34 results on '"Tran, Van Du T."'
Search Results
2. A Federated Database for Obesity Research: An IMI-SOPHIA Study
- Author
-
Delfin, Carl, primary, Dragan, Iulian, additional, Kuznetsov, Dmitry, additional, Tajes, Juan Fernandez, additional, Smit, Femke, additional, Coral, Daniel E., additional, Farzaneh, Ali, additional, Haugg, André, additional, Hungele, Andreas, additional, Niknejad, Anne, additional, Hall, Christopher, additional, Jacobs, Daan, additional, Marek, Diana, additional, Fraser, Diane P., additional, Thuillier, Dorothee, additional, Ahmadizar, Fariba, additional, Mehl, Florence, additional, Pattou, Francois, additional, Burdet, Frederic, additional, Hawkes, Gareth, additional, Arts, Ilja C. W., additional, Blanch, Jordi, additional, Van Soest, Johan, additional, Fernández-Real, José-Manuel, additional, Boehl, Juergen, additional, Fink, Katharina, additional, van Greevenbroek, Marleen M. J., additional, Kavousi, Maryam, additional, Minten, Michiel, additional, Prinz, Nicole, additional, Ipsen, Niels, additional, Franks, Paul W., additional, Ramos, Rafael, additional, Holl, Reinhard W., additional, Horban, Scott, additional, Duarte-Salles, Talita, additional, Tran, Van Du T., additional, Raverdy, Violeta, additional, Leal, Yenny, additional, Lenart, Adam, additional, Pearson, Ewan, additional, Sparsø, Thomas, additional, Giordano, Giuseppe N., additional, Ioannidis, Vassilios, additional, Soh, Keng, additional, Frayling, Timothy M., additional, Le Roux, Carel W., additional, and Ibberson, Mark, additional
- Published
- 2024
- Full Text
- View/download PDF
3. A Federated Database for Obesity Research: An IMI-SOPHIA Study
- Author
-
RWE/Causal inference, Child Health, Delfin, Carl, Dragan, Iulian, Kuznetsov, Dmitry, Tajes, Juan Fernandez, Smit, Femke, Coral, Daniel E, Farzaneh, Ali, Haugg, André, Hungele, Andreas, Niknejad, Anne, Hall, Christopher, Jacobs, Daan, Marek, Diana, Fraser, Diane P, Thuillier, Dorothee, Ahmadizar, Fariba, Mehl, Florence, Pattou, Francois, Burdet, Frederic, Hawkes, Gareth, Arts, Ilja C W, Blanch, Jordi, Van Soest, Johan, Fernández-Real, José-Manuel, Boehl, Juergen, Fink, Katharina, van Greevenbroek, Marleen M J, Kavousi, Maryam, Minten, Michiel, Prinz, Nicole, Ipsen, Niels, Franks, Paul W, Ramos, Rafael, Holl, Reinhard W, Horban, Scott, Duarte-Salles, Talita, Tran, Van Du T, Raverdy, Violeta, Leal, Yenny, Lenart, Adam, Pearson, Ewan, Sparsø, Thomas, Giordano, Giuseppe N, Ioannidis, Vassilios, Soh, Keng, Frayling, Timothy M, Le Roux, Carel W, Ibberson, Mark, RWE/Causal inference, Child Health, Delfin, Carl, Dragan, Iulian, Kuznetsov, Dmitry, Tajes, Juan Fernandez, Smit, Femke, Coral, Daniel E, Farzaneh, Ali, Haugg, André, Hungele, Andreas, Niknejad, Anne, Hall, Christopher, Jacobs, Daan, Marek, Diana, Fraser, Diane P, Thuillier, Dorothee, Ahmadizar, Fariba, Mehl, Florence, Pattou, Francois, Burdet, Frederic, Hawkes, Gareth, Arts, Ilja C W, Blanch, Jordi, Van Soest, Johan, Fernández-Real, José-Manuel, Boehl, Juergen, Fink, Katharina, van Greevenbroek, Marleen M J, Kavousi, Maryam, Minten, Michiel, Prinz, Nicole, Ipsen, Niels, Franks, Paul W, Ramos, Rafael, Holl, Reinhard W, Horban, Scott, Duarte-Salles, Talita, Tran, Van Du T, Raverdy, Violeta, Leal, Yenny, Lenart, Adam, Pearson, Ewan, Sparsø, Thomas, Giordano, Giuseppe N, Ioannidis, Vassilios, Soh, Keng, Frayling, Timothy M, Le Roux, Carel W, and Ibberson, Mark
- Published
- 2024
4. A Federated Database for Obesity Research:An IMI-SOPHIA Study
- Author
-
Delfin, Carl, Dragan, Iulian, Kuznetsov, Dmitry, Tajes, Juan Fernandez, Smit, Femke, Coral, Daniel E., Farzaneh, Ali, Haugg, Andre, Hungele, Andreas, Niknejad, Anne, Hall, Christopher, Jacobs, Daan, Marek, Diana, Fraser, Diane P., Thuillier, Dorothee, Ahmadizar, Fariba, Mehl, Florence, Pattou, Francois, Burdet, Frederic, Hawkes, Gareth, Arts, Ilja C. W., Blanch, Jordi, Van Soest, Johan, Fernandez-Real, Jose-Manuel, Boehl, Juergen, Fink, Katharina, van Greevenbroek, Marleen M. J., Kavousi, Maryam, Minten, Michiel, Prinz, Nicole, Ipsen, Niels, Franks, Paul W., Ramos, Rafael, Holl, Reinhard W., Horban, Scott, Duarte-Salles, Talita, Tran, Van Du T., Raverdy, Violeta, Leal, Yenny, Lenart, Adam, Pearson, Ewan, Sparso, Thomas, Giordano, Giuseppe N., Ioannidis, Vassilios, Soh, Keng, Frayling, Timothy M., Le Roux, Carel W., Ibberson, Mark, Delfin, Carl, Dragan, Iulian, Kuznetsov, Dmitry, Tajes, Juan Fernandez, Smit, Femke, Coral, Daniel E., Farzaneh, Ali, Haugg, Andre, Hungele, Andreas, Niknejad, Anne, Hall, Christopher, Jacobs, Daan, Marek, Diana, Fraser, Diane P., Thuillier, Dorothee, Ahmadizar, Fariba, Mehl, Florence, Pattou, Francois, Burdet, Frederic, Hawkes, Gareth, Arts, Ilja C. W., Blanch, Jordi, Van Soest, Johan, Fernandez-Real, Jose-Manuel, Boehl, Juergen, Fink, Katharina, van Greevenbroek, Marleen M. J., Kavousi, Maryam, Minten, Michiel, Prinz, Nicole, Ipsen, Niels, Franks, Paul W., Ramos, Rafael, Holl, Reinhard W., Horban, Scott, Duarte-Salles, Talita, Tran, Van Du T., Raverdy, Violeta, Leal, Yenny, Lenart, Adam, Pearson, Ewan, Sparso, Thomas, Giordano, Giuseppe N., Ioannidis, Vassilios, Soh, Keng, Frayling, Timothy M., Le Roux, Carel W., and Ibberson, Mark
- Abstract
Obesity is considered by many as a lifestyle choice rather than a chronic progressive disease. The Innovative Medicines Initiative (IMI) SOPHIA (Stratification of Obesity Phenotypes to Optimize Future Obesity Therapy) project is part of a momentum shift aiming to provide better tools for the stratification of people with obesity according to disease risk and treatment response. One of the challenges to achieving these goals is that many clinical cohorts are siloed, limiting the potential of combined data for biomarker discovery. In SOPHIA, we have addressed this challenge by setting up a federated database building on open-source DataSHIELD technology. The database currently federates 16 cohorts that are accessible via a central gateway. The database is multi-modal, including research studies, clinical trials, and routine health data, and is accessed using the R statistical programming environment where statistical and machine learning analyses can be performed at a distance without any disclosure of patient-level data. We demonstrate the use of the database by providing a proof-of-concept analysis, performing a federated linear model of BMI and systolic blood pressure, pooling all data from 16 studies virtually without any analyst seeing individual patient-level data. This analysis provided similar point estimates compared to a meta-analysis of the 16 individual studies. Our approach provides a benchmark for reproducible, safe federated analyses across multiple study types provided by multiple stakeholders.
- Published
- 2024
5. Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue
- Author
-
Caputo, Tiziana, Tran, Van Du T., Bararpour, Nasim, Winkler, Carine, Aguileta, Gabriela, Trang, Khanh Bao, Giordano Attianese, Greta M. P., Wilson, Anne, Thomas, Aurelien, Pagni, Marco, Guex, Nicolas, Desvergne, Béatrice, and Gilardi, Federica
- Published
- 2021
- Full Text
- View/download PDF
6. Multi-omics subgroups associated with glycaemic deterioration in type 2 diabetes: an IMI-RHAPSODY Study.
- Author
-
Shiying Li, Dragan, Iulian, Tran, Van Du T., Chun Ho Fung, Kuznetsov, Dmitry, Hansen, Michael K., Beulens, Joline W. J., t Hart, Leen M., Slieker, Roderick C., Donnelly, Louise A., Gerl, Mathias J., Klose, Christian, Mehl, Florence, Simons, Kai, Elders, Petra J. M., Pearson, Ewan R., Rutter, Guy A., and Ibberson, Mark
- Subjects
TYPE 2 diabetes ,MULTIOMICS ,INTERLEUKIN receptors ,BLOOD lipids ,INSULIN ,INSULIN sensitivity ,INSULIN aspart - Abstract
Introduction: Type 2 diabetes (T2D) onset, progression and outcomes differ substantially between individuals. Multi-omics analyses may allow a deeper understanding of these differences and ultimately facilitate personalised treatments. Here, in an unsupervised "bottom-up" approach, we attempt to group T2D patients based solely on -omics data generated from plasma. Methods: Circulating plasma lipidomic and proteomic data from two independent clinical cohorts, Hoorn Diabetes Care System (DCS) and Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS), were analysed using Similarity Network Fusion. The resulting patient network was analysed with Logistic and Cox regression modelling to explore relationships between plasma -omic profiles and clinical characteristics. Results: From a total of 1,134 subjects in the two cohorts, levels of 180 circulating plasma lipids and 1195 proteins were used to separate patients into two subgroups. These differed in terms of glycaemic deterioration (Hazard Ratio=0.56;0.73), insulin sensitivity and secretion (C-peptide, p=3.7e-11;2.5e-06, DCS and GoDARTS, respectively; Homeostatic model assessment 2 (HOMA2)-B; -IR; -S, p=0.0008;4.2e-11;1.1e-09, only in DCS). The main molecular signatures separating the two groups included triacylglycerols, sphingomyelin, testican-1 and interleukin 18 receptor. Conclusions: Using an unsupervised network-based fusion method on plasma lipidomics and proteomics data from two independent cohorts, we were able to identify two subgroups of T2D patients differing in terms of disease severity. The molecular signatures identified within these subgroups provide insights into disease mechanisms and possibly new prognostic markers for T2D. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
7. An in vitro approach to understand contribution of kidney cells to human urinary extracellular vesicles
- Author
-
Barreiro, Karina, primary, Lay, Abigail C., additional, Leparc, German, additional, Tran, Van Du T., additional, Rosler, Marcel, additional, Dayalan, Lusyan, additional, Burdet, Frederic, additional, Ibberson, Mark, additional, Coward, Richard J. M., additional, Huber, Tobias B., additional, Krämer, Bernhard K., additional, Delic, Denis, additional, and Holthofer, Harry, additional
- Published
- 2023
- Full Text
- View/download PDF
8. On permuted super-secondary structures of transmembrane β-barrel proteins
- Author
-
Tran, Van Du T., Chassignet, Philippe, and Steyaert, Jean-Marc
- Published
- 2014
- Full Text
- View/download PDF
9. Using in vivo transcriptomics and RNA enrichment to identify genes involved in virulence of Candida glabrata
- Author
-
Schrevens, Sanne, primary, Durandau, Eric, additional, Tran, Van Du T., additional, and Sanglard, Dominique, additional
- Published
- 2022
- Full Text
- View/download PDF
10. Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation
- Author
-
Lemberg, Christina, de San Vicente, Kontxi Martinez, Fróis-Martins, Ricardo, Altmeier, Simon, Tran, Van Du T, Mertens, Sarah, Amorim-Vaz, Sara, Rai, Laxmi Shanker, d’Enfert, Christophe, Pagni, Marco, Sanglard, Dominique, LeibundGut-Landmann, Salomé, Universität Zürich [Zürich] = University of Zurich (UZH), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Institute of Microbiology [University of Lausanne] (IMUL), Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Biologie et Pathogénicité fongiques - Fungal Biology and Pathogenicity (BPF), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swiss National Science Foundation to SLL (grants N˚ 310030_166206, CRSII5_173863, 310030_166206, CRSII5_173863 and CRSII3_141848), Fondation pour la Recherche Médicale (FRM, DBF20160635719), Swiss Federal Government, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 812969,H2020-MSCA-ITN-2018,FunHoMic(2019), University of Zurich, Krysan, Damian J, and LeibundGut-Landmann, Salomé
- Subjects
2403 Immunology ,Virulence ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,2404 Microbiology ,Immunology ,2405 Parasitology ,Mouth Mucosa ,Microbiology ,Fungal Proteins ,Mice ,1311 Genetics ,Candidiasis, Oral ,Virology ,Candida albicans ,1312 Molecular Biology ,2406 Virology ,Genetics ,570 Life sciences ,biology ,Animals ,Parasitology ,Symbiosis ,Molecular Biology ,[SDV.AEN]Life Sciences [q-bio]/Food and Nutrition ,10244 Institute of Virology - Abstract
International audience; As part of the human microbiota, the fungus Candida albicans colonizes the oral cavity and other mucosal surfaces of the human body. Commensalism is tightly controlled by complex interactions of the fungus and the host to preclude fungal elimination but also fungal overgrowth and invasion, which can result in disease. As such, defects in antifungal T cell immunity render individuals susceptible to oral thrush due to interrupted immunosurveillance of the oral mucosa. The factors that promote commensalism and ensure persistence of C. albicans in a fully immunocompetent host remain less clear. Using an experimental model of C. albicans oral colonization in mice we explored fungal determinants of commensalism in the oral cavity. Transcript profiling of the oral isolate 101 in the murine tongue tissue revealed a characteristic metabolic profile tailored to the nutrient poor conditions in the stratum corneum of the epithelium where the fungus resides. Metabolic adaptation of isolate 101 was also reflected in enhanced nutrient acquisition when grown on oral mucosa substrates. Persistent colonization of the oral mucosa by C. albicans also correlated inversely with the capacity of the fungus to induce epithelial cell damage and to elicit an inflammatory response. Here we show that these immune evasive properties of isolate 101 are explained by a strong attenuation of a number of virulence genes, including those linked to filamentation. De-repression of the hyphal program by deletion or conditional repression of NRG1 abolished the commensal behaviour of isolate 101, thereby establishing a central role of this factor in the commensal lifestyle of C. albicans in the oral niche of the host.Author summary : The oral microbiota represents an important part of the human microbiota and includes several hundreds to several thousands of bacterial and fungal species. One of the most prominent fungus colonizing the oral cavity is the yeast Candida albicans. While the presence of C. albicans usually remains unnoticed, the fungus can under certain circumstances cause lesions on the lining of the mouth referred to as oral thrush or contribute to other common oral diseases such as caries. Maintaining C. albicans commensalism in the oral mucosa is therefore of utmost importance for oral health and overall wellbeing. While overt fungal growth and disease is limited by immunosurveillance mechanisms during homeostasis, C. albicans strives to survive and evades elimination from the host. Here, we show that while commensalism in the oral cavity is characterized by a restricted fungal virulence and hyphal program, enforcing filamentation in a commensal isolate is sufficient for driving pathogenicity and fungus-induced inflammation in the oral mucosa thwarting persistent colonization. Our results further support a critical role for specialized nutrient acquisition allowing the fungus to thrive in the nutrient poor environment of the squamous epithelium. Together, this work revealed key determinants of C. albicans commensalism in the oral niche.
- Published
- 2022
11. Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation
- Author
-
Krysan, Damian J, Krysan, D J ( Damian J ), Lemberg, Christina; https://orcid.org/0000-0003-4327-3394, de San Vicente, Kontxi Martinez; https://orcid.org/0000-0003-3320-7035, Fróis-Martins, Ricardo, Altmeier, Simon; https://orcid.org/0000-0003-2514-0299, Tran, Van Du T; https://orcid.org/0000-0003-2074-5029, Mertens, Sarah, Amorim-Vaz, Sara, Rai, Laxmi Shanker; https://orcid.org/0000-0002-7974-0196, d'Enfert, Christophe; https://orcid.org/0000-0002-6235-3886, Pagni, Marco, Sanglard, Dominique; https://orcid.org/0000-0002-5244-4178, LeibundGut-Landmann, Salomé; https://orcid.org/0000-0002-5724-4837, Krysan, Damian J, Krysan, D J ( Damian J ), Lemberg, Christina; https://orcid.org/0000-0003-4327-3394, de San Vicente, Kontxi Martinez; https://orcid.org/0000-0003-3320-7035, Fróis-Martins, Ricardo, Altmeier, Simon; https://orcid.org/0000-0003-2514-0299, Tran, Van Du T; https://orcid.org/0000-0003-2074-5029, Mertens, Sarah, Amorim-Vaz, Sara, Rai, Laxmi Shanker; https://orcid.org/0000-0002-7974-0196, d'Enfert, Christophe; https://orcid.org/0000-0002-6235-3886, Pagni, Marco, Sanglard, Dominique; https://orcid.org/0000-0002-5244-4178, and LeibundGut-Landmann, Salomé; https://orcid.org/0000-0002-5724-4837
- Abstract
As part of the human microbiota, the fungus Candida albicans colonizes the oral cavity and other mucosal surfaces of the human body. Commensalism is tightly controlled by complex interactions of the fungus and the host to preclude fungal elimination but also fungal overgrowth and invasion, which can result in disease. As such, defects in antifungal T cell immunity render individuals susceptible to oral thrush due to interrupted immunosurveillance of the oral mucosa. The factors that promote commensalism and ensure persistence of C. albicans in a fully immunocompetent host remain less clear. Using an experimental model of C. albicans oral colonization in mice we explored fungal determinants of commensalism in the oral cavity. Transcript profiling of the oral isolate 101 in the murine tongue tissue revealed a characteristic metabolic profile tailored to the nutrient poor conditions in the stratum corneum of the epithelium where the fungus resides. Metabolic adaptation of isolate 101 was also reflected in enhanced nutrient acquisition when grown on oral mucosa substrates. Persistent colonization of the oral mucosa by C. albicans also correlated inversely with the capacity of the fungus to induce epithelial cell damage and to elicit an inflammatory response. Here we show that these immune evasive properties of isolate 101 are explained by a strong attenuation of a number of virulence genes, including those linked to filamentation. De-repression of the hyphal program by deletion or conditional repression of NRG1 abolished the commensal behaviour of isolate 101, thereby establishing a central role of this factor in the commensal lifestyle of C. albicans in the oral niche of the host.
- Published
- 2022
12. Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation
- Author
-
Lemberg, Christina, primary, de San Vicente, Kontxi Martinez, additional, Fróis-Martins, Ricardo, additional, Altmeier, Simon, additional, Tran, Van Du T., additional, Amorim-Vaz, Sara, additional, Rai, Laxmi Shanker, additional, d’Enfert, Christophe, additional, Pagni, Marco, additional, Sanglard, Dominique, additional, and LeibundGut-Landmann, Salomé, additional
- Published
- 2021
- Full Text
- View/download PDF
13. Using in vivotranscriptomics and RNA enrichment to identify genes involved in virulence of Candida glabrata
- Author
-
Schrevens, Sanne, Durandau, Eric, Tran, Van Du T., and Sanglard, Dominique
- Abstract
ABSTRACTCandidaspecies are the most commonly isolated opportunistic fungal pathogens in humans. Candida albicanscauses most of the diagnosed infections, closely followed by Candida glabrata. C. albicansis well studied, and many genes have been shown to be important for infection and colonization of the host. It is however less clear how C. glabratainfects the host. With the help of fungal RNA enrichment, we here investigated for the first time the transcriptomic profile of C. glabrataduring urinary tract infection (UTI) in mice. In the UTI model, bladders and kidneys are major target organs and therefore fungal transcriptomes were addressed in these organs. Our results showed that, next to adhesins and proteases, nitrogen metabolism and regulation play a vital role during C. glabrataUTI. Genes involved in nitrogen metabolism were upregulated and among them we show that DUR1,2(urea amidolyase) and GAP1(amino acid permease) were important for virulence. Furthermore, we confirmed the importance of the glyoxylate cycle in the host and identified MLS1(malate synthase) as an important gene necessary for C. glabratavirulence. In conclusion, our study shows with the support of in vivotranscriptomics how C. glabrataadapts to host conditions.
- Published
- 2022
- Full Text
- View/download PDF
14. Function Analysis of MBF1, a Factor Involved in the Response to Amino Acid Starvation and Virulence in Candida albicans
- Author
-
Amorim-Vaz, Sara, primary, Coste, Alix T., additional, Tran, Van Du T., additional, Pagni, Marco, additional, and Sanglard, Dominique, additional
- Published
- 2021
- Full Text
- View/download PDF
15. MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
- Author
-
Moretti, Sébastien, primary, Tran, Van Du T, additional, Mehl, Florence, additional, Ibberson, Mark, additional, and Pagni, Marco, additional
- Published
- 2020
- Full Text
- View/download PDF
16. Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue
- Author
-
Caputo, Tiziana, primary, Tran, Van Du T., additional, Bararpour, Nasim, additional, Winkler, Carine, additional, Aguileta, Gabriela, additional, Trang, Khanh Bao, additional, Giordano Attianese, Greta M. P., additional, Wilson, Anne, additional, Thomas, Aurelien, additional, Pagni, Marco, additional, Guex, Nicolas, additional, Desvergne, Béatrice, additional, and Gilardi, Federica, additional
- Published
- 2020
- Full Text
- View/download PDF
17. Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
- Author
-
Kirchner, Florian R., primary, Littringer, Katharina, additional, Altmeier, Simon, additional, Tran, Van Du T., additional, Schönherr, Franziska, additional, Lemberg, Christina, additional, Pagni, Marco, additional, Sanglard, Dominique, additional, Joller, Nicole, additional, and LeibundGut-Landmann, Salomé, additional
- Published
- 2019
- Full Text
- View/download PDF
18. Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis
- Author
-
Tran, Van Du T, primary, Moretti, Sébastien, additional, Coste, Alix T, additional, Amorim-Vaz, Sara, additional, Sanglard, Dominique, additional, and Pagni, Marco, additional
- Published
- 2018
- Full Text
- View/download PDF
19. MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.
- Author
-
Moretti, Sébastien, Tran, Van Du T, Mehl, Florence, Ibberson, Mark, and Pagni, Marco
- Published
- 2021
- Full Text
- View/download PDF
20. Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis
- Author
-
Tran, Van Du T., primary, Moretti, Sébastien, additional, Coste, Alix T., additional, Amorim-Vaz, Sara, additional, Sanglard, Dominique, additional, and Pagni, Marco, additional
- Published
- 2017
- Full Text
- View/download PDF
21. Comparative Genomics of Two Sequential Candida glabrata Clinical Isolates
- Author
-
Vale-Silva, Luis, primary, Beaudoing, Emmanuel, additional, Tran, Van Du T, additional, and Sanglard, Dominique, additional
- Published
- 2017
- Full Text
- View/download PDF
22. Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis.
- Author
-
Tran, Van Du T, Moretti, Sébastien, Coste, Alix T, Amorim-Vaz, Sara, Sanglard, Dominique, and Pagni, Marco
- Subjects
- *
GENES , *BIOINFORMATICS , *MICE , *METABOLISM - Abstract
Motivation Genome-scale metabolic networks and transcriptomic data represent complementary sources of knowledge about an organism's metabolism, yet their integration to achieve biological insight remains challenging. Results We investigate here condition-specific series of metabolic sub-networks constructed by successively removing genes from a comprehensive network. The optimal order of gene removal is deduced from transcriptomic data. The sub-networks are evaluated via a fitness function, which estimates their degree of alteration. We then consider how a gene set, i.e. a group of genes contributing to a common biological function, is depleted in different series of sub-networks to detect the difference between experimental conditions. The method, named metaboGSE, is validated on public data for Yarrowia lipolytica and mouse. It is shown to produce GO terms of higher specificity compared to popular gene set enrichment methods like GSEA or topGO. Availability and implementation The metaboGSE R package is available at https://CRAN.R-project.org/package=metaboGSE. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
23. Integrative Transcriptome and Proteome Profiling of Insulin-Resistant Kidney Cell Models and Patient Biopsies Reveals Common and Cell Type-Specific Mechanisms Underpinning Diabetic Kidney Disease
- Author
-
Coward, Richard, Lay, Abigail C., Tran, Van Du T., Nair, Viji, Betin, Virginie M., Burdet, Frédéric, Mehl, Florence, Kryvokhyzha, Dmytro, Ahmad, Abrar, Lewis, Philip A., Wilson, Marieangela C., Menon, Rajasree, Otto, Edgar A., Heesom, Kate J., Looker, Helen C., Nelson, Robert G., Ju, Wenjun, Kretzler, Matthias, Satchell, Simon C., and Gomez, Maria F.
- Published
- 2023
- Full Text
- View/download PDF
24. RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection
- Author
-
Tran, Van Du T., primary, De Coi, Niccolò, additional, Feuermann, Marc, additional, Schmid-Siegert, Emanuel, additional, Băguţ, Elena-Tatiana, additional, Mignon, Bernard, additional, Waridel, Patrice, additional, Peter, Corinne, additional, Pradervand, Sylvain, additional, Pagni, Marco, additional, and Monod, Michel, additional
- Published
- 2016
- Full Text
- View/download PDF
25. Detection of generic differential RNA processing events from RNA-seq data
- Author
-
Tran, Van Du T, primary, Souiai, Oussema, additional, Romero-Barrios, Natali, additional, Crespi, Martin, additional, and Gautheret, Daniel, additional
- Published
- 2016
- Full Text
- View/download PDF
26. Supersecondary structure prediction of transmembrane beta-barrel proteins
- Author
-
Tran, Van Du T, Chassignet, Philippe, Steyaert, Jean-Marc, Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Algorithms and Models for Integrative Biology (AMIB ), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Recherche en Informatique (LRI), Laboratoire d'informatique de l'École polytechnique [Palaiseau] ( LIX ), Centre National de la Recherche Scientifique ( CNRS ) -École polytechnique ( X ), Algorithms and Models for Integrative Biology ( AMIB ), Centre National de la Recherche Scientifique ( CNRS ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ) -École polytechnique ( X ) -Laboratoire de Recherche en Informatique ( LRI ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Inria Saclay - Ile de France, and Institut National de Recherche en Informatique et en Automatique ( Inria )
- Subjects
Models, Molecular ,Protein Folding ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Amino Acid Motifs ,Computational Biology ,Membrane Proteins ,Algorithms ,[ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM] - Abstract
International audience; We introduce a graph-theoretic model for predicting the supersecondary structure of transmembrane β-barrel proteins--a particular class of proteins that performs diverse important functions but it is difficult to determine their structure with experimental methods. This ab initio model resolves the protein folding problem based on pseudo-energy minimization with the aid of a simple probabilistic filter. It also allows for determining structures whose barrel follows a given permutation on the arrangement of β-strands, and allows for rapidly discriminating the transmembrane β-barrels from other kinds of proteins. The model is fairly accurate, robust and can be run very efficiently on PC-like computers, thus proving useful for genome screening.
- Published
- 2013
27. RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans
- Author
-
Amorim-Vaz, Sara, primary, Tran, Van Du T., additional, Pradervand, Sylvain, additional, Pagni, Marco, additional, Coste, Alix T., additional, and Sanglard, Dominique, additional
- Published
- 2015
- Full Text
- View/download PDF
28. miRBoost: boosting support vector machines for microRNA precursor classification
- Author
-
Tran, Van Du T., primary, Tempel, Sebastien, additional, Zerath, Benjamin, additional, Zehraoui, Farida, additional, and Tahi, Fariza, additional
- Published
- 2015
- Full Text
- View/download PDF
29. A graph-theoretic approach for classification and structure prediction of transmembrane β-barrel proteins
- Author
-
Tran, Van Du T, primary, Chassignet, Philippe, additional, Sheikh, Saad, additional, and Steyaert, Jean-Marc, additional
- Published
- 2012
- Full Text
- View/download PDF
30. RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In VivoApplied to the Fungus Candida albicans
- Author
-
Amorim-Vaz, Sara, Tran, Van Du T., Pradervand, Sylvain, Pagni, Marco, Coste, Alix T., and Sanglard, Dominique
- Abstract
ABSTRACTIn vivotranscriptional analyses of microbial pathogens are often hampered by low proportions of pathogen biomass in host organs, hindering the coverage of full pathogen transcriptome. We aimed to address the transcriptome profiles of Candida albicans, the most prevalent fungal pathogen in systemically infected immunocompromised patients, during systemic infection in different hosts. We developed a strategy for high-resolution quantitative analysis of the C. albicanstranscriptome directly from early and late stages of systemic infection in two different host models, mouse and the insect Galleria mellonella. Our results show that transcriptome sequencing (RNA-seq) libraries were enriched for fungal transcripts up to 1,600-fold using biotinylated bait probes to capture C. albicanssequences. This enrichment biased the read counts of only ~3% of the genes, which can be identified and removed based on a prioricriteria. This allowed an unprecedented resolution of C. albicanstranscriptome in vivo, with detection of over 86% of its genes. The transcriptional response of the fungus was surprisingly similar during infection of the two hosts and at the two time points, although some host- and time point-specific genes could be identified. Genes that were highly induced during infection were involved, for instance, in stress response, adhesion, iron acquisition, and biofilm formation. Of the in vivo-regulated genes, 10% are still of unknown function, and their future study will be of great interest. The fungal RNA enrichment procedure used here will help a better characterization of the C. albicansresponse in infected hosts and may be applied to other microbial pathogens.IMPORTANCEUnderstanding the mechanisms utilized by pathogens to infect and cause disease in their hosts is crucial for rational drug development. Transcriptomic studies may help investigations of these mechanisms by determining which genes are expressed specifically during infection. This task has been difficult so far, since the proportion of microbial biomass in infected tissues is often extremely low, thus limiting the depth of sequencing and comprehensive transcriptome analysis. Here, we adapted a technology to capture and enrich C. albicansRNA, which was next used for deep RNA sequencing directly from infected tissues from two different host organisms. The high-resolution transcriptome revealed a large number of genes that were so far unknown to participate in infection, which will likely constitute a focus of study in the future. More importantly, this method may be adapted to perform transcript profiling of any other microbes during host infection or colonization.
- Published
- 2015
- Full Text
- View/download PDF
31. Using <italic>in vivo</italic> transcriptomics and RNA enrichment to identify genes involved in virulence of <italic>Candida glabrata</italic>.
- Author
-
Schrevens, Sanne, Durandau, Eric, Tran, Van Du T., and Sanglard, Dominique
- Abstract
Abstract
Candida species are the most commonly isolated opportunistic fungal pathogens in humans. These species exhibit very different infection strategies, since they acquired pathogenesis independently throughout evolution.Candida albicans causes most of the diagnosed infections, closely followed byCandida glabrata .C. albicans is well studied, and many genes have been shown to be important for infection and colonization of the host. It is, however, less clear howC. glabrata infects the host. With the help of a fungal RNA enrichment technology, we here investigated for the first time the transcriptomic profile ofC. glabrata during urinary tract infection (UTI) in mice in order to determine which pathways and genes are regulated in the host compared toin vitro conditions. In the UTI model, bladders and kidneys are major target organs and therefore fungal transcriptomes were addressed in these organs. Our results showed that, next to adhesins and proteases, which seem to have a specific expression profile that may be linked to the niche in which the fungus grows, nitrogen metabolism and regulation play a vital role duringC. glabrata UTI. Genes involved in nitrogen metabolism were upregulated and among them we show thatDUR1,2 (urea amidolyase) andGAP1 (amino acid permease) are important for virulence. Furthermore, we confirmed the importance of the glyoxylate cycle in the host and identifiedMLS1 (malate synthase) as an important gene necessary forC. glabrata virulence. In conclusion, our study shows with the support ofin vivo transcriptomics howC. glabrata adapts to host conditions. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
32. Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation.
- Author
-
Lemberg C, Martinez de San Vicente K, Fróis-Martins R, Altmeier S, Tran VDT, Mertens S, Amorim-Vaz S, Rai LS, d'Enfert C, Pagni M, Sanglard D, and LeibundGut-Landmann S
- Subjects
- Animals, Fungal Proteins, Mice, Mouth Mucosa microbiology, Symbiosis, Virulence, Candida albicans, Candidiasis, Oral microbiology
- Abstract
As part of the human microbiota, the fungus Candida albicans colonizes the oral cavity and other mucosal surfaces of the human body. Commensalism is tightly controlled by complex interactions of the fungus and the host to preclude fungal elimination but also fungal overgrowth and invasion, which can result in disease. As such, defects in antifungal T cell immunity render individuals susceptible to oral thrush due to interrupted immunosurveillance of the oral mucosa. The factors that promote commensalism and ensure persistence of C. albicans in a fully immunocompetent host remain less clear. Using an experimental model of C. albicans oral colonization in mice we explored fungal determinants of commensalism in the oral cavity. Transcript profiling of the oral isolate 101 in the murine tongue tissue revealed a characteristic metabolic profile tailored to the nutrient poor conditions in the stratum corneum of the epithelium where the fungus resides. Metabolic adaptation of isolate 101 was also reflected in enhanced nutrient acquisition when grown on oral mucosa substrates. Persistent colonization of the oral mucosa by C. albicans also correlated inversely with the capacity of the fungus to induce epithelial cell damage and to elicit an inflammatory response. Here we show that these immune evasive properties of isolate 101 are explained by a strong attenuation of a number of virulence genes, including those linked to filamentation. De-repression of the hyphal program by deletion or conditional repression of NRG1 abolished the commensal behaviour of isolate 101, thereby establishing a central role of this factor in the commensal lifestyle of C. albicans in the oral niche of the host., Competing Interests: We have read the journal’s policy and the authors of this manuscript have the following competing interests:Simon Altmeier is now an employee of Novartis. His findings presented in this paper are solely his views and are independent from Novartis work. The other authors have no competing interest to declare.
- Published
- 2022
- Full Text
- View/download PDF
33. Comparative Genomics of Two Sequential Candida glabrata Clinical Isolates.
- Author
-
Vale-Silva L, Beaudoing E, Tran VDT, and Sanglard D
- Subjects
- Chromosomes, Fungal genetics, Fungal Proteins genetics, Genetic Variation, Genome, Fungal genetics, Humans, INDEL Mutation genetics, Molecular Sequence Annotation, Nucleotides genetics, Polymorphism, Single Nucleotide genetics, Candida glabrata genetics, Candida glabrata isolation & purification, Genomics
- Abstract
Candida glabrata is an important fungal pathogen which develops rapid antifungal resistance in treated patients. It is known that azole treatments lead to antifungal resistance in this fungal species and that multidrug efflux transporters are involved in this process. Specific mutations in the transcriptional regulator PDR1 result in upregulation of the transporters. In addition, we showed that the PDR1 mutations can contribute to enhance virulence in animal models. In this study, we were interested to compare genomes of two specific C. glabrata -related isolates, one of which was azole susceptible (DSY562) while the other was azole resistant (DSY565). DSY565 contained a PDR1 mutation (L280F) and was isolated after a time-lapse of 50 d of azole therapy. We expected that genome comparisons between both isolates could reveal additional mutations reflecting host adaptation or even additional resistance mechanisms. The PacBio technology used here yielded 14 major contigs (sizes 0.18-1.6 Mb) and mitochondrial genomes from both DSY562 and DSY565 isolates that were highly similar to each other. Comparisons of the clinical genomes with the published CBS138 genome indicated important genome rearrangements, but not between the clinical strains. Among the unique features, several retrotransposons were identified in the genomes of the investigated clinical isolates. DSY562 and DSY565 each contained a large set of adhesin-like genes (101 and 107, respectively), which exceed by far the number of reported adhesins (63) in the CBS138 genome. Comparison between DSY562 and DSY565 yielded 17 nonsynonymous SNPs (among which the was the expected PDR1 mutation) as well as small size indels in coding regions (11) but mainly in adhesin-like genes. The genomes contained a DNA mismatch repair allele of MSH2 known to be involved in the so-called hyper-mutator phenotype of this yeast species and the number of accumulated mutations between both clinical isolates is consistent with the presence of a MSH2 defect. In conclusion, this study is the first to compare genomes of C. glabrata sequential clinical isolates using the PacBio technology as an approach. The genomes of these isolates taken in the same patient at two different time points exhibited limited variations, even if submitted to the host pressure., (Copyright © 2017 Vale-Silva et al.)
- Published
- 2017
- Full Text
- View/download PDF
34. Supersecondary structure prediction of transmembrane beta-barrel proteins.
- Author
-
Tran Vdu T, Chassignet P, and Steyaert JM
- Subjects
- Algorithms, Amino Acid Motifs, Computational Biology methods, Protein Folding, Membrane Proteins chemistry, Models, Molecular
- Abstract
We introduce a graph-theoretic model for predicting the supersecondary structure of transmembrane β-barrel proteins--a particular class of proteins that performs diverse important functions but it is difficult to determine their structure with experimental methods. This ab initio model resolves the protein folding problem based on pseudo-energy minimization with the aid of a simple probabilistic filter. It also allows for determining structures whose barrel follows a given permutation on the arrangement of β-strands, and allows for rapidly discriminating the transmembrane β-barrels from other kinds of proteins. The model is fairly accurate, robust and can be run very efficiently on PC-like computers, thus proving useful for genome screening.
- Published
- 2013
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.