Search

Your search keyword '"Hettne K."' showing total 26 results
Start Over Author "Hettne K."
26 results on '"Hettne K."'

1. The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data

Author

Wittenburg, P., Sustkova, H. Pergl, Montesanti, A., Bloemers, S. M., de Waard, S. H., Musen, M. A., Graybeal, J. B., Hettne, K. M., Jacobsen, A., Pergl, R., Hooft, R. W. W., Staiger, C., van Gelder, C. W. G., Knijnenburg, S. L., van Arkel, A. C., Meerman, B., Wilkinson, M. D., Sansone, S-A, Rocca-Serra, P., McQuilton, P., Gonzalez-Beltran, A. N., Aben, G. J. C., Henning, P., Alencar, S., Ribeiro, C., Silva, C. R. L., Sayao, L., Sales, L., Veiga, V., Lima, J., Dib, S., Xavier, P., Murtinho, R., Tendel, J., Schaap, B. F., Brouwer, P. M., Gavai, A. K., Bouzembrak, Y., Marvin, H. J. P., Mons, A., Kuhn, T., Gambardella, A. A., Azevedo, R. de Miranda, Muhonen, V., van der Naald, M., Smit, N. W., Buys, M. J., de Bruin, T. F., Schoots, F., Goodson, H. J. E., Rzepa, H. S., Jeffery, K. G., Shanahan, H. P., Axton, M., Tkachenko, V., Maya, A. D., Meyers, N. K., Conlon, M., Haak, L. L., and Schultes, E. A.

Subjects
Computer Science - Digital Libraries
Abstract

There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recognizing that high quality metadata are essential to make datasets FAIR, members of the GO FAIR Initiative and the Research Data Alliance (RDA) have initiated a series of workshops to encourage the creation of Metadata for Machines (M4M), enabling any self-identified stakeholder to define and promote the reuse of standardized, comprehensive machine-actionable metadata. The funders of scientific research recognize that they have an important role to play in ensuring that experimental results are FAIR, and that high quality metadata and careful planning for FAIR data stewardship are central to these goals. We describe the outcome of a recent M4M workshop that has led to a pilot programme involving two national science funders, the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW). These funding organizations will explore new technologies to define at the time that a request for proposals is issued the minimal set of machine-actionable metadata that they would like investigators to use to annotate their datasets, to enable investigators to create such metadata to help make their data FAIR, and to develop data-stewardship plans that ensure that experimental data will be managed appropriately abiding by the FAIR principles. The FAIR Funders design envisions a data-management workflow having seven essential stages, where solution providers are openly invited to participate. The initial pilot programme will launch using existing computer-based tools of those who attended the M4M Workshop., Comment: This is a pre-print of the FAIR Funders pilot, an outcome of the first Metadata for Machines workshop, see: https://www.go-fair.org/resources/go-fair-workshop-series/metadata-for-machines-workshops/. Corresponding author: E. A Schultes, ORCID 0000-0001-8888-635X

Published
2019

2. Huntington Disease Gene Expression Signatures in Blood Compared to Brain of YAC128 Mice as Candidates for Monitoring of Pathology

Author

Kuijper, E.C., Toonen, L.J.A., Overzier, M., Tsonaka, R., Hettne, K., Roos, M., Roon-Mom, W.M.C. van, and Mina, E.

Subjects
Huntingtin Protein, YAC128 mice, Neuroscience (miscellaneous), Brain, Mice, Transgenic, Biomarker, Corpus Striatum, Disease Models, Animal, Mice, Cellular and Molecular Neuroscience, Huntington Disease, Neurology, Disease Progression, Animals, Network analysis, Gene expression, Transcriptome, Biological Phenomena
Abstract

While the genetic cause of Huntington disease (HD) is known since 1993, still no cure exists. Therapeutic development would benefit from a method to monitor disease progression and treatment efficacy, ideally using blood biomarkers. Previously, HD-specific signatures were identified in human blood representing signatures in human brain, showing biomarker potential. Since drug candidates are generally first screened in rodent models, we aimed to identify HD signatures in blood and brain of YAC128 HD mice and compare these with previously identified human signatures. RNA sequencing was performed on blood withdrawn at two time points and four brain regions from YAC128 and control mice. Weighted gene co-expression network analysis was used to identify clusters of co-expressed genes (modules) associated with the HD genotype. These HD-associated modules were annotated via text-mining to determine the biological processes they represented. Subsequently, the processes from mouse blood were compared with mouse brain, showing substantial overlap, including protein modification, cell cycle, RNA splicing, nuclear transport, and vesicle-mediated transport. Moreover, the disease-associated processes shared between mouse blood and brain were highly comparable to those previously identified in human blood and brain. In addition, we identified HD blood-specific pathology, confirming previous findings for peripheral pathology in blood. Finally, we identified hub genes for HD-associated blood modules and proposed a strategy for gene selection for development of a disease progression monitoring panel.

Published
2022
Full Text
View/download PDF

3. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Author

Grapotte M., Saraswat M., Bessiere C., Menichelli C., Ramilowski J. A., Severin J., Hayashizaki Y., Itoh M., Tagami M., Murata M., Kojima-Ishiyama M., Noma S., Noguchi S., Kasukawa T., Hasegawa A., Suzuki H., Nishiyori-Sueki H., Frith M. C., Abugessaisa I., Aitken S., Aken B. L., Alam I., Alam T., Alasiri R., Alhendi A. M. N., Alinejad-Rokny H., Alvarez M. J., Andersson R., Arakawa T., Araki M., Arbel T., Archer J., Archibald A. L., Arner E., Arner P., Asai K., Ashoor H., Astrom G., Babina M., Baillie J. K., Bajic V. B., Bajpai A., Baker S., Baldarelli R. M., Balic A., Bansal M., Batagov A. O., Batzoglou S., Beckhouse A. G., Beltrami A. P., Beltrami C. A., Bertin N., Bhattacharya S., Bickel P. J., Blake J. A., Blanchette M., Bodega B., Bonetti A., Bono H., Bornholdt J., Bttcher M., Bougouffa S., Boyd M., Breda J., Brombacher F., Brown J. B., Bult C. J., Burroughs A. M., Burt D. W., Busch A., Caglio G., Califano A., Cameron C. J., Cannistraci C. V., Carbone A., Carlisle A. J., Carninci P., Carter K. W., Cesselli D., Chang J. -C., Chen J. C., Chen Y., Chierici M., Christodoulou J., Ciani Y., Clark E. L., Coskun M., Dalby M., Dalla E., Daub C. O., Davis C. A., de Hoon M. J. L., de Rie D., Denisenko E., Deplancke B., Detmar M., Deviatiiarov R., Di Bernardo D., Diehl A. D., Dieterich L. C., Dimont E., Djebali S., Dohi T., Dostie J., Drablos F., Edge A. S. B., Edinger M., Ehrlund A., Ekwall K., Elofsson A., Endoh M., Enomoto H., Enomoto S., Faghihi M., Fagiolini M., Farach-Carson M. C., Faulkner G. J., Favorov A., Fernandes A. M., Ferrai C., Forrest A. R. R., Forrester L. M., Forsberg M., Fort A., Francescatto M., Freeman T. C., Frith M., Fukuda S., Funayama M., Furlanello C., Furuno M., Furusawa C., Gao H., Gazova I., Gebhard C., Geier F., Geijtenbeek T. B. H., Ghosh S., Ghosheh Y., Gingeras T. R., Gojobori T., Goldberg T., Goldowitz D., Gough J., Greco D., Gruber A. J., Guhl S., Guigo R., Guler R., Gusev O., Gustincich S., Ha T. J., Haberle V., Hale P., Hallstrom B. M., Hamada M., Handoko L., Hara M., Harbers M., Harrow J., Harshbarger J., Hase T., Hashimoto K., Hatano T., Hattori N., Hayashi R., Herlyn M., Hettne K., Heutink P., Hide W., Hitchens K. J., Sui S. H., 't Hoen P. A. C., Hon C. C., Hori F., Horie M., Horimoto K., Horton P., Hou R., Huang E., Huang Y., Hugues R., Hume D., Ienasescu H., Iida K., Ikawa T., Ikemura T., Ikeo K., Inoue N., Ishizu Y., Ito Y., Ivshina A. V., Jankovic B. R., Jenjaroenpun P., Johnson R., Jorgensen M., Jorjani H., Joshi A., Jurman G., Kaczkowski B., Kai C., Kaida K., Kajiyama K., Kaliyaperumal R., Kaminuma E., Kanaya T., Kaneda H., Kapranov P., Kasianov A. S., Katayama T., Kato S., Kawaguchi S., Kawai J., Kawaji H., Kawamoto H., Kawamura Y. I., Kawasaki S., Kawashima T., Kempfle J. S., Kenna T. J., Kere J., Khachigian L., Kiryu H., Kishima M., Kitajima H., Kitamura T., Kitano H., Klaric E., Klepper K., Klinken S. P., Kloppmann E., Knox A. J., Kodama Y., Kogo Y., Kojima M., Kojima S., Komatsu N., Komiyama H., Kono T., Koseki H., Koyasu S., Kratz A., Kukalev A., Kulakovskiy I., Kundaje A., Kunikata H., Kuo R., Kuo T., Kuraku S., Kuznetsov V. A., Kwon T. J., Larouche M., Lassmann T., Law A., Le-Cao K. -A., Lecellier C. -H., Lee W., Lenhard B., Lennartsson A., Li K., Li R., Lilje B., Lipovich L., Lizio M., Lopez G., Magi S., Mak G. K., Makeev V., Manabe R., Mandai M., Mar J., Maruyama K., Maruyama T., Mason E., Mathelier A., Matsuda H., Medvedeva Y. A., Meehan T. F., Mejhert N., Meynert A., Mikami N., Minoda A., Miura H., Miyagi Y., Miyawaki A., Mizuno Y., Morikawa H., Morimoto M., Morioka M., Morishita S., Moro K., Motakis E., Motohashi H., Mukarram A. K., Mummery C. L., Mungall C. J., Murakawa Y., Muramatsu M., Nagasaka K., Nagase T., Nakachi Y., Nakahara F., Nakai K., Nakamura K., Nakamura Y., Nakazawa T., Nason G. P., Nepal C., Nguyen Q. H., Nielsen L. K., Nishida K., Nishiguchi K. M., Nishiyori H., Nitta K., Notredame C., Ogishima S., Ohkura N., Ohno H., Ohshima M., Ohtsu T., Okada Y., Okada-Hatakeyama M., Okazaki Y., Oksvold P., Orlando V., Ow G. S., Ozturk M., Pachkov M., Paparountas T., Parihar S. P., Park S. -J., Pascarella G., Passier R., Persson H., Philippens I. H., Piazza S., Plessy C., Pombo A., Ponten F., Poulain S., Poulsen T. M., Pradhan S., Prezioso C., Pridans C., Qin X. -Y., Quackenbush J., Rackham O., Ramilowski J., Ravasi T., Rehli M., Rennie S., Rito T., Rizzu P., Robert C., Roos M., Rost B., Roudnicky F., Roy R., Rye M. B., Sachenkova O., Saetrom P., Sai H., Saiki S., Saito M., Saito A., Sakaguchi S., Sakai M., Sakaue S., Sakaue-Sawano A., Sandelin A., Sano H., Sasamoto Y., Sato H., Saxena A., Saya H., Schafferhans A., Schmeier S., Schmidl C., Schmocker D., Schneider C., Schueler M., Schultes E. A., Schulze-Tanzil G., Semple C. A., Seno S., Seo W., Sese J., Sheng G., Shi J., Shimoni Y., Shin J. W., SimonSanchez J., Sivertsson A., Sjostedt E., Soderhall C., Laurent G. S., Stoiber M. H., Sugiyama D., Summers K. M., Suzuki A. M., Suzuki K., Suzuki M., Suzuki N., Suzuki T., Swanson D. J., Swoboda R. K., Taguchi A., Takahashi H., Takahashi M., Takamochi K., Takeda S., Takenaka Y., Tam K. T., Tanaka H., Tanaka R., Tanaka Y., Tang D., Taniuchi I., Tanzer A., Tarui H., Taylor M. S., Terada A., Terao Y., Testa A. C., Thomas M., Thongjuea S., Tomii K., Triglia E. T., Toyoda H., Tsang H. G., Tsujikawa M., Uhlen M., Valen E., van de Wetering M., van Nimwegen E., Velmeshev D., Verardo R., Vitezic M., Vitting-Seerup K., von Feilitzen K., Voolstra C. R., Vorontsov I. E., Wahlestedt C., Wasserman W. W., Watanabe K., Watanabe S., Wells C. A., Winteringham L. N., Wolvetang E., Yabukami H., Yagi K., Yamada T., Yamaguchi Y., Yamamoto M., Yamamoto Y., Yamanaka Y., Yano K., Yasuzawa K., Yatsuka Y., Yo M., Yokokura S., Yoneda M., Yoshida E., Yoshida Y., Yoshihara M., Young R., Young R. S., Yu N. Y., Yumoto N., Zabierowski S. E., Zhang P. G., Zucchelli S., Zwahlen M., Chatelain C., Brehelin L., Grapotte, M., Saraswat, M., Bessiere, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S., Aken, B. L., Alam, I., Alam, T., Alasiri, R., Alhendi, A. M. N., Alinejad-Rokny, H., Alvarez, M. J., Andersson, R., Arakawa, T., Araki, M., Arbel, T., Archer, J., Archibald, A. L., Arner, E., Arner, P., Asai, K., Ashoor, H., Astrom, G., Babina, M., Baillie, J. K., Bajic, V. B., Bajpai, A., Baker, S., Baldarelli, R. M., Balic, A., Bansal, M., Batagov, A. O., Batzoglou, S., Beckhouse, A. G., Beltrami, A. P., Beltrami, C. A., Bertin, N., Bhattacharya, S., Bickel, P. J., Blake, J. A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J. B., Bult, C. J., Burroughs, A. M., Burt, D. W., Busch, A., Caglio, G., Califano, A., Cameron, C. J., Cannistraci, C. V., Carbone, A., Carlisle, A. J., Carninci, P., Carter, K. W., Cesselli, D., Chang, J. -C., Chen, J. C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E. L., Coskun, M., Dalby, M., Dalla, E., Daub, C. O., Davis, C. A., de Hoon, M. J. L., de Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A. D., Dieterich, L. C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A. S. B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-Carson, M. C., Faulkner, G. J., Favorov, A., Fernandes, A. M., Ferrai, C., Forrest, A. R. R., Forrester, L. M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T. C., Frith, M., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T. B. H., Ghosh, S., Ghosheh, Y., Gingeras, T. R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A. J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T. J., Haberle, V., Hale, P., Hallstrom, B. M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K. J., Sui, S. H., 't Hoen, P. A. C., Hon, C. C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Ivshina, A. V., Jankovic, B. R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A. S., Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y. I., Kawasaki, S., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S. P., Kloppmann, E., Knox, A. J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V. A., Kwon, T. J., Larouche, M., Lassmann, T., Law, A., Le-Cao, K. -A., Lecellier, C. -H., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G. K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y. A., Meehan, T. F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A. K., Mummery, C. L., Mungall, C. J., Murakawa, Y., Muramatsu, M., Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakazawa, T., Nason, G. P., Nepal, C., Nguyen, Q. H., Nielsen, L. K., Nishida, K., Nishiguchi, K. M., Nishiyori, H., Nitta, K., Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-Hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G. S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S. P., Park, S. -J., Pascarella, G., Passier, R., Persson, H., Philippens, I. H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T. M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X. -Y., Quackenbush, J., Rackham, O., Ramilowski, J., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M. B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-Sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E. A., Schulze-Tanzil, G., Semple, C. A., Seno, S., Seo, W., Sese, J., Sheng, G., Shi, J., Shimoni, Y., Shin, J. W., Simonsanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G. S., Stoiber, M. H., Sugiyama, D., Summers, K. M., Suzuki, A. M., Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D. J., Swoboda, R. K., Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K. T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M. S., Terada, A., Terao, Y., Testa, A. C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E. T., Toyoda, H., Tsang, H. G., Tsujikawa, M., Uhlen, M., Valen, E., van de Wetering, M., van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-Seerup, K., von Feilitzen, K., Voolstra, C. R., Vorontsov, I. E., Wahlestedt, C., Wasserman, W. W., Watanabe, K., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R. S., Yu, N. Y., Yumoto, N., Zabierowski, S. E., Zhang, P. G., Zucchelli, S., Zwahlen, M., Chatelain, C., Brehelin, L., Institute of Biotechnology, Biosciences, Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), National Institute of Advanced Industrial Science and Technology (AIST), SANOFI Recherche, University of British Columbia (UBC), Experimental Immunology, Infectious diseases, AII - Infectious diseases, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)

Subjects
0301 basic medicine, General Physics and Astronomy, Genome, Mice, 0302 clinical medicine, Transcription (biology), Promoter Regions, Genetic, Transcription Initiation, Genetic, 0303 health sciences, Multidisciplinary, 1184 Genetics, developmental biology, physiology, High-Throughput Nucleotide Sequencing, Neurodegenerative Diseases, 222 Other engineering and technologies, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], humanities, Enhancer Elements, Genetic, Microsatellite Repeat, Transcription Initiation Site, Sequence motif, Transcription Initiation, Human, Enhancer Elements, Neural Networks, Science, 610 Medicine & health, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Promoter Regions, 03 medical and health sciences, Computer, Deep Learning, Tandem repeat, Genetic, Clinical Research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Machine learning, Genetics, Animals, Humans, Polymorphism, Enhancer, Transcriptomics, Gene, A549 Cell, 030304 developmental biology, Polymorphism, Genetic, Neurodegenerative Disease, Base Sequence, Animal, Genome, Human, Human Genome, Computational Biology, Promoter, General Chemistry, 113 Computer and information sciences, Cap analysis gene expression, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Cardiovascular and Metabolic Diseases, A549 Cells, Minion, Generic health relevance, 3111 Biomedicine, Neural Networks, Computer, 610 Medizin und Gesundheit, 030217 neurology & neurosurgery, FANTOM consortium, Microsatellite Repeats
Abstract

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism., Nature Communications, 12 (1), ISSN:2041-1723

Published
2020
Full Text
View/download PDF

4. The use or generation of biomedical data and existing medicines to discover and establish new treatments for patients with rare diseases - recommendations of the IRDiRC Data Mining and Repurposing Task Force

Author

Southall, N.T., Natarajan, M., Lau, L.P.L., Jonker, A.H., Deprez, B., Guilliams, T., Hunter, L., Rademaker, C.M.A., Hivert, V., Ardigo, D., Cavalla, D., Colvis, C., Hettne, K., t'Hoen, P.B., Kant, C., Krischer, J., Marin, F., Quintana, J., Rademaker, C., Reed, J., Southali, N., Tsigkos, S., Thompson, R., and IRDiRC Data Min Repurposing Task

Subjects
Big Data, 0301 basic medicine, Biomedical Research, Databases, Factual, Computer science, IRDiRC, lcsh:Medicine, Drug development, computer.software_genre, Orphan drug, 03 medical and health sciences, Rare Diseases, 0302 clinical medicine, Humans, Genetics(clinical), Pharmacology (medical), Position Statement, Data mining, Genetics (clinical), Repurposing, Pace, Task force, lcsh:R, Repositioning, Drug Repositioning, General Medicine, Precision medicine, 3. Good health, Drug repositioning, 030104 developmental biology, Therapies, computer, Rare disease, Orphan medical product, 030217 neurology & neurosurgery
Abstract

The number of available therapies for rare diseases remains low, as fewer than 6% of rare diseases have an approved treatment option. The International Rare Diseases Research Consortium (IRDiRC) set up the multi-stakeholder Data Mining and Repurposing (DMR) Task Force to examine the potential of applying biomedical data mining strategies to identify new opportunities to use existing pharmaceutical compounds in new ways and to accelerate the pace of drug development for rare disease patients. In reviewing past successes of data mining for drug repurposing, and planning for future biomedical research capacity, the DMR Task Force identified four strategic infrastructure investment areas to focus on in order to accelerate rare disease research productivity and drug development: (1) improving the capture and sharing of self-reported patient data, (2) better integration of existing research data, (3) increasing experimental testing capacity, and (4) sharing of rare disease research and development expertise. Additionally, the DMR Task Force also recommended a number of strategies to increase data mining and repurposing opportunities for rare diseases research as well as the development of individualized and precision medicine strategies.

Published
2019
Full Text
View/download PDF

5. Tracking disease progression non-invasively in Duchenne and Becker muscular dystrophies

Author

Spitali, P., Hettne, K., Tsonaka, R., Charrout, M., Bergen, J. van den, Koeks, Z., Kan, H.E., Hooijmans, M.T., Roos, A., Straub, V., Muntoni, F., Al-Khalili-Szigyarto, C., Koel-Simmelink, M.J., Teunissen, C.E., Lochmuller, H., Niks, E.H., Aartsma-Rus, A., Clinical chemistry, Amsterdam Neuroscience - Neurodegeneration, and Amsterdam Reproduction & Development (AR&D)

Subjects
musculoskeletal diseases, Duchenne muscular dystrophy, Proteomics, Sarcopenia, Becker muscular dystrophy, Longitudinal analysis, Biomarker
Abstract

Background: Analysis of muscle biopsies allowed to characterize the pathophysiological changes of Duchenne and Becker muscular dystrophies (D/BMD) leading to the clinical phenotype. Muscle tissue is often investigated during interventional dose finding studies to show in situ proof of concept and pharmacodynamics effect of the tested drug. Less invasive readouts are needed to objectively monitor patients' health status, muscle quality, and response to treatment. The identification of serum biomarkers correlating with clinical function and able to anticipate functional scales is particularly needed for personalized patient management and to support drug development programs. Methods: A large-scale proteomic approach was used to identify serum biomarkers describing pathophysiological changes (e.g. loss of muscle mass), association with clinical function, prediction of disease milestones, association with in vivo 31P magnetic resonance spectroscopy data and dystrophin levels in muscles. Cross-sectional comparisons were performed to compare DMD patients, BMD patients, and healthy controls. A group of DMD patients was followed up for a median of 4.4 years to allow monitoring of individual disease trajectories based on yearly visits. Results: Cross-sectional comparison enabled to identify 10 proteins discriminating between healthy controls, DMD and BMD patients. Several proteins (285) were able to separate DMD from healthy, while 121 proteins differentiated between BMD and DMD; only 13 proteins separated BMD and healthy individuals. The concentration of specific proteins in serum was significantly associated with patients' performance (e.g. BMP6 serum levels and elbow flexion) or dystrophin levels (e.g. TIMP2) in BMD patients. Analysis of longitudinal trajectories allowed to identify 427 proteins affected over time indicating loss of muscle mass, replacement of muscle by adipose tissue, and cardiac involvement. Over-representation analysis of longitudinal data allowed to highlight proteins that could be used as pharmacodynamic biomarkers for drugs currently in clinical development. Conclusions: Serum proteomic analysis allowed to not only discriminate among DMD, BMD, and healthy subjects, but it enabled to detect significant associations with clinical function, dystrophin levels, and disease progression.

Published
2018
Full Text
View/download PDF

6. Metabolomics analysis in serum of muscular dystrophy patients

Author

Spitali, P., primary, Hettne, K., additional, Tsonaka, R., additional, Sabir, E., additional, Seyer, A., additional, Hemerik, J.B.A., additional, Goeman, J.J., additional, Picillo, E., additional, Ergoli, M., additional, Politano, L., additional, and Aartsma-Rus, A., additional

Published
2018
Full Text
View/download PDF

8. Longitudinal proteomic analysis of sera allows to non-invasively monitor disease progression in Duchenne muscular dystrophy

Author

Spitali, P., Tsonaka, R., Hettne, K., Koeks, Z., Roos, A., Straub, V., Domingos, J. Piscos, Muntoni, F., Al-Khalili-Szigyarto, Cristina, Lochmueller, H., Niks, E., Aartsma-Rus, A., Spitali, P., Tsonaka, R., Hettne, K., Koeks, Z., Roos, A., Straub, V., Domingos, J. Piscos, Muntoni, F., Al-Khalili-Szigyarto, Cristina, Lochmueller, H., Niks, E., and Aartsma-Rus, A.

Abstract

QC 20171106

Published
2017
Full Text
View/download PDF

9. Early career researchers want Open Science

Author

Farnham, A, Kurz, C, Oeztuerk, MA, Solbiati, M, Myllyntaus, O, Meekes, J, Pham, TM, Paz, C, Langiewicz, M, Andrews, S, Kanninen, L, Agbemabiese, C, Guler, AT, Durieux, J, Jasim, S, Viessmann, O, Frattini, S, Yembergenova, D, Benito, CM, Porte, M, Grangeray-Vilmint, A, Curiel, RP, Rehncrona, C, Malas, T, Esposito, F, Hettne, K, Farnham, A, Kurz, C, Oeztuerk, MA, Solbiati, M, Myllyntaus, O, Meekes, J, Pham, TM, Paz, C, Langiewicz, M, Andrews, S, Kanninen, L, Agbemabiese, C, Guler, AT, Durieux, J, Jasim, S, Viessmann, O, Frattini, S, Yembergenova, D, Benito, CM, Porte, M, Grangeray-Vilmint, A, Curiel, RP, Rehncrona, C, Malas, T, Esposito, F, and Hettne, K

Abstract

Open Science is encouraged by the European Union and many other political and scientific institutions. However, scientific practice is proving slow to change. We propose, as early career researchers, that it is our task to change scientific research into open scientific research and commit to Open Science principles.

Published
2017

11. Why workflows break — understanding and combating decay in Taverna workflows

Author

Zhao, J, Gómez-Pérez, J, Belhajjame, K, Klyne, G, García-Cuesta, E, Garrido, A, Hettne, K, Roos, M, Roure, D, and Goble, C

Abstract

Workflows provide a popular means for preserving scientific methods by explicitly encoding their process. However, some of them are subject to a decay in their ability to be re-executed or reproduce the same results over time, largely due to the volatility of the resources required for workflow executions. This paper provides an analysis of the root causes of workflow decay based on an empirical study of a collection of Taverna workflows from the myExperiment repository. Although our analysis was based on a specific type of workflow, the outcomes and methodology should be applicable to workflows from other systems, at least those whose executions also rely largely on accessing third-party resources. Based on our understanding about decay we recommend a minimal set of auxiliary resources to be preserved together with the workflows as an aggregation object and provide a software tool for end-users to create such aggregations and to assess their completeness. ©2012 IEEE.

Published
2012
Full Text
View/download PDF

13. Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles

Author

Dharuri, H, Henneman, Peter, Demirkan, Ayse, van Klinken, JB, Mook, Dennis, Wang-Sattler, R, Gieger, C, Adamski, J, Hettne, K, Roos, M (Marco), Suhre, K, Duijn, Cornelia, van Dijk, KW, 't Hoen, PAC, Dharuri, H, Henneman, Peter, Demirkan, Ayse, van Klinken, JB, Mook, Dennis, Wang-Sattler, R, Gieger, C, Adamski, J, Hettne, K, Roos, M (Marco), Suhre, K, Duijn, Cornelia, van Dijk, KW, and 't Hoen, PAC

Abstract

Background: Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) that associate with clinical phenotypes, but these SNPs usually explain just a small part of the heritability and have relatively modest effect sizes. In contrast, SNPs that associate with metabolite levels generally explain a higher percentage of the genetic variation and demonstrate larger effect sizes. Still, the discovery of SNPs associated with metabolite levels is challenging since testing all metabolites measured in typical metabolomics studies with all SNPs comes with a severe multiple testing penalty. We have developed an automated workflow approach that utilizes prior knowledge of biochemical pathways present in databases like KEGG and BioCyc to generate a smaller SNP set relevant to the metabolite. This paper explores the opportunities and challenges in the analysis of GWAS of metabolomic phenotypes and provides novel insights into the genetic basis of metabolic variation through the re-analysis of published GWAS datasets. Results: Re-analysis of the published GWAS dataset from Illig et al. (Nature Genetics, 2010) using a pathway-based workflow (http://www.myexperiment.org/packs/319.html), confirmed previously identified hits and identified a new locus of human metabolic individuality, associating Aldehyde dehydrogenase family1 L1 (ALDH1L1) with serine/glycine ratios in blood. Replication in an independent GWAS dataset of phospholipids (Demirkan et al., PLoS Genetics, 2012) identified two novel loci supported by a Conclusions: We demonstrate the utility of automated exploitation of background knowledge present in pathway databases for the analysis of GWAS datasets of metabolomic phenotypes. We report novel loci and potential biochemical mechanisms that contribute to our understanding of the genetic basis of metabolic variation and its relationship to disease development and progression.

Published
2013

16. Best practices for workflow design: How to prevent workflow decay

Author

Hettne, K., Wolstencroft, K., Belhajjame, K., Goble, C., Eleni Mina, Dharuri, H., Verdes-Montenegro, L., Garrido, J., Roure, D., Roos, M., Paschke, Adrian, Burger, Albert, Romano, Paolo, Marshall, M. Scott, and Splendiani, Andrea

Subjects
Best practices, InformationSystems_INFORMATIONSYSTEMSAPPLICATIONS, Scientific workflows, Decay
Abstract

In this position paper we present a set of best practices for workflow design to prevent workflow decay and increase reuse and re-purposing of scientific workflows. MyExperiment provides access to a large number of scientific workflows. However, scientists find it difficult to reuse or re-purpose these workflows for mainly two reasons: workflows suffer from decay over time and lack sufficient metadata to understand their purpose. We argue that good workflow design is a prerequisite for repairing a workflow, or redesigning an equivalent workflow pattern with new components. We present a set of best practices for workflow design and the semantic tooling that is being developed in the Workflow4Ever (Wf4Ever) project to support these best practices.

18. Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients.

Author

Signorelli M, Ebrahimpoor M, Veth O, Hettne K, Verwey N, García-Rodríguez R, Tanganyika-deWinter CL, Lopez Hernandez LB, Escobar Cedillo R, Gómez Díaz B, Magnusson OT, Mei H, Tsonaka R, Aartsma-Rus A, and Spitali P

Subjects
Animals, Disease Progression, Gene Expression Profiling, Humans, Mice, Mice, Inbred mdx, Muscle, Skeletal, Transcriptome, Muscular Dystrophy, Duchenne genetics
Abstract

DMD is a rare disorder characterized by progressive muscle degeneration and premature death. Therapy development is delayed by difficulties to monitor efficacy non-invasively in clinical trials. In this study, we used RNA-sequencing to describe the pathophysiological changes in skeletal muscle of 3 dystrophic mouse models. We show how dystrophic changes in muscle are reflected in blood by analyzing paired muscle and blood samples. Analysis of repeated blood measurements followed the dystrophic signature at five equally spaced time points over a period of seven months. Treatment with two antisense drugs harboring different levels of dystrophin recovery identified genes associated with safety and efficacy. Evaluation of the blood gene expression in a cohort of DMD patients enabled the comparison between preclinical models and patients, and the identification of genes associated with physical performance, treatment with corticosteroids and body measures. The presented results provide evidence that blood RNA-sequencing can serve as a tool to evaluate disease progression in dystrophic mice and patients, as well as to monitor response to (dystrophin-restoring) therapies in preclinical drug development and in clinical trials., (© 2021 The Authors. Published under the terms of the CC BY 4.0 license.)

Published
2021
Full Text
View/download PDF

19. Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods.

Author

Ebrahimpoor M, Spitali P, Hettne K, Tsonaka R, and Goeman J

Subjects
Animals, Confidence Intervals, Genome-Wide Association Study, Humans, Mice, Models, Statistical, Genomics methods
Abstract

Studying sets of genomic features is increasingly popular in genomics, proteomics and metabolomics since analyzing at set level not only creates a natural connection to biological knowledge but also offers more statistical power. Currently, there are two gene-set testing approaches, self-contained and competitive, both of which have their advantages and disadvantages, but neither offers the final solution. We introduce simultaneous enrichment analysis (SEA), a new approach for analysis of feature sets in genomics and other omics based on a new unified null hypothesis, which includes the self-contained and competitive null hypotheses as special cases. We employ closed testing using Simes tests to test this new hypothesis. For every feature set, the proportion of active features is estimated, and a confidence bound is provided. Also, for every unified null hypotheses, a $P$-value is calculated, which is adjusted for family-wise error rate. SEA does not need to assume that the features are independent. Moreover, users are allowed to choose the feature set(s) of interest after observing the data. We develop a novel pipeline and apply it on RNA-seq data of dystrophin-deficient mdx mice, showcasing the flexibility of the method. Finally, the power properties of the method are evaluated through simulation studies., (© The Author(s) 2019. Published by Oxford University Press.)

Published
2020
Full Text
View/download PDF

20. Longitudinal metabolomic analysis of plasma enables modeling disease progression in Duchenne muscular dystrophy mouse models.

Author

Tsonaka R, Signorelli M, Sabir E, Seyer A, Hettne K, Aartsma-Rus A, and Spitali P

Subjects
Animals, Cross-Sectional Studies, Disease Progression, Longitudinal Studies, Mice, Mice, Inbred mdx, Disease Models, Animal, Metabolome, Muscle, Skeletal metabolism, Muscle, Skeletal pathology, Muscular Dystrophy, Duchenne blood, Muscular Dystrophy, Duchenne pathology
Abstract

Duchenne muscular dystrophy is a severe pediatric neuromuscular disorder caused by the lack of dystrophin. Identification of biomarkers is needed to support and accelerate drug development. Alterations of metabolites levels in muscle and plasma have been reported in pre-clinical and clinical cross-sectional comparisons. We present here a 7-month longitudinal study comparing plasma metabolomic data in wild-type and mdx mice. A mass spectrometry approach was used to study metabolites in up to five time points per mouse at 6, 12, 18, 24 and 30 weeks of age, providing an unprecedented in depth view of disease trajectories. A total of 106 metabolites were studied. We report a signature of 31 metabolites able to discriminate between healthy and disease at various stages of the disease, covering the acute phase of muscle degeneration and regeneration up to the deteriorating phase. We show how metabolites related to energy production and chachexia (e.g. glutamine) are affected in mdx mice plasma over time. We further show how the signature is connected to molecular targets of nutraceuticals and pharmaceutical compounds currently in development as well as to the nitric oxide synthase pathway (e.g. arginine and citrulline). Finally, we evaluate the signature in a second longitudinal study in three independent mouse models carrying 0, 1 or 2 functional copies of the dystrophin paralog utrophin. In conclusion, we report an in-depth metabolomic signature covering previously identified associations and new associations, which enables drug developers to peripherally assess the effect of drugs on the metabolic status of dystrophic mice., (© The Author(s) 2020. Published by Oxford University Press.)

Published
2020
Full Text
View/download PDF

21. Cross-sectional serum metabolomic study of multiple forms of muscular dystrophy.

Author

Spitali P, Hettne K, Tsonaka R, Sabir E, Seyer A, Hemerik JBA, Goeman JJ, Picillo E, Ergoli M, Politano L, and Aartsma-Rus A

Subjects
Adolescent, Adult, Female, Humans, Male, Middle Aged, Muscles pathology, Muscular Dystrophies classification, Muscular Dystrophies pathology, Muscular Dystrophies, Limb-Girdle blood, Muscular Dystrophies, Limb-Girdle pathology, Muscular Dystrophy, Duchenne blood, Muscular Dystrophy, Duchenne pathology, Muscular Dystrophy, Facioscapulohumeral blood, Muscular Dystrophy, Facioscapulohumeral pathology, Myotonic Dystrophy blood, Myotonic Dystrophy pathology, Young Adult, Metabolomics, Muscles metabolism, Muscular Dystrophies blood
Abstract

Muscular dystrophies are characterized by a progressive loss of muscle tissue and/or muscle function. While metabolic alterations have been described in patients'-derived muscle biopsies, non-invasive readouts able to describe these alterations are needed in order to objectively monitor muscle condition and response to treatment targeting metabolic abnormalities. We used a metabolomic approach to study metabolites concentration in serum of patients affected by multiple forms of muscular dystrophy such as Duchenne and Becker muscular dystrophies, limb-girdle muscular dystrophies type 2A and 2B, myotonic dystrophy type 1 and facioscapulohumeral muscular dystrophy. We show that 15 metabolites involved in energy production, amino acid metabolism, testosterone metabolism and response to treatment with glucocorticoids were differentially expressed between healthy controls and Duchenne patients. Five metabolites were also able to discriminate other forms of muscular dystrophy. In particular, creatinine and the creatine/creatinine ratio were significantly associated with Duchenne patients performance as assessed by the 6-minute walk test and north star ambulatory assessment. The obtained results provide evidence that metabolomics analysis of serum samples can provide useful information regarding muscle condition and response to treatment, such as to glucocorticoids treatment., (© 2018 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.)

Published
2018
Full Text
View/download PDF

22. Early career researchers want Open Science.

Author

Farnham A, Kurz C, Öztürk MA, Solbiati M, Myllyntaus O, Meekes J, Pham TM, Paz C, Langiewicz M, Andrews S, Kanninen L, Agbemabiese C, Guler AT, Durieux J, Jasim S, Viessmann O, Frattini S, Yembergenova D, Benito CM, Porte M, Grangeray-Vilmint A, Curiel RP, Rehncrona C, Malas T, Esposito F, and Hettne K

Subjects
Databases as Topic, Research Personnel, Science
Abstract

Open Science is encouraged by the European Union and many other political and scientific institutions. However, scientific practice is proving slow to change. We propose, as early career researchers, that it is our task to change scientific research into open scientific research and commit to Open Science principles.

Published
2017
Full Text
View/download PDF

23. Common disease signatures from gene expression analysis in Huntington's disease human blood and brain.

Author

Mina E, van Roon-Mom W, Hettne K, van Zwet E, Goeman J, Neri C, A C 't Hoen P, Mons B, and Roos M

Subjects
Biomarkers blood, Biomarkers metabolism, Brain pathology, Disease Progression, Gene Expression genetics, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Humans, Huntington Disease genetics, Brain metabolism, Huntington Disease blood, Huntington Disease metabolism
Abstract

Background: Huntington's disease (HD) is a devastating brain disorder with no effective treatment or cure available. The scarcity of brain tissue makes it hard to study changes in the brain and impossible to perform longitudinal studies. However, peripheral pathology in HD suggests that it is possible to study the disease using peripheral tissue as a monitoring tool for disease progression and/or efficacy of novel therapies. In this study, we investigated if blood can be used to monitor disease severity and progression in brain. Since previous attempts using only gene expression proved unsuccessful, we compared blood and brain Huntington's disease signatures in a functional context., Methods: Microarray HD gene expression profiles from three brain regions were compared to the transcriptome of HD blood generated by next generation sequencing. The comparison was performed with a combination of weighted gene co-expression network analysis and literature based functional analysis (Concept Profile Analysis). Uniquely, our comparison of blood and brain datasets was not based on (the very limited) gene overlap but on the similarity between the gene annotations in four different semantic categories: "biological process", "cellular component", "molecular function" and "disease or syndrome"., Results: We identified signatures in HD blood reflecting a broad pathophysiological spectrum, including alterations in the immune response, sphingolipid biosynthetic processes, lipid transport, cell signaling, protein modification, spliceosome, RNA splicing, vesicle transport, cell signaling and synaptic transmission. Part of this spectrum was reminiscent of the brain pathology. The HD signatures in caudate nucleus and BA4 exhibited the highest similarity with blood, irrespective of the category of semantic annotations used. BA9 exhibited an intermediate similarity, while cerebellum had the least similarity. We present two signatures that were shared between blood and brain: immune response and spinocerebellar ataxias., Conclusions: Our results demonstrate that HD blood exhibits dysregulation that is similar to brain at a functional level, but not necessarily at the level of individual genes. We report two common signatures that can be used to monitor the pathology in brain of HD patients in a non-invasive manner. Our results are an exemplar of how signals in blood data can be used to represent brain disorders. Our methodology can be used to study disease specific signatures in diseases where heterogeneous tissues are involved in the pathology.

Published
2016
Full Text
View/download PDF

24. Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles.

Author

Dharuri H, Henneman P, Demirkan A, van Klinken JB, Mook-Kanamori DO, Wang-Sattler R, Gieger C, Adamski J, Hettne K, Roos M, Suhre K, Van Duijn CM, van Dijk KW, and 't Hoen PA

Subjects
Genome-Wide Association Study, Humans, Linear Models, Polymorphism, Single Nucleotide, Software, Workflow, Computational Biology methods, Databases, Genetic, Electronic Data Processing, Metabolic Networks and Pathways genetics, Metabolome
Abstract

Background: Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) that associate with clinical phenotypes, but these SNPs usually explain just a small part of the heritability and have relatively modest effect sizes. In contrast, SNPs that associate with metabolite levels generally explain a higher percentage of the genetic variation and demonstrate larger effect sizes. Still, the discovery of SNPs associated with metabolite levels is challenging since testing all metabolites measured in typical metabolomics studies with all SNPs comes with a severe multiple testing penalty. We have developed an automated workflow approach that utilizes prior knowledge of biochemical pathways present in databases like KEGG and BioCyc to generate a smaller SNP set relevant to the metabolite. This paper explores the opportunities and challenges in the analysis of GWAS of metabolomic phenotypes and provides novel insights into the genetic basis of metabolic variation through the re-analysis of published GWAS datasets., Results: Re-analysis of the published GWAS dataset from Illig et al. (Nature Genetics, 2010) using a pathway-based workflow (http://www.myexperiment.org/packs/319.html), confirmed previously identified hits and identified a new locus of human metabolic individuality, associating Aldehyde dehydrogenase family1 L1 (ALDH1L1) with serine/glycine ratios in blood. Replication in an independent GWAS dataset of phospholipids (Demirkan et al., PLoS Genetics, 2012) identified two novel loci supported by additional literature evidence: GPAM (Glycerol-3 phosphate acyltransferase) and CBS (Cystathionine beta-synthase). In addition, the workflow approach provided novel insight into the affected pathways and relevance of some of these gene-metabolite pairs in disease development and progression., Conclusions: We demonstrate the utility of automated exploitation of background knowledge present in pathway databases for the analysis of GWAS datasets of metabolomic phenotypes. We report novel loci and potential biochemical mechanisms that contribute to our understanding of the genetic basis of metabolic variation and its relationship to disease development and progression.

Published
2013
Full Text
View/download PDF

25. Connecting small molecules to nuclear receptor pathways.

Author

Hettne K, Cases M, Boyer S, and Mestres J

Subjects
Drug Design, Humans, Proteasome Endopeptidase Complex metabolism, Signal Transduction, Receptors, Cytoplasmic and Nuclear metabolism
Abstract

Many efforts are currently being made to connect small molecules to target proteins by extracting pharmacological data from bibliographic sources and storing them in annotated chemical libraries. Here, small molecules are further connected to biological pathways, with particular focus to pathways involving members of the nuclear receptor family. The results bring to light the relative importance for molecules on gaining selectivity at the target level, when the target has an intrinsic promiscuity at the pathway level, and highlight the implications for drug discovery to address current challenges related to poor drug efficacy and toxicity. Details on the main limitations encountered during the molecule-to-target-to-pathway annotation process are also discussed.

Published
2007
Full Text
View/download PDF

26. Chemical and biological profiling of an annotated compound library directed to the nuclear receptor family.

Author

Cases M, García-Serna R, Hettne K, Weeber M, van der Lei J, Boyer S, and Mestres J

Subjects
Drug Design, Ligands, Molecular Structure, Organic Chemicals pharmacology, Receptors, Cytoplasmic and Nuclear drug effects, Structure-Activity Relationship, Combinatorial Chemistry Techniques methods, Receptors, Cytoplasmic and Nuclear chemistry
Abstract

Nuclear receptors form a family of ligand-activated transcription factors that regulate a wide variety of biological processes and are thus generally considered relevant targets in drug discovery. We have constructed an annotated compound library directed to nuclear receptors (NRacl) as a means for integrating the chemical and biological data being generated within this family. Special care has been put in the appropriate storage of annotations by using hierarchical classification schemes for both molecules and nuclear receptors, which takes the ability to extract knowledge from annotated compound libraries to another level. Analysis of NRacl has ultimately led to the identification of scaffolds with highly promiscuous nuclear receptor profiles and to the classification of nuclear receptor groups with similar scaffold promiscuity patterns. This information can be exploited in the design of probing libraries for deorphanization activities as well as for devising screening batteries to address selectivity issues.

Published
2005
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results