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1. Erratum to: Building bridges for innovation in ageing: Synergies between action groups of the EIP on AHA

Author

Bousquet, Jean, Bewick, M., Cano, A., Eklund, P., Fico, G., Goswami, N., Guldemond, N. A., Henderson, D., Hinkema, M. J., Liotta, G., Mair, A., Molloy, W., Monaco, A., Monsonis-Paya, I., Nizinska, A., Papadopoulos, H., Pavlickova, A., Pecorelli, S., Prados-Torres, A., Roller-Wirnsberger, R. E., Somekh, D., Vera-Muñoz, C., Visser, F., Farrell, J., Malva, J., Andersen Ranberg, K., Camuzat, T., Carriazo, A. M., Crooks, G., Gutter, Z., Iaccarino, G., de Keenoy, E. Manuel, Moda, G., Rodriguez-Mañas, L., Vontetsianos, T., Abreu, C., Alonso, J., Alonso-Bouzon, C., Ankri, J., Arredondo, M. T., Avolio, F., Bedbrook, A., Białoszewski, A. Z., Blain, H., Bourret, R., Cabrera-Umpierrez, M. F., Catala, A., O’Caoimh, R., Cesari, M., Chavannes, N. H., Correia-Da-Sousa, J., Dedeu, T., Ferrando, M., Ferri, M., Fokkens, W. J., Garcia-Lizana, F., Guérin, O., Hellings, P. W., Haahtela, T., Illario, M., Inzerilli, M. C., Lodrup Carlsen, K. C., Kardas, P., Keil, T., Maggio, M., Mendez-Zorrilla, A., Menditto, E., Mercier, J., Michel, J. P., Murray, R., Nogues, M., O’Byrne-Maguire, I., Pappa, D., Parent, A. S., Pastorino, M., Robalo-Cordeiro, C., Samolinski, B., Siciliano, P., Teixeira, A. M., Tsartara, S. I., Valiulis, A., Vandenplas, O., Vasankari, T., Vellas, B., Vollenbroek-Hutten, M., Wickman, M., Yorgancioglu, A., Zuberbier, T., Barbagallo, M., Canonica, G. W., Klimek, L., Maggi, S., Aberer, W., Akdis, C., Adcock, I. M., Agache, I., Albera, C., Alonso-Trujillo, F., Angel Guarcia, M., Annesi-Maesano, I., Apostolo, J., Arshad, S. H., Attalin, V., Avignon, A., Bachert, C., Baroni, I., Bel, E., Benson, M., Bescos, C., Blasi, F., Barbara, C., Bergmann, K. C., Bernard, P. L., Bonini, S., Bousquet, P. J., Branchini, B., Brightling, C. E., Bruguière, V., Bunu, C., Bush, A., Caimmi, D. P., Calderon, M. A., Canovas, G., Cardona, V., Carlsen, K. H., Cesario, A., Chkhartishvili, E., Chiron, R., Chivato, T., Chung, K. F., D’Angelantonio, M., de Carlo, G., Cholley, D., Chorin, F., Combe, B., Compas, B., Costa, D. J., Costa, E., Coste, O., Coupet, A. -L., Crepaldi, G., Custovic, A., Dahl, R., Dahlen, S. E., Demoly, P., Devillier, P., Didier, A., Dinh-Xuan, A. T., Djukanovic, R., Dokic, D., du Toit, G., Dubakiene, R., Dupeyron, A., Emuzyte, R., Fiocchi, A., Wagner, A., Fletcher, M., Fonseca, J., Fougère, B., Gamkrelidze, A., Garces, G., Garcia-Aymeric, J., Garcia-Zapirain, B., Gemicioğlu, B., Gouder, C., Hellquist-Dahl, B., Hermosilla-Gimeno, I., Héve, D., Holland, C., Humbert, M., Hyland, M., Johnston, S. L., Just, J., Jutel, M., Kaidashev, I. P., Kaitov, M., Kalayci, O., Kalyoncu, A. F., Keijser, W., Kerstjens, H., Knezović, J., Kowalski, M., Koppelman, G. H., Kotska, T., Kovac, M., Kull, I., Kuna, P., Kvedariene, V., Lepore, V., Macnee, W., Maggio, M., Magnan, A., Majer, I., Manning, P., Marcucci, M., Marti, T., Masoli, M., Melen, E., Miculinic, N., Mihaltan, F., Milenkovic, B., Millot-Keurinck, J., Mlinarić, H., Momas, I., Montefort, S., Morais-Almeida, M., Moreno-Casbas, T., Mösges, R., Mullol, J., Nadif, R., Nalin, M., Navarro-Pardo, E., Nekam, K., Ninot, G., Paccard, D., Pais, S., Palummeri, E., Panzner, P., Papadopoulos, N. K., Papanikolaou, C., Passalacqua, G., Pastor, E., Perrot, M., Plavec, D., Popov, T. A., Postma, D. S., Price, D., Raffort, N., Reuzeau, J. C., Robine, J. M., Rodenas, F., Robusto, F., Roche, N., Romano, A., Romano, V., Rosado-Pinto, J., Roubille, F., Ruiz, F., Ryan, D., Salcedo, T., Schmid-Grendelmeier, P., Schulz, H., Schunemann, H. J., Serrano, E., Sheikh, A., Shields, M., Siafakas, N., Scichilone, N., Siciliano, P., Skrindo, I., Smit, H. A., Sourdet, S., Sousa-Costa, E., Spranger, O., Sooronbaev, T., Sruk, V., Sterk, P. J., Todo-Bom, A., Touchon, J., Tramontano, D., Triggiani, M., Tsartara, S. I., Valero, A. L., Valovirta, E., van Ganse, E., van Hage, M., van den Berge, M., Vandenplas, O., Ventura, M. T., Vergara, I., Vezzani, G., Vidal, D., Viegi, G., Wagemann, M., Whalley, B., Wickman, M., Wilson, N., Yiallouros, P. K., Žagar, M., Zaidi, A., Zidarn, M., Hoogerwerf, E. J., Usero, J., Zuffada, R., Senn, A., and de Oliveira-Alves, B.

Published
2023
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2. Modules, networks and systems medicine for understanding disease and aiding diagnosis

Author

Gustafsson, Mika, Nestor, Colm E, Zhang, Huan, Barabási, Albert-László, Baranzini, Sergio, Brunak, Sören, Chung, Kian Fan, Federoff, Howard J, Gavin, Anne-Claude, Meehan, Richard R, Picotti, Paola, Pujana, Miguel Ángel, Rajewsky, Nikolaus, Smith, Kenneth GC, Sterk, Peter J, Villoslada, Pablo, and Benson, Mikael

Subjects
Biological Sciences, Genetics, Biotechnology, Lung, Obesity, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Good Health and Well Being, Clinical Sciences
Abstract

Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation.

Published
2014

6. Building bridges for innovation in ageing: Synergies between action groups of the EIP on AHA

Author

Bousquet, Jean, Bewick, M., Cano, A., Eklund, P., Fico, G., Goswami, N., Guldemond, N. A., Henderson, D., Hinkema, M. J., Liotta, G., Mair, A., Molloy, W., Monaco, A., Monsonis-Paya, I., Nizinska, A., Papadopoulos, H., Pavlickova, A., Pecorelli, S., Prados-Torres, A., Roller-Wirnsberger, R. E., Somekh, D., Vera-Muñoz, C., Visser, F., Farrell, J., Malva, J., Andersen Ranberg, K., Camuzat, T., Carriazo, A. M., Crooks, G., Gutter, Z., Iaccarino, G., de Keenoy, E. Manuel, Moda, G., Rodriguez-Mañas, L., Vontetsianos, T., Abreu, C., Alonso, J., Alonso-Bouzon, C., Ankri, J., Arredondo, M. T., Avolio, F., Bedbrook, A., Białoszewski, A. Z., Blain, H., Bourret, R., Cabrera-Umpierrez, M. F., Catala, A., O’Caoimh, R., Cesari, M., Chavannes, N. H., Correia-Da-Sousa, J., Dedeu, T., Ferrando, M., Ferri, M., Fokkens, W. J., Garcia-Lizana, F., Guérin, O., Hellings, P. W., Haahtela, T., Illario, M., Inzerilli, M. C., Lodrup Carlsen, K. C., Kardas, P., Keil, T., Maggio, M., Mendez-Zorrilla, A., Menditto, E., Mercier, J., Michel, J. P., Murray, R., Nogues, M., O’Byrne-Maguire, I., Pappa, D., Parent, A. S., Pastorino, M., Robalo-Cordeiro, C., Samolinski, B., Siciliano, P., Teixeira, A. M., Tsartara, S. I., Valiulis, A., Vandenplas, O., Vasankari, T., Vellas, B., Vollenbroek-Hutten, M., Wickman, M., Yorgancioglu, A., Zuberbier, T., Barbagallo, M., Canonica, G. W., Klimek, L., Maggi, S., Aberer, W., Akdis, C., Adcock, I. M., Agache, I., Albera, C., Alonso-Trujillo, F., Angel Guarcia, M., Annesi-Maesano, I., Apostolo, J., Arshad, S. H., Attalin, V., Avignon, A., Bachert, C., Baroni, I., Bel, E., Benson, M., Bescos, C., Blasi, F., Barbara, C., Bergmann, K. C., Bernard, P. L., Bonini, S., Bousquet, P. J., Branchini, B., Brightling, C. E., Bruguière, V., Bunu, C., Bush, A., Caimmi, D. P., Calderon, M. A., Canovas, G., Cardona, V., Carlsen, K. H., Cesario, A., Chkhartishvili, E., Chiron, R., Chivato, T., Chung, K. F., D’Angelantonio, M., de Carlo, G., Cholley, D., Chorin, F., Combe, B., Compas, B., Costa, D. J., Costa, E., Coste, O., Coupet, A. -L., Crepaldi, G., Custovic, A., Dahl, R., Dahlen, S. E., Demoly, P., Devillier, P., Didier, A., Dinh-Xuan, A. T., Djukanovic, R., Dokic, D., du Toit, G., Dubakiene, R., Dupeyron, A., Emuzyte, R., Fiocchi, A., Wagner, A., Fletcher, M., Fonseca, J., Fougère, B., Gamkrelidze, A., Garces, G., Garcia-Aymeric, J., Garcia-Zapirain, B., Gemicioğlu, B., Gouder, C., Hellquist-Dahl, B., Hermosilla-Gimeno, I., Héve, D., Holland, C., Humbert, M., Hyland, M., Johnston, S. L., Just, J., Jutel, M., Kaidashev, I. P., Kaitov, M., Kalayci, O., Kalyoncu, A. F., Keijser, W., Kerstjens, H., Knezović, J., Kowalski, M., Koppelman, G. H., Kotska, T., Kovac, M., Kull, I., Kuna, P., Kvedariene, V., Lepore, V., Macnee, W., Maggio, M., Magnan, A., Majer, I., Manning, P., Marcucci, M., Marti, T., Masoli, M., Melen, E., Miculinic, N., Mihaltan, F., Milenkovic, B., Millot-Keurinck, J., Mlinarić, H., Momas, I., Montefort, S., Morais-Almeida, M., Moreno-Casbas, T., Mösges, R., Mullol, J., Nadif, R., Nalin, M., Navarro-Pardo, E., Nekam, K., Ninot, G., Paccard, D., Pais, S., Palummeri, E., Panzner, P., Papadopoulos, N. K., Papanikolaou, C., Passalacqua, G., Pastor, E., Perrot, M., Plavec, D., Popov, T. A., Postma, D. S., Price, D., Raffort, N., Reuzeau, J. C., Robine, J. M., Rodenas, F., Robusto, F., Roche, N., Romano, A., Romano, V., Rosado-Pinto, J., Roubille, F., Ruiz, F., Ryan, D., Salcedo, T., Schmid-Grendelmeier, P., Schulz, H., Schunemann, H. J., Serrano, E., Sheikh, A., Shields, M., Siafakas, N., Scichilone, N., Siciliano, P., Skrindo, I., Smit, H. A., Sourdet, S., Sousa-Costa, E., Spranger, O., Sooronbaev, T., Sruk, V., Sterk, P. J., Todo-Bom, A., Touchon, J., Tramontano, D., Triggiani, M., Tsartara, S. I., Valero, A. L., Valovirta, E., van Ganse, E., van Hage, M., van den Berge, M., Vandenplas, O., Ventura, M. T., Vergara, I., Vezzani, G., Vidal, D., Viegi, G., Wagemann, M., Whalley, B., Wickman, M., Wilson, N., Yiallouros, P. K., Žagar, M., Zaidi, A., Zidarn, M., Hoogerwerf, E. J., Usero, J., Zuffada, R., Senn, A., and de Oliveira-Alves, B.

Published
2017
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8. Identification of oropharyngeal microbiome-driven asthma and wheezing clusters in children

Author

Abdel-Aziz, M I, primary, Thorsen, J, additional, Hashimoto, S, additional, Vijverberg, S J H, additional, Neerincx, A H, additional, Brinkman, P, additional, Aalderen, W V, additional, Stokholm, J, additional, Roggenbuck-Wedemeyer, M, additional, Vissing, N H, additional, Mortensen, M S, additional, Brejnrod, A D, additional, Fleming, L J, additional, Murray, C S, additional, Fowler, S J, additional, Frey, U, additional, Bush, A, additional, Singer, F, additional, Hedlin, G, additional, Nordlund, B, additional, Shaw, D E, additional, Chung, K F, additional, Adcock, I M, additional, Djukanovic, R, additional, Auffray, C, additional, Bansal, A T, additional, Sousa, A R, additional, Wagers, S S, additional, Chawes, B L, additional, Bønnelykke, K, additional, Sørensen, S J, additional, Kraneveld, A D, additional, Sterk, P J, additional, Roberts, G, additional, Bisgaard, H, additional, and Maitland-Van Der Zee, A H, additional

Published
2022
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10. Lipid phenotyping of lung epithelial lining fluid in healthy human volunteers

Author

Brandsma, Joost, Goss, Victoria M., Yang, Xian, Bakke, Per S., Caruso, Massimo, Chanez, Pascal, Dahlén, Sven-Erik, Fowler, Stephen J., Horvath, Ildiko, Krug, Norbert, Montuschi, Paolo, Sanak, Marek, Sandström, Thomas, Shaw, Dominick E., Chung, Kian Fan, Singer, Florian, Fleming, Louise J., Sousa, Ana R., Pandis, Ioannis, Bansal, Aruna T., Sterk, Peter J., Djukanović, Ratko, Postle, Anthony D., and The U-BIOPRED Study Group

Published
2018
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11. A computational framework for complex disease stratification from multiple large-scale datasets

Author

De Meulder, Bertrand, Lefaudeux, Diane, Bansal, Aruna T., Mazein, Alexander, Chaiboonchoe, Amphun, Ahmed, Hassan, Balaur, Irina, Saqi, Mansoor, Pellet, Johann, Ballereau, Stéphane, Lemonnier, Nathanaël, Sun, Kai, Pandis, Ioannis, Yang, Xian, Batuwitage, Manohara, Kretsos, Kosmas, van Eyll, Jonathan, Bedding, Alun, Davison, Timothy, Dodson, Paul, Larminie, Christopher, Postle, Anthony, Corfield, Julie, Djukanovic, Ratko, Chung, Kian Fan, Adcock, Ian M., Guo, Yi-Ke, Sterk, Peter J., Manta, Alexander, Rowe, Anthony, Baribaud, Frédéric, Auffray, Charles, and the U-BIOPRED Study Group and the eTRIKS Consortium

Published
2018
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13. Prospective Detection of Early Lung Cancer in Patients With COPD in Regular Care by Electronic Nose Analysis of Exhaled Breath

Author

de Vries, Rianne, Farzan, Niloufar, Fabius, Timon, De Jongh, Frans H.C., Jak, Patrick M.C., Haarman, Eric G., Snoey, Erik, In ’T Veen, Johannes C.C.M., Dagelet, Yennece W.F., Maitland-Van Der Zee, Anke-Hilse, Lucas, Annelies, Van Den Heuvel, Michel M., Wolf-Lansdorf, Marguerite, Muller, Mirte, Baas, Paul, and Sterk, Peter J.

Abstract

Patients with COPD are at high risk of lung cancer developing, but no validated predictive biomarkers have been reported to identify these patients. Molecular profiling of exhaled breath by electronic nose (eNose) technology may qualify for early detection of lung cancer in patients with COPD.

Published
2023
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17. Cover Image

Author

Brinkman, P., van de Pol, M. A., Gerritsen, M. G., Bos, L. D., Dekker, T., Smids, B. S., Sinha, A., Majoor, C. J., Sneeboer, M. M., Knobel, H. H., Vink, T. J., de Jongh, F. H., Lutter, R., Sterk, P. J., and Fens, N.

Published
2017
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18. Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation

Author

Mikus, M. S., Kolmert, J., Andersson, L. I., Ostling, J., Knowles, R. G., Gomez, C., Ericsson, M., Thorngren, J. -O., Khoonsari, P. E., Dahlen, B., Kupczyk, M., de Meulder, B., Auffray, C., Bakke, P. S., Beghe, Bianca, Bel, E. H., Caruso, M., Chanez, P., Chawes, B., Fowler, S. J., Gaga, M., Geiser, T., Gjomarkaj, M., Horvath, I., Howarth, P. H., Johnston, S. L., Joos, G., Krug, N., Montuschi, P., Musial, J., Nizankowska-Mogilnicka, E., Olsson, H. K., Papi, A., Rabe, K. F., Sandstrom, T., Shaw, D. E., Siafakas, N. M., Uhlen, M., Riley, J. H., Bates, S., Middelveld, R. J. M., Wheelock, C. E., Chung, K. F., Adcock, I. M., Sterk, P. J., Djukanovic, R., Nilsson, P., Dahlen, S. -E., James, A., Ahmed, H., Balgoma, D., Bansal, A. T., Baribaud, F., Bigler, J., Billing, B., Bisgaard, H., Boedigheimer, M. J., Bonnelykke, K., Brandsma, J., Brinkman, P., Bucchioni, E., Burg, D., Bush, A., Chaiboonchoe, A., Checa, T., Compton, C. H., Corfield, J., Cunoosamy, D., D'Amico, A., Emma, R., Erpenbeck, V. J., Erzen, D., Fichtner, K., Fitch, N., Fleming, L. J., Formaggio, E., Frey, U., Gahlemann, M., Goss, V., Guo, Y. -K., Hashimoto, S., Haughney, J., Hedlin, G., Hekking, P. -P. W., Higenbottam, T., Hohlfeld, J. M., Holweg, C. T. J., Knox, A. J., Konradsen, J., Lazarinis, N., Lefaudeux, D., Li, T., Loza, M. J., Lutter, R., Manta, A., Masefield, S., Matthews, J. G., Mazein, A., Meiser, A., Miralpeix, M., Mores, N., Murray, C. S., Myles, D., Naz, S., Nordlund, B., Pahus, L., Pandis, I., Pavlidis, S., Postle, A., Powel, P., Rao, N., Reinke, S., Roberts, A., Roberts, G., Rowe, A., Schofield, J. P. R., Seibold, W., Selby, A., Sigmund, R., Singer, F., Sjodin, M., Skipp, P. J., Sousa, A. R., Sun, K., Thornton, B., Uddin, M., van Aalderen, W. M., van Geest, M., Vestbo, J., Vissing, N. H., Wagener, A. H., Wagers, S. S., Weiszhart, Z., Wheelock, A., Wilson, S. J., Yasinska, V., Brusselle, G. G., Campbell, D. A., Contoli, M., Damm, K., de Rudder, I., Delin, I., Devautour, C., Duplaga, M., Eduards, M., Ek, A., Ekstrom, T., Figiel, E., Gaber, F., Gauw, S., Gawlewicz-Mroczka, A., Gerding, D., Haque, S., Hewitt, L., Hiemstra, P. S., Holgate, S. T., Holloway, J., Kania, A., Kanniess, F., Karlsson, O., Kips, J. C., Kumlin, M., Lantz, A. -S., Magnussen, H., Mallia, P., Martling, I., Meziane, L., Oikonomidou, E., Olsson, M., Pace, E., Papadopouli, E., Papadopoulos, N., Plataki, M., Profita, M., Reinius, L. E., Richter, K., Robinson, D. S., Romagnoli, M., Samara, K., Schelfhout, V., Skedinger, M., Stamataki, E., ten Brinke, A., Vachier, I., Wallen-Nielsen, E., van Veen, I., Weersink, E., Zervas, E., and Ziolkowska-Graca, B.

Subjects
Blood Proteins, Humans, Inflammation, Proteomics, Severity of Illness Index, Steroids, Asthma, Quality of Life
Published
2022

19. ARIA 2016: Care pathways implementing emerging technologies for predictive medicine in rhinitis and asthma across the life cycle

Author

Bousquet, J., Hellings, P. W., Agache, I., Bedbrook, A., Bachert, C., Bergmann, K. C., Bewick, M., Bindslev-Jensen, C., Bosnic-Anticevitch, S., Bucca, C., Caimmi, D. P., Camargos, P. A. M., Canonica, G. W., Casale, T., Chavannes, N. H., Cruz, A. A., De Carlo, G., Dahl, R., Demoly, P., Devillier, P., Fonseca, J., Fokkens, W. J., Guldemond, N. A., Haahtela, T., Illario, M., Just, J., Keil, T., Klimek, L., Kuna, P., Larenas-Linnemann, D., Morais-Almeida, M., Mullol, J., Murray, R., Naclerio, R., O’Hehir, R. E., Papadopoulos, N. G., Pawankar, R., Potter, P., Ryan, D., Samolinski, B., Schunemann, H. J., Sheikh, A., Simons, F. E. R., Stellato, C., Todo-Bom, A., Tomazic, P. V., Valiulis, A., Valovirta, E., Ventura, M. T., Wickman, M., Young, I., Yorgancioglu, A., Zuberbier, T., Aberer, W., Akdis, C. A., Akdis, M., Annesi-Maesano, I., Ankri, J., Ansotegui, I. J., Anto, J. M., Arnavielhe, S., Asarnoj, A., Arshad, H., Avolio, F., Baiardini, I., Barbara, C., Barbagallo, M., Bateman, E. D., Beghé, B., Bel, E. H., Bennoor, K. S., Benson, M., Białoszewski, A. Z., Bieber, T., Bjermer, L., Blain, H., Blasi, F., Boner, A. L., Bonini, M., Bonini, S., Bosse, I., Bouchard, J., Boulet, L. P., Bourret, R., Bousquet, P. J., Braido, F., Briggs, A. H., Brightling, C. E., Brozek, J., Buhl, R., Bunu, C., Burte, E., Bush, A., Caballero-Fonseca, F., Calderon, M. A., Camuzat, T., Cardona, V., Carreiro-Martins, P., Carriazo, A. M., Carlsen, K. H., Carr, W., Cepeda Sarabia, A. M., Cesari, M., Chatzi, L., Chiron, R., Chivato, T., Chkhartishvili, E., Chuchalin, A. G., Chung, K. F., Ciprandi, G., de Sousa, J. Correia, Cox, L., Crooks, G., Custovic, A., Dahlen, S. E., Darsow, U., Dedeu, T., Deleanu, D., Denburg, J. A., De Vries, G., Didier, A., Dinh-Xuan, A. T., Dokic, D., Douagui, H., Dray, G., Dubakiene, R., Durham, S. R., Du Toit, G., Dykewicz, M. S., Eklund, P., El-Gamal, Y., Ellers, E., Emuzyte, R., Farrell, J., Fink Wagner, A., Fiocchi, A., Fletcher, M., Forastiere, F., Gaga, M., Gamkrelidze, A., Gemicioğlu, B., Gereda, J. E., van Wick, R. Gerth, González Diaz, S., Grisle, I., Grouse, L., Gutter, Z., Guzmán, M. A., Hellquist-Dahl, B., Heinrich, J., Horak, F., Hourihane, J. O’. B., Humbert, M., Hyland, M., Iaccarino, G., Jares, E. J., Jeandel, C., Johnston, S. L., Joos, G., Jonquet, O., Jung, K. S., Jutel, M., Kaidashev, I., Khaitov, M., Kalayci, O., Kalyoncu, A. F., Kardas, P., Keith, P. K., Kerkhof, M., Kerstjens, H. A. M., Khaltaev, N., Kogevinas, M., Kolek, V., Koppelman, G. H., Kowalski, M. L., Kuitunen, M., Kull, I., Kvedariene, V., Lambrecht, B., Lau, S., Laune, D., Le, L. T. T., Lieberman, P., Lipworth, B., Li, J., Lodrup Carlsen, K. C., Louis, R., Lupinek, C., MacNee, W., Magar, Y., Magnan, A., Mahboub, B., Maier, D., Majer, I., Malva, J., Manning, P., De Manuel Keenoy, E., Marshall, G. D., Masjedi, M. R., Mathieu-Dupas, E., Maurer, M., Mavale-Manuel, S., Melén, E., Melo-Gomes, E., Meltzer, E. O., Mercier, J., Merk, H., Miculinic, N., Mihaltan, F., Milenkovic, B., Millot-Keurinck, J., Mohammad, Y., Momas, I., Mösges, R., Muraro, A., Namazova-Baranova, L., Nadif, R., Neffen, H., Nekam, K., Nieto, A., Niggemann, B., Nogueira-Silva, L., Nogues, M., Nyembue, T. D., Ohta, K., Okamoto, Y., Okubo, K., Olive-Elias, M., Ouedraogo, S., Paggiaro, P., Pali-Schöll, I., Palkonen, S., Panzner, P., Papi, A., Park, H. S., Passalacqua, G., Pedersen, S., Pereira, A. M., Pfaar, O., Picard, R., Pigearias, B., Pin, I., Plavec, D., Pohl, W., Popov, T. A., Portejoie, F., Postma, D., Poulsen, L. K., Price, D., Rabe, K. F., Raciborski, F., Roberts, G., Robalo-Cordeiro, C., Rodenas, F., Rodriguez-Mañas, L., Rolland, C., Roman Rodriguez, M., Romano, A., Rosado-Pinto, J., Rosario, N., Rottem, M., Sanchez-Borges, M., Sastre-Dominguez, J., Scadding, G. K., Scichilone, N., Schmid-Grendelmeier, P., Serrano, E., Shields, M., Siroux, V., Sisul, J. C., Skrindo, I., Smit, H. A., Solé, D., Sooronbaev, T., Spranger, O., Stelmach, R., Sterk, P. J., Strandberg, T., Sunyer, J., Thijs, C., Triggiani, M., Valenta, R., Valero, A., van Eerd, M., van Ganse, E., van Hague, M., Vandenplas, O., Varona, L. L., Vellas, B., Vezzani, G., Vazankari, T., Viegi, G., Vontetsianos, T., Wagenmann, M., Walker, S., Wang, D. Y., Wahn, U., Werfel, T., Whalley, B., Williams, D. M., Williams, S., Wilson, N., Wright, J., Yawn, B. P., Yiallouros, P. K., Yusuf, O. M., Zaidi, A., Zar, H. J., Zernotti, M. E., Zhang, L., Zhong, N., and Zidarn, M.

Published
2016
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24. Temporal Fluctuation of Systemic Markers in Urine During a Nasal Rhinovirus Challenge in Healthy and Asthmatic Subjects

Author

Sinha, A., Wheelock, C.E., Xu, Binbin, Frey, U., Sterk, P. J., Lutter, R., Chaleckis, R., VU University Medical Center [Amsterdam], Karolinska Institutet [Stockholm], EuroMov - Digital Health in Motion (Euromov DHM), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Montpellier (UM), Bern University Hospital [Berne] (Inselspital), Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA), and Gunma University

Subjects
[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, 3. Good health
Abstract

International audience; Biological processes are dynamic as reflected by temporal fluctuations of biomarkers. These dynamics underline the adaptive capacity of physiological systems to respond to external perturbations. We have captured differences in the pattern of fluctuations in biomarkers sampled locally at the sites of respiratory infection between healthy individuals and asthma patients, before and after perturbation by rhinovirus exposure [Sinha et al, eLife]. The detection of fluctuating biomarker signals in a systemic matrix, e.g. urine could aid in the development of better prognostic, non-invasive markers for monitoring disease progression especially during loss-of-control/exacerbation events due to viral exposures in asthma. Aims:Probe and compare temporal fluctuations of metabolomic signatures in the systemic circulation (urine) after a rhinovirus (RV-16) challenge in healthy and asthmatic subjects. Methods: In this prospective follow-up study, urine from 12 healthy individuals and 12 asthma patients was sampled thrice weekly for 3 months. After two months (stable phase) individuals were exposed to a 100 TCID50 Rhinovirus 16 and followed for another month (unstable phase). Non-targeted metabolomics data were acquiredwith liquid chromatography-mass spectrometry (LC-MS) using HILIC chromatography in positive ionization mode. Urine specific gravity (SG) was measured to normalize urine concentration and to reduce matrix effects. Data was processed independently using MZmine, MS-DIAL and Profinder software packages.A modified robust regression analysis technique, LASSO (least absolute shrinkage and selection operator) was applied on the mass spectrometric fragments to compare healthy and asthma groups both before and after rhinovirus challenge interventions. The machine learning pipeline was applied to the non-targeted metabolomics dataset and selected features were identified using an in-house chemical library. Results: We have identified a total of 164 metabolites in urine, several of which were found differentially regulated in healthy and asthmatic volunteers before and after the challenge (See Figure 1). Interestingly carnitine species decreased during the Rhinovirus challenge. Decreases in urinary carnitines have been previously observed in relationto asthma severity levels which confirm and substantiate our findings. Derivates of GABA (γ-aminobutyric acid) were also found to be differentially regulated. Conclusions: Our studyreports for the first time the fluctuating signals of metabolites in systemic signals in response to an exogenous trigger in the local nasal compartment in healthy and asthmaticsubjects. Carnitine compounds could prove to be useful markers of viral infection. The differential regulation of urinary metabolites could be useful to monitor patient prognosis andspot viral infections.

Published
2021

25. Lumacaftor/ivacaftor changes the lung microbiome and metabolome in cystic fibrosis patients

Author

Neerincx, Anne H., Whiteson, Katrine, Phan, Joann L., Brinkman, Paul, Abdel-Aziz, Mahmoud I., Weersink, Els J.M., Altenburg, Josje, Majoor, Christof J., Maitland-van der Zee, Anke H., Bos, Lieuwe D.J., Haarman, E., Rutjes, N. W., Terheggen-Lagro, S. W.J., Seljogi, D., Kemper, E. M., Lutter, R., Vijverberg, S. J., Vonk, S. E.M., Adriaens, N., Lub, R., van Brederode, M., van der Schaaf, L., Verkleij, M., van Gilst, N. A., Hofsteenge, G. H., Brackel, C. L.H., Lakeman, P., Bon, I. C.M., Tanner, S. P.M., Sterk, P. J., Longo, C., Sinha, A., Fenn, D., Lammers, A., Richards, L. B., van Bragt, J. M., Kos, R., Dagelet, J. W.F., Lone-Latif, S. J.A., Schultz, M. J., Smit, M. R., Hagens, L. A., Pulmonary medicine, Pediatrics, Amsterdam Reproduction & Development (AR&D), Psychiatry, CCA - Cancer biology and immunology, Pulmonology, AII - Inflammatory diseases, Graduate School, APH - Personalized Medicine, Paediatric Pulmonology, Intensive Care Medicine, and ACS - Heart failure & arrhythmias

Subjects
Pulmonary and Respiratory Medicine, Lung microbiome, medicine.medical_specialty, Cystic Fibrosis, medicine.disease_cause, Cystic fibrosis, Gastroenterology, Ivacaftor, 03 medical and health sciences, chemistry.chemical_compound, Internal medicine, Medicine, Microbiome, 030304 developmental biology, 0303 health sciences, 030306 microbiology, business.industry, Pseudomonas aeruginosa, Lumacaftor, Original Articles, medicine.disease, Epithelial fluid transport, chemistry, Sputum, medicine.symptom, business, medicine.drug
Abstract

Rationale Targeted cystic fibrosis (CF) therapy with lumacaftor/ivacaftor partly restores chloride channel function and improves epithelial fluid transport in the airways. Consequently, changes may occur in the microbiome, which is adapted to CF lungs. Objectives To investigate the effects of lumacaftor/ivacaftor on respiratory microbial composition and microbial metabolic activity by repeatedly sampling the lower respiratory tract. Methods This was a single-centre longitudinal observational cohort study in adult CF patients with a homozygous Phe508del mutation. Lung function measurements and microbial cultures of sputum were performed as part of routine care. An oral and nasal wash, and a breath sample, were collected before and every 3 months after starting therapy, for up to 12 months. Results Twenty patients were included in this study. Amplicon 16S RNA and metagenomics sequencing revealed that Pseudomonas aeruginosa was most abundant in sputum and seemed to decrease after 6 months of treatment, although this did not reach statistical significance after correction for multiple testing. Two types of untargeted metabolomics analyses in sputum showed a change in metabolic composition between 3 and 9 months that almost returned to baseline levels after 12 months of treatment. The volatile metabolic composition of breath was significantly different after 3 months and remained different from baseline until 12 months follow-up. Conclusions After starting CF transmembrane conductance regulator (CFTR) modulating treatment in CF patients with a homozygous Phe508del mutation, a temporary and moderate change in the lung microbiome is observed, which is mainly characterised by a reduction in the relative abundance of Pseudomonas aeruginosa., Lumacaftor/ivacaftor in adult cystic fibrosis patients with homozygous Phe508del results in temporal and moderate changes in lung microbiome and metabolome, that are mainly characterised by a reduction in the relative abundance of Pseudomonas aeruginosa https://bit.ly/3pcPUfX

Published
2021

31. Three phenotypes of adult-onset asthma

Author

Amelink, M., de Nijs, S. B., de Groot, J. C., van Tilburg, P. M. B., van Spiegel, P. I., Krouwels, F. H., Lutter, R., Zwinderman, A. H., Weersink, E. J. M., ten Brinke, A., Sterk, P. J., and Bel, E. H.

Published
2013
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39. Novel Type 2-high gene clusters associated with corticosteroid sensitivity in COPD

Author

Faiz, A., primary, Pavlidis, S., additional, Kuo, C.S., additional, Rowe, A., additional, Hiemstra, P. S., additional, Timens, W., additional, Berg, M., additional, Wisman, M., additional, Guo, Y., additional, Djukanovic, R., additional, Sterk, P. J., additional, Nawijn, M.C., additional, Adcock, I. M., additional, Chung, K. F., additional, and van den Berge, M., additional

Published
2020
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45. Treatable traits in the European U-BIOPRED adult asthma cohorts

Author

Simpson, Andrew J., Hekking, Pieter-Paul, Shaw, Dominick E., Fleming, L. J., Roberts, Graham, Riley, John H., Bates, Stewart, Sousa, A. R., Bansal, A. T., Pandis, Ioannis, Sun, K., Bakke, Per S., Caruso, Massimo, Dahlen, Barbro, Dahlen, Sven-Erik, Horvath, Ildiko, Krug, Norbert, Montuschi, Paolo, Sandstrom, Thomas, Singer, Florian, Adcock, I. M., Wagers, Scott S., Djukanovic, R., Chung, Kian Fan, Sterk, P. J., Fowler, S. J., Ahmed, H., Auffray, C., Bakke, P., Baribaud, F., Bates, S., Bel, E. H., Bigler, J., Bisgaard, H., Boedigheimer, M. J., Bonnelykke, K., Brandsma, J., Brinkman, P., Bucchioni, E., Burg, D., Bush, A., Caruso, M., Chaiboonchoe, A., Chanez, P., Chung, F. K., Compton, C. H., Corfield, J., D'Amico, A., Dahlen, B., Dahlen, S. E., De Meulder, B., Erpenbeck, V. J., Erzen, D., Fichtner, K., Fitch, N., Formaggio, E., Frey, U., Gahlemann, M., Geiser, T., Goss, V., Guo, Y., Hashimoto, S., Haughney, J., Hedlin, G., Hekking, P. W., Higenbottam, T., Hohlfeld, J. M., Holweg, C., Horvath, I., Howarth, P., James, A. J., Knowles, R., Knox, A. J., Krug, N., Lefaudeux, D., Loza, M. J., Lutter, R., Manta, A., Masefield, S., Matthews, J. G., Mazein, A., Meiser, A., Middelveld, R. J. M., Miralpeix, M., Montuschi, P., Mores, N., Murray, C. S., Musial, J., Myles, D., Pahus, L., Pandis, I., Pavlidis, S., Postle, A., Powel, P., Pratico, G., Puig Valls, M., Rao, N., Riley, J., Roberts, A., Roberts, G., Rowe, A., Sandstrom, T., Schofield, J. P. R., Seibold, W., Selby, A., Shaw, D. E., Sigmund, R., Singer, F., Skipp, P. J., van Aalderen, W. M., van Geest, M., Vestbo, J., Vissing, N. H., Wagener, A. H., Wagers, S. S., Weiszhart, Z., Wheelock, C. E., and Wilson, S. J.

Abstract

mprovements in asthma outcomes have stalled over the past decade, which may be attributed to treating patients on the basis of a generic diagnostic label. The taxonomy “Treatable Traits” was proposed by Agusti et al (2016) as a precision medicine approach for the diagnosis and management of chronic airway diseases that is based on the identification of genetic, phenotypic and psychosocial characteristics for which therapeutic interventions are known to improve respiratory health ...

Published
2019

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