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A Systems medicine approach to chronic inflammatory disease

Deliverables

Public project website

Eurice will be in charge of the set-up and maintenance of the public project website, which will serve as an additional showcase for presenting the project’s activities and achievements.

SYSCID movie

In addition to standard print materials such as project leaflets and posters, audio-visual material like a project movie will be produced to support dissemination to the interested public including patients.

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Publications

A Proposal for a Study on Treatment Selection and Lifestyle Recommendations in Chronic Inflammatory Diseases: A Danish Multidisciplinary Collaboration on Prognostic Factors and Personalised Medicine

Author(s): Vibeke Andersen, Uffe Holmskov, Signe Sørensen, Mohamad Jawhara, Karina Andersen, Anette Bygum, Lone Hvid, Jakob Grauslund, Jimmi Wied, Henning Glerup, Ulrich Fredberg, Jan Villadsen, Søren Kjær, Jan Fallingborg, Seyed Moghadd, Torben Knudsen, Jacob Brodersen, Jesper Frøjk, Jens Dahlerup, Ole Nielsen, Robin Christensen, Anders Bojesen, Grith Sorensen, Steffen Thiel, Nils Færgeman, Ivan Brands
Published in: Nutrients, Issue 9/5, 2017, Page(s) 499, ISSN 2072-6643
DOI: 10.3390/nu9050499

Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation

Author(s): Xia Shen, Lucija Klarić, Sodbo Sharapov, Massimo Mangino, Zheng Ning, Di Wu, Irena Trbojević-Akmačić, Maja Pučić-Baković, Igor Rudan, Ozren Polašek, Caroline Hayward, Timothy D. Spector, James F. Wilson, Gordan Lauc, Yurii S. Aulchenko
Published in: Nature Communications, Issue 8/1, 2017, ISSN 2041-1723
DOI: 10.1038/s41467-017-00453-3

Increased Tryptophan Metabolism Is Associated With Activity of Inflammatory Bowel Diseases

Author(s): Susanna Nikolaus, Berenice Schulte, Natalie Al-Massad, Florian Thieme, Dominik M. Schulte, Johannes Bethge, Ateequr Rehman, Florian Tran, Konrad Aden, Robert Häsler, Natalie Moll, Gregor Schütze, Markus J. Schwarz, Georg H. Waetzig, Philip Rosenstiel, Michael Krawczak, Silke Szymczak, Stefan Schreiber
Published in: Gastroenterology, Issue 153/6, 2017, Page(s) 1504-1516.e2, ISSN 0016-5085
DOI: 10.1053/j.gastro.2017.08.028

Impact of red and processed meat and fibre intake on treatment outcomes among patients with chronic inflammatory diseases:protocol for a prospective cohort study of prognostic factors and personalised medicine

Author(s): Christensen, Robin; Heitmann, Berit L; Andersen, Karina Winther; Nielsen, Ole Haagen; Sørensen, Signe Bek; Jawhara, Mohamad; Bygum, Anette; Hvid, Lone; Grauslund, Jakob; Wied, Jimmi; Glerup, Henning; Fredberg, Ulrich; Villadsen, Jan Alexander; Kjær, Søren Geill; Fallingborg, Jan; Moghadd, Seyed A G R; Knudsen, Torben; Brodersen, Jacob; Frøjk, Jesper; Dahlerup, Jens Frederik; Bojesen, Anders Bo
Published in: BMJ Open, Issue 1, 2018, ISSN 2044-6055
DOI: 10.1136/bmjopen-2017-018166

Overview of methodologies for T-cell receptor repertoire analysis

Author(s): Elisa Rosati, C Marie Dowds, Evaggelia Liaskou, Eva Kristine Klemsdal Henriksen, Tom H Karlsen, Andre Franke
Published in: BMC Biotechnology, Issue 17/1, 2017, ISSN 1472-6750
DOI: 10.1186/s12896-017-0379-9

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes

Author(s): Yukihide Momozawa, Julia Dmitrieva, Emilie Théâtre, Valérie Deffontaine, Souad Rahmouni, Benoît Charloteaux, François Crins, Elisa Docampo, Mahmoud Elansary, Ann-Stephan Gori, Christelle Lecut, Rob Mariman, Myriam Mni, Cécile Oury, Ilya Altukhov, Dmitry Alexeev, Yuri Aulchenko, Leila Amininejad, Gerd Bouma, Frank Hoentjen, Mark Löwenberg, Bas Oldenburg, Marieke J. Pierik, Andrea E. vander M
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
DOI: 10.1038/s41467-018-04365-8

Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner

Author(s): Morgane Sonia Thion, Donovan Low, Aymeric Silvin, Jinmiao Chen, Pauline Grisel, Jonas Schulte-Schrepping, Ronnie Blecher, Thomas Ulas, Paola Squarzoni, Guillaume Hoeffel, Fanny Coulpier, Eleni Siopi, Friederike Sophie David, Claus Scholz, Foo Shihui, Josephine Lum, Arlaine Anne Amoyo, Anis Larbi, Michael Poidinger, Anne Buttgereit, Pierre-Marie Lledo, Melanie Greter, Jerry Kok Yen Chan, Ido Amit,
Published in: Cell, Issue 172/3, 2018, Page(s) 500-516.e16, ISSN 0092-8674
DOI: 10.1016/j.cell.2017.11.042

Systems Medicine in Chronic Inflammatory Diseases

Author(s): Joachim L. Schultze, Philip Rosenstiel
Published in: Immunity, Issue 48/4, 2018, Page(s) 608-613, ISSN 1074-7613
DOI: 10.1016/j.immuni.2018.03.022

The resilience of the intestinal microbiota influences health and disease

Author(s): Felix Sommer, Jacqueline Moltzau Anderson, Richa Bharti, Jeroen Raes, Philip Rosenstiel
Published in: Nature Reviews Microbiology, Issue 15/10, 2017, Page(s) 630-638, ISSN 1740-1526
DOI: 10.1038/nrmicro.2017.58

Glycosylation of Immunoglobulin G Associates With Clinical Features of Inflammatory Bowel Diseases

Author(s): Mirna Šimurina, Noortje de Haan, Frano Vučković, Nicholas A. Kennedy, Jerko Štambuk, David Falck, Irena Trbojević-Akmačić, Florent Clerc, Genadij Razdorov, Anna Khon, Anna Latiano, Renata D'Incà, Silvio Danese, Stephan Targan, Carol Landers, Marla Dubinsky, Dermot P.B. McGovern, Vito Annese, Manfred Wuhrer, Gordan Lauc, Harry Campbell, Vlatka Zoldoš, Iain K. Permberton, Daniel Kolarich, D
Published in: Gastroenterology, Issue 154/5, 2018, Page(s) 1320-1333.e10, ISSN 0016-5085
DOI: 10.1053/j.gastro.2018.01.002

Profiling and genetic control of the murine immunoglobulin G glycome

Author(s): Jasminka Krištić, Olga O. Zaytseva, Ramesh Ram, Quang Nguyen, Mislav Novokmet, Frano Vučković, Marija Vilaj, Irena Trbojević-Akmačić, Marija Pezer, Kathleen M. Davern, Grant Morahan, Gordan Lauc
Published in: Nature Chemical Biology, Issue 14/5, 2018, Page(s) 516-524, ISSN 1552-4450
DOI: 10.1038/s41589-018-0034-3

Low galactosylation of IgG associates with higher risk for future diagnosis of rheumatoid arthritis during 10 years of follow-up

Author(s): Ivan Gudelj, Perttu P. Salo, Irena Trbojević-Akmačić, Malena Albers, Dragan Primorac, Markus Perola, Gordan Lauc
Published in: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Issue 1864/6, 2018, Page(s) 2034-2039, ISSN 0925-4439
DOI: 10.1016/j.bbadis.2018.03.018

N-glycome of the Lysosomal Glycocalyx is Altered in Niemann-Pick Type C Disease (NPC) Model Cells

Author(s): Marko Kosicek, Ivan Gudelj, Anita Horvatic, Tanja Jovic, Frano Vuckovic, Gordan Lauc, Silva Hecimovic
Published in: Molecular & Cellular Proteomics, Issue 17/4, 2018, Page(s) 631-642, ISSN 1535-9476
DOI: 10.1074/mcp.RA117.000129

The association between subclass-specific IgG Fc N-glycosylation profiles and hypertension in the Uygur, Kazak, Kirgiz, and Tajik populations

Author(s): JN Liu, M Dolikun, J Štambuk, I Trbojević-Akmačić, J Zhang, H Wang, DQ Zheng, XY Zhang, HL Peng, ZY Zhao, D Liu, Y Sun, Q Sun, QH Li, JX Zhang, M Sun, WJ Cao, A Momčilović, G. Razdorov, LJ Wu, A Russell, YX Wang, MS Song, G Lauc, W Wang
Published in: Journal of Human Hypertension, 2018, ISSN 0950-9240
DOI: 10.1038/s41371-018-0071-0

Quantitative microbiome profiling links gut community variation to microbial load

Author(s): Doris Vandeputte, Gunter Kathagen, Kevin D’hoe, Sara Vieira-Silva, Mireia Valles-Colomer, João Sabino, Jun Wang, Raul Y. Tito, Lindsey De Commer, Youssef Darzi, Séverine Vermeire, Gwen Falony, Jeroen Raes
Published in: Nature, Issue 551, 2017, Page(s) 507-511, ISSN 0028-0836
DOI: 10.1038/nature24460

Vedolizumab is associated with changes in innate rather than adaptive immunity in patients with inflammatory bowel disease

Author(s): Sebastian Zeissig, Elisa Rosati, C Marie Dowds, Konrad Aden, Johannes Bethge, Berenice Schulte, Wei Hung Pan, Neha Mishra, Maaz Zuhayra, Marlies Marx, Maren Paulsen, Anne Strigli, Claudio Conrad, Dörthe Schuldt, Anupam Sinha, Henriette Ebsen, Sabin-Christin Kornell, Susanna Nikolaus, Alexander Arlt, Dieter Kabelitz, Mark Ellrichmann, Ulf Lützen, Philip C Rosenstiel, Andre Franke, Stefan Schreibe
Published in: Gut, 2018, ISSN 0017-5749
DOI: 10.1136/gutjnl-2018-316023

Evaluation of interleukin-6 and its soluble receptor components sIL-6R and sgp130 as markers of inflammation in inflammatory bowel diseases

Author(s): Susanna Nikolaus, Georg H. Waetzig, Sven Butzin, Monika Ziolkiewicz, Natalie Al-Massad, Florian Thieme, Ulf Lövgren, Birgitte B. Rasmussen, Torsten M. Reinheimer, Dirk Seegert, Philip Rosenstiel, Silke Szymczak, Stefan Schreiber
Published in: International Journal of Colorectal Disease, Issue 33/7, 2018, Page(s) 927-936, ISSN 0179-1958
DOI: 10.1007/s00384-018-3069-8

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome

Author(s): Kate Joanne Howell, Judith Kraiczy, Komal M. Nayak, Marco Gasparetto, Alexander Ross, Claire Lee, Tim N. Mak, Bon-Kyoung Koo, Nitin Kumar, Trevor Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Published in: Gastroenterology, Issue 154/3, 2018, Page(s) 585-598, ISSN 0016-5085
DOI: 10.1053/j.gastro.2017.10.007

Deep molecular phenotypes link complex disorders and physiological insult to CpG methylation

Author(s): Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana T Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Marija Pezer, Gordan Lauc, Johann
Published in: Human Molecular Genetics, Issue 27/6, 2018, Page(s) 1106-1121, ISSN 0964-6906
DOI: 10.1093/hmg/ddy006

Identification of Disease-associated Traits and Clonotypes in the T Cell Receptor Repertoire of Monozygotic Twins Affected by Inflammatory Bowel Diseases

Author(s): Elisa Rosati, Mikhail V Pogorelyy, C Marie Dowds, Frederik T Moller, Signe B Sorensen, Yuri B Lebedev, Norbert Frey, Stefan Schreiber, Martina E Spehlmann, Vibeke Andersen, Ilgar Z Mamedov, Andre Franke
Published in: Journal of Crohn's and Colitis, 2019, ISSN 1873-9946
DOI: 10.1093/ecco-jcc/jjz179

aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data

Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Published in: BMC Genomics, Issue 20/1, 2019, ISSN 1471-2164
DOI: 10.1186/s12864-019-5686-1

Biomarkers of Whole-Grain and Cereal-Fiber Intake in Human Studies: A Systematic Review of the Available Evidence and Perspectives

Author(s): Mohamad Jawhara, Signe Bek Sørensen, Berit Lilienthal Heitmann, Vibeke Andersen
Published in: Nutrients, Issue 11/12, 2019, Page(s) 2994, ISSN 2072-6643
DOI: 10.3390/nu11122994

Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system

Author(s): Goran Josipović, Vanja Tadić, Marija Klasić, Vladimir Zanki, Ivona Bečeheli, Felicia Chung, Akram Ghantous, Toma Keser, Josip Madunić, Maria Bošković, Gordan Lauc, Zdenko Herceg, Aleksandar Vojta, Vlatka Zoldoš
Published in: Nucleic Acids Research, Issue 47/18, 2019, Page(s) 9637-9657, ISSN 0305-1048
DOI: 10.1093/nar/gkz709

Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics

Author(s): Stefanie Warnat-Herresthal, Konstantinos Perrakis, Bernd Taschler, Matthias Becker, Kevin Baßler, Marc Beyer, Patrick Günther, Jonas Schulte-Schrepping, Lea Seep, Kathrin Klee, Thomas Ulas, Torsten Haferlach, Sach Mukherjee, Joachim L. Schultze
Published in: iScience, Issue 23/1, 2020, Page(s) 100780, ISSN 2589-0042
DOI: 10.1016/j.isci.2019.100780

Update on the pathogenesis of central nervous system lupus

Author(s): Dionysis Nikolopoulos, Antonis Fanouriakis, Dimitrios T. Boumpas
Published in: Current Opinion in Rheumatology, Issue 31/6, 2019, Page(s) 669-677, ISSN 1040-8711
DOI: 10.1097/bor.0000000000000655

Increased central adiposity is associated with pro-inflammatory immunoglobulin G N-glycans

Author(s): Alyce C. Russell, Agnieszka Kepka, Irena Trbojević-Akmačić, Ivo Ugrina, Manshu Song, Jennie Hui, Michael Hunter, Simon M. Laws, Gordan Lauc, Wei Wang
Published in: Immunobiology, Issue 224/1, 2019, Page(s) 110-115, ISSN 0171-2985
DOI: 10.1016/j.imbio.2018.10.002

Analysis of the B cell receptor repertoire in six immune-mediated diseases

Author(s): R. J. M. Bashford-Rogers, L. Bergamaschi, E. F. McKinney, D. C. Pombal, F. Mescia, J. C. Lee, D. C. Thomas, S. M. Flint, P. Kellam, D. R. W. Jayne, P. A. Lyons, K. G. C. Smith
Published in: Nature, Issue 574/7776, 2019, Page(s) 122-126, ISSN 0028-0836
DOI: 10.1038/s41586-019-1595-3

ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS–STING

Author(s): Konrad Aden, Florian Tran, Go Ito, Raheleh Sheibani-Tezerji, Simone Lipinski, Jan W. Kuiper, Markus Tschurtschenthaler, Svetlana Saveljeva, Joya Bhattacharyya, Robert Häsler, Kareen Bartsch, Anne Luzius, Marlene Jentzsch, Maren Falk-Paulsen, Stephanie T. Stengel, Lina Welz, Robin Schwarzer, Björn Rabe, Winfried Barchet, Stefan Krautwald, Gunther Hartmann, Manolis Pasparakis, Richard S. Blumberg,
Published in: The Journal of Experimental Medicine, Issue 215/11, 2018, Page(s) 2868-2886, ISSN 0022-1007
DOI: 10.1084/jem.20171029

Combined genetic and transcriptome analysis of patients with SLE: distinct, targetable signatures for susceptibility and severity

Author(s): Nikolaos I Panousis, George K Bertsias, Halit Ongen, Irini Gergianaki, Maria G Tektonidou, Maria Trachana, Luciana Romano-Palumbo, Deborah Bielser, Cedric Howald, Cristina Pamfil, Antonis Fanouriakis, Despoina Kosmara, Argyro Repa, Prodromos Sidiropoulos, Emmanouil T Dermitzakis, Dimitrios T Boumpas
Published in: Annals of the Rheumatic Diseases, Issue 78/8, 2019, Page(s) 1079-1089, ISSN 0003-4967
DOI: 10.1136/annrheumdis-2018-214379

Transcriptional Signature Derived from Murine Tumor-Associated Macrophages Correlates with Poor Outcome in Breast Cancer Patients

Author(s): Sander Tuit, Camilla Salvagno, Theodore S. Kapellos, Cheei-Sing Hau, Lea Seep, Marie Oestreich, Kathrin Klee, Karin E. de Visser, Thomas Ulas, Joachim L. Schultze
Published in: Cell Reports, Issue 29/5, 2019, Page(s) 1221-1235.e5, ISSN 2211-1247
DOI: 10.1016/j.celrep.2019.09.067