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1. The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation

Author

Farhadova, Sabina, primary, Ghousein, Amani, additional, Charon, François, additional, Surcis, Caroline, additional, Gomez-Velazques, Melisa, additional, Roidor, Clara, additional, Di Michele, Flavio, additional, Borensztein, Maud, additional, De Sario, Albertina, additional, Esnault, Cyril, additional, Noordermeer, Daan, additional, Moindrot, Benoit, additional, and Feil, Robert, additional

Published
2024
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4. Blood co-expression modules identify potential modifier genes of diabetes and lung function in cystic fibrosis

Author

Pineau, Fanny, Caimmi, Davide, Magalhães, Milena, Fremy, Enora, Mohamed, Abdillah, Mely, Laurent, Leroy, Sylvie, Murris, Marlene, Claustres, Mireille, Chiron, Raphaël, De Sario, Albertina, 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), Centres de Ressources et de Compétences de la Mucoviscidose [Montpellier] (CRCM [Montpellier]), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Arnaud de Villeneuve-Service des Maladies Respiratoires, Centre de Ressources et de Compétences en Mucoviscidose [Lyon] (CRCM [Lyon]), Hospices Civils de Lyon (HCL)-CHU Lyon-Hôpital Renée Sabran [CHU - HCL], Hospices Civils de Lyon (HCL), Centre de Ressources et de Compétences en Mucoviscidose [Nice] (CRCM [Nice]), Les Hôpitaux Pédiatriques de Nice CHU-Lenval, Centre de Ressources et de Compétences en Mucoviscidose [Toulouse] (CRCM [Toulouse]), CHU Toulouse [Toulouse]-Hôpital Larrey [Toulouse], CHU Toulouse [Toulouse], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), DE SARIO, Albertina, Centre de Ressources et de Compétences en Mucoviscidose [CHU Toulouse] (CRCM Toulouse), Service Pneumologie et allergologie pédiatrique [CHU Toulouse], Pôle Enfants [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Enfants [CHU Toulouse], and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)

Subjects
Male, Cystic Fibrosis, Pulmonology, [SDV]Life Sciences [q-bio], Cystic Fibrosis Transmembrane Conductance Regulator, Pulmonary Function, Gene Expression, Comorbidity, Pathology and Laboratory Medicine, White Blood Cells, Endocrinology, Animal Cells, Medicine and Health Sciences, Lung, Gene Ontologies, Pseudomonas Aeruginosa, Genomics, Bacterial Pathogens, [SDV] Life Sciences [q-bio], Genetic Diseases, Medical Microbiology, Medicine, Female, Pathogens, Cellular Types, Research Article, Adult, Cell Binding, Cell Physiology, Endocrine Disorders, Science, Immune Cells, Immunology, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Microbiology, Autosomal Recessive Diseases, Pseudomonas, Diabetes Mellitus, Genetics, Humans, Pseudomonas Infections, Microbial Pathogens, Clinical Genetics, Genes, Modifier, Blood Cells, Bacteria, Organisms, Biology and Life Sciences, Computational Biology, Cell Biology, Genome Analysis, Fibrosis, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Metabolic Disorders, Mutation, Transcriptome, Developmental Biology
Abstract

International audience; Cystic fibrosis (CF) is a rare genetic disease that affects the respiratory and digestive systems. Lung disease is variable among CF patients and associated with the development of comorbidities and chronic infections. The rate of lung function deterioration depends not only on the type of mutations in CFTR, the disease-causing gene, but also on modifier genes. In the present study, we aimed to identify genes and pathways that (i) contribute to the pathogenesis of cystic fibrosis and (ii) modulate the associated comorbidities. We profiled blood samples in CF patients and healthy controls and analyzed RNA-seq data with Weighted Gene Correlation Network Analysis (WGCNA). Interestingly, lung function, body mass index, the presence of diabetes, and chronic P. aeruginosa infections correlated with four modules of co-expressed genes. Detailed inspection of networks and hub genes pointed to cell adhesion, leukocyte trafficking and production of reactive oxygen species as central mechanisms in lung function decline and cystic fibrosis-related diabetes. Of note, we showed that blood is an informative surrogate tissue to study the contribution of inflammation to lung disease and diabetes in CF patients. Finally, we provided evidence that WGCNA is useful to analyze-omic datasets in rare genetic diseases as patient cohorts are inevitably small.

Published
2020
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13. Dynamic changes of DNA methylation and lung disease in cystic fibrosis: lessons from a monogenic disease

Author

Magalhães, Milena, primary, Tost, Jörg, additional, Pineau, Fanny, additional, Rivals, Isabelle, additional, Busato, Florence, additional, Alary, Nathan, additional, Mely, Laurent, additional, Leroy, Sylvie, additional, Murris, Marlène, additional, Caimmi, Davide, additional, Claustres, Mireille, additional, Chiron, Raphaël, additional, and De Sario, Albertina, additional

Published
2018
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14. Genomic structure of a copy of the human TPTE gene which encompasses 87kb on the short arm of chromosome 21

Author

Guipponi, Michel, Yaspo, Marie-Laure, Riesselman, Lisa, Chen, Haiming, De Sario, Albertina, Roizès, Gérard, Antonarakis, Stylianos E., Guipponi, Michel, Yaspo, Marie-Laure, Riesselman, Lisa, Chen, Haiming, De Sario, Albertina, Roizès, Gérard, and Antonarakis, Stylianos E.

Abstract

The testis-expressed human TPTE is a putative transmembrane tyrosine phosphatase, probably involved in signal transduction pathways of the endocrine and/or the spermatogenetic function of the testis. TPTE was mapped to the pericentromeric region of human chromosomes 21 and 13, and to chromosomes 15, 22, and Y. It is unknown which of the TPTE copies are transcribed, contain intronic sequences, and/or have open reading frames. Here, in silico analysis of the genomic sequence of human chromosome 21 allowed the determination of the genomic structure of a copy of the TPTE gene. This copy consists of 24 exons and spans approximately 87kb. The mapping position of this copy of TPTE on the short arm of chromosome 21 was confirmed by FISH using the BAC 15L0C0 clone as a probe that contains almost the entire TPTE gene. This is the first description of the genomic sequence of a non-RNR gene on the short arm of human acrocentric chromosomes

Published
2018

15. DNA methylation at modifier genes of lung disease severity is altered in cystic fibrosis

Author

Magalhães, Milena, primary, Rivals, Isabelle, additional, Claustres, Mireille, additional, Varilh, Jessica, additional, Thomasset, Mélodie, additional, Bergougnoux, Anne, additional, Mely, Laurent, additional, Leroy, Sylvie, additional, Corvol, Harriet, additional, Guillot, Loïc, additional, Murris, Marlène, additional, Beyne, Emmanuelle, additional, Caimmi, Davide, additional, Vachier, Isabelle, additional, Chiron, Raphaël, additional, and De Sario, Albertina, additional

Published
2017
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16. Mapping of the juxtacentromeric heterochromatin-euchromatin frontier of human chromosome 21

Author

Grunau, Christoph, Buard, Jerome, Brun, Marie-Elisabeth, and De Sario, Albertina

Subjects
Chromatin -- Genetic aspects, Chromatin -- Research, Chromosome mapping -- Analysis, Human chromosome 21 -- Research, Methylation -- Analysis, Health
Abstract

A study used the juxtacentromeric region of human chromosome 21 as a model system to map for the first time at less than or equal to 100-kb resolution a transition from constitutive heterochromatin to euchromatin. Results revealed that the juxtacentromeric region of the long arm of chromosome 21 is composed of a proximal compartment that is separated from the euchromatic compartment of the chromosome arm by a cluster of histone isoforms H3K9Me3 and H3K27Me 715-822 kb from the centromeric [alpha]-satellite block.

Published
2006

17. Heterochromatic Genes Undergo Epigenetic Changes and Escape Silencing in Immunodeficiency

Author

Brun, Marie-Elisabeth, Lana, Erica, Rivals, Isabelle, Lefranc, Gérard, Sarda, Pierre, Claustres, Mireille, Mégarbané, André, De Sario, Albertina, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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), Equipe de Statistique Appliquée (UMRS 1158) (ESA), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Neurophysiologie Respiratoire Expérimentale et Clinique, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Unité de Génétique Médicale et Foetopathologie, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), and Institut Jérôme Lejeune

Subjects
[SDV]Life Sciences [q-bio], human activities, humanities
Abstract

International audience; Immunodeficiency, Centromeric Instability, Facial Anomalies (ICF) syndrome is a rare autosomal recessive disorder that is characterized by a marked immunodeficiency, severe hypomethylation of the classical satellites 2 and 3 associated with disruption of constitutive heterochromatin, and facial anomalies. Sixty percent of ICF patients have mutations in the DNMT3B (DNA methyltransferase 3B) gene, encoding a de novo DNA methyltransferase. In the present study, we have shown that, in ICF lymphoblasts and peripheral blood, juxtacentromeric heterochromatic genes undergo dramatic changes in DNA methylation, indicating that they are bona fide targets of the DNMT3B protein. DNA methylation in heterochromatic genes dropped from about 80% in normal cells to approximately 30% in ICF cells. Hypomethylation was observed in five ICF patients and was associated with activation of these silent genes. Although DNA hypomethylation occurred in all the analyzed heterochromatic genes and in all the ICF patients, gene expression was restricted to some genes, every patient having his own group of activated genes. Histone modifications were preserved in ICF patients. Heterochromatic genes were associated with histone modifications that are typical of inactive chromatin: they had low acetylation on H3 and H4 histones and were slightly enriched in H3K9Me 3 , both in ICF and controls. This was also the case for those heterochromatic genes that escaped silencing. This finding suggests that gene activation was not generalized to all the cells, but rather was restricted to a clonal cell population that may contribute to the phenotypic variability observed in ICF syndrome. A slight increase in H3K27 monomethylation was observed both in heterochromatin and active euchromatin in ICF patients; however, no correlation between this modification and activation of heterochromatic genes was found.

Published
2011
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20. A balance between activating and repressive histone modifications regulatescystic fibrosis transmembrane conductance regulator (CFTR) expression in vivo

Author

Bergougnoux, Anne, primary, Rivals, Isabelle, additional, Liquori, Alessandro, additional, Raynal, Caroline, additional, Varilh, Jessica, additional, Magalhães, Milena, additional, Perez, Marie-José, additional, Bigi, Nicole, additional, Des Georges, Marie, additional, Chiron, Raphaël, additional, Squalli-Houssaini, Ahmed Saad, additional, Claustres, Mireille, additional, and De Sario, Albertina, additional

Published
2014
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21. Frequent DNA hypomethylation of human juxtacentromeric BAGE loci in cancer.

Author

UCL - SSS/DDUV - Institut de Duve, Grunau, Christoph, Sanchez, Cecilia, Ehrlich, Melanie, van der Bruggen, Pierre, Hindermann, Winfried, Rodriguez, Carmen, Krieger, Sophie, Dubeau, Louis, Fiala, Emerich, De Sario, Albertina, UCL - SSS/DDUV - Institut de Duve, Grunau, Christoph, Sanchez, Cecilia, Ehrlich, Melanie, van der Bruggen, Pierre, Hindermann, Winfried, Rodriguez, Carmen, Krieger, Sophie, Dubeau, Louis, Fiala, Emerich, and De Sario, Albertina

Abstract

The BAGE (B melanoma antigens) sequence family contains 15 nearly identical sequences that are in the juxtacentromeric regions of chromosomes 9, 13, 18, and 21. BAGE loci are expressed in male germ tissue and in a high percentage of cancers and cancer cell lines. We analyzed the DNA methylation state of the sequences in or near the promoters of the BAGE loci by a quantitative bisulfite and PCR-based assay (multiplex COBRA) using MboI and HphI in 18 somatic tissue samples, 4 testis and 4 sperm samples, and 48 tumors and tumor cell lines. In 94% of the control somatic tissue samples, DNA was highly methylated in the analyzed regions. In contrast, 98% of tumor DNA samples displayed hypomethylation. Also, DNA from testes and sperm was hypomethylated in at least one of the BAGE loci. BAGE transcripts were observed in only 47% of the analyzed tumor samples. Consequently, we propose BAGE hypomethylation as a new, highly informative epigenetic biomarker for the diagnosis of cancer, whose hypomethylation in cancer may be causally related to that of juxtacentromeric satellite DNA.

Published
2005

29. Centromeres and Neocentromeres.

Author

Walker, John M., Sgaramella, Vittorio, Eridani, Sandro, Roizés, Gérard, Grunau, Christoph, Buard, Jérôme, De Sario, Albertina, and Puechberty, Jacques

Abstract

A functional centromere is formed by a chromosomal domain that very often, but not always, is recognizable by a primary constriction in metaphasic chromosomes. It is associated with a kinetochore through which a link is established with the microtubules, which pull the sister chromatids toward the poles of the two daughter cells during cell division. Centromeres therefore mediate chromosome segregation during mitosis and meiosis, but in ways that are relatively different. For instance, binding of the two sister chromatids is normally destroyed at anaphase in mitosis whereas binding is maintained in meiosis all along the first division until anaphase of the second is reached. The same locus is, however, in charge of the two distinct processes. [ABSTRACT FROM AUTHOR]

Published
2004
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38. Prenatal Ultrasound Suspicion of Cystic Fibrosis in a Multiethnic Population: Is Extensive CFTR Genotyping Needed?

Author

Mekki, Chadia, Aissat, Abdel, Mirlesse, Véronique, Mayer Lacrosniere, Sophie, Eche, Elsa, Le Floch, Annick, Whalen, Sandra, Prud'Homme, Cecile, Remus, Christelle, Funalot, Benoit, Castaigne, Vanina, Fanen, Pascale, de Becdelièvre, Alix, and De Sario, Albertina

Subjects
FETAL ultrasonic imaging, CYSTIC fibrosis, ULTRASONIC imaging, FETAL abnormalities, MOLECULAR diagnosis, SUSPICION, ETHNICITY
Abstract

In families without a Cystic Fibrosis (CF) history, fetal ultrasound bowel abnormalities can unexpectedly reveal the disease. Isolated or in association, the signs can be fetal bowel hyperechogenicity, intestinal loop dilatation and non-visualization of fetal gallbladder. In these cases, search for CF transmembrane conductance regulator (CFTR) gene mutations is part of the recommended diagnostic practices, with a search for frequent mutations according to ethnicity, and, in case of the triad of signs, with an exhaustive study of the gene. However, the molecular diagnosis remains a challenge in populations without well-known frequent pathogenic variants. We present a multiethnic cohort of 108 pregnancies with fetal bowel abnormalities in which the parents benefited from an exhaustive study of the CFTR gene. We describe the new homozygous p.Cys1410* mutation in a fetus of African origin. We did not observe the most frequent p.Phe508del mutation in our cohort but evidenced variants undetected by our frequent mutations kit. Thanks to the progress of sequencing techniques and despite the difficulties of interpretation occasionally encountered, we discuss the need to carry out a comprehensive CFTR study in all patients in case of fetal bowel abnormalities. [ABSTRACT FROM AUTHOR]

Published
2021
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39. Modulation of Ion Transport to Restore Airway Hydration in Cystic Fibrosis.

Author

Reihill, James A., Douglas, Lisa E. J., Martin, S. Lorraine, and De Sario, Albertina

Subjects
ION transport (Biology), CYSTIC fibrosis, BURKHOLDERIA infections, CYSTIC fibrosis transmembrane conductance regulator, GLYCOCALYX, HYDRATION, ION channels
Abstract

Cystic fibrosis (CF) is a life-limiting genetic disorder caused by loss-of-function mutations in the gene which codes for the CF transmembrane conductance regulator (CFTR) Cl− channel. Loss of Cl− secretion across the apical membrane of airway lining epithelial cells results in dehydration of the airway surface liquid (ASL) layer which impairs mucociliary clearance (MCC), and as a consequence promotes bacterial infection and inflammation of the airways. Interventions that restore airway hydration are known to improve MCC. Here we review the ion channels present at the luminal surface of airway epithelial cells that may be targeted to improve airway hydration and MCC in CF airways. [ABSTRACT FROM AUTHOR]

Published
2021
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40. Genomic structure of a copy of the human TPTE gene which encompasses 87kb on the short arm of chromosome 21

Author

Guipponi, Michel, Yaspo, Marie-Laure, Riesselman, Lisa, Chen, Haiming, De Sario, Albertina, Roizès, Gérard, Antonarakis, Stylianos E., Guipponi, Michel, Yaspo, Marie-Laure, Riesselman, Lisa, Chen, Haiming, De Sario, Albertina, Roizès, Gérard, and Antonarakis, Stylianos E.

Abstract

The testis-expressed human TPTE is a putative transmembrane tyrosine phosphatase, probably involved in signal transduction pathways of the endocrine and/or the spermatogenetic function of the testis. TPTE was mapped to the pericentromeric region of human chromosomes 21 and 13, and to chromosomes 15, 22, and Y. It is unknown which of the TPTE copies are transcribed, contain intronic sequences, and/or have open reading frames. Here, in silico analysis of the genomic sequence of human chromosome 21 allowed the determination of the genomic structure of a copy of the TPTE gene. This copy consists of 24 exons and spans approximately 87kb. The mapping position of this copy of TPTE on the short arm of chromosome 21 was confirmed by FISH using the BAC 15L0C0 clone as a probe that contains almost the entire TPTE gene. This is the first description of the genomic sequence of a non-RNR gene on the short arm of human acrocentric chromosomes

41. DNA methylation changes in cystic fibrosis: Cause or consequence?

Author

Albertina De Sario, Madeleine Scott, DE SARIO, Albertina, Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, and Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)

Subjects
Epigenomics, 0301 basic medicine, [SDV]Life Sciences [q-bio], [SDV.GEN] Life Sciences [q-bio]/Genetics, 030105 genetics & heredity, Biology, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, Cystic fibrosis, Transcriptome, cystic fibrosis, 03 medical and health sciences, reactive oxygen species, Genetics, medicine, Animals, Humans, Epigenetics, Enhancer, Genetics (clinical), chemistry.chemical_classification, Reactive oxygen species, [SDV.GEN]Life Sciences [q-bio]/Genetics, DNA methylation, Genomics, medicine.disease, Phenotype, infection, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, chemistry, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, enhancers, phenotypic variability, Reactive Oxygen Species
Abstract

International audience; Twin and sibling studies have shown that lung disease severity is variable among cystic fibrosis (CF) patients and affected to the same extent by genetic and nonheritable factors. Genetic factors have been thoroughly assessed, whereas the molecular mechanisms whereby nonheritable factors contribute to the phenotypic variability of CF patients are still unknown. Epigenetic modifications may represent the missing link between nonheritable factors and phenotypic variation in CF. Herein, we review recent studies showing that DNA methylation is altered in CF and we address three possible factors responsible for these variations: (i) overproduction of reactive oxygen species, (ii) depletion of DNA methylation cofactors and (iii) susceptibility to acute and chronic bacterial infections. Also, we hypothesize that the unique DNA methylation profile of each patient can modulate the phenotype and discuss the interest of implementing integrated genomic, epigenomic and transcriptomic studies to further understand the clinical diversity of CF patients (Graphical Abstract).

Published
2020
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42. Report of the seventh international workshop on human chromosome 21 mapping 1997.

Author

Gardiner, K. and Yaspo, M.-L.

Subjects
CONFERENCES & conventions, HUMAN gene mapping, HUMAN chromosome 21, HUMAN genome
Abstract

The seventh international chromosome 21 workshop was held at the Sorat-Spree Bogen Hotel in Berlin, Germany, from September 12-14, 1997. The meeting was supported by the Deutsches Human Genome Projekt and the Max Planck Institute for Molecular Genetics. Over 70 attendees coming from 14 countries participated in the workshop. Human chromosome 21 represents one of the chromosomes in the most advanced state of analysis in the Human Genome Initiative. The 7th in the series of chromosome 21 workshops reflected the transition from historically reported mapping efforts towards large scale genomic sequencing, in silico gene identification, and functional characterization of genes.

Published
1998
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