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6 results on '"DRF/IRCM/SREIT/LREG"'

1. New susceptibility loci for cutaneous melanoma risk and progression revealed using a porcine model

Author

Bourneuf, Emmanuelle, Jordi Estellé, Jordi, Blin, Amandine, Créchet, Francoise, Schneider, Maria-Del-Pilar, Gilbert, Hélène, Brossard, Myriam, Vaysse, Amaury, Lathrop, Mark, Vincent-Naulleau, Silvia, Demenais, Florence, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), DRF/IRCM/SREIT/LREG, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Santé et de la Recherche Médicale (INSERM), Taxonomie - Collections (TC), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées, Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7), Université Sorbonne Paris Cité (COMUE) (USPC), Innovation Centre, P&G, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), and Université de Toulouse (UT)

Subjects
pig, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], melanoma, GWAS, [INFO]Computer Science [cs], comparative genomics, Research Paper, biomedical model
Abstract

International audience; Despite major advances, it is estimated that a large part of melanoma predisposing genes remains to be discovered. Animal models of spontaneous diseases are valuable tools and experimental crosses can be used to identify and fine-map new susceptibility loci associated with melanoma. We performed a Genome-Wide Association Study (GWAS) of melanoma occurrence and progression (clinical ulceration and presence of metastasis) in a porcine model of spontaneous melanoma, the MeLiM pig. Five loci on chromosomes 2, 5, 7, 8 and 16 showed genome-wide significant associations ( p < 5 × 10 –6 ) with either one of these phenotypes. Suggestive associations ( p < 5 × 10 –5 ) were also found at 16 additional loci. Moreover, comparison of the porcine results to those reported by human melanoma GWAS indicated shared association signals notably at CDKAL1 and TERT loci but also nearby CCND1 , FTO, PLA2G6 and TMEM 38B-RAD23B loci. Extensive search of the literature revealed a potential key role of genes at the identified porcine loci in tumor invasion ( DST , PLEKHA5, CBY1 , LIMK2 and ETV5 ) and immune response modulation ( ETV5 , HERC3 and DICER1 ) of the progression phenotypes. These biological processes are consistent with the clinico-pathological features of MeLiM tumors and can open new routes for future melanoma research in humans.

Published
2018
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2. Survey of allele specific expression in bovine muscle

Author

Guillocheau, Gabriel, El Hou, Abdelmajid, Meerssemann, Cédric, Esquerré, Diane, Rebours, Emmanuelle, Letaief, Rabia, Simao, Morgane, Hypolite, Nicolas, Bourneuf, Emmanuelle, Bruneau, Nicolas, Vaiman, Anne, Vander Jagt, Christy, Chamberlain, Amanda, Rocha, Dominique, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université de Limoges (UNILIM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, DRF/IRCM/SREIT/LREG, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Agriculture Victoria Research, Agence Nationale de la Recherche ANR-05-GANI-005 ANR-05-GANI-017-01 / APIS-GENE 01-2005-QualviGenA-02 / French National Research Agency (Regulomix project) ANR-09-GENM-011, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), and Université de Toulouse (UT)-Université de Toulouse (UT)

Subjects
aldehyde oxidase, rna-seq, microrna expression, binding-site, gene, differentiation, identification, polymorphism, transcriptome, deficiency, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], animal structures, Genotype, Quantitative Trait Loci, lcsh:Medicine, Allelic Imbalance, Polymorphism, Single Nucleotide, Article, Animals, Muscle, Skeletal, lcsh:Science, 3' Untranslated Regions, Alleles, lcsh:R, Phenotype, Cattle, lcsh:Q, Autre (Sciences du Vivant), Genome-Wide Association Study
Abstract

International audience; Allelic imbalance is a common phenomenon in mammals that plays an important role in gene regulation. An Allele Specific Expression (ASE) approach can be used to detect variants with a cis-regulatory effect on gene expression. In cattle, this type of study has only been done once in Holstein. In our study we performed a genome-wide analysis of ASE in 19 Limousine muscle samples. We identified 5,658 ASE SNPs (Single Nucleotide Polymorphisms showing allele specific expression) in 13% of genes with detectable expression in the Longissimus thoraci muscle. Interestingly we found allelic imbalance in AOX1, PALLD and CAST genes. We also found 2,107 ASE SNPs located within genomic regions associated with meat or carcass traits. In order to identify causative cis-regulatory variants explaining ASE we searched for SNPs altering binding sites of transcription factors or microRNAs. We identified one SNP in the 3'UTR region of PRNP that could be a causal regulatory variant modifying binding sites of several miRNAs. We showed that ASE is frequent within our muscle samples. Our data could be used to elucidate the molecular mechanisms underlying gene expression imbalance.

Published
2019
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3. Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues

Author

Maroilley, Tatiana, Berri, Mustapha, Lemonnier, Gaetan, Esquerré, D., Chevaleyre, Claire, Melo, Sandrine, MEURENS, François, Coville, Jean-Luc, Leplat, Jean Jacques, Rau, Andrea, Bed'Hom, Bertrand, Vincent-Naulleau, Silvia, Mercat, Marie-José, Billon, Yvon, Lepage, Patricia, Rogel-Gaillard, Claire, Estellé, Jordi, Canadian Space Agency (CSA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut de radiobiologie cellulaire et moléculaire (iRCM), Service de radiobiologie expérimentale et innovation technologiques (SREIT), Laboratoire de Radiologie et d'Etude du génome, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), DRF/IRCM/SREIT/LREG, Institut du Porc (IFIP), Génétique, Expérimentation et Système Innovants (GenESI), Institut National de la Recherche Agronomique (INRA), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), SUS-FLORA project (ANR-10-GENM-016) of the French National Agency and internal funds of INRA’s Animal Genetics Division, Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Laboratoire de radiobiologie et d'étude du génome (LREG), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), INRA, ANR-10-GENM-0016,SUS_FLORA,Contribution du microbiote intestinal à l'homéostasie du système immunitaire chez le porc: approches génétiques et génomiques(2010), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
Male, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Lymphoid Tissue, Swine, T-Lymphocytes, education, lcsh:Medicine, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Peyer's Patches, Ileum, Exome Sequencing, Animals, Mesentery, lcsh:Science, ComputingMilieux_MISCELLANEOUS, B-Lymphocytes, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], lcsh:R, Cell Differentiation, Jejunum, [SDV.IMM]Life Sciences [q-bio]/Immunology, lcsh:Q, Female, Lymph Nodes, Transcriptome
Abstract

International audience; The epithelium of the intestinal mucosa and the gut-associated lymphoid tissues (GALT) constitute an essential physical and immunological barrier against pathogens. In order to study the specificities of the GALT transcriptome in pigs, we compared the transcriptome profiles of jejunal and ileal Peyer's patches (PPs), mesenteric lymph nodes (MLNs) and peripheral blood (PB) of four male piglets by RNA-Seq. We identified 1,103 differentially expressed (DE) genes between ileal PPs (IPPs) and jejunal PPs (JPPs), and six times more DE genes between PPs and MLNs. The master regulator genes FOXP3, GATA3, STAT4, TBX21 and RORC were less expressed in IPPs compared to JPPs, whereas the transcription factor BCL6 was found more expressed in IPPs. In comparison between IPPs and JPPs, our analyses revealed predominant differential expression related to the differentiation of T cells into Th1, Th2, Th17 and iTreg in JPPs. Our results were consistent with previous reports regarding a higher T/B cells ratio in JPPs compared to IPPs. We found antisense transcription for respectively 24%, 22% and 14% of the transcripts detected in MLNs, PPs and PB, and significant positive correlations between PB and GALT transcriptomes. Allele-specific expression analyses revealed both shared and tissue-specific cis-genetic control of gene expression.

Published
2018
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4. Fine phenotyping of swine immune cells by multicolor flow cytometry

Author

Blanc, Fany, Prevost-Blondel, Armelle, Piton, Guillaume, Bouguyon, Edwige, Leplat, Jean Jacques, Andreoletti, Fabrice, Bourneuf, Emmanuelle, Bertho, Nicolas, Vincent-Naulleau, Silvia, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), 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), Université Paris Descartes - Paris 5 (UPD5), DRF/IRCM/SREIT/LREG, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA). FRA., and ProdInra, Migration

Subjects
[SDV.IMM] Life Sciences [q-bio]/Immunology, [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.IMM]Life Sciences [q-bio]/Immunology
Abstract

National audience; Immunological research in a species such as the pig is of great importance for its direct impact on the veterinary control of the pig husbandry and thus the economy of the pig industry as well as for the development of biomedical model. In order to monitor all cell types simultaneously from peripheral whole blood cells from MeLiM pigs (melanoma-bearing minipigs), we compiled the available knowledge to develop gating strategies for multicolor flow cytometry. Lineage, exclusion and activation markers allowed us to identify lymphoid (αβ and δ T cells, B cells, NK and NKT cells) and myeloid cells (dendritic cells, monocytes, granulocytes). The subsets of T lymphocytes were also distinguished according to their helper, cytotoxic or regulatory functions. In contrast with published data, we found that the anti-human CD19 antibody (clone BD3) did not stain B cells efficiently, and we provided a new strategy to detect different B cell subsets according to their maturation status. In particular, their loss of MHCII and CD21 expression correlated with the increase of circulating total IgG concentration. Myeloid cells display a very heterogeneous expression of CD172a, CD14, CD163, PG68A and MHCII. Whereas PG68A were considered as a pan-granulocyte marker, we found that eosinophils were PG68A-/low using May-Grünwald-Giemsa stainings. We also characterized different monocyte subsets, corresponding to differential activation status. As a direct application of this strategy, we could monitor pigs from 3 to 21 weeks of age to gain knowledge about the maturation of pig immune system from weaning to puberty. This immuno-phenotyping has also been extended to a high-throughput approach, which provides new perspectives to qualify the immune capacity of pigs in production. Finally, our fine strategy based on multicolor flow cytometry will be valuable to monitor the regulation of the immune response notably in case of inflammation, disease progression or treatment in swine.

Published
2018

5. Genetic individual variability of vaccine responses in pigs

Author

Fany BLANC, Gaetan Lemonnier, Jean Jacques Leplat, Edwige Bouguyon, Yvon Billon, Jordi Estelle, Claire Gaillard, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, DRF/IRCM/SREIT/LREG, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), UE 1372 Génétique, Expérimentation et Système Innovants, Institut National de la Recherche Agronomique (INRA)-Génétique animale (G.A.)-Physiologie Animale et Systèmes d'Elevage (PHASE), Institut National de la Recherche Agronomique (INRA)-Génétique, Expérimentation et Système Innovants (GenESI), European Project: 633184, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Génétique, Expérimentation et Système Innovants (GenESI), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], education, health care economics and organizations
Abstract

Genetic individual variability of vaccine responses in pigs. 36. Conference of the International Society for Animal Genetics (ISAG)

Published
2017

6. Survey of allele specific expression in bovine muscle.

Author

Guillocheau GM, El Hou A, Meersseman C, Esquerré D, Rebours E, Letaief R, Simao M, Hypolite N, Bourneuf E, Bruneau N, Vaiman A, Vander Jagt CJ, Chamberlain AJ, and Rocha D

Subjects
3' Untranslated Regions genetics, Allelic Imbalance genetics, Allelic Imbalance physiology, Animals, Cattle, Genome-Wide Association Study, Genotype, Phenotype, Polymorphism, Single Nucleotide genetics, Quantitative Trait Loci genetics, Alleles, Muscle, Skeletal metabolism
Abstract

Allelic imbalance is a common phenomenon in mammals that plays an important role in gene regulation. An Allele Specific Expression (ASE) approach can be used to detect variants with a cis-regulatory effect on gene expression. In cattle, this type of study has only been done once in Holstein. In our study we performed a genome-wide analysis of ASE in 19 Limousine muscle samples. We identified 5,658 ASE SNPs (Single Nucleotide Polymorphisms showing allele specific expression) in 13% of genes with detectable expression in the Longissimus thoraci muscle. Interestingly we found allelic imbalance in AOX1, PALLD and CAST genes. We also found 2,107 ASE SNPs located within genomic regions associated with meat or carcass traits. In order to identify causative cis-regulatory variants explaining ASE we searched for SNPs altering binding sites of transcription factors or microRNAs. We identified one SNP in the 3'UTR region of PRNP that could be a causal regulatory variant modifying binding sites of several miRNAs. We showed that ASE is frequent within our muscle samples. Our data could be used to elucidate the molecular mechanisms underlying gene expression imbalance.

Published
2019
Full Text
View/download PDF

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