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2. Theme 02 - Genetics and Genomics.

Author

Baindoor, S., Gibriel, H., Donovan, P., Veno, M., Kjems, J., van den Berg, L., van Es, M., Prehn, J., Biasetti, L., Troakes, C., King, A., Smith, B., Grant, O., Gromicho, M., Simão, S., Pronto-Laborinho, A., Oliveira Santos, M., De Carvalho, M., Domínguez-Rubio, R., and Lombardo, P.

Subjects
AMYOTROPHIC lateral sclerosis, GENETICS, GENOMICS, RESEARCH personnel
Abstract

The text is a list of authors who have contributed to an article titled "Theme 02 - Genetics and Genomics" in the journal "Amyotrophic Lateral Sclerosis & Frontotemporal Degeneration." The article likely discusses the role of genetics and genomics in the development and progression of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). The list of authors is extensive and includes researchers from various institutions and countries, indicating a diverse range of perspectives and expertise in the field. [Extracted from the article]

Published
2023
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4. Chitosan/siRNA functionalized titanium surface via a layer-by-layer approach for in vitro sustained gene silencing and osteogenic promotion

Author

Song W, Song X, Yang C, Gao S, Klausen LH, Zhang Y, Dong M, and Kjems J

Subjects
Medicine (General), R5-920
Abstract

Wen Song,1,* Xin Song,2,* Chuanxu Yang,2 Shan Gao,2 Lasse Hyldgaard Klausen,2 Yumei Zhang,1 Mingdong Dong,2 Jørgen Kjems21State Key Laboratory of Military Stomatology, Department of Prosthetic Dentistry, School of Stomatology, The Fourth Military Medical University, Xi’an, People’s Republic of China; 2Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark*These authors contributed equally to this workAbstract: Titanium surface modification is crucial to improving its bioactivity, mainly its bone binding ability in bone implant materials. In order to functionalize titanium with small interfering RNA (siRNA) for sustained gene silencing in nearby cells, the layer-by-layer (LbL) approach was applied using sodium hyaluronate and chitosan/siRNA (CS/siRNA) nanoparticles as polyanion and polycation, respectively, to build up the multilayered film on smooth titanium surfaces. The CS/siRNA nanoparticle characterization was analyzed first. Dynamic contact angle, atomic force microscopy, and scanning electron microscopy were used to monitor the layer accumulation. siRNA loaded in the film was quantitated and the release profile of film in phosphate-buffered saline was studied. In vitro knockdown effect and cytotoxicity evaluation of the film were investigated using H1299 human lung carcinoma cells expressing green fluorescent protein (GFP). The transfection of human osteoblast-like cell MG63 and H1299 were performed and the osteogenic differentiation of MG63 on LbL film was analyzed. The CS/siRNA nanoparticles exhibited nice size distribution. During formation of the film, the surface wettability, topography, and roughness were alternately changed, indicating successful adsorption of the individual layers. The scanning electron microscope images clearly demonstrated the hybrid structure between CS/siRNA nanoparticles and sodium hyaluronate polymer. The cumulated load of siRNA increased linearly with the bilayer number and, more importantly, a gradual release of the film allowed the siRNA to be maintained on the titanium surface over approximately 1 week. In vitro transfection revealed that the LbL film-associated siRNA could consistently suppress GFP expression in H1299 without showing significant cytotoxicity. The LbL film loading with osteogenic siRNA could dramatically increase the osteogenic differentiation in MG63. In conclusion, LbL technology can potentially modify titanium surfaces with specific gene-regulatory siRNAs to enhance biofunction.Keywords: sustained gene silencing, osteogenic differentiation, chitosan, small interfering RNA, titanium

Published
2015

7. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, N., Almouzni, G., Gorski, S., Aerts, S., Amit, I., Bertero, M., Bock, C., Bredenoord, A., Cavalli, G., Chiocca, S., Clevers, H., Strooper, B., Eggert, A., Ellenberg, J., Fernández, X., Figlerowicz, M., Gasser, S., Hubner, N., Kjems, J., Knoblich, J., Krabbe, G., Lichter, P., Linnarsson, S., Marine, J., Marioni, J., Marti-Renom, M., Netea, M., Nickel, D., Nollmann, M., Novak, H., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F., Torres-Padilla, M., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M., Voet, T., Alberi, L., Alexander, S., Alexandrov, T., Arenas, E., Bagni, C., Balderas, R., Bandelli, A., Becher, B., Becker, M., Beerenwinkel, N., Benkirame, M., Beyer, M., Bickmore, W., Biessen, E., Blomberg, N., Blumcke, I., Bodenmiller, B., Borroni, B., Boumpas, D., Bourgeron, T., Bowers, S., Braeken, D., Brooksbank, C., Brose, N., Bruining, H., Bury, J., Caporale, N., Cattoretti, G., Chabane, N., Chneiweiss, H., Cook, S., Curatolo, P., de Jonge, M., Deplancke, B., de Witte, P., Dimmeler, S., Draganski, B., Drews, A., Dumbrava, C., Engelhardt, S., Gasser, T., Giamarellos-Bourboulis, E., Graff, C., Grün, D., Gut, I., Hansson, O., Henshall, D., Herland, A., Heutink, P., Heymans, S., Heyn, H., Huch, M., Huitinga, I., Jackowiak, P., Jongsma, K., Journot, L., Junker, J., Katz, S., Kehren, J., Kempa, S., Kirchhof, P., Klein, C., Koralewska, N., Korbel, J., Kühnemund, M., Lamond, A., Lauwers, E., Le Ber, I., Leinonen, V., Tobon, A., Lundberg, E., Lunkes, A., Maatz, H., Mann, M., Marelli, L., Matser, V., Matthews, P., Mechta-Grigoriou, F., Menon, R., Nielsen, A., Pagani, M., Pasterkamp, R., Pitkänen, A., Popescu, V., Pottier, C., Puisieux, A., Rademakers, R., Reiling, D., Reiner, O., Remondini, D., Ritchie, C., Rohrer, J., Saliba, A., Sanchez-Valle, R., Santosuosso, A., Sauter, A., Scheltema, R., Scheltens, P., Schiller, H., Schneider, A., Seibler, P., Sheehan-Rooney, K., Shields, D., Sleegers, K., Smit, A., Smith, K., Smolders, I., Synofzik, M., Tam, W., Teichmann, S., Thom, M., Turco, M., van Beusekom, H., Vandenberghe, R., den Hoecke, S., de Poel, I., van der Ven, A., van der Zee, J., van Lunzen, J., van Minnebruggen, G., Paesschen, W., van Swieten, J., van Vught, R., Verhage, M., Verstreken, P., Villa, C., Vogel, J., von Kalle, C., Walter, J., Weckhuysen, S., Weichert, W., Wood, L., Ziegler, A., Zipp, F., HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., Medical Research Council (MRC), UK DRI Ltd, TWINCORE, Zentrum für experimentelle und klinische Infektionsforschung GmbH,Feodor-Lynen Str. 7, 30625 Hannover, Germany., Barcelona Supercomputing Center, LifeTime Community Working Groups, Cardiology, Neurology, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Human genetics, Rajewsky N., Almouzni G., Gorski S.A., Aerts S., Amit I., Bertero M.G., Bock C., Bredenoord A.L., Cavalli G., Chiocca S., Clevers H., De Strooper B., Eggert A., Ellenberg J., Fernandez X.M., Figlerowicz M., Gasser S.M., Hubner N., Kjems J., Knoblich J.A., Krabbe G., Lichter P., Linnarsson S., Marine J.-C., Marioni J.C., Marti-Renom M.A., Netea M.G., Nickel D., Nollmann M., Novak H.R., Parkinson H., Piccolo S., Pinheiro I., Pombo A., Popp C., Reik W., Roman-Roman S., Rosenstiel P., Schultze J.L., Stegle O., Tanay A., Testa G., Thanos D., Theis F.J., Torres-Padilla M.-E., Valencia A., Vallot C., van Oudenaarden A., Vidal M., Voet T., Alberi L., Alexander S., Alexandrov T., Arenas E., Bagni C., Balderas R., Bandelli A., Becher B., Becker M., Beerenwinkel N., Benkirame M., Beyer M., Bickmore W., Biessen E.E.A.L., Blomberg N., Blumcke I., Bodenmiller B., Borroni B., Boumpas D.T., Bourgeron T., Bowers S., Braeken D., Brooksbank C., Brose N., Bruining H., Bury J., Caporale N., Cattoretti G., Chabane N., Chneiweiss H., Cook S.A., Curatolo P., de Jonge M.I., Deplancke B., de Witte P., Dimmeler S., Draganski B., Drews A., Dumbrava C., Engelhardt S., Gasser T., Giamarellos-Bourboulis E.J., Graff C., Grun D., Gut I., Hansson O., Henshall D.C., Herland A., Heutink P., Heymans S.R.B., Heyn H., Huch M., Huitinga I., Jackowiak P., Jongsma K.R., Journot L., Junker J.P., Katz S., Kehren J., Kempa S., Kirchhof P., Klein C., Koralewska N., Korbel J.O., Kuhnemund M., Lamond A.I., Lauwers E., Le Ber I., Leinonen V., Tobon A.L., Lundberg E., Lunkes A., Maatz H., Mann M., Marelli L., Matser V., Matthews P.M., Mechta-Grigoriou F., Menon R., Nielsen A.F., Pagani M., Pasterkamp R.J., Pitkanen A., Popescu V., Pottier C., Puisieux A., Rademakers R., Reiling D., Reiner O., Remondini D., Ritchie C., Rohrer J.D., Saliba A.-E., Sanchez-Valle R., Santosuosso A., Sauter A., Scheltema R.A., Scheltens P., Schiller H.B., Schneider A., Seibler P., Sheehan-Rooney K., Shields D., Sleegers K., Smit A.B., Smith K.G.C., Smolders I., Synofzik M., Tam W.L., Teichmann S., Thom M., Turco M.Y., van Beusekom H.M.M., Vandenberghe R., Van den Hoecke S., Van de Poel I., van der Ven A., van der Zee J., van Lunzen J., van Minnebruggen G., Van Paesschen W., van Swieten J., van Vught R., Verhage M., Verstreken P., Villa C.E., Vogel J., von Kalle C., Walter J., Weckhuysen S., Weichert W., Wood L., Ziegler A.-G., Zipp F., Center for Neurogenomics and Cognitive Research, Functional Genomics, Rajewsky, N, Almouzni, G, Gorski, S, Aerts, S, Amit, I, Bertero, M, Bock, C, Bredenoord, A, Cavalli, G, Chiocca, S, Clevers, H, De Strooper, B, Eggert, A, Ellenberg, J, Fernández, X, Figlerowicz, M, Gasser, S, Hubner, N, Kjems, J, Knoblich, J, Krabbe, G, Lichter, P, Linnarsson, S, Marine, J, Marioni, J, Marti-Renom, M, Netea, M, Nickel, D, Nollmann, M, Novak, H, Parkinson, H, Piccolo, S, Pinheiro, I, Pombo, A, Popp, C, Reik, W, Roman-Roman, S, Rosenstiel, P, Schultze, J, Stegle, O, Tanay, A, Testa, G, Thanos, D, Theis, F, Torres-Padilla, M, Valencia, A, Vallot, C, van Oudenaarden, A, Vidal, M, Voet, T, Cattoretti, G, Alliance for Modulation in Epilepsy, Pharmaceutical and Pharmacological Sciences, Experimental Pharmacology, RS: Carim - H02 Cardiomyopathy, MUMC+: MA Med Staf Spec Cardiologie (9), and Cardiologie

Subjects
0301 basic medicine, Male, Artificial intelligence, Legislation, Medical, [SDV]Life Sciences [q-bio], Molecular datasets, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Cell- and Tissue-Based Therapy, Diseases, LifeTime Community Working Groups, Disease, Biomarkers, Systems biology, Health data, Pharmacology, Toxicology and Pharmaceutics(all), 0302 clinical medicine, Conjunts de dades, ethics [Delivery of Health Care], Health care, Pathology, Medicine, European healthcare, BRAIN, Single-cell multi-omics, GENE-EXPRESSION, Multidisciplinary, methods [Medicine], Education, Medical, Settore BIO/13, Intel.ligència artificial, 3. Good health, ALZHEIMERS-DISEASE, Europe, Health, Management system, Perspective, Female, ddc:500, Single-Cell Analysis, Biomarkers, Diseases, Systems biology, Complex diseases, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], medicine.medical_specialty, General Science & Technology, Cells, MEDLINE, cell-based interceptive medicine, LifeTime Initiative, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Clinical datasets, Artificial Intelligence, REVEALS, LifeTime Community, standards [Medicine], Humans, OMICS, RECONSTRUCTION, Intensive care medicine, trends [Medicine], trends [Delivery of Health Care], business.industry, Disease progression, standards [Delivery of Health Care], methods [Delivery of Health Care], 030104 developmental biology, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], single cell, personalized therapy, machine learning, bioinformatics, systems biology, disease, cell-based interceptive medicine, Early Diagnosis, Cardiovascular and Metabolic Diseases, Human medicine, business, Delivery of Health Care, 030217 neurology & neurosurgery, Cell based
Abstract

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade., The LifeTime initiative is an ambitious, multidisciplinary programme that aims to improve healthcare by tracking individual human cells during disease processes and responses to treatment in order to develop and implement cell-based interceptive medicine in Europe.

Published
2020
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8. Fabrication and characterization of a rapid prototyped tissue engineering scaffold with embedded multicomponent matrix for controlled drug release

Author

Chen M, Le DQ, Hein S, Li P, Nygaard JV, Kassem M, Kjems J, Besenbacher F, and Bünger C

Subjects
Medicine (General), R5-920
Abstract

Muwan Chen,1,2 Dang QS Le,1,2 San Hein,2 Pengcheng Li,1 Jens V Nygaard,2 Moustapha Kassem,3 Jørgen Kjems,2 Flemming Besenbacher,2 Cody Bünger11Orthopaedic Research Lab, Aarhus University Hospital, Aarhus C, Denmark; 2Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark; 3Department of Endocrinology and Metabolism, Odense University Hospital, Odense C, DenmarkAbstract: Bone tissue engineering implants with sustained local drug delivery provide an opportunity for better postoperative care for bone tumor patients because these implants offer sustained drug release at the tumor site and reduce systemic side effects. A rapid prototyped macroporous polycaprolactone scaffold was embedded with a porous matrix composed of chitosan, nanoclay, and β-tricalcium phosphate by freeze-drying. This composite scaffold was evaluated on its ability to deliver an anthracycline antibiotic and to promote formation of mineralized matrix in vitro. Scanning electronic microscopy, confocal imaging, and DNA quantification confirmed that immortalized human bone marrow-derived mesenchymal stem cells (hMSC-TERT) cultured in the scaffold showed high cell viability and growth, and good cell infiltration to the pores of the scaffold. Alkaline phosphatase activity and osteocalcin staining showed that the scaffold was osteoinductive. The drug-release kinetics was investigated by loading doxorubicin into the scaffold. The scaffolds comprising nanoclay released up to 45% of the drug for up to 2 months, while the scaffold without nanoclay released 95% of the drug within 4 days. Therefore, this scaffold can fulfill the requirements for both bone tissue engineering and local sustained release of an anticancer drug in vitro. These results suggest that the scaffold can be used clinically in reconstructive surgery after bone tumor resection. Moreover, by changing the composition and amount of individual components, the scaffold can find application in other tissue engineering areas that need local sustained release of drug.Keywords: nanoclay, chitosan, scaffold, tissue engineering, drug delivery system

Published
2012

9. Additional file 1 of The transcriptional landscape and biomarker potential of circular RNAs in prostate cancer

Author

Hansen, Emma Bollmann, Freds��e, Jacob, Okholm, Trine Line Hauge, Ulh��i, Benedicte Parm, Klingenberg, S��ren, Jensen, J��rgen Bjerggaard, Kjems, J��rgen, Bouchelouche, Kirsten, Borre, Michael, Damgaard, Christian Kroun, Pedersen, Jakob Skou, Kristensen, Lasse Sommer, and S��rensen, Karina Dalsgaard

Abstract

Additional file 1. Supplementary Methods.

Published
2022
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10. Additional file 2 of The transcriptional landscape and biomarker potential of circular RNAs in prostate cancer

Author

Hansen, Emma Bollmann, Freds��e, Jacob, Okholm, Trine Line Hauge, Ulh��i, Benedicte Parm, Klingenberg, S��ren, Jensen, J��rgen Bjerggaard, Kjems, J��rgen, Bouchelouche, Kirsten, Borre, Michael, Damgaard, Christian Kroun, Pedersen, Jakob Skou, Kristensen, Lasse Sommer, and S��rensen, Karina Dalsgaard

Abstract

Additional file 2. Fig. S1: Flow charts of inclusion/exclusion in cohort 1 (training) according to the REMARK guidelines. Fig. S2: Flow charts of inclusion/exclusion for cohorts 2-4. Fig. S3: Clustering of abundant circRNAs in cohort 1. Fig. S4: Association of abundant circRNAs to metastatic disease. Fig. S5: Association of abundant circRNAs to key clinicopathological parameters. Fig. S6: circKDM1A holds prognostic potential in prostate cancer patients. Fig. S7: circRNA candidates show both correlations and substantial differences between levels in EV-enriched plasma and in prostate tissue samples.

Published
2022
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14. Publisher Correction: The RNA Atlas expands the catalog of human non-coding RNAs (Nature Biotechnology, (2021), 39, 11, (1453-1465), 10.1038/s41587-021-00936-1)

Author

Lorenzi, Lucia, Chiu, Hua-Sheng, Avila Cobos, Francisco, Gross, Stephen, Volders, Pieter-Jan, Cannoodt, Robrecht, Nuytens, Justine, Vanderheyden, Katrien, Anckaert, Jasper, Lefever, Steve, Tay, Aidan P., de Bony, Eric J., Trypsteen, Wim, Gysens, Fien, Vromman, Marieke, Goovaerts, Tine, Hansen, Thomas Birkballe, Kuersten, Scott, Nijs, Nele, Taghon, Tom, Vermaelen, Karim, Bracke, Ken R., Saeys, Yvan, de Meyer, Tim, Deshpande, Nandan P., Anande, Govardhan, Chen, Ting-Wen, Wilkins, Marc R., Unnikrishnan, Ashwin, de Preter, Katleen, Kjems, J. rgen, Koster, Jan, Schroth, Gary P., Vandesompele, Jo, Sumazin, Pavel, Mestdagh, Pieter, Oncogenomics, AII - Cancer immunology, and CCA - Cancer biology and immunology

Abstract

In the version of this article initially published online, Pavel Sumazin’s affilation was given as Cancer Research Institute Ghent (CRIG), Ghent, Belgium. The correct affiliation is Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX, USA. The error has been corrected in the print, PDF and HTML versions of the article.

Published
2021

17. Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine (Nature, (2020), 587, 7834, (377-386), 10.1038/s41586-020-2715-9)

Author

Rajewsky, N. Almouzni, G. Gorski, S.A. Aerts, S. Amit, I. Bertero, M.G. Bock, C. Bredenoord, A.L. Cavalli, G. Chiocca, S. Clevers, H. De Strooper, B. Eggert, A. Ellenberg, J. Fernández, X.M. Figlerowicz, M. Gasser, S.M. Hubner, N. Kjems, J. Knoblich, J.A. Krabbe, G. Lichter, P. Linnarsson, S. Marine, J.-C. Marioni, J.C. Marti-Renom, M.A. Netea, M.G. Nickel, D. Nollmann, M. Novak, H.R. Parkinson, H. Piccolo, S. Pinheiro, I. Pombo, A. Popp, C. Reik, W. Roman-Roman, S. Rosenstiel, P. Schultze, J.L. Stegle, O. Tanay, A. Testa, G. Thanos, D. Theis, F.J. Torres-Padilla, M.-E. Valencia, A. Vallot, C. van Oudenaarden, A. Vidal, M. Voet, T. Alberi, L. Alexander, S. Alexandrov, T. Arenas, E. Bagni, C. Balderas, R. Bandelli, A. Becher, B. Becker, M. Beerenwinkel, N. Benkirane, M. Beyer, M. Bickmore, W.A. Biessen, E.E.A.L. Blomberg, N. Blumcke, I. Bodenmiller, B. Borroni, B. Boumpas, D.T. Bourgeron, T. Bowers, S. Braeken, D. Brooksbank, C. Brose, N. Bruining, H. Bury, J. Caporale, N. Cattoretti, G. Chabane, N. Chneiweiss, H. Cook, S.A. Curatolo, P. de Jonge, M.I. Deplancke, B. de Witte, P. Dimmeler, S. Draganski, B. Drews, A. Dumbrava, C. Engelhardt, S. Gasser, T. Giamarellos-Bourboulis, E.J. Graff, C. Grün, D. Gut, I.G. Hansson, O. Henshall, D.C. Herland, A. Heutink, P. Heymans, S.R.B. Heyn, H. Huch, M. Huitinga, I. Jackowiak, P. Jongsma, K.R. Journot, L. Junker, J.P. Katz, S. Kehren, J. Kempa, S. Kirchhof, P. Klein, C. Koralewska, N. Korbel, J.O. Kühnemund, M. Lamond, A.I. Lauwers, E. Le Ber, I. Leinonen, V. López-Tobón, A. Lundberg, E. Lunkes, A. Maatz, H. Mann, M. Marelli, L. Matser, V. Matthews, P.M. Mechta-Grigoriou, F. Menon, R. Nielsen, A.F. Pagani, M. Pasterkamp, R.J. Pitkänen, A. Popescu, V. Pottier, C. Puisieux, A. Rademakers, R. Reiling, D. Reiner, O. Remondini, D. Ritchie, C. Rohrer, J.D. Saliba, A.-E. Sanchez-Valle, R. Santosuosso, A. Sauter, A. Scheltema, R.A. Scheltens, P. Schiller, H.B. Schneider, A. Seibler, P. Sheehan-Rooney, K. Shields, D.J. Sleegers, K. Smit, A.B. Smith, K.G.C. Smolders, I. Synofzik, M. Tam, W.L. Teichmann, S.A. Thom, M. Turco, M.Y. van Beusekom, H.M.M. Vandenberghe, R. Van den Hoecke, S. van de Poel, I. van der Ven, A. van der Zee, J. van Lunzen, J. van Minnebruggen, G. van Oudenaarden, A. Van Paesschen, W. van Swieten, J.C. van Vught, R. Verhage, M. Verstreken, P. Villa, C.E. Vogel, J. von Kalle, C. Walter, J. Weckhuysen, S. Weichert, W. Wood, L. Ziegler, A.-G. Zipp, F. LifeTime Community Working Groups

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING
Abstract

In this Perspective, owing to an error in the HTML, the surname of author Alejandro López-Tobón of the LifeTime Community Working Groups consortium was indexed as ‘Tobon’ rather than ‘López-Tobón’ and the accents were missing. The HTML version of the original Perspective has been corrected; the PDF and print versions were always correct. © 2021, The Author(s).

Published
2021

18. The RNA Atlas expands the catalog of human non-coding RNAs

Author

Lorenzi, L, Chiu, HS, Avila Cobos, F, Gross, S, Volders, PJ, Cannoodt, R, Nuytens, J, Vanderheyden, K, Anckaert, J, Lefever, S, Tay, AP, de Bony, EJ, Trypsteen, W, Gysens, F, Vromman, M, Goovaerts, T, Hansen, TB, Kuersten, S, Nijs, N, Taghon, T, Vermaelen, K, Bracke, KR, Saeys, Y, De Meyer, T, Deshpande, NP ; https://orcid.org/0000-0002-0324-8728, Anande, G, Chen, TW, Wilkins, MR ; https://orcid.org/0000-0002-5700-5684, Unnikrishnan, A ; https://orcid.org/0000-0001-5168-8755, De Preter, K, Kjems, J, Koster, J, Schroth, GP, Vandesompele, J, Sumazin, P, Mestdagh, P, Lorenzi, L, Chiu, HS, Avila Cobos, F, Gross, S, Volders, PJ, Cannoodt, R, Nuytens, J, Vanderheyden, K, Anckaert, J, Lefever, S, Tay, AP, de Bony, EJ, Trypsteen, W, Gysens, F, Vromman, M, Goovaerts, T, Hansen, TB, Kuersten, S, Nijs, N, Taghon, T, Vermaelen, K, Bracke, KR, Saeys, Y, De Meyer, T, Deshpande, NP ; https://orcid.org/0000-0002-0324-8728, Anande, G, Chen, TW, Wilkins, MR ; https://orcid.org/0000-0002-5700-5684, Unnikrishnan, A ; https://orcid.org/0000-0001-5168-8755, De Preter, K, Kjems, J, Koster, J, Schroth, GP, Vandesompele, J, Sumazin, P, and Mestdagh, P

Abstract

Existing compendia of non-coding RNA (ncRNA) are incomplete, in part because they are derived almost exclusively from small and polyadenylated RNAs. Here we present a more comprehensive atlas of the human transcriptome, which includes small and polyA RNA as well as total RNA from 300 human tissues and cell lines. We report thousands of previously uncharacterized RNAs, increasing the number of documented ncRNAs by approximately 8%. To infer functional regulation by known and newly characterized ncRNAs, we exploited pre-mRNA abundance estimates from total RNA sequencing, revealing 316 microRNAs and 3,310 long non-coding RNAs with multiple lines of evidence for roles in regulating protein-coding genes and pathways. Our study both refines and expands the current catalog of human ncRNAs and their regulatory interactions. All data, analyses and results are available for download and interrogation in the R2 web portal, serving as a basis for future exploration of RNA biology and function.

Published
2021

19. Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine (Nature, (2020), 587, 7834, (377-386), 10.1038/s41586-020-2715-9)

Author

Rajewsky, N. Almouzni, G. Gorski, S.A. Aerts, S. Amit, I. Bertero, M.G. Bock, C. Bredenoord, A.L. Cavalli, G. Chiocca, S. Clevers, H. De Strooper, B. Eggert, A. Ellenberg, J. Fernández, X.M. Figlerowicz, M. Gasser, S.M. Hubner, N. Kjems, J. Knoblich, J.A. Krabbe, G. Lichter, P. Linnarsson, S. Marine, J.-C. Marioni, J.C. Marti-Renom, M.A. Netea, M.G. Nickel, D. Nollmann, M. Novak, H.R. Parkinson, H. Piccolo, S. Pinheiro, I. Pombo, A. Popp, C. Reik, W. Roman-Roman, S. Rosenstiel, P. Schultze, J.L. Stegle, O. Tanay, A. Testa, G. Thanos, D. Theis, F.J. Torres-Padilla, M.-E. Valencia, A. Vallot, C. van Oudenaarden, A. Vidal, M. Voet, T. Alberi, L. Alexander, S. Alexandrov, T. Arenas, E. Bagni, C. Balderas, R. Bandelli, A. Becher, B. Becker, M. Beerenwinkel, N. Benkirane, M. Beyer, M. Bickmore, W.A. Biessen, E.E.A.L. Blomberg, N. Blumcke, I. Bodenmiller, B. Borroni, B. Boumpas, D.T. Bourgeron, T. Bowers, S. Braeken, D. Brooksbank, C. Brose, N. Bruining, H. Bury, J. Caporale, N. Cattoretti, G. Chabane, N. Chneiweiss, H. Cook, S.A. Curatolo, P. de Jonge, M.I. Deplancke, B. de Witte, P. Dimmeler, S. Draganski, B. Drews, A. Dumbrava, C. Engelhardt, S. Gasser, T. Giamarellos-Bourboulis, E.J. Graff, C. Grün, D. Gut, I.G. Hansson, O. Henshall, D.C. Herland, A. Heutink, P. Heymans, S.R.B. Heyn, H. Huch, M. Huitinga, I. Jackowiak, P. Jongsma, K.R. Journot, L. Junker, J.P. Katz, S. Kehren, J. Kempa, S. Kirchhof, P. Klein, C. Koralewska, N. Korbel, J.O. Kühnemund, M. Lamond, A.I. Lauwers, E. Le Ber, I. Leinonen, V. López-Tobón, A. Lundberg, E. Lunkes, A. Maatz, H. Mann, M. Marelli, L. Matser, V. Matthews, P.M. Mechta-Grigoriou, F. Menon, R. Nielsen, A.F. Pagani, M. Pasterkamp, R.J. Pitkänen, A. Popescu, V. Pottier, C. Puisieux, A. Rademakers, R. Reiling, D. Reiner, O. Remondini, D. Ritchie, C. Rohrer, J.D. Saliba, A.-E. Sanchez-Valle, R. Santosuosso, A. Sauter, A. Scheltema, R.A. Scheltens, P. Schiller, H.B. Schneider, A. Seibler, P. Sheehan-Rooney, K. Shields, D.J. Sleegers, K. Smi and Rajewsky, N. Almouzni, G. Gorski, S.A. Aerts, S. Amit, I. Bertero, M.G. Bock, C. Bredenoord, A.L. Cavalli, G. Chiocca, S. Clevers, H. De Strooper, B. Eggert, A. Ellenberg, J. Fernández, X.M. Figlerowicz, M. Gasser, S.M. Hubner, N. Kjems, J. Knoblich, J.A. Krabbe, G. Lichter, P. Linnarsson, S. Marine, J.-C. Marioni, J.C. Marti-Renom, M.A. Netea, M.G. Nickel, D. Nollmann, M. Novak, H.R. Parkinson, H. Piccolo, S. Pinheiro, I. Pombo, A. Popp, C. Reik, W. Roman-Roman, S. Rosenstiel, P. Schultze, J.L. Stegle, O. Tanay, A. Testa, G. Thanos, D. Theis, F.J. Torres-Padilla, M.-E. Valencia, A. Vallot, C. van Oudenaarden, A. Vidal, M. Voet, T. Alberi, L. Alexander, S. Alexandrov, T. Arenas, E. Bagni, C. Balderas, R. Bandelli, A. Becher, B. Becker, M. Beerenwinkel, N. Benkirane, M. Beyer, M. Bickmore, W.A. Biessen, E.E.A.L. Blomberg, N. Blumcke, I. Bodenmiller, B. Borroni, B. Boumpas, D.T. Bourgeron, T. Bowers, S. Braeken, D. Brooksbank, C. Brose, N. Bruining, H. Bury, J. Caporale, N. Cattoretti, G. Chabane, N. Chneiweiss, H. Cook, S.A. Curatolo, P. de Jonge, M.I. Deplancke, B. de Witte, P. Dimmeler, S. Draganski, B. Drews, A. Dumbrava, C. Engelhardt, S. Gasser, T. Giamarellos-Bourboulis, E.J. Graff, C. Grün, D. Gut, I.G. Hansson, O. Henshall, D.C. Herland, A. Heutink, P. Heymans, S.R.B. Heyn, H. Huch, M. Huitinga, I. Jackowiak, P. Jongsma, K.R. Journot, L. Junker, J.P. Katz, S. Kehren, J. Kempa, S. Kirchhof, P. Klein, C. Koralewska, N. Korbel, J.O. Kühnemund, M. Lamond, A.I. Lauwers, E. Le Ber, I. Leinonen, V. López-Tobón, A. Lundberg, E. Lunkes, A. Maatz, H. Mann, M. Marelli, L. Matser, V. Matthews, P.M. Mechta-Grigoriou, F. Menon, R. Nielsen, A.F. Pagani, M. Pasterkamp, R.J. Pitkänen, A. Popescu, V. Pottier, C. Puisieux, A. Rademakers, R. Reiling, D. Reiner, O. Remondini, D. Ritchie, C. Rohrer, J.D. Saliba, A.-E. Sanchez-Valle, R. Santosuosso, A. Sauter, A. Scheltema, R.A. Scheltens, P. Schiller, H.B. Schneider, A. Seibler, P. Sheehan-Rooney, K. Shields, D.J. Sleegers, K. Smi

Abstract

In this Perspective, owing to an error in the HTML, the surname of author Alejandro López-Tobón of the LifeTime Community Working Groups consortium was indexed as ‘Tobon’ rather than ‘López-Tobón’ and the accents were missing. The HTML version of the original Perspective has been corrected; the PDF and print versions were always correct. © 2021, The Author(s).

Published
2021

24. Magnetic structure of the heavy-fermion compound U2Zn17

Author

Cox, DE, Shirane, G, Shapiro, SM, Aeppli, G, Fisk, Z, Smith, JL, Kjems, J, and Ott, HR

Subjects
Physical Sciences, Chemical Sciences, Engineering, Fluids & Plasmas
Abstract

The phase transition of U2Zn17 at 9.7 K has been investigated by neutron powder diffraction. The transition corresponds to the onset of antiferromagnetic order where the U moments are oriented antiparallel to their nearest neighbors within the basal planes and the near neighbor along the c^ axis of this rhombohedral compound. At 5 K, the ordered moments lie within the basal planes and are of magnitude (0.8±0.1)1/4B, which is substantially below the paramagnetic moment of 2.251/4B/U atom given by high-temperature susceptibility data. © 1986 The American Physical Society.

Published
1986

25. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, N, Almouzni, G, Gorski, S, Aerts, S, Amit, I, Bertero, M, Bock, C, Bredenoord, A, Cavalli, G, Chiocca, S, Clevers, H, De Strooper, B, Eggert, A, Ellenberg, J, Fernández, X, Figlerowicz, M, Gasser, S, Hubner, N, Kjems, J, Knoblich, J, Krabbe, G, Lichter, P, Linnarsson, S, Marine, J, Marioni, J, Marti-Renom, M, Netea, M, Nickel, D, Nollmann, M, Novak, H, Parkinson, H, Piccolo, S, Pinheiro, I, Pombo, A, Popp, C, Reik, W, Roman-Roman, S, Rosenstiel, P, Schultze, J, Stegle, O, Tanay, A, Testa, G, Thanos, D, Theis, F, Torres-Padilla, M, Valencia, A, Vallot, C, van Oudenaarden, A, Vidal, M, Voet, T, Cattoretti, G, Rajewsky, Nikolaus, Almouzni, Geneviève, Gorski, Stanislaw A, Aerts, Stein, Amit, Ido, Bertero, Michela G, Bock, Christoph, Bredenoord, Annelien L, Cavalli, Giacomo, Chiocca, Susanna, Clevers, Hans, De Strooper, Bart, Eggert, Angelika, Ellenberg, Jan, Fernández, Xosé M, Figlerowicz, Marek, Gasser, Susan M, Hubner, Norbert, Kjems, Jørgen, Knoblich, Jürgen A, Krabbe, Grietje, Lichter, Peter, Linnarsson, Sten, Marine, Jean-Christophe, Marioni, John, Marti-Renom, Marc A, Netea, Mihai G, Nickel, Dörthe, Nollmann, Marcelo, Novak, Halina R, Parkinson, Helen, Piccolo, Stefano, Pinheiro, Inês, Pombo, Ana, Popp, Christian, Reik, Wolf, Roman-Roman, Sergio, Rosenstiel, Philip, Schultze, Joachim L, Stegle, Oliver, Tanay, Amos, Testa, Giuseppe, Thanos, Dimitris, Theis, Fabian J, Torres-Padilla, Maria-Elena, Valencia, Alfonso, Vallot, Céline, van Oudenaarden, Alexander, Vidal, Marie, Voet, Thierry, Cattoretti, Giorgio, Rajewsky, N, Almouzni, G, Gorski, S, Aerts, S, Amit, I, Bertero, M, Bock, C, Bredenoord, A, Cavalli, G, Chiocca, S, Clevers, H, De Strooper, B, Eggert, A, Ellenberg, J, Fernández, X, Figlerowicz, M, Gasser, S, Hubner, N, Kjems, J, Knoblich, J, Krabbe, G, Lichter, P, Linnarsson, S, Marine, J, Marioni, J, Marti-Renom, M, Netea, M, Nickel, D, Nollmann, M, Novak, H, Parkinson, H, Piccolo, S, Pinheiro, I, Pombo, A, Popp, C, Reik, W, Roman-Roman, S, Rosenstiel, P, Schultze, J, Stegle, O, Tanay, A, Testa, G, Thanos, D, Theis, F, Torres-Padilla, M, Valencia, A, Vallot, C, van Oudenaarden, A, Vidal, M, Voet, T, Cattoretti, G, Rajewsky, Nikolaus, Almouzni, Geneviève, Gorski, Stanislaw A, Aerts, Stein, Amit, Ido, Bertero, Michela G, Bock, Christoph, Bredenoord, Annelien L, Cavalli, Giacomo, Chiocca, Susanna, Clevers, Hans, De Strooper, Bart, Eggert, Angelika, Ellenberg, Jan, Fernández, Xosé M, Figlerowicz, Marek, Gasser, Susan M, Hubner, Norbert, Kjems, Jørgen, Knoblich, Jürgen A, Krabbe, Grietje, Lichter, Peter, Linnarsson, Sten, Marine, Jean-Christophe, Marioni, John, Marti-Renom, Marc A, Netea, Mihai G, Nickel, Dörthe, Nollmann, Marcelo, Novak, Halina R, Parkinson, Helen, Piccolo, Stefano, Pinheiro, Inês, Pombo, Ana, Popp, Christian, Reik, Wolf, Roman-Roman, Sergio, Rosenstiel, Philip, Schultze, Joachim L, Stegle, Oliver, Tanay, Amos, Testa, Giuseppe, Thanos, Dimitris, Theis, Fabian J, Torres-Padilla, Maria-Elena, Valencia, Alfonso, Vallot, Céline, van Oudenaarden, Alexander, Vidal, Marie, Voet, Thierry, and Cattoretti, Giorgio

Abstract

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.

Published
2020

27. Preface

Author

Kjems, J;ørgen, primary, Egebjerg, Jan, additional, and Christiansen, Jan, additional

Published
1998
Full Text
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28. 448 A comprehensive analysis of coding and non coding transcriptomic changes in cutaneous squamous cell carcinoma

Author

Das Mahapatra, K., primary, Pasquali, L., additional, Søndergaard, J.N., additional, Lapins, J., additional, Németh, I.B., additional, Baltás, E., additional, Kemény, L., additional, Moldovan, L., additional, Kjems, J., additional, Kutter, C., additional, Sonkoly, E., additional, Kristensen, L.S., additional, and Pivarcsi, A., additional

Published
2019
Full Text
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37. Singlet Ground-State Dimer Systems Cs3Cr2Br9 and Cs3Cr2Cl9

Author

Kjems, J. K., Petitgrand, D., Feile, R., Leuenberger, B., Güdel, H. U., Cardona, Manuel, editor, Fulde, Peter, editor, Queisser, Han-Joachim, editor, Lovesey, Stephen W., editor, Balucani, Umberto, editor, Borsa, Ferdinando, editor, and Tognetti, Valerio, editor

Published
1984
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50. Electrospun PVA-PCL-HAB scaffold for craniofacial bone regeneration

Author

Prabha, R. D., Kraft, D. C., Melsen, B., Varma, H., Nair, P. D., Kjems, J., and Kassem, M.

Abstract

Bone tissue engineering for craniofacial region is considered challenging owing to its physiologic and anatomical complexities. A porous bioactive scaffold promoting osteogenesis and angio- genesis is required for clinical applications. We have developed an electrospun polyvinyl alcohol (PVA) poly-caprolactone (PCL)- triphasic bioceramic(HAB) scaffold to biomimic native tissue and we tested its ability to support osteogenic differentiation of stromal stem cells ( MSC) and its suitability for regeneration of craniofa- cial defects. Physiochemical characterizations of the scaffold, including con- tact angle measurements, showed that PVA-PCL-HAB was more hydrophilic than PCL alone or PCL-HAB combined (P < 0.05). Ion release profile studies using ICP-OES of the scaffold showed release of calcium and silica ions, required for initiation of bioactivity. SEM and EDS analyses revealed apatite formation on stimulated body fluid immersed scaffold samples. Culturing human adult dental pulp stem cells (DPSC) and human bone marrow derived MSC seeded on PVA-PCL-HAB scaffold showed enhanced cell proliferation and in vitro osteoblastic differentiation. Cell-containing scaffolds were implanted subcutaneously in immune deficient mice. Histologic ex- amination of retrieved implant sections stained with H&E, Col- lagenType I and Human Vimentin antibody demonstrated that the cells survived in vivo in the implants for at least 8 weeks with evidence of osteoblastic differentiation and angiogenesis within the implants. Our results suggest that PVA-PCL-HAB scaffold can support growth and osteoblast differentiation of MSC and thus should be considered for clinical use in craniofacial tissue regeneration

Published
2015
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