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4. Anti-Human Herpesvirus 6 A/B Antibodies Titers Correlate With Multiple Sclerosis-Associated Retrovirus Envelope Expression

Author

Pérez-Pérez, Silvia, primary, Domínguez-Mozo, María I., additional, García-Martínez, M. Ángel, additional, García-Frontini, M. Celeste, additional, Villarrubia, Noelia, additional, Costa-Frossard, Lucienne, additional, Villar, Luisa M., additional, Arroyo, Rafael, additional, and Álvarez-Lafuente, Roberto, additional

Published
2021
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11. Erratum to: Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps (Nature Genetics, (2016), 48, 11, (1303-1312), 10.1038/ng.3668)

Author

Iotchkova, V., Huang, J., Morris, J. A., Jain, D., Barbieri, C., Ukovich, Walter, Min, J. L., Chen, L., Astle, W., Cocca, M., Deelen, P., Elding, H., Farmaki, A. -E., Franklin, C. S., Franberg, M., Gaunt, T. R., Hofman, A., Jiang, T., Kleber, M. E., Lachance, G., Luan, J., Malerba, G., Matchan, A., Mead, D., Memari, Y., Ntalla, I., Panoutsopoulou, K., Pazoki, R., Perry, J. R. B., Rivadeneira, F., Sabater-Lleal, M., Sennblad, B., Shin, S. -Y., Southam, L., Traglia, M., van Dijk, F., van Leeuwen, E. M., Zaza, G., Zhang, W., Amin, N., Butterworth, A., Chambers, J. C., Dedoussis, G., Dehghan, A., Franco, O. H., Franke, L., Frontini, M., Gambaro, G., Gasparini, P., Hamsten, A., Isaacs, A., Kooner, J. S., Kooperberg, C., Langenberg, C., Marz, W., Scott, R. A., Swertz, M. A., Toniolo, D., Uitterlinden, A. G., van Duijn, C. M., Watkins, H., Zeggini, E., Maurano, M. T., Timpson, N. J., Reiner, A. P., Auer, P. L., Soranzo, N., Iotchkova, V., Huang, J., Morris, J. A., Jain, D., Barbieri, C., Ukovich, Walter, Min, J. L., Chen, L., Astle, W., Cocca, M., Deelen, P., Elding, H., Farmaki, A. -E., Franklin, C. S., Franberg, M., Gaunt, T. R., Hofman, A., Jiang, T., Kleber, M. E., Lachance, G., Luan, J., Malerba, G., Matchan, A., Mead, D., Memari, Y., Ntalla, I., Panoutsopoulou, K., Pazoki, R., Perry, J. R. B., Rivadeneira, F., Sabater-Lleal, M., Sennblad, B., Shin, S. -Y., Southam, L., Traglia, M., van Dijk, F., van Leeuwen, E. M., Zaza, G., Zhang, W., Amin, N., Butterworth, A., Chambers, J. C., Dedoussis, G., Dehghan, A., Franco, O. H., Franke, L., Frontini, M., Gambaro, G., Gasparini, P., Hamsten, A., Isaacs, A., Kooner, J. S., Kooperberg, C., Langenberg, C., Marz, W., Scott, R. A., Swertz, M. A., Toniolo, D., Uitterlinden, A. G., van Duijn, C. M., Watkins, H., Zeggini, E., Maurano, M. T., Timpson, N. J., Reiner, A. P., Auer, P. L., and Soranzo, N.

Subjects
Author correction
Abstract

In the version of the article published, the surname of author Aaron Isaacs is misspelled as Issacs.

Published
2018

12. Platelet function is modified by common sequence variation in megakaryocyte super enhancers

Author

Petersen, R., Lambourne, J.J., Javierre, B.M., Grassi, L., Martens, J.H.A., Stegle, O., Richardson, S., Vallier, L., Roberts, D.J., Freson, K., Wernisch, L., Stunnenberg, H., Danesh, J., and Frontini, M.

Subjects
Molecular Biology, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries)
Abstract

Contains fulltext : 177883.pdf (Publisher’s version ) (Open Access) 12 p.

Published
2017

15. Detection of Atherosclerotic Inflammation by $^{68}$Ga-DOTATATE PET Compared to [$^{18}$F]FDG PET Imaging

Author

Tarkin, JM, Joshi, FR, Evans, NR, Chowdhury, MM, Figg, NL, Shah, AV, Starks, LT, Martin-Garrido, A, Manavaki, R, Yu, E, Kuc, RE, Grassi, L, Kreuzhuber, R, Kostadima, MA, Frontini, M, Kirkpatrick, PJ, Coughlin, PA, Gopalan, D, Fryer, TD, Buscombe, JR, Groves, AM, Ouwehand, WH, Bennett, MR, Warburton, EA, Davenport, AP, Rudd, JHF, Tarkin, Jason [0000-0002-9132-120X], Evans, Nicholas [0000-0002-7640-4701], Manavaki, Roido [0000-0002-4384-6626], Grassi, Luigi [0000-0002-6308-7540], Frontini, Mattia [0000-0001-8074-6299], Ouwehand, Willem [0000-0002-7744-1790], Bennett, Martin [0000-0002-2565-1825], Davenport, Anthony [0000-0002-2096-3117], Rudd, James [0000-0003-2243-3117], and Apollo - University of Cambridge Repository

Subjects
somatostatin receptor, positron emission tomography, inflammation, atherosclerosis, molecular imaging, macrophages
Abstract

$\textbf{Background}$ Inflammation drives atherosclerotic plaque rupture. Although inflammation can be measured using fluorine-18-labeled fluorodeoxyglucose positron emission tomography ([$^{18}$F]FDG PET), [$^{18}$F]FDG lacks cell specificity, and coronary imaging is unreliable because of myocardial spillover. $\textbf{Objectives}$ Objectives This study tested the efficacy of gallium-68-labeled DOTATATE ($^{68}$Ga-DOTATATE), a somatostatin receptor subtype-2 (SST2)-binding PET tracer, for imaging atherosclerotic inflammation. $\textbf{Methods}$ We confirmed $^{68}$Ga-DOTATATE binding in macrophages and excised carotid plaques. $^{68}$Ga-DOTATATE PET imaging was compared to [$^{18}$F]FDG PET imaging in 42 patients with atherosclerosis. $\textbf{Results}$ Target $\textit{SSTR2}$ gene expression occurred exclusively in “proinflammatory” M1 macrophages, specific $^{68}$Ga-DOTATATE ligand binding to SST$_{2}$ receptors occurred in CD68-positive macrophage-rich carotid plaque regions, and carotid $\textit{SSTR2}$ mRNA was highly correlated with in vivo $^{68}$Ga-DOTATATE PET signals (r = 0.89; 95% confidence interval [CI]: 0.28 to 0.99; p = 0.02). $^{68}$Ga-DOTATATE mean of maximum tissue-to-blood ratios (mTBR$_{max}$) correctly identified culprit versus nonculprit arteries in patients with acute coronary syndrome (median difference: 0.69; interquartile range [IQR]: 0.22 to 1.15; p = 0.008) and transient ischemic attack/stroke (median difference: 0.13; IQR: 0.07 to 0.32; p = 0.003). $^{68}$Ga-DOTATATE mTBR$_{max}$ predicted high-risk coronary computed tomography features (receiver operating characteristics area under the curve [ROC AUC]: 0.86; 95% CI: 0.80 to 0.92; p < 0.0001), and correlated with Framingham risk score (r = 0.53; 95% CI: 0.32 to 0.69; p

Published
2017

17. Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.

Author

Grassi, L., Pourfarzad, F., Ullrich, S., Merkel, A., Were, F., Carrillo-de-Santa-Pau, E., Yi, G., Hiemstra, I.H., Tool, A.T., Mul, E., Perner, J., Janssen-Megens, E.M., Berentsen, K., Kerstens, H.H.D., Habibi, E., Gut, M., Yaspo, M.L., Linser, M., Lowy, E., Datta, A., Clarke, L., Flicek, P., Vingron, M., Roos, D., Berg, T.K. van den, Heath, S., Rico, D., Frontini, M., Kostadima, M., Gut, I., Valencia, A., Ouwehand, W.H., Stunnenberg, H., Martens, J.H.A., Kuijpers, T.W., Grassi, L., Pourfarzad, F., Ullrich, S., Merkel, A., Were, F., Carrillo-de-Santa-Pau, E., Yi, G., Hiemstra, I.H., Tool, A.T., Mul, E., Perner, J., Janssen-Megens, E.M., Berentsen, K., Kerstens, H.H.D., Habibi, E., Gut, M., Yaspo, M.L., Linser, M., Lowy, E., Datta, A., Clarke, L., Flicek, P., Vingron, M., Roos, D., Berg, T.K. van den, Heath, S., Rico, D., Frontini, M., Kostadima, M., Gut, I., Valencia, A., Ouwehand, W.H., Stunnenberg, H., Martens, J.H.A., and Kuijpers, T.W.

Abstract

Contains fulltext : 195014.pdf (publisher's version ) (Open Access), Neutrophils are short-lived blood cells that play a critical role in host defense against infections. To better comprehend neutrophil functions and their regulation, we provide a complete epigenetic overview, assessing important functional features of their differentiation stages from bone marrow-residing progenitors to mature circulating cells. Integration of chromatin modifications, methylation, and transcriptome dynamics reveals an enforced regulation of differentiation, for cellular functions such as release of proteases, respiratory burst, cell cycle regulation, and apoptosis. We observe an early establishment of the cytotoxic capability, while the signaling components that activate these antimicrobial mechanisms are transcribed at later stages, outside the bone marrow, thus preventing toxic effects in the bone marrow niche. Altogether, these data reveal how the developmental dynamics of the chromatin landscape orchestrate the daily production of a large number of neutrophils required for innate host defense and provide a comprehensive overview of differentiating human neutrophils.

Published
2018

18. Erratum to: Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps

Author

Iotchkova, V. (Valentina), Huang, J. (Jie), Morris, J.A. (John A), Jain, D. (Deepti), Barbieri, C. (Caterina), Walter, K. (Klaudia), Min, J. (Josine), Chen, L. (Lu), Astle, W. (William), Cocca, M. (Massimilian), Deelen, P. (Patrick), Elding, H. (Heather), Farmaki, A.-E. (Aliki-Eleni), Franklin, C.S. (Christopher), Frånberg, M. (Mattias), Gaunt, T.R. (Tom), Hofman, A. (Albert), Jiang, T. (Tao), Kleber, M.E. (Marcus), Lachance, G. (Genevieve), Luan, J., Malerba, G. (Giovanni), Matchan, A. (Angela), Mead, D. (Daniel), Memari, Y. (Yasin), Ntalla, I. (Ioanna), Panoutsopoulou, K. (Kalliope), Pazoki, R. (Raha), Perry, J.R.B. (John R B), Rivadeneira Ramirez, F. (Fernando), Sabater-Lleal, M. (Maria), Sennblad, B. (Bengt), Shin, S.-Y., Southam, L. (Lorraine), Traglia, M. (Michela), Dijk, F. (Freerk) van, Leeuwen, E.M. (Elisa) van, Zaza, G. (Gianluigi), Zhang, W. (Weihua), Amin, N. (Najaf), Butterworth, A. (Adam), Chambers, J.C. (John C), Dedoussis, G.V. (George), Dehghan, A. (Abbas), Franco, O.H. (Oscar), Franke, L. (Lude), Frontini, M. (Mattia), Gambaro, G. (Giovanni), Gasparini, P. (Paolo), Hamsten, A. (Anders), Isaacs, A.J. (Aaron), Kooner, J.S. (Jaspal S.), Kooperberg, C. (Charles), Langenberg, C. (Claudia), März, W. (Winfried), Scott, R.A. (Robert), Swertz, M.A. (Morris A), Toniolo, D. (Daniela), Uitterlinden, A.G. (André), Duijn, C.M. (Cornelia) van, Watkins, H. (Hugh), Zeggini, E. (Eleftheria), Maurano, M.T. (Matthew T.), Timpson, N.J. (Nicholas), Reiner, A.P. (Alexander P), Auer, P.L. (Paul L), Soranzo, N. (Nicole), Iotchkova, V. (Valentina), Huang, J. (Jie), Morris, J.A. (John A), Jain, D. (Deepti), Barbieri, C. (Caterina), Walter, K. (Klaudia), Min, J. (Josine), Chen, L. (Lu), Astle, W. (William), Cocca, M. (Massimilian), Deelen, P. (Patrick), Elding, H. (Heather), Farmaki, A.-E. (Aliki-Eleni), Franklin, C.S. (Christopher), Frånberg, M. (Mattias), Gaunt, T.R. (Tom), Hofman, A. (Albert), Jiang, T. (Tao), Kleber, M.E. (Marcus), Lachance, G. (Genevieve), Luan, J., Malerba, G. (Giovanni), Matchan, A. (Angela), Mead, D. (Daniel), Memari, Y. (Yasin), Ntalla, I. (Ioanna), Panoutsopoulou, K. (Kalliope), Pazoki, R. (Raha), Perry, J.R.B. (John R B), Rivadeneira Ramirez, F. (Fernando), Sabater-Lleal, M. (Maria), Sennblad, B. (Bengt), Shin, S.-Y., Southam, L. (Lorraine), Traglia, M. (Michela), Dijk, F. (Freerk) van, Leeuwen, E.M. (Elisa) van, Zaza, G. (Gianluigi), Zhang, W. (Weihua), Amin, N. (Najaf), Butterworth, A. (Adam), Chambers, J.C. (John C), Dedoussis, G.V. (George), Dehghan, A. (Abbas), Franco, O.H. (Oscar), Franke, L. (Lude), Frontini, M. (Mattia), Gambaro, G. (Giovanni), Gasparini, P. (Paolo), Hamsten, A. (Anders), Isaacs, A.J. (Aaron), Kooner, J.S. (Jaspal S.), Kooperberg, C. (Charles), Langenberg, C. (Claudia), März, W. (Winfried), Scott, R.A. (Robert), Swertz, M.A. (Morris A), Toniolo, D. (Daniela), Uitterlinden, A.G. (André), Duijn, C.M. (Cornelia) van, Watkins, H. (Hugh), Zeggini, E. (Eleftheria), Maurano, M.T. (Matthew T.), Timpson, N.J. (Nicholas), Reiner, A.P. (Alexander P), Auer, P.L. (Paul L), and Soranzo, N. (Nicole)

Abstract

In the version of the article published, the surname of author Aaron Isaacs is misspelled as Issacs.

Published
2018
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19. Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

Author

Ecker, S., Chen, L., Pancaldi, V., Bagger, F.O., Fernandez, J.M., Carrillo de Santa Pau, E., Juan, D., Mann, A.L., Watt, S., Casale, F.P., Sidiropoulos, N., Rapin, N., Merkel, A., Stunnenberg, H., Stegle, O., Frontini, M., Downes, K., Pastinen, T., Kuijpers, T.W., Rico, D., Valencia, A., Beck, S., Soranzo, N., Paul, D.S., and Albers, C.A.

Subjects
Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Molecular Biology
Abstract

Contains fulltext : 169675.pdf (Publisher’s version ) (Open Access) BACKGROUND: A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. RESULTS: We apply a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+CD16- monocytes, CD66b+CD16+ neutrophils, and CD4+CD45RA+ naive T cells from the same 125 healthy individuals. We discover substantially increased variability in neutrophils compared to monocytes and T cells. In neutrophils, genes with hypervariable expression are found to be implicated in key immune pathways and are associated with cellular properties and environmental exposure. We also observe increased sex-specific gene expression differences in neutrophils. Neutrophil-specific DNA methylation hypervariable sites are enriched at dynamic chromatin regions and active enhancers. CONCLUSIONS: Our data highlight the importance of transcriptional and epigenetic variability for the key role of neutrophils as the first responders to inflammatory stimuli. We provide a resource to enable further functional studies into the plasticity of immune cells, which can be accessed from: http://blueprint-dev.bioinfo.cnio.es/WP10/hypervariability .

Published
2017

20. Information recovery from low coverage whole-genome bisulfite sequencing

Author

Libertini, E., Heath, S., Hamoudi, R., Gut, M., Ziller, M., Czyz, A., Ruotti, V., Stunnenberg, H., Frontini, M., Ouwehand, W., and Meissner, A.

Subjects
food and beverages
Abstract

The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs). Using this tool, we demonstrate recovery of ∼30% of the lost DMP information content as DMCs even at very low (5X) coverage. This constitutes twice the amount that can be recovered using an existing method based on differentially methylated regions (DMRs). In addition, we explored the relationship between COMETs and haplotypes in lymphoblastoid cell lines of African and European origin. Using best fit analysis, we show COMETs to be correlated in a population-specific manner, suggesting that this type of dynamic segmentation may be useful for integrated (epi)genome-wide association studies in the future.

Published
2016

21. Fenoldopam to prevent renal replacement therapy after cardiac surgery. Design of the FENO-HSR study

Author

Landoni, G, Bove, T, Pasero, D, Comis, M, Orando, S, Pinelli, F, Guarracino, F, Corcione, A, Galdieri, N, Zucchetti, M, Maglioni, E, Biagioli, B, Pala, G, Frontini, M, Caramelli, F, Persi, B, Renzini, M, Paoletti, F, Lorini, F, Morelli, A, Alvaro, G, Bianco, R, Pittarello, D, Manzato, A, Pedersini, G, Mizzi, A, Lojacono, N, Leoncini, P, Iovino, T, Cariello, C, Baldassarri, R, Camata, A, Padua, G, Frascaroli, G, Leonardi S, Bignami, E, Zangrillo, A, Landoni G, Bove T, Pasero D, Comis M, Orando S, Pinelli F, Guarracino F, Corcione A, Galdieri N, Zucchetti M, Maglioni E, Biagioli B, Pala G, Frontini M, Caramelli F, Persi B, Renzini M, Paoletti F, Lorini F, Morelli A, Alvaro G, Bianco R, Pittarello D, Manzato A, Pedersini G, Mizzi A, Lojacono N, Leoncini P, Iovino T, Cariello C, Baldassarri R, Camata AM, Padua G, Frascaroli G, Bignami E, Zangrillo A, Landoni, G, Bove, T, Pasero, D, Comis, M, Orando, S, Pinelli, F, Guarracino, F, Corcione, A, Galdieri, N, Zucchetti, M, Maglioni, E, Biagioli, B, Pala, G, Frontini, M, Caramelli, F, Persi, B, Renzini, M, Paoletti, F, Lorini, F, Morelli, A, Alvaro, G, Bianco, R, Pittarello, D, Manzato, A, Pedersini, G, Mizzi, A, Lojacono, N, Leoncini, P, Iovino, T, Cariello, C, Baldassarri, R, Camata, A, Padua, G, Frascaroli, G, Leonardi S, Bignami, E, Zangrillo, A, Landoni G, Bove T, Pasero D, Comis M, Orando S, Pinelli F, Guarracino F, Corcione A, Galdieri N, Zucchetti M, Maglioni E, Biagioli B, Pala G, Frontini M, Caramelli F, Persi B, Renzini M, Paoletti F, Lorini F, Morelli A, Alvaro G, Bianco R, Pittarello D, Manzato A, Pedersini G, Mizzi A, Lojacono N, Leoncini P, Iovino T, Cariello C, Baldassarri R, Camata AM, Padua G, Frascaroli G, Bignami E, and Zangrillo A

Abstract

Introduction: Acute kidney injury requiring renal replacement therapy is a serious complication following cardiac surgery associated with poor clinical outcomes. Until now no drug showed nephroprotective effects. Fenoldopam is a dopamine-1 receptor agonist which seems to be effective in improving postoperative renal function. The aim of this paper is to describe the design of the FENO-HSR study, planned to assess the effect of a continuous infusion of fenoldopam in reducing the need for renal replacement therapy in patients with acute kidney injury after cardiac surgery. Methods: We're performing a double blind, placebo-controlled multicentre randomized trial in over 20 Italian hospitals. Patients who develop acute renal failure defined as R of RIFLE score following cardiac surgery are randomized to receive a 96-hours continuous infusion of either fenoldopam (0.025-0.3 µg/kg/min) or placebo. Results: The primary endpoint will be the rate of renal replacement therapy. Secondary endpoints will be: mortality, time on mechanical ventilation, length of intensive care unit and hospital stay, peak serum creatinine and the rate of acute renal failure (following the RIFLE score). Conclusions: This trial is planned to assess if fenoldopam could improve relevant outcomes in patients undergoing cardiac surgery who develop acute renal dysfunction. Results of this double-blind randomized trial could provide important insights to improve the management strategy of patients at high risk for postoperative acute kidney injury.

Published
2010

22. Fenoldopam to prevent renal replacement therapy after cardiac surgery. Design of the FENO-HSR study

Author

Landoni G, Bove T, Pasero D, Comis M, Orando S, Pinelli F, Guarracino F, Corcione A, Galdieri N, Zucchetti M, Maglioni E, Biagioli B, Pala G, Frontini M, Caramelli F, Persi B, Renzini M, Paoletti F, Lorini F, Morelli A, Alvaro G, Bianco R, Pittarello D, Manzato A, Pedersini G, Mizzi A, Lojacono N, Leoncini P, Iovino T, Cariello C, Baldassarri R, Camata AM, Padua G, Frascaroli G, Leonardi S, Bignami E, Zangrillo A, Landoni, Giovanni, Bove, T, Pasero, D, Comis, M, Orando, S, Pinelli, F, Guarracino, F, Corcione, A, Galdieri, N, Zucchetti, M, Maglioni, E, Biagioli, B, Pala, G, Frontini, M, Caramelli, F, Persi, B, Renzini, M, Paoletti, F, Lorini, L, Morelli, A, Alvaro, G, Bianco, R, Pittarello, D, Manzato, A, Pedersini, G, Mizzi, A, Lojacono, N, Leoncini, P, Iovino, T, Cariello, C, Baldassarri, R, Camata, Am, Padua, G, Frascaroli, G, Leonardi, S, Bignami, E, Zangrillo, Alberto, Landoni, G, Lorini, F, Camata, A, Leonardi S, and Zangrillo, A

Subjects
cardiac surgical procedure, Research-Article, fenoldopam, anesthesia, cardiac surgical procedures, acute renal failure, renal replacement therapy, cardiac surgery
Abstract

Introduction: Acute kidney injury requiring renal replacement therapy is a serious complication following cardiac surgery associated with poor clinical outcomes. Until now no drug showed nephroprotective effects. Fenoldopam is a dopamine-1 receptor agonist which seems to be effective in improving postoperative renal function. The aim of this paper is to describe the design of the FENO-HSR study, planned to assess the effect of a continuous infusion of fenoldopam in reducing the need for renal replacement therapy in patients with acute kidney injury after cardiac surgery. Methods: We're performing a double blind, placebo-controlled multicentre randomized trial in over 20 Italian hospitals. Patients who develop acute renal failure defined as R of RIFLE score following cardiac surgery are randomized to receive a 96-hours continuous infusion of either fenoldopam (0.025-0.3 µg/kg/min) or placebo. Results: The primary endpoint will be the rate of renal replacement therapy. Secondary endpoints will be: mortality, time on mechanical ventilation, length of intensive care unit and hospital stay, peak serum creatinine and the rate of acute renal failure (following the RIFLE score). Conclusions: This trial is planned to assess if fenoldopam could improve relevant outcomes in patients undergoing cardiac surgery who develop acute renal dysfunction. Results of this double-blind randomized trial could provide important insights to improve the management strategy of patients at high risk for postoperative acute kidney injury.

Published
2010

23. 1-year outcomes after transfemoral transcatheter or surgical aortic valve replacement: Results from the Italian OBSERVANT study

Author

Tamburino, C, Barbanti, M, D'Errigo, P, Ranucci, M, Onorati, F, Covello, R, Santini, F, Rosato, S, Santoro, G, Fusco, D, Grossi, C, Seccareccia, F, Marra, S, D'Amico, M, Gaita, F, Moretti, C, De Benedictis, M, Aranzulla, T, Pistis, G, Reale, M, Bedogni, F, Brambilla, N, Ferrario, M, Ferrero, L, Vicinelli, P, Colombo, A, Chieffo, A, Ferrari, A, Inglese, L, Casilli, F, Ettori, F, Frontini, M, Antona, C, Piccaluga, E, Klugmann, S, De Marco, F, Tespili, M, Saino, A, Leonzi, O, Rizzi, A, Grisolia, E, Franceschini Grisolia, E, Isabella, G, Fraccaro, C, Bernardi, G, Bisceglia, T, Armellini, I, Vischi, M, Parodi, E, Vignali, L, Ardissimo, D, Marzocchi, A, Marrozzini, C, Cremonesi, A, Colombo, F, Giannini, C, Pierli, C, Iadanza, A, Meucci, F, Berti, S, Mariani, M, Tomai, F, Ghini, A, Violini, R, Confessore, P, Crea, F, Giubilato, S, Sardella, G, Mancone, M, Ribichini, F, Vassanelli, C, Dandale, R, Giudice, P, Vigorito, F, Liso, A, Specchia, L, Indolfi, C, Spaccarotella, C, Stabile, A, Gandolfo, C, Ussia, G, Comoglio, C, Dyrda, O, Rinaldi, M, Salizzoni, S, Micalizzi, E, Di Gregorio, O, Scoti, P, Costa, R, Casabona, R, Del Ponte, S, Panisi, P, Spira, G, Troise, G, Messina, A, Viganò, M, Aiello, M, Alfieri, O, Denti, P, Menicanti, L, Agnelli, B, Donatelli, F, Muneretto, C, Rambaldini, M, Gamba, A, Tasca, G, Ferrazzi, P, Terzi, A, Gelpi, G, Martinelli, L, Bruschi, G, Graffigna, A, Mazzucco, A, Pappalardo, A, Gatti, G, Livi, U, Pompei, E, Coppola, R, Gucciardo, M, Albertini, A, Caprili, L, Ghidoni, I, Gabbieri, D, La Marra, M, Aquino, T, Gherli, T, Policlinico, S, Di Bartolomeo, R, Savini, C, Popoff, G, Innocenti, D, Bortolotti, U, Pratali, S, Stefano, P, Blanzola, C, Glauber, M, Cerillo, A, Chiaramonti, F, Pardini, A, Fioriello, F, Torracca, L, Rescigno, G, De Paulis, R, Nardella, S, Musumeci, F, Luzi, G, Possati, G, Bonalumi, G, Covino, E, Pollari, F, Sinatra, R, Roscitano, A, Chiariello, L, Nardi, P, Lonobile, T, Baldascino, F, Di Benedetto, G, Mastrogiovanni, G, Piazza, L, Marmo, J, Vosa, C, De Amicis, V, Speziale, G, Visicchio, G, Spirito, R, Gregorini, R, Villani, M, Pano, M, Bortone, A, De Luca Tupputi Schinosa, L, De Cillis, E, Gaeta, R, Di Natale, M, Cassese, M, Antonazzo, A, Argano, V, Santaniello, E, Patanè, L, Gentile, M, Tribastone, S, Follis, F, Montalbano, G, Pilato, M, Stringi, V, Patanè, F, Salamone, G, Ruvolo, G, Pisano, C, Mignosa, C, Bivona, A, Cirio, E, Lixi, G, Maraschini, A, Badoni, G, Onorato, F, De Palma, R, Scandotto, S, Orlando, A, Copello, F, Borgia, P, Marchetta, F, and Porcu, R

Subjects
aortic stenosis, implantation, intermediate risk, transcatheter aortic valve, Settore MED/23 - Chirurgia Cardiaca
Published
2015

24. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

Author

Chen, L., Ge, B., Casale, F.P., Vasquez, L., Kwan, T., Garrido-Martin, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., Datta, A., Richardson, D., Burden, F., Mead, D., Mann, A.L., Fernandez, J.M., Rowlston, S., Wilder, S.P., Farrow, S., Shao, X., Lambourne, J.J., Redensek, A., Albers, C.A., Amstislavskiy, V., Ashford, S., Berentsen, K., Bomba, L., Bourque, G., Bujold, D., Busche, S., Caron, M., Chen, S.H., Cheung, W., Delaneau, O., Dermitzakis, E.T., Elding, H., Colgiu, I., Bagger, F.O., Flicek, P., Habibi, E., Iotchkova, V., Janssen-Megens, E., Kim, B., Lehrach, H., Lowy, E., Mandoli, A., Matarese, F., Maurano, M.T., Morris, J.A., Pancaldi, V., Pourfarzad, F., Rehnstrom, K., Rendon, A., Risch, T., Sharifi, N., Simon, M.M., Sultan, M., Valencia, A., Walter, K., Wang, S.Y., Frontini, M., Antonarakis, S.E., Clarke, L., Yaspo, M.L., Beck, S., Guigo, R., Rico, D., Martens, J.H., Ouwehand, W.H., Kuijpers, T.W., Paul, D.S., Stunnenberg, H.G., Stegle, O., Downes, K., Pastinen, T., Soranzo, N., Chen, L., Ge, B., Casale, F.P., Vasquez, L., Kwan, T., Garrido-Martin, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., Datta, A., Richardson, D., Burden, F., Mead, D., Mann, A.L., Fernandez, J.M., Rowlston, S., Wilder, S.P., Farrow, S., Shao, X., Lambourne, J.J., Redensek, A., Albers, C.A., Amstislavskiy, V., Ashford, S., Berentsen, K., Bomba, L., Bourque, G., Bujold, D., Busche, S., Caron, M., Chen, S.H., Cheung, W., Delaneau, O., Dermitzakis, E.T., Elding, H., Colgiu, I., Bagger, F.O., Flicek, P., Habibi, E., Iotchkova, V., Janssen-Megens, E., Kim, B., Lehrach, H., Lowy, E., Mandoli, A., Matarese, F., Maurano, M.T., Morris, J.A., Pancaldi, V., Pourfarzad, F., Rehnstrom, K., Rendon, A., Risch, T., Sharifi, N., Simon, M.M., Sultan, M., Valencia, A., Walter, K., Wang, S.Y., Frontini, M., Antonarakis, S.E., Clarke, L., Yaspo, M.L., Beck, S., Guigo, R., Rico, D., Martens, J.H., Ouwehand, W.H., Kuijpers, T.W., Paul, D.S., Stunnenberg, H.G., Stegle, O., Downes, K., Pastinen, T., and Soranzo, N.

Abstract

Contains fulltext : 167824.pdf (Publisher’s version ) (Open Access)

Published
2016

25. DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

Author

Farlik, M., Halbritter, F., Muller, F, Choudry, F.A., Ebert, P., Klughammer, J., Farrow, S., Santoro, A., Ciaurro, V., Mathur, A., Uppal, R., Stunnenberg, H.G., Ouwehand, W.H., Laurenti, E., Lengauer, T., Frontini, M., Bock, C., Farlik, M., Halbritter, F., Muller, F, Choudry, F.A., Ebert, P., Klughammer, J., Farrow, S., Santoro, A., Ciaurro, V., Mathur, A., Uppal, R., Stunnenberg, H.G., Ouwehand, W.H., Laurenti, E., Lengauer, T., Frontini, M., and Bock, C.

Abstract

Contains fulltext : 165947.pdf (publisher's version ) (Open Access)

Published
2016

26. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

Author

Astle, W.J., Elding, H., Jiang, T., Allen, D., Ruklisa, D., Mann, A.L., Mead, D., Bouman, H., Riveros-Mckay, F., Kostadima, M.A., Lambourne, J.J., Sivapalaratnam, S., Downes, K., Kundu, K., Bomba, L., Berentsen, K., Bradley, J.R., Daugherty, L.C., Delaneau, O., Freson, K., Garner, S.F., Grassi, L., Guerrero, J., Haimel, M., Janssen-Megens, E.M., Kaan, A., Kamat, M., Kim, B., Mandoli, A., Marchini, J., Martens, J.H.A., Meacham, S., Megy, K., O'Connell, J., Petersen, R., Sharifi, N., Sheard, S.M., Staley, J.R., Tuna, S., Ent, M. van der, Walter, K., Wang, S., Wheeler, E., Wilder, S.P., Iotchkova, V., Moore, C., Sambrook, J., Stunnenberg, H.G., Di Angelantonio, E., Kaptoge, S., Kuijpers, T.W., Carrillo-de-Santa-Pau, E., Juan, D., Rico, D., Valencia, A., Chen, L, Ge, B., Vasquez, L., Kwan, T., Garrido-Martin, D., Watt, S., Yang, Y., Guigo, R., Beck, S., Paul, D.S., Pastinen, T., Bujold, D., Bourque, G., Frontini, M., Danesh, J., Roberts, D.J., Ouwehand, W.H., Butterworth, A.S., Soranzo, N., Astle, W.J., Elding, H., Jiang, T., Allen, D., Ruklisa, D., Mann, A.L., Mead, D., Bouman, H., Riveros-Mckay, F., Kostadima, M.A., Lambourne, J.J., Sivapalaratnam, S., Downes, K., Kundu, K., Bomba, L., Berentsen, K., Bradley, J.R., Daugherty, L.C., Delaneau, O., Freson, K., Garner, S.F., Grassi, L., Guerrero, J., Haimel, M., Janssen-Megens, E.M., Kaan, A., Kamat, M., Kim, B., Mandoli, A., Marchini, J., Martens, J.H.A., Meacham, S., Megy, K., O'Connell, J., Petersen, R., Sharifi, N., Sheard, S.M., Staley, J.R., Tuna, S., Ent, M. van der, Walter, K., Wang, S., Wheeler, E., Wilder, S.P., Iotchkova, V., Moore, C., Sambrook, J., Stunnenberg, H.G., Di Angelantonio, E., Kaptoge, S., Kuijpers, T.W., Carrillo-de-Santa-Pau, E., Juan, D., Rico, D., Valencia, A., Chen, L, Ge, B., Vasquez, L., Kwan, T., Garrido-Martin, D., Watt, S., Yang, Y., Guigo, R., Beck, S., Paul, D.S., Pastinen, T., Bujold, D., Bourque, G., Frontini, M., Danesh, J., Roberts, D.J., Ouwehand, W.H., Butterworth, A.S., and Soranzo, N.

Abstract

Contains fulltext : 163344.pdf (Publisher’s version ) (Open Access)

Published
2016

27. Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems

Author

Schuyler, R.P., Merkel, A., Raineri, E., Altucci, L., Vellenga, E., Martens, J.H.A., Pourfarzad, F., Kuijpers, T.W., Burden, F., Farrow, S., Downes, K., Ouwehand, W.H., Clarke, L., Datta, A., Lowy, E., Flicek, P., Frontini, M., Stunnenberg, H., Martin-Subero, J.I., Gut, I., Heath, S., Schuyler, R.P., Merkel, A., Raineri, E., Altucci, L., Vellenga, E., Martens, J.H.A., Pourfarzad, F., Kuijpers, T.W., Burden, F., Farrow, S., Downes, K., Ouwehand, W.H., Clarke, L., Datta, A., Lowy, E., Flicek, P., Frontini, M., Stunnenberg, H., Martin-Subero, J.I., Gut, I., and Heath, S.

Abstract

Contains fulltext : 161704.pdf (publisher's version ) (Open Access)

Published
2016

28. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

Author

Javierre, B.M., Burren, O.S., Wilder, S.P., Kreuzhuber, R., Hill, S.M., Sewitz, S., Cairns, J., Wingett, S.W., Varnai, C., Thiecke, M.J., Burden, F., Farrow, S., Cutler, A.J., Rehnstrom, K., Downes, K., Grassi, L., Kostadima, M., Freire-Pritchett, P., Wang, F, Stunnenberg, H., Todd, J.A., Zerbino, D.R., Stegle, O., Ouwehand, W.H., Frontini, M., Wallace, C., Spivakov, M., Fraser, P., Javierre, B.M., Burren, O.S., Wilder, S.P., Kreuzhuber, R., Hill, S.M., Sewitz, S., Cairns, J., Wingett, S.W., Varnai, C., Thiecke, M.J., Burden, F., Farrow, S., Cutler, A.J., Rehnstrom, K., Downes, K., Grassi, L., Kostadima, M., Freire-Pritchett, P., Wang, F, Stunnenberg, H., Todd, J.A., Zerbino, D.R., Stegle, O., Ouwehand, W.H., Frontini, M., Wallace, C., Spivakov, M., and Fraser, P.

Abstract

Contains fulltext : 161816.pdf (publisher's version ) (Open Access)

Published
2016

29. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

Author

Breeze, C.E., Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., Iotchkova, V., Frontini, M., Downes, K., Ouwehand, W.H., Laperle, J., Jacques, P.E., Bourque, G., Bergmann, A.K., Siebert, R., Vellenga, E., Saeed, S., Matarese, F., Martens, J.H.A., Stunnenberg, H., Teschendorff, A.E., Herrero, J., Birney, E., Dunham, I., Beck, S., Breeze, C.E., Paul, D.S., van Dongen, J., Butcher, L.M., Ambrose, J.C., Barrett, J.E., Lowe, R., Rakyan, V.K., Iotchkova, V., Frontini, M., Downes, K., Ouwehand, W.H., Laperle, J., Jacques, P.E., Bourque, G., Bergmann, A.K., Siebert, R., Vellenga, E., Saeed, S., Matarese, F., Martens, J.H.A., Stunnenberg, H., Teschendorff, A.E., Herrero, J., Birney, E., Dunham, I., and Beck, S.

Abstract

Contains fulltext : 161675.pdf (publisher's version ) (Open Access)

Published
2016

30. Saturation analysis for whole-genome bisulfite sequencing data

Author

Libertini, E., Heath, S.C., Hamoudi, R.A., Gut, M., Ziller, M.J., Herrero, J., Czyz, A., Ruotti, V., Stunnenberg, H., Frontini, M., Ouwehand, W.H., Meissner, A., Gut, I.G., Beck, S., Libertini, E., Heath, S.C., Hamoudi, R.A., Gut, M., Ziller, M.J., Herrero, J., Czyz, A., Ruotti, V., Stunnenberg, H., Frontini, M., Ouwehand, W.H., Meissner, A., Gut, I.G., and Beck, S.

Abstract

Item does not contain fulltext

Published
2016

31. Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps

Author

Iotchkova, V. (Valentina), Huang, J. (Jian), Morris, J.A. (John A), Jain, D. (Deepti), Barbieri, C. (Caterina), Walter, K. (Klaudia), Min, J. (Josine), Chen, L. (Lu), Astle, W. (William), Cocca, M. (Massimiliano), Deelen, P. (Patrick), Elding, H. (Heather), Farmaki, A.-E. (Aliki-Eleni), Franklin, C.S. (Christopher), Frånberg, M. (Mattias), Gaunt, T.R. (Tom), Hofman, A. (Albert), Jiang, T. (Tao), Kleber, M.E. (Marcus), Lachance, G. (Genevieve), Luan, J. (Jian'An), Malerba, G. (Giovanni), Matchan, A. (Angela), Mead, D. (Daniel), Memari, Y. (Yasin), Ntalla, I. (Ioanna), Panoutsopoulou, K. (Kalliope), Pazoki, R. (Raha), Perry, J.R.B. (John), Rivadeneira Ramirez, F. (Fernando), Sabater-Lleal, M. (Maria), Sennblad, B. (Bengt), Shin, S.-Y., Southam, L. (Lorraine), Traglia, M. (Michela), Dijk, F. (Freerk) van, Leeuwen, E.M. (Elisa) van, Zaza, G. (Gianluigi), Zhang, W. (Weihua), Amin, N. (Najaf), Butterworth, A.S. (Adam), Chambers, J.C. (John), Dedoussis, G.V. (George), Dehghan, A. (Abbas), Franco, O.H. (Oscar), Franke, L. (Lude), Frontini, M. (Mattia), Gambaro, G. (Giovanni), Gasparini, P. (Paolo), Hamsten, A. (Anders), Issacs, A. (Aaron), Kooner, J.S. (Jaspal S.), Kooperberg, C. (Charles), Langenberg, C. (Claudia), März, W. (Winfried), Scott, R.A. (Robert), Swertz, M.A. (Morris A), Toniolo, D. (Daniela), Uitterlinden, A.G. (André), Duijn, C.M. (Cornelia) van, Watkins, H. (Hugh), Zeggini, E. (Eleftheria), Maurano, M.T. (Matthew T.), Timpson, N.J. (Nicholas), Reiner, A. (Alexander), Auer, P. (Paul), Soranzo, N. (Nicole), Iotchkova, V. (Valentina), Huang, J. (Jian), Morris, J.A. (John A), Jain, D. (Deepti), Barbieri, C. (Caterina), Walter, K. (Klaudia), Min, J. (Josine), Chen, L. (Lu), Astle, W. (William), Cocca, M. (Massimiliano), Deelen, P. (Patrick), Elding, H. (Heather), Farmaki, A.-E. (Aliki-Eleni), Franklin, C.S. (Christopher), Frånberg, M. (Mattias), Gaunt, T.R. (Tom), Hofman, A. (Albert), Jiang, T. (Tao), Kleber, M.E. (Marcus), Lachance, G. (Genevieve), Luan, J. (Jian'An), Malerba, G. (Giovanni), Matchan, A. (Angela), Mead, D. (Daniel), Memari, Y. (Yasin), Ntalla, I. (Ioanna), Panoutsopoulou, K. (Kalliope), Pazoki, R. (Raha), Perry, J.R.B. (John), Rivadeneira Ramirez, F. (Fernando), Sabater-Lleal, M. (Maria), Sennblad, B. (Bengt), Shin, S.-Y., Southam, L. (Lorraine), Traglia, M. (Michela), Dijk, F. (Freerk) van, Leeuwen, E.M. (Elisa) van, Zaza, G. (Gianluigi), Zhang, W. (Weihua), Amin, N. (Najaf), Butterworth, A.S. (Adam), Chambers, J.C. (John), Dedoussis, G.V. (George), Dehghan, A. (Abbas), Franco, O.H. (Oscar), Franke, L. (Lude), Frontini, M. (Mattia), Gambaro, G. (Giovanni), Gasparini, P. (Paolo), Hamsten, A. (Anders), Issacs, A. (Aaron), Kooner, J.S. (Jaspal S.), Kooperberg, C. (Charles), Langenberg, C. (Claudia), März, W. (Winfried), Scott, R.A. (Robert), Swertz, M.A. (Morris A), Toniolo, D. (Daniela), Uitterlinden, A.G. (André), Duijn, C.M. (Cornelia) van, Watkins, H. (Hugh), Zeggini, E. (Eleftheria), Maurano, M.T. (Matthew T.), Timpson, N.J. (Nicholas), Reiner, A. (Alexander), Auer, P. (Paul), and Soranzo, N. (Nicole)

Abstract

Large-scale whole-genome sequence data sets offer novel opportunities to identify genetic variation underlying human traits. Here we apply genotype imputation based on whole-genome sequence data from the UK10K and 1000 Genomes Project into 35,981 study participants of European ancestry, followed by association analysis with 20 quantitative cardiometabolic and hematological traits. We describe 17 new associations, including 6 rare (minor allele frequency (MAF) < 1%) or low-frequency (1% < MAF < 5%) variants with platelet count (PLT), red blood cell indices (MCH and MCV) and HDL cholesterol. Applying fine-mapping analysis to 233 known and new loci associated with the 20 traits, we resolve the associations of 59 loci to credible sets of 20 or fewer variants and describe trait enrichments within regions of predicted regulatory function. These findings improve understanding of the allelic architecture of risk factors for cardiometabolic and hematological diseases and provide additional functional insights with the identification of potentially novel biological targets.

Published
2016
Full Text
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32. Development of the layered structure in a double-gated glass fiber-reinforced polypropylene injection molding: Experimental and simulated results.

Author

Quintana, M. C. and Frontini, M. P.

Subjects
*FIBER-reinforced plastics, *FIBER orientation, *POLYPROPYLENE, *INJECTION molding, *COMPUTER simulation
Abstract

The present study aims to experimentally validate numerical simulation of fiber orientation distribution performed by molding simulation software Moldex3D in a double-gated injection-molded glass fiber-filled (40 wt%) polypropylene box, by making a detailed comparison of predicted and experimentally measured fiber orientation distribution data. The modeling approach evaluated in this work consists in the implementation of the Folgar–Tucker rotary diffusion model with the invariant-based optimal fitting closure approximation for the fourth-order orientation tensor. The specimen used has a weld line in the center and sharp corners. This investigation characterizes in detail the development of the through-thickness layered structure at distinctive locations of the specimen. The sensitivity of fiber orientation distribution and the layered structure to changes upon injection time and melt temperature is also evaluated. The boxes display the typical layered laminate structure, with fibers aligned in the main flow direction near the walls (shell layer) and less oriented in the middle plane (core layer). The boxes injected at the lowest melt temperature display an additional skin layer. Unfortunately, simulation fails in predicting the five layers structure developed under these latter conditions. The grade of fiber orientation is deemed to be independent of process parameters but not the layered structure. [ABSTRACT FROM AUTHOR]

Published
2018
Full Text
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35. Cell cycle regulation of NF-YC nuclear localization

Author

Frontini M, Carol Imbriano, Manni I, and Mantovani R

Subjects
Cell Nucleus, cell cycle progression, Cell Cycle, Green Fluorescent Proteins, Cell Compartmentation, Histones, Myoblasts, Luminescent Proteins, Mice, Protein Subunits, CCAAT-Binding Factor, Microscopy, Fluorescence, CCAAT, CCAAT-Enhancer-Binding Proteins, NIH 3T3 Cells, Animals, Histone fold motifs, NF-Y, Cloning, Molecular
Abstract

NF-Y is a trimeric activator with histone fold, HFM, subunits that binds to the CCAAT-box and is required for a majority of cell cycle promoters, often in conjunction with E2Fs. In vivo binding of NF-Y is dynamic during the cell cycle and correlates with gene activation. We performed immunofluorescence studies on endogenous, GFP- and Flag-tagged overexpressed NF-Y subunits. NF-YA, NF-YB are nuclear proteins. Unexpectedly, NF-YC localizes both in cytoplamatic and nuclear compartments and its nuclear localization is determined by the interaction with its heterodimerization partner NF-YB. Most importantly, compartmentalization is regulated during the cell cycle of serum restimulated NIH3T3 cells, accumulating in the nucleus at the onset of S phase. These data point to the control of HFM heterodimerization as an important layer of NF-Y regulation during cell cycle progression.

Published
2004

36. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

Author

Saeed, S., Quintin, J., Kerstens, H.H., Rao, N.A., Aghajanirefah, A., Matarese, F., Cheng, S.C., Ratter, J., Berentsen, K., Ent, M.A. van der, Sharifi, N., Janssen-Megens, E.M., Huurne, M.C. ter, Mandoli, A., Schaik, T. van, Ng, A., Burden, F., Downes, K., Frontini, M., Kumar, V., Giamarellos-Bourboulis, E.J., Ouwehand, W.H., Meer, J.W.M. van der, Joosten, L.A., Wijmenga, C., Martens, J.H., Xavier, R.J., Logie, C., Netea, M.G., Stunnenberg, H.G., Saeed, S., Quintin, J., Kerstens, H.H., Rao, N.A., Aghajanirefah, A., Matarese, F., Cheng, S.C., Ratter, J., Berentsen, K., Ent, M.A. van der, Sharifi, N., Janssen-Megens, E.M., Huurne, M.C. ter, Mandoli, A., Schaik, T. van, Ng, A., Burden, F., Downes, K., Frontini, M., Kumar, V., Giamarellos-Bourboulis, E.J., Ouwehand, W.H., Meer, J.W.M. van der, Joosten, L.A., Wijmenga, C., Martens, J.H., Xavier, R.J., Logie, C., Netea, M.G., and Stunnenberg, H.G.

Abstract

Item does not contain fulltext, Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate of macrophages and susceptibility to secondary infections. We characterized the transcriptomes and epigenomes in four primary cell types: monocytes and in vitro-differentiated naive, tolerized, and trained macrophages. Inflammatory and metabolic pathways were modulated in macrophages, including decreased inflammasome activation, and we identified pathways functionally implicated in trained immunity. beta-glucan training elicits an exclusive epigenetic signature, revealing a complex network of enhancers and promoters. Analysis of transcription factor motifs in deoxyribonuclease I hypersensitive sites at cell-type-specific epigenetic loci unveiled differentiation and treatment-specific repertoires. Altogether, we provide a resource to understand the epigenetic changes that underlie innate immunity in humans.

Published
2014

37. Transcriptional diversity during lineage commitment of human blood progenitors

Author

Chen, L., Kostadima, M., Martens, J.H., Canu, G., Garcia, S.P., Turro, E., Downes, K., Macaulay, I.C., Bielczyk-Maczynska, E., Coe, S., Farrow, S., Poudel, P., Burden, F., Jansen, S.B., Astle, W.J., Attwood, A., Bariana, T., Bono, B. de, Breschi, A., Chambers, J.C., Consortium, B., Choudry, F.A., Clarke, L., Coupland, P., Ent, M. van der, Erber, W.N., Jansen, J.H., Favier, R., Fenech, M.E., Foad, N., Freson, K., Geet, C. Van, Gomez, K., Guigo, R., Hampshire, D., Kelly, A.M., Kerstens, H.H., Kooner, J.S., Laffan, M., Lentaigne, C., Labalette, C., Martin, T., Meacham, S., Mumford, A., Nürnberg, S., Palumbo, E., Reijden, B.A. van der, Richardson, D., Sammut, S.J., Slodkowicz, G., Tamuri, A.U., Vasquez, L., Voss, K., Watt, S., Westbury, S., Flicek, P., Loos, R., Goldman, N., Bertone, P., Read, R.J., Richardson, S., Cvejic, A., Soranzo, N., Ouwehand, W.H., Stunnenberg, H.G., Frontini, M., Rendon, A., Chen, L., Kostadima, M., Martens, J.H., Canu, G., Garcia, S.P., Turro, E., Downes, K., Macaulay, I.C., Bielczyk-Maczynska, E., Coe, S., Farrow, S., Poudel, P., Burden, F., Jansen, S.B., Astle, W.J., Attwood, A., Bariana, T., Bono, B. de, Breschi, A., Chambers, J.C., Consortium, B., Choudry, F.A., Clarke, L., Coupland, P., Ent, M. van der, Erber, W.N., Jansen, J.H., Favier, R., Fenech, M.E., Foad, N., Freson, K., Geet, C. Van, Gomez, K., Guigo, R., Hampshire, D., Kelly, A.M., Kerstens, H.H., Kooner, J.S., Laffan, M., Lentaigne, C., Labalette, C., Martin, T., Meacham, S., Mumford, A., Nürnberg, S., Palumbo, E., Reijden, B.A. van der, Richardson, D., Sammut, S.J., Slodkowicz, G., Tamuri, A.U., Vasquez, L., Voss, K., Watt, S., Westbury, S., Flicek, P., Loos, R., Goldman, N., Bertone, P., Read, R.J., Richardson, S., Cvejic, A., Soranzo, N., Ouwehand, W.H., Stunnenberg, H.G., Frontini, M., and Rendon, A.

Abstract

Item does not contain fulltext

Published
2014

39. SMIM1 underlies the Vel blood group and influences red blood cell traits

Author

Cvejic, A., Haer-Wigman, L., Stephens, J.C., Kostadima, M., Smethurst, P.A., Frontini, M., Akker, E. van den, Bertone, P., Bielczyk-Maczynska, E., Farrow, S., Fehrmann, R.S.N., Gray, A., Haas, M. de, Haver, V.G., Jordan, G., Karjalainen, J., Kerstens, H.H.D., Kiddle, G., Lloyd-Jones, H., Needs, M., Poole, J., Soussan, A.A., Rendon, A., Rieneck, K, Sambrook, J.G., Schepers, H., Sillje, H.H.W., Sipos, B., Swinkels, D.W., Tamuri, A.U., Verweij, N., Watkins, N.A., Westra, H.J., Stemple, D., Franke, L., Soranzo, N., Stunnenberg, H.G., Goldman, N., Harst, P. van der, Schoot, C.E. van der, Ouwehand, W.H., Albers, C.A., Cvejic, A., Haer-Wigman, L., Stephens, J.C., Kostadima, M., Smethurst, P.A., Frontini, M., Akker, E. van den, Bertone, P., Bielczyk-Maczynska, E., Farrow, S., Fehrmann, R.S.N., Gray, A., Haas, M. de, Haver, V.G., Jordan, G., Karjalainen, J., Kerstens, H.H.D., Kiddle, G., Lloyd-Jones, H., Needs, M., Poole, J., Soussan, A.A., Rendon, A., Rieneck, K, Sambrook, J.G., Schepers, H., Sillje, H.H.W., Sipos, B., Swinkels, D.W., Tamuri, A.U., Verweij, N., Watkins, N.A., Westra, H.J., Stemple, D., Franke, L., Soranzo, N., Stunnenberg, H.G., Goldman, N., Harst, P. van der, Schoot, C.E. van der, Ouwehand, W.H., and Albers, C.A.

Abstract

Item does not contain fulltext

Published
2013

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