 73 Pakistani children with severe obesity from consanguineous families.Initially, all subjects were screened for mutations in coding regions of leptin (LEP) and melanocortin 4 receptor (MC4R) genes by direct sequencing. Subjects negative for mutation in these genes were screened using microdroplet PCR enrichment and NGS. Genomic structural variation was assessed by genotyping. Serum leptin, insulin, and cortisol were determined by ELISA.Among 73 children with severe obesity (BMI SDS 3.0), we identified 22 probands and 5 relatives, carrying 10 different loss-of-function homozygous mutations in LEP, leptin receptor (LEPR), and MC4R genes, including 4 novel variants. Hypercortisolemia was significantly emphasized in LEP mutation carriers.The prevalence of pathogenic mutations in genes known to directly influence leptin-melanocortin signaling is 30% in our cohort. The results of this study emphasize the desirability of undertaking systematic and in-depth genetic analysis of cases with severe obesity in specific consanguineous populations.

Published
2015

32. Fond génétique partagé entre la pneumopathie interstitielle diffuse associée à la polyarthrite rhumatoïde et la fibrose pulmonaire idiopathique

Author

Sylvain Marchand-Adam, Christophe Béroud, Huguette Lioté, Nicolas Leulliot, Christelle Ménard, Nadia Nathan, Aline Frazier, P. Richette, Benoit Wallaert, J. Sibilia, Patrick Revy, Martin Soubrier, Steven Gazal, Bruno Crestani, Sébastien Ottaviani, Jean-Pierre Desvignes, Hilario Nunes, S. Amselem, Y. Allanore, Dominique Valeyre, N. Saidenberg, Aurélien Justet, Gabriel Thabut, Annick Clement, Vincent Cottin, Olivier Sand, Christophe Richez, P.A. Juge, Philippe Froguel, Catherine Boileau, Isabelle Callebaut, R.M. Flipo, T. Schaeverbeke, Amélie Bonnefond, Marie-Christophe Boissier, Marie-Pierre Debray, Baptiste Coustet, Philippe Dieudé, F. Dastot Le Moal, Caroline Kannengiesser, Lidwine Wemeau-Stervinou, Raphael Borie, Claire Dromer, and David Salgado

Subjects
Pulmonary and Respiratory Medicine, Rheumatology
Abstract

Introduction La pneumopathie interstitielle diffuse (PID) est l’une des causes majeure de mortalite chez les patients atteints de polyarthrite rhumatoide (PR). Malgre une prevalence et une mortalite importante, la physiopathologie de la PID associee a la PR (PR-PID) reste meconnue. La PR-PID partage plusieurs caracteristiques phenotypiques avec la fibrose pulmonaire idiopathique (FPI) telles que l’aspect de pneumopathie interstitielle commune sur le scanner et un pronostic tres severe. Enfin, les similitudes entre PR-PID et FPI concernent egalement les facteurs environnementaux (tabac,…) suggerant que ces deux pathologies pourraient egalement partager des facteurs de risques genetiques tels que ceux predisposant a la FPI familiale (FPF). Methodes Nous avons utilise des donnees d’exome obtenue par whole-exome sequencing (WES) de patients atteints de PR-PID provenant de differents centres de rhumatologie et de pneumologie francais. L’ensemble des patients PR-PID+ repondaient aux criteres ACR/EULAR 2010. Le diagnostic de PID etait realise apres analyse de scanner thoracique de haute resolution. Apres une analyse restrictive de 9 genes rapportes comme etant associes aux FPF, nous avons compare le nombre de mutations retrouvees parmi les patients PR-PID au nombre de mutations retrouvees chez des individus temoins. Un burden test a ete effectue pour definir l’exces de mutations chez les patients PR-PID au sein de ces 9 genes d’interet. Resultats Parmi les 101 patients PR-PID inclus, 12 (11,9 %) presentaient des mutations au sein des regions codantes des genes TERT, RTEL1, PARN et SFTPC. Le burden test comparant 81 patients PR-PID a 1010 individus temoins caucasiens europeens a confirme un exces de mutations parmi ces genes chez les patients PR-PID (P = 9,45 × 10−4 ; OR = 3,17 ; IC 95 % 1,53–6,12). Chez les patients PR-PID porteurs de mutations des genes TERT, RTEL1 et PARN, appartenant au complexe telomerase, la taille des telomeres etait significativement plus petite que celle observees chez les temoins (P = 2,87 × 10−2). Conclusion Ces resultats sont en faveur d’un fond genetique commun entre FPI et PR-PID, suggerant une physiopathologie commune entre ces deux pathologies. En cas de confirmation de ces resultats, les avancees therapeutiques realisees dans la prise en charge des FPI pourraient alors beneficier aux patients atteints de PR-PID.

Published
2016
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33. GATA6 inactivating mutations are associated with heart defects and, inconsistently, with pancreatic agenesis and diabetes

Author

Philippe Froguel, Amélie Bonnefond, Paul Czernichow, Marlène Huyvaert, François Pattou, Martine Vaxillaire, Latif Rachdi, Olivier Sand, Michel Polak, Julie Kerr-Conte, F. De Graeve, Raphael Scharfmann, Emmanuelle Durand, and B. Guerin

Subjects
Genetics, endocrine system, Mutation, GATA6, business.industry, Endocrinology, Diabetes and Metabolism, Permanent neonatal diabetes mellitus, Bioinformatics, medicine.disease, medicine.disease_cause, Diabetes mellitus genetics, medicine.anatomical_structure, Neonatal diabetes mellitus, Internal Medicine, medicine, PDX1, Pancreas, business, Exome sequencing
Abstract

To the Editor: Pancreatic agenesis is an extremely rare cause of permanent neonatal diabetes mellitus (NDM) in humans. It can be associated with severe intrauterine growth retardation as well as a plethora of abnormalities or malformations in the heart, biliary tract, gut, thyroid or brain [1–3]. To date, mutations in three genes have been shown to cause pancreatic agenesis, namely, PDX1 [1], PTF1A [2], and most recently GATA6 [3], all three of which encode transcription factors. The GATA6 study reported heterozygous coding mutations in a dozen individuals with permanent NDM presumed to be due to pancreatic agenesis [3]. The genetic evidence supporting the pathogenicity of these mutations seemed quite strong as the reported mutations had arisen de novo and none of these mutations was present in the 1,000 Genome Project database [3]. The authors concluded that GATA6 may have a key role in human pancreatic development, with strong implications for beta cell regenerative medicine in diabetes [3]. In the

Published
2012
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34. Mutations exomiques rares transmises au sein de familles de type MODY : analyse de corrélation avec la variabilité phénotypique et les défauts métaboliques précoces

Author

Martine Vaxillaire, Cécile Lecoeur, Emmanuelle Durand, Emmanuel Vaillant, Bénédicte Toussaint, Audrey Leloire, Franck De Graeve, Iandry Rabearivelo, Olivier Sand, Amélie Bonnefond, and Philippe Froguel

Subjects
Endocrinology, Endocrinology, Diabetes and Metabolism, Internal Medicine, General Medicine
Published
2017
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35. Les mutations du gène TMEM240 provoquent l'ataxie spinocérébelleuse 21 avec un retard mental et des troubles cognitifs sévères

Author

Giovanni Stevanin, Luc Buée, Olivier Sand, David Devos, Guillaume Grolez, Marie Lorraine Monin, Alexandra Durr, Caroline Moreau, Kathy Dujardin, Bernard Sablonnière, Vincent Huin, Alexis Brice, Cyril Goizet, Alexandre Genet, Alain Destée, Mathieu Anheim, Perrine Charles, Christine Delmaire, Jérôme Delplanque, Isabelle Strubi-Vuillaume, Delphine Dellacherie, Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer - U1172 Inserm - U837 (JPArc), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Lille Nord de France (COMUE)-Université de Lille, Département de neurologie[Lille], Université de Lille, Droit et Santé-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre de Biologie Pathologie [CHRU Lille] (Pôle de Pathologie), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Maladies Rares - Génétique et Métabolisme (MRGM), Université Bordeaux Segalen - Bordeaux 2-Hôpital Pellegrin-Service de Génétique Médicale du CHU de Bordeaux, Service de Neurologie [CHU Pitié-Salpêtrière], IFR70-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre for Integrative Biology - CBI (Inserm U964 - CNRS UMR7104 - IGBMC), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Departement de Neuroradiologie [Lille], Service de neuropédiatrie [CHU Lille], Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), and HESAM Université (HESAM)

Subjects
Cerebellum, MESH: Intellectual Disability / genetics, MESH: Introns, MESH: Exome / genetics, MESH: Amino Acid Sequence, MESH: Membrane Proteins / genetics, MESH: Spinocerebellar Degenerations / pathology, Autosomal dominant cerebellar ataxia, MESH: Child, Missense mutation, MESH: DNA Mutational Analysis, Exome, MESH: Spinocerebellar Degenerations / psychology, MESH: Cohort Studies, Exome sequencing, Genetics, MESH: Conserved Sequence, MESH: Membrane Proteins / physiology, MESH: Neuropsychological Tests, MESH: Cognition Disorders / psychology, MESH: Infant, 3. Good health, medicine.anatomical_structure, MESH: Young Adult, Spinocerebellar ataxia, medicine.symptom, MESH: Spinocerebellar Degenerations / genetics, MESH: Mutation / physiology, congenital, hereditary, and neonatal diseases and abnormalities, Ataxia, MESH: Pedigree, MESH: Age of Onset, MESH: Genetic Linkage, Biology, MESH: Intellectual Disability / psychology, MESH: Chromosomes, Human, Pair 1 / genetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Quantitative Biology - Genomics, Genomics (q-bio.GN), MESH: Adolescent, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, MESH: Molecular Sequence Data, Cerebellar ataxia, [SCCO.NEUR]Cognitive science/Neuroscience, MESH: Child, Preschool, MESH: Polymerase Chain Reaction, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, MESH: Male, MESH: France, MESH: Cognition Disorders / genetics, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, FOS: Biological sciences, TMEM240, Neurology (clinical), MESH: Intelligence Tests, MESH: Female, exome
Abstract

Autosomal dominant cerebellar ataxia corresponds to a clinically and genetically heterogeneous group of neurodegenerative disorders that primarily affect the cerebellum. Here, we report the identification of the causative gene in spinocerebellar ataxia 21, an autosomal-dominant disorder previously mapped to chromosome 7p21.3-p15.1. This ataxia was firstly characterized in a large French family with slowly progressive cerebellar ataxia, accompanied by severe cognitive impairment and mental retardation in two young children. Following the recruitment of 12 additional young family members, linkage analysis enabled us to definitively map the disease locus to chromosome 1p36.33-p36.32. The causative mutation, (c.509C>T/p.P170L) in the transmembrane protein gene TMEM240 , was identified by whole exome sequencing and then was confirmed by Sanger sequencing and co-segregation analyses. Index cases from 368 French families with autosomal-dominant cerebellar ataxia were also screened for mutations. In seven cases, we identified a range of missense mutations (c.509C>T/p.P170L, c.239C>T/p.T80M, c.346C>T/p.R116C, c.445G>A/p.E149K, c.511C>T/p.R171W), and a stop mutation (c.489C>G/p.Y163*) in the same gene. TMEM240 is a small, strongly conserved transmembrane protein of unknown function present in cerebellum and brain. Spinocerebellar ataxia 21 may be a particular early-onset disease associated with severe cognitive impairment. * Abbreviations : SCA : spinocerebellar ataxia SPATAX : network of hereditary forms of spastic paraplegias and cerebellar ataxias

Published
2014
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36. O59 Identification de nouvelles mutations associées au diabète néonatal grâce à l’utilisation de techniques (pan) génomiques incluant le séquençage de nouvelle génération

Author

Amélie Bonnefond, Olivier Sand, Michel Polak, Kanetee Busiah, Martine Vaxillaire, Emmanuelle Durand, Raphael Scharfmann, P. Froguel, J. Philippe, Emmanuel Vaillant, Suna Hancili, and M. Hafez

Subjects
Endocrinology, Endocrinology, Diabetes and Metabolism, Internal Medicine, General Medicine
Abstract

Introduction Le diabete neonatal (DN) est une forme rare de diabete non autoimmun (~1/180 000 naissances), qui est tres heterogene dans ses presentations cliniques et etiologies genetiques. Le diagnostic moleculaire permet de definir un traitement optimal et un suivi adapte des patients et de leur famille. Les techniques (pan) genomiques incluant le sequencage de nouvelle generation (NGS) representent un nouveau paradigme dans ce contexte. Patients et methodes Vingt patients avec diabete non auto-immun d’une cohorte multicentrique (dont 12 diagnostiques avant 6 mois, et 7 de type syndromique) et 24 patients d’origine egyptienne (diagnostic Resultats Deux mutations homozygotes non repertoriees ont ete identifiees chez deux patients avec DN, nes de parents consanguins (porteurs de la mutation a l’etat heterozygote): RFX6- (Regulatory Factor X-6) -p.V506G, associee a un retard de croissance intra-uterin (RCIU), une hypoplasie du pancreas et des anomalies du developpement intestinal ; et NEUROG3- (Neurogenin-3) -p.Q4*, associee a un RCIU, une hypoplasie de la vesicule biliaire et une dysplasie neurointestinale. Par ailleurs, trois nouvelles mutations, deleteres et probablement causales, ont ete identifiees chez trois patients d’origine egyptienne: GCK- (Glucokinase) -p.S151P (homozygote), ABCC8/SUR1-p.Q19E (heterozygote) et GATA6- (GATA-binding protein-6) -p.P91S (heterozygote). Conclusion Une exploration (pan) genomique combinant plusieurs approches de NGS est un pre-requis pour le diagnostic etiologique des differentes formes de DN. La variabilite des âges au diagnostic et des manifestations cliniques, notamment dans la cohorte egyptienne, est en faveur d’une heterogeneite genetique qui reste a evaluer au niveau de l’exome (ou genome) entier. Declaration d’interet Les auteurs declarent ne pas avoir d’interet direct ou indirect (financier ou en nature) avec un organisme prive, industriel ou commercial en relation avec le sujet presente.

Published
2015
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37. Novel LEPR mutations in obese Pakistani children identified by PCR-based enrichment and next generation sequencing

Author

Sadia, Saeed, Amélie, Bonnefond, Jaida, Manzoor, Julien, Philippe, Emmanuelle, Durand, Mohsin, Arshad, Olivier, Sand, Taeed A, Butt, Mario, Falchi, Muhammad, Arslan, and Philippe, Froguel

Subjects
Male, Homozygote, Infant, Exons, Sequence Analysis, DNA, Polymerase Chain Reaction, Severity of Illness Index, Pedigree, Cohort Studies, Consanguinity, Phenotype, Case-Control Studies, Mutation, Humans, Receptor, Melanocortin, Type 4, Receptors, Leptin, Female, Pakistan, Obesity
Abstract

Mutations in leptin receptor gene (LEPR) result in early onset extreme adiposity. However, their prevalence in different populations is not known. Indeed, LEPR screening by gold standard Sanger sequencing has been limited by its large size and the cost. One-step PCR-based targeted enrichment could be an option for rapid and cost effective molecular diagnosis of monogenic forms of obesity.The study is based on 39 unrelated severely obese Pakistani children, previously shown to be negative for leptin (LEP) and melanocortin 4 receptor (MC4R) gene mutations, from an initial cohort of 62 probands. Patient samples were analyzed by microdroplet PCR-enrichment (RainDance technologies) targeting coding exons of 26 obesity-associated genes combined with next generation sequencing. Hormone levels were analyzed by ELISA.The analysis revealed two novel homozygous LEPR mutations, an essential splice site mutation in exon 15 (c.2396-1 GT), and a nonsense mutation in exon 10 (c.1675 GA). Both probands had high leptin levels and were phenotypically indistinguishable from age-matched leptin-deficient subjects from the same population.The two subjects carrying homozygous LEPR mutations, reported here for the first time in the Pakistani population, constitute 3% of the whole cohort of severely obese children (compared to 17% for LEP and 3% for MC4R).

Published
2013

38. Highly sensitive diagnosis of 43 monogenic forms of diabetes or obesity through one-step PCR-based enrichment in combination with next-generation sequencing

Author

Luis Castaño, Jean Muller, Rosa de Diego Martínez, J. Philippe, Olivier Sand, Michel Polak, Franck De Graeve, Hélène Cavé, Amélie Bonnefond, Philippe Froguel, Véronique Dhennin, Muhammad Arslan, Martine Vaxillaire, Jean-Louis Mandel, Emmanuelle Durand, Sadia Saeed, and Iandry Rabearivelo

Subjects
Adolescent, Endocrinology, Diabetes and Metabolism, Genetic counseling, Cost-Benefit Analysis, Locus (genetics), Computational biology, Polymerase Chain Reaction, Sensitivity and Specificity, DNA sequencing, symbols.namesake, Diabetes mellitus genetics, Diabetes mellitus, Internal Medicine, Diabetes Mellitus, Medicine, Humans, Obesity, Indel, Child, Gene, Advanced and Specialized Nursing, Sanger sequencing, business.industry, High-Throughput Nucleotide Sequencing, medicine.disease, Child, Preschool, Mutation, symbols, business
Abstract

OBJECTIVE Accurate etiological diagnosis of monogenic forms of diabetes and obesity is useful as it can lead to marked improvements in patient care and genetic counseling. Currently, molecular diagnosis based on Sanger sequencing is restricted to only a few genes, as this technology is expensive, time-consuming, and labor-intensive. High-throughput next-generation sequencing (NGS) provides an opportunity to develop innovative cost-efficient methods for sensitive diabetes and obesity multigene screening. RESEARCH DESIGN AND METHODS We assessed a new method based on PCR enrichment in microdroplets (RainDance Technologies) and NGS using the Illumina HiSeq2000 for the molecular diagnosis of 43 forms of monogenic diabetes or obesity. Forty patients carrying a known causal mutation for those subtypes according to diagnostic laboratories were blindly reanalyzed. RESULTS Except for one variant, we reidentified all causal mutations in each patient associated with an almost-perfect sequencing of the targets (mean of 98.6%). We failed to call one highly complex indel, although we identified a dramatic drop of coverage at this locus. In three patients, we detected other mutations with a putatively deleterious effect in addition to those reported by the genetic diagnostic laboratories. CONCLUSIONS Our NGS approach provides an efficient means of highly sensitive screening for mutations in genes associated with monogenic forms of diabetes and obesity. As cost and time to deliver results have been key barriers to uncovering a molecular cause in the many undiagnosed cases likely to exist, the present methodology should be considered in patients displaying features of monogenic diabetes or obesity.

Published
2013

39. KLHL3 mutations cause familial hyperkalemic hypertension by impairing ion transport in the distal nephron

Author

Daniel Trujillano, Patrick Niaudet, Amélie Bonnefond, Xavier Jeunemaitre, Pascal Houillier, Olivier Sand, Mark J. Caulfield, Geneviève Beaurain, Stéphanie Miserey-Lenkei, Paul Landais, Robert J. Unwin, Georg Ehret, Chebel Mourani, Olivier Chabre, Vincent L.M. Esnault, Corinne Isnard Bagnis, Christophe Simian, Juliette Hadchouel, Patrick Bruneval, Stephan Ossowski, Béatrice Fiquet, Christelle Soukaseum, Hélène Louis-Dit-Picard, Christel Thauvin, Emmanuelle Vidal-Petiot, Julien Barc, Olena Pylypenko, Steven D. Soroka, Nabila Bouatia-Naji, Michel Delahousse, Philippe Froguel, Jean-Jacques Schott, Xavier Estivill, Jens Koenig, Chantal Mandet, Vincent Probst, Martin Konrad, Françoise Broux, Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Mécanismes moléculaires du transport intracellulaire, Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Epidemiology Unit, Addenbrooke's Hospital-Medical Research Council (MRC), Motilité structurale, Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université libre de Bruxelles (ULB), Service Génétique, Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service d'endocrinologie, CHU Grenoble-Hôpital Michallon, Service de transplantation rénale, Hôpital Foch [Suresnes], Service de néphrologie, Centre Hospitalier Universitaire de Nice (CHU Nice), Pharmaceut, Med & Sci Affairs, Novartis, Centre de Recherche des Cordeliers (CRC), Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de néphrologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University Children's Hospital, Munster, Westfälische Wilhelms-Universität Münster (WWU), Aide à la Décision pour une Médecine Personnalisé - Laboratoire de Biostatistique, Epidémiologie et Recherche Clinique - EA 2415 (AIDMP), Université Montpellier 1 (UM1)-Université de Montpellier (UM), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre hospitalier universitaire de Nantes (CHU Nantes), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), UFR de médecine (Université de Bourgogne), Université de Bourgogne (UB), Royal Free and University College Medical School, Center for Nephrology, Laboratoire de Recherche en Imagerie : Méthodes d'imagerie des Échanges transcapillaires (LRI - EA4062), Universitat Pompeu Fabra [Barcelona] (UPF), Génétique des maladies multifactorielles (GMM), Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), Ehret, Georg Benedikt, Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de Néphrologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Unité de recherche de l'institut du thorax (ITX-lab), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique Intégrative et Modélisation des Maladies Métaboliques (EGID), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Université Libre de Bruxelles [Bruxelles] (ULB), Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale, Université Paris Diderot - Paris 7 (UPD7)-École pratique des hautes études (EPHE)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Génétique Médicale, Hopital, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), and Universitat Pompeu Fabra [Barcelona]

Subjects
Male, Carrier Proteins/genetics, Pseudohypoaldosteronism/genetics/metabolism/physiopathology, Pseudohypoaldosteronism, [SDV]Life Sciences [q-bio], Blood Pressure, 030204 cardiovascular system & hematology, Nephrons/metabolism, Kidney, 0302 clinical medicine, Missense mutation, Child, ComputingMilieux_MISCELLANEOUS, Genetics, ddc:616, Aged, 80 and over, 0303 health sciences, biology, Microfilament Proteins, Middle Aged, WNK1, Phenotype, Sodium Chloride Symporters, WNK4, Ubiquitin ligase, Female, Signal Transduction, Adult, medicine.medical_specialty, Adolescent, Blood Pressure/genetics, Ion Transport/genetics, Molecular Sequence Data, Polymorphism, Single Nucleotide, 03 medical and health sciences, Young Adult, Internal medicine, medicine, Humans, Amino Acid Sequence, Sodium Chloride Symporters/genetics/metabolism, 030304 developmental biology, Adaptor Proteins, Signal Transducing, Aged, Ion Transport, Base Sequence, urogenital system, Kidney metabolism, Nephrons, Sequence Analysis, DNA, medicine.disease, Kidney/metabolism, Endocrinology, Ion homeostasis, biology.protein, Carrier Proteins
Abstract

Familial hyperkalemic hypertension (FHHt) is a Mendelian form of arterial hypertension that is partially explained by mutations in WNK1 and WNK4 that lead to increased activity of the Na(+)-Cl(-) cotransporter (NCC) in the distal nephron. Using combined linkage analysis and whole-exome sequencing in two families, we identified KLHL3 as a third gene responsible for FHHt. Direct sequencing of 43 other affected individuals revealed 11 additional missense mutations that were associated with heterogeneous phenotypes and diverse modes of inheritance. Polymorphisms at KLHL3 were not associated with blood pressure. The KLHL3 protein belongs to the BTB-BACK-kelch family of actin-binding proteins that recruit substrates for Cullin3-based ubiquitin ligase complexes. KLHL3 is coexpressed with NCC and downregulates NCC expression at the cell surface. Our study establishes a role for KLHL3 as a new member of the complex signaling pathway regulating ion homeostasis in the distal nephron and indirectly blood pressure.

Published
2012
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40. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

Author

Denis Thieffry, Carl Herrmann, Morgane Thomas-Chollier, Olivier Sand, Matthieu Defrance, Jacques van Helden, Max Planck Institute for Molecular Genetics (MPIMG), Max-Planck-Gesellschaft, Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universidad Nacional Autónoma de México (UNAM), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université libre de Bruxelles (ULB), Alexander von Humboldt foundation (to M.T.C.), Agence Nationale de la Recherche (ANR) partner of the ERASysBio+ initiative supported under the EU ERA-NET Plus scheme in FP7, ANR Young Researchers Grant ‘CardiHox’ (to C.H.), the Belgian Program on Interuniversity Attraction Poles, initiated by the Belgian Federal Science Policy Office [project P6/25 (BioMaGNet)], EU-funded COST action [BM1006 ‘Next Generation Sequencing Data Analysis Network’], FP7 MICROME Collaborative Project (‘Microbial genomics and bio-informatics’, contract number 222886-2). Funding for open access charge: Belgian Program on Interuniversity Attraction Poles [project P6/25 (BioMaGNet)]., European Project: 222886,EC:FP7:KBBE,FP7-KBBE-2007-2A,MICROME(2009), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Spinelli, Lionel, and The Microme Project: A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics - MICROME - - EC:FP7:KBBE2009-12-01 - 2013-11-30 - 222886 - VALID

Subjects
Chromatin Immunoprecipitation, Sequence analysis, [SDV]Life Sciences [q-bio], Time efficiency, P300-CBP Transcription Factors, Genome browser, Computational biology, Biology, Genome, p300-CBP Transcription Factors -- metabolism, Mice, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, Genetics, Animals, p300-CBP Transcription Factors, Regulatory Elements, Transcriptional, Nucleotide Motifs, Transcription Factors -- metabolism, Embryonic Stem Cells, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology, 0303 health sciences, Massively Parallel (Deep) Sequencing, Sequence Analysis, DNA, Genomics, Sciences bio-médicales et agricoles, Chip, Visualization, [SDV] Life Sciences [q-bio], Methods Online, Motif (music), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Embryonic Stem Cells -- metabolism, Software, 030217 neurology & neurosurgery, Transcription Factors, Computational Methods
Abstract

ChIP-seq is increasingly used to characterize transcription factor binding and chromatin marks at a genomic scale. Various tools are now available to extract binding motifs from peak data sets. However, most approaches are only available as command-line programs, or via a website but with size restrictions. We present peak-motifs, a computational pipeline that discovers motifs in peak sequences, compares them with databases, exports putative binding sites for visualization in the UCSC genome browser and generates an extensive report suited for both naive and expert users. It relies on time- and memory-efficient algorithms enabling the treatment of several thousand peaks within minutes. Regarding time efficiency, peak-motifs outperforms all comparable tools by several orders of magnitude. We demonstrate its accuracy by analyzing data sets ranging from 4000 to 1,28,000 peaks for 12 embryonic stem cell-specific transcription factors. In all cases, the program finds the expected motifs and returns additional motifs potentially bound by cofactors. We further apply peak-motifs to discover tissue-specific motifs in peak collections for the p300 transcriptional co-activator. To our knowledge, peak-motifs is the only tool that performs a complete motif analysis and offers a user-friendly web interface without any restriction on sequence size or number of peaks., Journal Article, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2012
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41. The EMBRACE web service collection

Author

Teresa K. Attwood, Philip McDermott, Steve Pettifer, David G. Pisano, Gert Vriend, Edita Bartaseviciute, Inge Jonassen, Dave Thorne, Jon Ison, Kristoffer Rapacki, Jean Salzemann, Matúš Kalaš, Inb Partners, Vincent Breton, Andrew B. Clegg, Olivier Sand, Mahmut Uludag, Heinz Stockinger, Ali Liaquat, Graham Cameron, Maarten L. Hekkelman, Christophe Blanchet, José M. Fernández, Peter Rice, Erik Bongcam-Rudloff, Jose Manuel Rodriguez, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Chemical and physical biology [NCMLS 7], Web standards, Genetics and epigenetic pathways of disease [NCMLS 6], Web development, Web 2.0, Bioinformatics, 0206 medical engineering, Matematikk og naturvitenskap: 400::Basale biofag: 470::Bioinformatikk: 475 [VDP], Services computing, 02 engineering and technology, Biology, computer.software_genre, Biological Science Disciplines, World Wide Web, 03 medical and health sciences, Web Services, Genetics, Matematikk og Naturvitenskap: 400 [VDP], Registries, 030304 developmental biology, WS-Addressing, 0303 health sciences, Internet, business.industry, WS-I Basic Profile, Information Dissemination, Computational Biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Systems Integration, Mathematics and natural scienses: 400::Basic biosciences: 470::Bioinformatics: 475 [VDP], Web service, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, WS-Policy, computer, Biologie, 020602 bioinformatics, Software
Abstract

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions. © The Author(s) 2010. Published by Oxford University Press., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2010
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42. Molecular Diagnosis of Neonatal Diabetes Mellitus Using Next-Generation Sequencing of the Whole Exome

Author

Sophie Gallina, Christine Bellanné-Chantelot, Kanetee Busiah, Louis Letourneau, Olivier Sand, Amélie Bonnefond, Philippe Froguel, Michel Polak, Albane Simon, Stéphane Lobbens, Robert Sladek, Martine Vaxillaire, Franck De Graeve, Emmanuelle Durand, Raphael Scharfmann, Jérôme Delplanque, Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (GI3M), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Génétique des maladies multifactorielles (GMM), Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), McGill University = Université McGill [Montréal, Canada], Pancréas endocrine et diabète de l'enfant, Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Human Genetics [Montréal], Service d'endocrinologie, gynécologie et diabétologie pédiatriques [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut de recherche en biothérapie [IRB], Génétique des maladies multifactorielles [GMM], Université de Lille, Droit et Santé, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)], Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)

Subjects
endocrine system diseases, lcsh:Medicine, 030209 endocrinology & metabolism, Bioinformatics, Polymorphism, Single Nucleotide, ABCC8, DNA sequencing, Infant, Newborn, Diseases, Frameshift mutation, 03 medical and health sciences, symbols.namesake, Diabetes mellitus genetics, 0302 clinical medicine, Neonatal diabetes mellitus, medicine, Diabetes Mellitus, Humans, Diabetes and Endocrinology/Type 2 Diabetes, lcsh:Science, Exome, Exome sequencing, Genetics and Genomics/Genetics of Disease, 030304 developmental biology, Sanger sequencing, Genetics and Genomics/Medical Genetics, 0303 health sciences, [SDV.MHEP.PED]Life Sciences [q-bio]/Human health and pathology/Pediatrics, Multidisciplinary, biology, lcsh:R, Infant, Newborn, nutritional and metabolic diseases, Genetics and Genomics, Exons, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, medicine.disease, 3. Good health, Diabetes and Endocrinology, Molecular Diagnostic Techniques, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Mutation, symbols, biology.protein, lcsh:Q, Genetics and Genomics/Gene Discovery, Chromosomes, Human, Pair 6, Research Article
Abstract

International audience; Background: Accurate molecular diagnosis of monogenic non-autoimmune neonatal diabetes mellitus (NDM) is critical for patient care, as patients carrying a mutation in KCNJ11 or ABCC8 can be treated by oral sulfonylurea drugs instead of insulin therapy. This diagnosis is currently based on Sanger sequencing of at least 42 PCR fragments from the KCNJ11, ABCC8, and INS genes. Here, we assessed the feasibility of using the next-generation whole exome sequencing (WES) for the NDM molecular diagnosis.Methodology/Principal Findings: We carried out WES for a patient presenting with permanent NDM, for whom mutations in KCNJ11, ABCC8 and INS and abnormalities in chromosome 6q24 had been previously excluded. A solution hybridization selection was performed to generate WES in 76 bp paired-end reads, by using two channels of the sequencing instrument. WES quality was assessed using a high-resolution oligonucleotide whole-genome genotyping array. From our WES with high-quality reads, we identified a novel non-synonymous mutation in ABCC8 (c.1455G>C/p.Q485H), despite a previous negative sequencing of this gene. This mutation, confirmed by Sanger sequencing, was not present in 348 controls and in the patient's mother, father and young brother, all of whom are normoglycemic.Conclusions/Significance: WES identified a novel de novo ABCC8 mutation in a NDM patient. Compared to the current Sanger protocol, WES is a comprehensive, cost-efficient and rapid method to identify mutations in NDM patients. We suggest WES as a near future tool of choice for further molecular diagnosis of NDM cases, negative for chr6q24, KCNJ11 and INS abnormalities

Published
2010
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43. Integrating sequence, evolution and functional genomics in regulatory genomics

Author

Olivier Sand, Esko Ukkonen, Thomas Manke, Richard M.R. Coulson, Kimmo Palin, Jacques van Helden, Alvis Brazma, Martin Vingron, Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université libre de Bruxelles (ULB), and Spinelli, Lionel

Subjects
Clinomics, [SDV]Life Sciences [q-bio], Genomics, Computational biology, Review, Biology, Genome, Structural genomics, Evolution, Molecular, 03 medical and health sciences, Regulatory Elements, Transcriptional, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Comparative genomics, 0303 health sciences, Base Sequence, 030302 biochemistry & molecular biology, Computational genomics, Computational Biology, [SDV] Life Sciences [q-bio], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Databases, Nucleic Acid, Functional genomics, Protein Structure Initiative
Abstract

Finding transcription factor binding sites in regulatory regions of the genome, With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome.

Published
2009

44. Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (2): impacts of post-partum negative energy balance on stromal, glandular and luminal epithelial cells

Author

Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongzhi Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Göran Andersson, Patrice Humblot, and Gilles Charpigny

Subjects
Negative energy balance, Endometrium, Cell type-specific, Transcriptome, LCM, RNA-seq, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background In post-partum dairy cows, the energy needs to satisfy high milk production induces a status of more or less pronounced Negative Energy Balance (NEB). NEB associated with fat mobilization impairs reproductive function. In a companion paper, we described constitutive gene expression in the three main endometrial cell types (stromal, glandular and luminal epithelial cells) isolated by laser capture micro-dissection (LCM) showing the specificities of their transcriptomic profiles. This study investigates the specific impact of NEB on gene expression in these cells around 80 days after parturition at day 15 of the oestrus cycle and describes their specific response to NEB. Results Following the description of their constitutive expression, the transcriptome profiles obtained by RNA sequencing of the three cells types revealed that differences related to the severity of NEB altered mainly specific patterns of expression related to individual cell types. Number of differentially expressed genes between severe NEB (SNEB) and mild NEB (MNEB) cows was higher in ST than in LE and GE, respectively. SNEB was associated with differential expression of genes coding for proteins involved in metabolic processes and embryo-maternal interactions in ST. Under-expression of genes encoding proteins with functions related to cell structure was found in GE whereas genes encoding proteins participating in pro-inflammatory pathways were over-expressed. Genes associated to adaptive immunity were under-expressed in LE. Conclusion The severity of NEB after calving is associated with changes in gene expression around 80 days after parturition corresponding to the time of breeding. Specific alterations in GEs are associated with activation of pro-inflammatory mechanisms. Concomitantly, changes in the expression of genes encoding proteins involved in cell interactions and maternal recognition of pregnancy takes place in ST. The combination of these effects possibly altering the uterine environment and embryo maternal interactions may negatively influence the establishment of pregnancy.

Published
2021
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45. Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells

Author

Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongzhi Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Göran Andersson, Patrice Humblot, and Gilles Charpigny

Subjects
Cow, Endometrium, Cell type-specific, Transcriptome, LCM, RNA-seq, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole endometrium which is a complex tissue. Consequently, the knowledge of cell-specific gene expression, when analysis performed with whole endometrium, is still weak and obviously limits the relevance of the results of gene expression studies. Thus, the aim of this study was to characterize specific transcriptome of the three main cell-types of the bovine endometrium at day-15 of the estrus cycle. Results In the RNA-Seq analysis, the number of expressed genes detected over 10 transcripts per million was 6622, 7814 and 8242 for LE, GE and ST respectively. ST expressed exclusively 1236 genes while only 551 transcripts were specific to the GE and 330 specific to LE. For ST, over-represented biological processes included many regulation processes and response to stimulus, cell communication and cell adhesion, extracellular matrix organization as well as developmental process. For GE, cilium organization, cilium movement, protein localization to cilium and microtubule-based process were the only four main biological processes enriched. For LE, over-represented biological processes were enzyme linked receptor protein signaling pathway, cell-substrate adhesion and circulatory system process. Conclusion The data show that each endometrial cell-type has a distinct molecular signature and provide a significantly improved overview on the biological process supported by specific cell-types. The most interesting result is that stromal cells express more genes than the two epithelial types and are associated with a greater number of pathways and ontology terms.

Published
2021
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46. Pressurized intra-peritoneal aerosol chemotherapy (PIPAC): increased intraperitoneal pressure does not affect distribution patterns but leads to deeper penetration depth of doxorubicin in a sheep model

Author

Myriam Mimouni, Christophe Richard, Pierre Adenot, Martine Letheule, Anne Tarrade, Olivier Sandra, Michèle Dahirel, Thomas Lilin, Benoit Lecuelle, Valérie Gélin, Julien Cohen, Arnaud Fauconnier, François Vialard, Cyrille Huchon, and Pascale Chavatte-Palmer

Subjects
Sheep, Doxorubicin, PIPAC, Intraperitoneum pressure, Peritoneal carcinomatosis, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Pressurized Intra-Peritoneal Aerosol Chemotherapy (PIPAC) is an innovative treatment against peritoneal carcinomatosis. Doxorubicin is a common intra-venous chemotherapy used for peritoneal carcinomatosis and for PIPAC. This study evaluated the impact of increased PIPAC intraperitoneal pressure on the distribution and cell penetration of doxorubicin in a sheep model. Methods Doxorubicin was aerosolized using PIPAC into the peritoneal cavity of 6 ewes (pre-alpes breed): N = 3 with 12 mmHg intraperitoneal pressure (“group 12”) and N = 3 with 20 mmHg (“group 20”). Samples from peritoneum (N = 6), ovarian (N = 1), omentum (N = 1) and caecum (N = 1) were collected for each ewe. The number of doxorubicin positive cells was determined using the ratio between doxorubicine fluorescence-positive cell nuclei (DOXO+) over total number of DAPI positive cell nuclei (DAPI+). Penetration depth (μm) was defined as the distance between the luminal surface and the location of the deepest DOXO+ nuclei over the total number of cell nuclei that were stained with DAPI. Penetration depth (μm) was defined as the distance between the luminal surface and the location of the deepest DOXO+ nuclei. Results DOXO+ nuclei were identified in 87% of samples. All omental samples, directly localized in front of the nebulizer head, had 100% DOXO+ nuclei whereas very few nuclei were DOXO+ for caecum. Distribution patterns were not different between the two groups but penetration depth in ovary and caecum samples was significantly deeper in group 20. Conclusions This study showed that applying a higher intra-peritoneal pressure during PIPAC treatment leads to a deeper penetration of doxorubicin in ovarian and caecum but does not affect distribution patterns.

Published
2021
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47. NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

Author

Yves Deville, Olivier Sand, Gilles Vanderstocken, Gipsi Lima-Mendez, Sylvain Brohée, Karoline Faust, Jacques van Helden, Rekin's Janky, Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université libre de Bruxelles (ULB), UCL - FSA/INGI - Département d'ingénierie informatique, and Spinelli, Lionel

Subjects
Theoretical computer science, Interface (Java), SOAP, computer.internet_protocol, [SDV]Life Sciences [q-bio], Biology, Bioinformatics, computer.software_genre, Set (abstract data type), 03 medical and health sciences, 0302 clinical medicine, Protein Interaction Mapping, Genetics, Computer Graphics, Cluster Analysis, Cluster analysis, ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology, Oligonucleotide Array Sequence Analysis, 0303 health sciences, Internet, Articles, Sciences bio-médicales et agricoles, [SDV] Life Sciences [q-bio], Gene Expression Regulation, 030220 oncology & carcinogenesis, Path (graph theory), Web service, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Graph operations, computer, Biological network, Metabolic Networks and Pathways, Software, Signal Transduction
Abstract

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources., Journal Article, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2008

48. Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services-an example with ChIP-chip data

Author

Morgane Thomas-Chollier, Jacques van Helden, Olivier Sand, Eric Vervisch, Spinelli, Lionel, Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), and Université libre de Bruxelles (ULB)

Subjects
Chromatin Immunoprecipitation, SOAP, computer.internet_protocol, Interface (Java), [SDV]Life Sciences [q-bio], Computational biology, Biology, computer.software_genre, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Factor (programming language), Microchip Analytical Procedures, Regulatory Elements, Transcriptional, Promoter Regions, Genetic, Protocol (object-oriented programming), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, computer.programming_language, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Internet, 0303 health sciences, Binding Sites, Programming language, Computational Biology, [SDV] Life Sciences [q-bio], ComputingMethodologies_PATTERNRECOGNITION, Workflow, Multigene Family, Data set (IBM mainframe), Web service, Perl, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software, 030217 neurology & neurosurgery, Transcription Factors
Abstract

This protocol shows how to access the Regulatory Sequence Analysis Tools (RSAT) via a programmatic interface in order to automate the analysis of multiple data sets. We describe the steps for writing a Perl client that connects to the RSAT Web services and implements a workflow to discover putative cis-acting elements in promoters of gene clusters. In the presented example, we apply this workflow to lists of transcription factor target genes resulting from ChIP-chip experiments. For each factor, the protocol predicts the binding motifs by detecting significantly overrepresented hexanucleotides in the target promoters and generates a feature map that displays the positions of putative binding sites along the promoter sequences. This protocol is addressed to bioinformaticians and biologists with programming skills (notions of Perl). Running time is approximately 6 min on the example data set.

Published
2008

49. Evaluating the prediction of cis-acting regulatory elements in genome sequences

Author

J. van Helden, Olivier Sand, and Jean Valéry Turatsinze

Subjects
Regulation of gene expression, Genetics, Regulatory sequence, Gene expression, Morphogenesis, Transcriptional regulation, Computational biology, Biology, Genome, Transcription factor, Gene
Abstract

Transcriptional regulation plays an essential role in all steps of morphogenesis, by controlling the specific subsets of genes that will be expressed in different cell types, and at different times during embryonic development. The control of gene expression is also crucial to maintain the basic cellular functions (e.g. cell divisions) and the response of the organism to its environment (e.g. metabolic regulation). The spatio-temporal control of gene expression is ensured by interactions between transcription factors and specific loci, called cis-acting regulatory elements.

Published
2008
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50. RSAT: regulatory sequence analysis tools

Author

Olivier Sand, Rekin's Janky, Sylvain Brohée, Jacques van Helden, Jean Valéry Turatsinze, Matthieu Defrance, Eric Vervisch, Morgane Thomas-Chollier, Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), and Université libre de Bruxelles (ULB)

Subjects
0106 biological sciences, Interface (Java), [SDV]Life Sciences [q-bio], Biology, computer.software_genre, 01 natural sciences, 03 medical and health sciences, User-Computer Interface, Software, Genetics, Ensembl, Pattern matching, Regulatory Elements, Transcriptional, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Internet, Software suite, Information retrieval, business.industry, Suite, Articles, Genomics, Sciences bio-médicales et agricoles, Workflow, Web service, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, 010606 plant biology & botany
Abstract

The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published., Journal Article, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2008
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