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  1. Article ; Online: Microarray Analysis of Whole-Transcriptome RNAs Including Non-Coding RNAs.

    Thuillier, Quentin / Behm-Ansmant, Isabelle

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2300, Page(s) 143–164

    Abstract: Non-coding RNAs participate in most cellular processes and play a causative role in several diseases. In addition to their relevance as targets or tools for therapy, ncRNAs have been extensively detected in body fluids supporting their role as easily ... ...

    Abstract Non-coding RNAs participate in most cellular processes and play a causative role in several diseases. In addition to their relevance as targets or tools for therapy, ncRNAs have been extensively detected in body fluids supporting their role as easily accessible and minimally invasive biomarkers. However, the precise measurement of circulating ncRNAs remains challenging due to their low abundance and the heterogeneity of the ncRNA population (size, polyadenylation status, circular forms). Microarrays constitute a very powerful method to analyze the expression level and the splicing pattern of circulating ncRNAs since they preserve sample integrity (no need to remove globin or rRNA) and allow precise quantification of low-abundance transcripts (no limitation by read depth). This chapter describes the protocols used in our lab to extract and purify total RNAs from PAXgene RNA Blood Tubes and to perform RNA labeling and hybridization on the Clariom™ D microarrays from Affymetrix.
    MeSH term(s) Blood Specimen Collection ; Gene Expression Profiling ; Humans ; Oligonucleotide Array Sequence Analysis/methods ; RNA, Untranslated/blood ; RNA, Untranslated/chemistry ; RNA, Untranslated/genetics ; Staining and Labeling ; Whole Exome Sequencing/methods
    Chemical Substances RNA, Untranslated
    Language English
    Publishing date 2021-04-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1386-3_14
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Substructure analyzer: a user-friendly workflow for rapid exploration and accurate analysis of cellular bodies in fluorescence microscopy images

    Heckler, Géraud / Aigueperse, Christelle / Hettal, Liza / Thuillier, Quentin / de Chaumont, Fabrice / Dallongeville, Stéphane / Behm-Ansmant, Isabelle

    Journal of visualized experiments. 2020 July 15, , no. 161

    2020  

    Abstract: The last decade has been characterized by breakthroughs in fluorescence microscopy techniques illustrated by spatial resolution improvement but also in live-cell imaging and high-throughput microscopy techniques. This led to a constant increase in the ... ...

    Abstract The last decade has been characterized by breakthroughs in fluorescence microscopy techniques illustrated by spatial resolution improvement but also in live-cell imaging and high-throughput microscopy techniques. This led to a constant increase in the amount and complexity of the microscopy data for a single experiment. Because manual analysis of microscopy data is very time consuming, subjective, and prohibits quantitative analyses, automation of bioimage analysis is becoming almost unavoidable. We built an informatics workflow called Substructure Analyzer to fully automate signal analysis in bioimages from fluorescent microscopy. This workflow is developed on the user-friendly open-source platform Icy and is completed by functionalities from ImageJ. It includes the pre-processing of images to improve the signal to noise ratio, the individual segmentation of cells (detection of cell boundaries) and the detection/quantification of cell bodies enriched in specific cell compartments. The main advantage of this workflow is to propose complex bio-imaging functionalities to users without image analysis expertise through a user-friendly interface. Moreover, it is highly modular and adapted to several issues from the characterization of nuclear/cytoplasmic translocation to the comparative analysis of different cell bodies in different cellular sub-structures. The functionality of this workflow is illustrated through the study of the Cajal (coiled) Bodies under oxidative stress (OS) conditions. Data from fluorescence microscopy show that their integrity in human cells is impacted a few hours after the induction of OS. This effect is characterized by a decrease of coilin nucleation into characteristic Cajal Bodies, associated with a nucleoplasmic redistribution of coilin into an increased number of smaller foci. The central role of coilin in the exchange between CB components and the surrounding nucleoplasm suggests that OS induced redistribution of coilin could affect the composition and the functionality of Cajal Bodies.
    Keywords automation ; bioimaging ; fluorescence microscopy ; humans ; oxidative stress ; quantitative analysis ; signal-to-noise ratio ; user interface
    Language English
    Dates of publication 2020-0715
    Size p. e60990.
    Publishing place Journal of Visualized Experiments
    Document type Article
    ZDB-ID 2259946-0
    ISSN 1940-087X
    ISSN 1940-087X
    DOI 10.3791/60990
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Substructure Analyzer: A User-Friendly Workflow for Rapid Exploration and Accurate Analysis of Cellular Bodies in Fluorescence Microscopy Images.

    Heckler, Géraud / Aigueperse, Christelle / Hettal, Liza / Thuillier, Quentin / de Chaumont, Fabrice / Dallongeville, Stéphane / Behm-Ansmant, Isabelle

    Journal of visualized experiments : JoVE

    2020  , Issue 161

    Abstract: The last decade has been characterized by breakthroughs in fluorescence microscopy techniques illustrated by spatial resolution improvement but also in live-cell imaging and high-throughput microscopy techniques. This led to a constant increase in the ... ...

    Abstract The last decade has been characterized by breakthroughs in fluorescence microscopy techniques illustrated by spatial resolution improvement but also in live-cell imaging and high-throughput microscopy techniques. This led to a constant increase in the amount and complexity of the microscopy data for a single experiment. Because manual analysis of microscopy data is very time consuming, subjective, and prohibits quantitative analyses, automation of bioimage analysis is becoming almost unavoidable. We built an informatics workflow called Substructure Analyzer to fully automate signal analysis in bioimages from fluorescent microscopy. This workflow is developed on the user-friendly open-source platform Icy and is completed by functionalities from ImageJ. It includes the pre-processing of images to improve the signal to noise ratio, the individual segmentation of cells (detection of cell boundaries) and the detection/quantification of cell bodies enriched in specific cell compartments. The main advantage of this workflow is to propose complex bio-imaging functionalities to users without image analysis expertise through a user-friendly interface. Moreover, it is highly modular and adapted to several issues from the characterization of nuclear/cytoplasmic translocation to the comparative analysis of different cell bodies in different cellular sub-structures. The functionality of this workflow is illustrated through the study of the Cajal (coiled) Bodies under oxidative stress (OS) conditions. Data from fluorescence microscopy show that their integrity in human cells is impacted a few hours after the induction of OS. This effect is characterized by a decrease of coilin nucleation into characteristic Cajal Bodies, associated with a nucleoplasmic redistribution of coilin into an increased number of smaller foci. The central role of coilin in the exchange between CB components and the surrounding nucleoplasm suggests that OS induced redistribution of coilin could affect the composition and the functionality of Cajal Bodies.
    MeSH term(s) Cell Body/metabolism ; Cell Nucleus ; Humans ; Microscopy, Fluorescence/methods ; Nuclear Proteins ; Workflow
    Chemical Substances Nuclear Proteins
    Language English
    Publishing date 2020-07-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/60990
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL.

    Alfeghaly, Charbel / Sanchez, Aymeric / Rouget, Raphael / Thuillier, Quentin / Igel-Bourguignon, Valérie / Marchand, Virginie / Branlant, Christiane / Motorin, Yuri / Behm-Ansmant, Isabelle / Maenner, Sylvain

    Nucleic acids research

    2021  Volume 49, Issue 9, Page(s) 4954–4970

    Abstract: Long non-coding RNAs have emerged as critical regulators of cell homeostasis by modulating gene expression at chromatin level for instance. Here, we report that the lncRNA ANRIL, associated with several pathologies, binds to thousands of loci dispersed ... ...

    Abstract Long non-coding RNAs have emerged as critical regulators of cell homeostasis by modulating gene expression at chromatin level for instance. Here, we report that the lncRNA ANRIL, associated with several pathologies, binds to thousands of loci dispersed throughout the mammalian genome sharing a 21-bp motif enriched in G/A residues. By combining ANRIL genomic occupancy with transcriptomic analysis, we established a list of 65 and 123 genes potentially directly activated and silenced by ANRIL in trans, respectively. We also found that Exon8 of ANRIL, mainly made of transposable elements, contributes to ANRIL genomic association and consequently to its trans-activity. Furthermore, we showed that Exon8 favors ANRIL's association with the FIRRE, TPD52L1 and IGFBP3 loci to modulate their expression through H3K27me3 deposition. We also investigated the mechanisms engaged by Exon8 to favor ANRIL's association with the genome. Our data refine ANRIL's trans-activity and highlight the functional importance of TEs on ANRIL's activity.
    MeSH term(s) DNA/chemistry ; DNA Transposable Elements ; Exons ; Gene Expression Regulation ; Genetic Loci ; Genome, Human ; HEK293 Cells ; Histones/metabolism ; Humans ; RNA/chemistry ; RNA, Long Noncoding/chemistry ; RNA, Long Noncoding/metabolism
    Chemical Substances CDKN2B antisense RNA, human ; DNA Transposable Elements ; Histones ; RNA, Long Noncoding ; RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2021-04-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab245
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Impact of natriuretic peptide polymorphisms on diastolic and metabolic function in a populational cohort: insights from the STANISLAS cohort.

    Xhaard, Constance / Rouget, Raphaël / Vodovar, Nicolas / Le Floch, Edith / Dandine-Roulland, Claire / Wagner, Sandra / Bacq-Daian, Delphine / Thuillier, Quentin / Boivin, Jean-Marc / Branlant, Christiane / Deleuze, Jean-François / Behm-Ansmant, Isabelle / Zannad, Faiez / Rossignol, Patrick / Girerd, Nicolas

    ESC heart failure

    2021  Volume 9, Issue 1, Page(s) 729–739

    Abstract: Aims: Elevated brain natriuretic peptide (BNP) and the N-terminal fragment of its pro-hormone (NT-proBNP) have become established biomarkers for heart failure and are associated with cardiovascular morbidity and mortality. Investigating sources of inter- ...

    Abstract Aims: Elevated brain natriuretic peptide (BNP) and the N-terminal fragment of its pro-hormone (NT-proBNP) have become established biomarkers for heart failure and are associated with cardiovascular morbidity and mortality. Investigating sources of inter-individual heterogeneity, particularly genetic factors, could help better identify patients at risk of future cardiovascular disease. The aim of this study was to estimate the heritability of circulating NT-proBNP levels, to perform a genome-wide association study (GWAS) and gene-candidate analysis focused on NPPB-NPPA genes on these levels, and to examine their association with cardiovascular or metabolic outcomes.
    Methods and results: A total of 1555 individuals from the STANISLAS study were included. The heritability of circulating NT-proBNP levels was estimated at 15%, with seven single nucleotide polymorphisms (SNPs) reaching the significant threshold in the GWAS. All above SNPs were located on the same gene cluster constituted of MTHFR, CLCN6, NPPA, NPPB, and C1orf167. NPPA gene expression was also associated with NT-proBNP levels. Moreover, six other SNPs from NPPA-NPPB genes were associated with diastolic function (lateral e' on echocardiography) and metabolic features (glycated haemoglobin).
    Conclusions: The heritability of natriuretic peptides appears relatively low (15%) and mainly based on the same gene cluster constituted of MTHFR, CLCN6, NPPA, NPPB, and C1orf167. Natriuretic peptide polymorphisms are associated with natriuretic peptide levels and diastolic function. These results suggest that natriuretic peptide polymorphisms may have an impact in the early stages of cardiovascular and metabolic disease.
    MeSH term(s) Atrial Natriuretic Factor/metabolism ; Cohort Studies ; Genome-Wide Association Study ; Humans ; Natriuretic Peptide, Brain/genetics ; Natriuretic Peptide, Brain/metabolism ; Natriuretic Peptides ; Polymorphism, Single Nucleotide
    Chemical Substances Natriuretic Peptides ; Natriuretic Peptide, Brain (114471-18-0) ; Atrial Natriuretic Factor (85637-73-6)
    Language English
    Publishing date 2021-11-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2814355-3
    ISSN 2055-5822 ; 2055-5822
    ISSN (online) 2055-5822
    ISSN 2055-5822
    DOI 10.1002/ehf2.13674
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Fatty acid desaturase genetic variations and dietary omega-3 fatty acid intake associate with arterial stiffness.

    Bäck, Magnus / Xhaard, Constance / Rouget, Raphael / Thuillier, Quentin / Plunde, Oscar / Larsson, Susanna C / Girerd, Nicolas / Ferreira, João Pedro / Boivin, Jean-Marc / Bozec, Erwan / Mercklé, Ludovic / Zannad, Faiez / Hoge, Axelle / Guillaume, Michèle / Dandine-Roulland, Claire / Floch, Edith Le / Bacq-Daian, Delphine / Deleuze, Jean-François / Van den Berghe, Laurie /
    Nazare, Julie-Anne / Laville, Martine / Branlant, Christiane / Behm-Ansmant, Isabelle / Wagner, Sandra / Rossignol, Patrick

    European heart journal open

    2022  Volume 2, Issue 2, Page(s) oeac016

    Abstract: Aims: Long-chain polyunsaturated fatty acids (PUFAs) generate diverse bioactive lipid mediators, which tightly regulate vascular inflammation. The effects of omega-3 PUFA supplementation in cardiovascular prevention however remain controversial. In ... ...

    Abstract Aims: Long-chain polyunsaturated fatty acids (PUFAs) generate diverse bioactive lipid mediators, which tightly regulate vascular inflammation. The effects of omega-3 PUFA supplementation in cardiovascular prevention however remain controversial. In addition to direct dietary intake, fatty acid desaturases (FADS) determine PUFA levels. Increased arterial stiffness represents an independent predictor of mortality and cardiovascular events. The aim of the present study was to determine the association of PUFA intake, FADS1 genotype, and FADS expression with arterial stiffness.
    Methods and results: A cross-sectional population-based cohort study of 1464 participants without overt cardiovascular disease was conducted. Dietary intake was assessed using a food frequency questionnaire. Arterial stiffness was assessed by carotid-femoral pulse wave velocity (cfPWV), and the FADS1 locus variant was determined. Blood cell transcriptomics was performed in a subset of 410 individuals. Pulse wave velocity was significantly associated with the FADS1 locus variant. Differential associations between PWV and omega-3 PUFA intake were observed depending on the FADS1 genotype. High omega-3 PUFA intake attenuated the FADS1 genotype-dependent associations. Carriers of the minor FADS1 locus variant exhibited increased expression of FADS2, which is associated with PWV.
    Conclusion: Taken together, these findings point to FADS1 genotype-dependent associations of omega-3 PUFA intake on subclinical cardiovascular disease. These findings may have implications for identifying responders and non-responders to omega-3 PUFA supplementation and open up for personalized dietary counselling in cardiovascular prevention.
    Language English
    Publishing date 2022-03-16
    Publishing country England
    Document type Journal Article
    ISSN 2752-4191
    ISSN (online) 2752-4191
    DOI 10.1093/ehjopen/oeac016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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