A Systems medicine approach to chronic inflammatory disease

Deliverables

Report on the maintenance of website, updating with project news, results, success information

A report on the maintenance of the Project Website including the updating with project news results and success Information will be submitted

Summer School on Systems Medicine

To disseminate knowledge and expertise also beyond SYSCID we will organize a summer school on Systems Medicine

Open access summary report

An open access questionnaire to assess each partners experiences with the process and their general opinion that has been developed by Eurice in direct collaboration with the infrastructure project OpenAIRE wwwopenaireeu will be used to collect partner feedback to be merged into an open access summary report at the end of the project

Final report on integrated analyses and model

This document will describe the machine learning methods employed for antigen prediction in the datasets integrated

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.

Publications

Transethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals not only shared but also ethnicity-specific disease associations

Author(s): Degenhardt, F., G. Mayr, M. Wendorff, G. Boucher, E. Ellinghaus, D. Ellinghaus, H. ElAbd, E. Rosati, M. Hübenthal, S. Juzenas, S. Abedian, H. Vahedi, B. K. Thelma, S. K. Yang, B. D. Ye, J. H. Cheon, L. W. Datta, N. E. Daryani, P. Ellul, M. Esaki, Y. Fuyuno, D. P. B. McGovern, T. Haritunians, M. Hong, G. Juyal, E. S. Jung, M. Kubo, S. Kugathasan, T. L. Lenz, S. Leslie, R. Malekzadeh, V. Midha, A.
Published in: Human Molecular Genetics, 2021, ISSN 0964-6906
Publisher: Oxford University Press
DOI: 10.1093/hmg/ddab017

Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation

Author(s): Kevin Baßler, Wataru Fujii, Theodore S Kapellos, Erika Dudkin, Nico Reusch, Ari Horne, Benedikt Reiz Malte D Luecken, Collins Osei-Sarpong, Stefanie Warnat-Herresthal, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Allon Wagner, Patrick Günther, Carmen Pizarro, Tina Schreiber, Rainer Knoll, Lisa Holsten, Charlotte Kröger, Elena De Domenico, Matthias Becker, Kristian Händler, Christian T Wohnhaas
Published in: Frontiers in Immunology, Issue 16643224, 2022, ISSN 1664-3224
Publisher: Frontiers Media SA
DOI: 10.3389/fimmu.2022.917232

Demyelination with autoimmune features: a distinct clinical entity? Results from a longitudinal cohort

Author(s): Dionysis Nikolopoulos, Dimitris Kitsos, Matilda Papathanasiou, Maria Chondrogianni, Aikaterini Theodorou, Panagiotis Garantziotis, Antigone Pieta, Triantafyllos Doskas, George Bertsias, Konstantinos Voumvourakis, Dimitrios T Boumpas, Antonis Fanouriakis
Published in: Rheumatology, Issue 14620324, 2021, ISSN 1462-0324
Publisher: Oxford University Press
DOI: 10.1093/rheumatology/keaa902

Cross-species transcriptome analysis for early detection and specific therapeutic targeting of human lupus nephritis

Author(s): Eleni Frangou, Panagiotis Garantziotis, Maria Grigoriou, Aggelos Banos, Dionysis Nikolopoulos, Antigone Pieta, Stavros A Doumas, Antonis Fanouriakis, Aikaterini Hatzioannou, Theodora Manolakou, Themis Alissafi, Panayotis Verginis, Emmanouil Athanasiadis, Emmanouil Dermitzakis, George Bertsias, Anastasia Filia, Dimitrios T Boumpas
Published in: Annals of the Rheumatic Diseases, Issue 00034967, 2022, ISSN 0003-4967
Publisher: BMJ Publishing Group
DOI: 10.1136/annrheumdis-2021-222069

Neutrophils in COVID-19

Author(s): Nico Reusch, Elena De Domenico, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Kevin Baßler, Joachim L. Schultze, Anna C. Aschenbrenner
Published in: Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2021.652470

Distinct Longitudinal Changes in Immunoglobulin G N-Glycosylation Associate with Therapy Response in Chronic Inflammatory Diseases

Author(s): Jerko Štambuk, Frano Vučković , Siniša Habazin, Maja Hanić, Mislav Novokmet, Susanna Nikolaus, Florian Tran, Stefan Schreiber, Andre Franke, Philip Rosenstiel, Gordan Lauc, Konrad Aden, Marija Pezer
Published in: International Journal of Molecular Sciences, Issue 14220067, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23158473

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Author(s): Benjamin Krämer, Rainer Knoll, Lorenzo Bonaguro, Michael To Vinh, Jan Raabe, Rosario Astaburuaga-García, Jonas Schulte-Schrepping, Kim Melanie Kaiser, Gereon J. Rieke, Jenny Bischoff, Malte B. Monin, Christoph Hoffmeister, Stefan Schlabe, Elena De Domenico, Nico Reusch Kristian Händler, Gary Reynolds, Nils Blüthgen, Gudrun Hack, Claudia Finnemann, Hans D. Nischalke, Christian P. Strassburg, Em
Published in: Immunity, Issue 00928674, 2021, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.immuni.2021.09.002

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

Author(s): Michael Scherer; Gilles Gasparoni; Souad Rahmouni; Tatiana I. Shashkova; Marion Arnoux; Edouard Louis; Arina Nostaeva; Diana Avalos; Emmanouil T. Dermitzakis; Emmanouil T. Dermitzakis; Yurii S. Aulchenko; Thomas Lengauer; Paul A. Lyons; Michel Georges; Jörn Walter
Published in: Epigenetics & Chromatin, Vol 14, Iss 1, Pp 1-17 (2021), Issue 17568935, 2021, ISSN 1756-8935
Publisher: BioMed Central
DOI: 10.17863/cam.77053

Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state

Author(s): Caterina Carraro, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Arik Horne, Marie Oestreich, Stefanie Warnat-Herresthal, Tim Helbing, Michele De Franco, Kristian Haendler, Sach Mukherjee, Thomas Ulas, Valentina Gandin, Richard Goettlich, Anna C Aschenbrenner, Joachim L Schultze, and Barbara Gatto
Published in: eLife, Issue 2050084X, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.78012

Swarm Learning for decentralized and confidential clinical machine learning

Author(s): Stefanie Warnat-Herresthal, Hartmut Schultze, Krishnaprasad Lingadahalli Shastry, Sathyanarayanan Manamohan, Saikat Mukherjee, Vishesh Garg, Ravi Sarveswara, Kristian Händler, Peter Pickkers, N. Ahmad Aziz, Sofia Ktena, Florian Tran, Michael Bitzer, Stephan Ossowski, Nicolas Casadei, Christian Herr, Daniel Petersheim, Uta Behrends, Fabian Kern, Tobias Fehlmann, Philipp Schommers, Clara Lehmann, M
Published in: Nature, Issue 594/7862, 2021, Page(s) 265-270, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-03583-3

Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19

Author(s): Elena De Domenico, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Matthias Becker, Kristian Händler, Joachim L. Schultze
Published in: STAR Protocols, Issue 1/3, 2020, Page(s) 100233, ISSN 2666-1667
Publisher: ScienceDirect
DOI: 10.1016/j.xpro.2020.100233

Differential associations between a priori diet quality scores and markers of cardiovascular health in women: cross-sectional analyses from TwinsUK

Author(s): Olatz Mompeo, Sarah E. Berry, Tim D. Spector, Cristina Menni, Massimo Mangino, Rachel Gibson
Published in: British Journal of Nutrition, 2020, Page(s) 1-11, ISSN 0007-1145
Publisher: CABI Publishing
DOI: 10.1017/s000711452000495x

Molecular Taxonomy of Systemic Lupus Erythematosus Through Data-Driven Patient Stratification: Molecular Endotypes and Cluster-Tailored Drugs

Author(s): Panagiotis Garantziotis, Dimitrios Nikolakis, Stavros Doumas, Eleni Frangou, George Sentis, Anastasia Filia, Antonis Fanouriakis, George Bertsias and Dimitrios T. Boumpas
Published in: Frontiers in Immunology, Issue 16643224, 2022, ISSN 1664-3224
Publisher: Froniters Media S.A.
DOI: 10.3389/fimmu.2022.860726

The Relation between Red Meat and Whole-Grain Intake and the Colonic Mucosal Barrier: A Cross-Sectional Study

Author(s): Mohamad Jawhara, Signe Bek Sørensen, Berit Lilienthal Heitmann, Þórhallur Ingi Halldórsson, Andreas Kristian Pedersen, Vibeke Andersen
Published in: Nutrients, Issue 12/6, 2020, Page(s) 1765, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu12061765

Association Between Human Gut Microbiome and N-Glycan Composition of Total Plasma Proteome

Author(s): Vyacheslav A Petrov , Sodbo Zh Sharapov, Lev Shagam, Arina V Nostaeva, Marija Pezer, Dalin Li, Maja Hanić, Dermot McGovern, Edouard Louis, Souad Rahmouni, Gordan Lauc, Michel Georges, Yurii S Aulchenko
Published in: Frontiers in Mircrobiology, Issue 1664302X, 2022, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.811922

Complement activation induces excessive T cell cytotoxicity in severe COVID-19

Author(s): Philipp Georg, Rosario Astaburuaga-García, Lorenzo Bonaguro, Sophia Brumhard, Laura Michalick, Lena, J. Lippert, Tomislav Kostevc, Christiane Gäbel, Maria Schneider, Mathias Streitz, Vadim Demichev, Ioanna Gemünd, Matthias Barone, Pinkus Tober-Lau, Elisa T. Helbig, David Hillus, Lev Petrov, Julia Stein, Hannah-Philine Dey, Daniela Paclik, Christina Iwert, Michael Mülleder, Simran, Kaur Aulakh,
Published in: Cell, Issue 00928674, 2021, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2021.12.040

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

Author(s): Urmo Võsa; Annique Claringbould; Annique Claringbould; Harm-Jan Westra; Marc Jan Bonder; Patrick Deelen; Biao Zeng; Holger Kirsten; Ashis Saha; Roman Kreuzhuber; Roman Kreuzhuber; Roman Kreuzhuber; Seyhan Yazar; Harm Brugge; Roy Oelen; Dylan H. de Vries; Monique G. P. van der Wijst; Silva Kasela; Natalia Pervjakova; Isabel Alves; Marie-Julie Favé; Mawusse Agbessi; Mark W. Christiansen; Rick Jans
Published in: Nature Genetics, Issue 24, 2021, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-021-00913-z

Differential Gene Expression in Circulating CD14+ Monocytes Indicates the Prognosis of Critically Ill Patients with Sepsis

Author(s): Anke Liepelt; Philipp Hohlstein; Hendrik Gussen; Jia Xue; Anna C. Aschenbrenner; Anna C. Aschenbrenner; Thomas Ulas; Lukas Buendgens; Klaudia Theresa Warzecha; Matthias Bartneck; Tom Luedde; Christian Trautwein; Joachim L. Schultze; Alexander Koch; Frank Tacke; Frank Tacke
Published in: Journal of Clinical Medicine, Issue 7, 2020, Page(s) 127, ISSN 2077-0383
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.18154/rwth-2020-04417

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

Author(s): Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna D. Gemünd, Nikoletta Rovina, Shobhit Agrawal, Kilian Dahm, Mart
Published in: Genome Medicine, Issue 13/1, 2021, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1186/s13073-020-00823-5

A novel unconventional T cell population enriched in Crohn's disease

Author(s): Rosati, Elisa, Gabriela Rios Martini, Mikhail V. Pogorelyy, Anastasia A. Minervina, Frauke Degenhardt, Mareike Wendorff, Soner Sari, Gabriele Mayr, Antonella Fazio, Christel Marie Dowds, Charlotte Hauser, Florian Tran, Witigo von Schönfels, Julius Pochhammer, Maria A. Salnikova, Charlot Jaeckel, Johannes Boy Gigla, Sanaz Sedghpour Sabet, Matthias Hübenthal, Esther Schiminsky, Stefan Schreiber, P
Published in: Gut, 2022, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2021-325373

Towards a European health research and innovation cloud (HRIC)

Author(s): F. M. Aarestrup, A. Albeyatti, W. J. Armitage, L. Augello, R. Balling, N. Benhabiles, G. Bertolini, J. G. Bjaalie,M. Black, N. Blomberg, P. Bogaert, M. Bubak, B. Claerhout, L. Clarke, B. De Meulder, G. D’Errico, A. Di Meglio, N. Forgo, C. Gans-Combe, A. E. Gray, I. Gut, A. Gyllenberg, G. Hemmrich-Stanisak, L. Hjorth, Y. Ioannidis, S. Jarmalaite, A. Kel, F. Kherif, J. O. Korbel, C. Larue, M. Lasz
Published in: Genome Medicine, Issue 1756994X, 2020, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1186/s13073-020-0713-z

Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases

Author(s): Konrad Aden, Ateequr Rehman, Silvio Waschina, Wei-Hung Pan, Alesia Walker, Marianna Lucio, Alejandro Mena Nunez, Richa Bharti, Johannes Zimmerman, Johannes Bethge, Berenice Schulte, Dominik Schulte, Andre Franke, Susanna Nikolaus, Johann Oltmann Schroeder, Doris Vandeputte, Jeroen Raes, Silke Szymczak, Georg H Waetzig, Rainald Zeuner, Philippe Schmitt-Kopplin, Christoph Kaleta, Stefan Schreiber, P
Published in: Gastroenterology, 2019, ISSN 0016-5085
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2019.07.025

Monocytes and Macrophages in COVID-19

Author(s): Rainer Knoll, Joachim L. Schultze, Jonas Schulte-Schrepping
Published in: Frontiers in Immunology, Issue 16624548, 2021, ISSN 1662-4548
Publisher: Frontiers Research Foundation
DOI: 10.3389/fimmu.2021.720109

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
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
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
Publisher: Nature Publishing Group
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
Publisher: W. B. Saunders Co., Ltd.
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
Publisher: BMJ Publishing Group
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
Publisher: BioMed Central
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
Publisher: Nature Publishing Group
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
Publisher: Cell Press
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
Publisher: Cell Press
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
Publisher: Nature Publishing Group
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
Publisher: W. B. Saunders Co., Ltd.
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
Publisher: Nature Publishing Group
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
Publisher: Elsevier BV
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
Publisher: American Society for Biochemistry and Molecular Biology Inc.
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
Publisher: Nature Publishing Group
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
Publisher: Nature Publishing Group
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
Publisher: BMJ Publishing Group
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
Publisher: Springer Verlag
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
Publisher: W. B. Saunders Co., Ltd.
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
Publisher: Oxford University Press
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
Publisher: Elsevier Science
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
Publisher: BioMed Central
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
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
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
Publisher: Oxford University Press
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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
Publisher: Cell Press
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
Publisher: Lippincott Williams & Wilkins Ltd.
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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
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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
Publisher: Nature Publishing Group
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
Publisher: Rockefeller University Press
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
Publisher: BMJ Publishing Group
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
Publisher: Cell Press
DOI: 10.1016/j.celrep.2019.09.067

NCX1 represents an ionic Na+ sensing mechanism in macrophages

Author(s): Patrick Neubert, Arne Homann, David Wendelborn, Anna-Lorena Bär, Luka Krampert, Maximilian Trum, Agnes Schröder, Stefan Ebner, Andrea Weichselbaum, Valentin Schatz, Peter Linz, Roland Veelken, Jonas Schulte-Schrepping, Anna C. Aschenbrenner, Thomas Quast, Christian Kurts, Sabrina Geisberger, Karl Kunzelmann, Karin Hammer, Katrina J. Binger, Jens Titze, Dominik N. Müller, Waldemar Kolanus, Joach
Published in: PLOS Biology, Issue 18/6, 2020, Page(s) e3000722, ISSN 1545-7885
Publisher: PLOS
DOI: 10.1371/journal.pbio.3000722

Regulatory T-cell Transcriptomic Reprogramming Characterizes Adverse Events by Checkpoint Inhibitors in Solid Tumors

Author(s): Maria Grigoriou, Aggelos Banos, Aikaterini Hatzioannou, Andreas Kloetgen, Panagiotis Kouzis, Despoina Aggouraki, Roubini Zakopoulou, Giorgos Bamias, Eva Kassi, Dimitrios Mavroudis, Aristotelis Bamias, Dimitrios T. Boumpas, Aristotelis Tsirigos, Helen Gogas, Themis Alissafi, Panayotis Verginis
Published in: Cancer Immunology Research, Issue 9/7, 2021, Page(s) 726-734, ISSN 2326-6066
Publisher: American Association for Cancer Research Inc.
DOI: 10.1158/2326-6066.cir-20-0969

Defining trained immunity and its role in health and disease

Author(s): Mihai G. Netea, Jorge Domínguez-Andrés, Luis B. Barreiro, Triantafyllos Chavakis, Maziar Divangahi, Elaine Fuchs, Leo A. B. Joosten, Jos W. M. van der Meer, Musa M. Mhlanga, Willem J. M. Mulder, Niels P. Riksen, Andreas Schlitzer, Joachim L. Schultze, Christine Stabell Benn, Joseph C. Sun, Ramnik J. Xavier, Eicke Latz
Published in: Nature Reviews Immunology, Issue 20/6, 2020, Page(s) 375-388, ISSN 1474-1733
Publisher: Nature Publishing Group
DOI: 10.1038/s41577-020-0285-6

Human variation in population-wide gene expression data predicts gene perturbation phenotype

Author(s): Bonaguro L, Schulte-Schrepping J, Carraro C, Sun LL, Reiz B, Gemünd I, Saglam A, Rahmouni S, Georges M, Arts P, Hoischen A, Joosten LAB, van de Veerdonk FL, Netea MG, Händler K, Mukherjee S, Ulas T, Schultze JL, Aschenbrenner AC.
Published in: iScience, 2022, ISSN 2589-0042
Publisher: Elsevier Inc.
DOI: 10.1016/j.isci.2022.105328

Baseline IgG-Fc N-glycosylation profile is associated with long-term outcome in a cohort of early inflammatory arthritis patients

Author(s): Thomas Sénard; Irini Flouri; Frano Vučković; Garyfalia Papadaki; Panagiota Goutakoli; Aggelos Banos; Maja Pučić-Baković; Marija Pezer; George Bertsias; Gordan Lauc; Prodromos Sidiropoulos
Published in: Arthritis Research & Therapy, Issue 14786362, 2022, ISSN 1478-6362
Publisher: Springer
DOI: 10.1186/s13075-022-02897-5

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Author(s): Jonas Schulte-Schrepping, Nico Reusch, Daniela Paclik, Kevin Baßler, Stephan Schlickeiser, Bowen Zhang, Benjamin Krämer, Tobias Krammer, Sophia Brumhard, Lorenzo Bonaguro, Elena De Domenico, Daniel Wendisch, Martin Grasshoff, Theodore S. Kapellos, Michael Beckstette, Tal Pecht, Adem Saglam, Oliver Dietrich, Henrik E. Mei, Axel R. Schulz, Claudia Conrad, Désirée Kunkel, Ehsan Vafadarnejad, Chen
Published in: Cell, Issue 182/6, 2020, Page(s) 1419-1440.e23, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2020.08.001

Genetic and Environmental Influences of Dietary Indices in a UK Female Twin Cohort

Author(s): Olatz Mompeo, Rachel Gibson, Paraskevi Christofidou, Tim D. Spector, Cristina Menni, Massimo Mangino
Published in: Twin Research and Human Genetics, Issue 23/6, 2020, Page(s) 330-337, ISSN 1832-4274
Publisher: Australian Academic Press Pty Ltd.
DOI: 10.1017/thg.2020.84

Decreased Immunoglobulin G Core Fucosylation, A Player in Antibody-dependent Cell-mediated Cytotoxicity, is Associated with Autoimmune Thyroid Diseases

Author(s): Tiphaine C. Martin, Mirna Šimurina, Marta Ząbczyńska, Marina Martinic Kavur, Magdalena Rydlewska, Marija Pezer, Kamila Kozłowska, Andrea Burri, Marija Vilaj, Renata Turek-Jabrocka, Milena Krnjajić-Tadijanović, Małgorzata Trofimiuk-Müldner, Ivo Ugrina, Anna Lityńska, Alicja Hubalewska-Dydejczyk, Irena Trbojevic-Akmacic, Ee Mun Lim, John P. Walsh, Ewa Pocheć, Tim D. Spector, Scott G. Wilso
Published in: Molecular & Cellular Proteomics, Issue 19/5, 2020, Page(s) 774-792, ISSN 1535-9476
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/mcp.ra119.001860

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Author(s): Joana P. Bernardes, Neha Mishra, Florian Tran, Thomas Bahmer, Lena Best, Johanna I. Blase, Dora Bordoni, Jeanette Franzenburg, Ulf Geisen, Jonathan Josephs-Spaulding, Philipp Köhler, Axel Künstner, Elisa Rosati, Anna C. Aschenbrenner, Petra Bacher, Nathan Baran, Teide Boysen, Burkhard Brandt, Niklas Bruse, Jonathan Dörr, Andreas Dräger, Gunnar Elke, David Ellinghaus, Julia Fischer, Michael For
Published in: Immunity, Issue 53/6, 2020, Page(s) 1296-1314.e9, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2020.11.017

A guide to systems-level immunomics

Author(s): Lorenzo Bonaguro, Jonas Schulte-Schrepping, Thomas Ulas, Anna C. Aschenbrenner, Marc Beyer, Joachim L. Schultze
Published in: nature immunology, Issue 15292908, 2022, ISSN 1529-2908
Publisher: Nature Publishing Group
DOI: 10.1038/s41590-022-01309-9

COVID-19 and the human innate immune system

Author(s): Joachim L. Schultze, Anna C. Aschenbrenner
Published in: Cell, Issue 184/7, 2021, Page(s) 1671-1692, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2021.02.029

Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Author(s): Neha Mishra, Konrad Aden, Johanna I Blase, Nathan Baran, Dora Bordoni, Florian Tran, Claudio Conrad, Diana Avalos, Charlot Jaeckel, Michael Scherer, Signe B Sørensen, Silja H Overgaard, Berenice Schulte, Susanna Nikolaus, Guillaume Rey, Gilles Gasparoni, Paul A Lyons, Joachim L Schultze, Jörn Walter, Vibeke Andersen, SYSCID Consortium, Emmanouil T Dermitzakis, Stefan Schreiber, Philip Rosenstiel
Published in: Genome Medicine, Issue 1756994X, 2022, ISSN 1756-994X
Publisher: BioMed Central
DOI: 10.1186/s13073-022-01112-z

Crohn’s-associated invariant T cells (CAITs) recognise small sulfonate molecules on CD1d

Author(s): Minervina, Anastasia A., Mikhail V. Pogorelyy, Steffen Paysen, Ulrich Luening, Frauke Degenhardt, Andre Franke, Paul G. Thomas, and Elisa Rosati
Published in: Gut, 2022, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2022-328684

Temporal variability in quantitative human gut microbiome profiles and implications for clinical research

Author(s): Doris Vandeputte, Lindsey De Commer, Raul Y Tito, Gunter Kathagen, João Sabino, Séverine Vermeire, Karoline Faust, Jeroen Raes
Published in: Nature communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27098-7

Glycosylation of IgG Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese

Author(s): Xiaoni Meng, Manshu Song, Marija Vilaj, Jerko Štambuk, Mamatyusupu Dolikun, Jie Zhang, Di Liu, Hao Wang, Xiaoyu Zhang, Jinxia Zhang, Weijie Cao, Ana Momčilović, Irena Trbojević-Akmačić, Xingang Li, Deqiang Zheng, Lijuan Wu, Xiuhua Guo, Youxin Wang, Gordan Lauc, Wei Wang
Published in: Journal of Personalized Medicine, Issue 11/7, 2021, Page(s) 614, ISSN 2075-4426
Publisher: MDPI
DOI: 10.3390/jpm11070614

Impact of fibre and red/processed meat intake on treatment outcomes among patients with chronic inflammatory diseases initiating biological therapy: A prospective cohort study

Author(s): Silja H. Overgaard1,2,3*, Signe B. Sørensen1,4, Heidi L. Munk5, Anders B. Nexøe4,6,7, Henning Glerup8, Rikke H. Henriksen8, Tanja Guldmann8, Natalia Pedersen9, Sanaz Saboori9, Lone Hvid10, Jens F. Dahlerup11, Christian L. Hvas11, Mohamad Jawhara1,4,12, Karina W. Andersen1,12, Andreas K. Pedersen13, Ole H. Nielsen14, Fredrik Bergenheim14, Jacob B. Brodersen3,15, Berit L. Heitmann16,17, Thorhallur
Published in: Frontiers in Nutrition, Issue 2296861X, 2019, ISSN 2296-861X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fnut.2022.985732

Therapeutic Interleukin-6 Trans-signaling Inhibition by Olamkicept (sgp130Fc) in Patients With Active Inflammatory Bowel Disease

Author(s): Stefan Schreiber, Konrad Aden, Joana P. Bernardes, Claudio Conrad, Florian Tran, Hanna Höper, Valery Volk, Neha Mishra, Johanna Ira Blase, Susanna Nikolaus, Johannes Bethge, Tanja Kühbacher, Christoph Röcken, Minhu Chen, Ian Cottingham, Niclas Petri, Birgitte B. Rasmussen, Juliane Lokau, Lennart Lenk, Christoph Garbers, Friedrich Feuerhake, Stefan Rose-John, Georg H. Waetzig, Philip Rosenstiel
Published in: Gastroenterology, Issue 160/7, 2021, Page(s) 2354-2366.e11, ISSN 0016-5085
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2021.02.062

An intrinsic role of IL-33 in Treg cell–mediated tumor immunoevasion

Author(s): Aikaterini Hatzioannou, Aggelos Banos, Theodore Sakelaropoulos, Constantinos Fedonidis, Maria-Sophia Vidali, Maren Köhne, Kristian Händler, Louis Boon, Ana Henriques, Vasiliki Koliaraki, Panagiotis Georgiadis, Jerome Zoidakis, Aikaterini Termentzi, Marc Beyer, Triantafyllos Chavakis, Dimitrios Boumpas, Aristotelis Tsirigos, Panayotis Verginis
Published in: Nature Immunology, Issue 21/1, 2020, Page(s) 75-85, ISSN 1529-2908
Publisher: Nature Publishing Group
DOI: 10.1038/s41590-019-0555-2

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