A Systems medicine approach to chronic inflammatory disease

Livrables

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

Auteurs: 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.
Publié dans: Human Molecular Genetics, 2021, ISSN 0964-6906
Éditeur: Oxford University Press
DOI: 10.1093/hmg/ddab017

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

Auteurs: 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
Publié dans: Frontiers in Immunology, Numéro 16643224, 2022, ISSN 1664-3224
Éditeur: Frontiers Media SA
DOI: 10.3389/fimmu.2022.917232

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

Auteurs: 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
Publié dans: Rheumatology, Numéro 14620324, 2021, ISSN 1462-0324
Éditeur: Oxford University Press
DOI: 10.1093/rheumatology/keaa902

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

Auteurs: 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
Publié dans: Annals of the Rheumatic Diseases, Numéro 00034967, 2022, ISSN 0003-4967
Éditeur: BMJ Publishing Group
DOI: 10.1136/annrheumdis-2021-222069

Neutrophils in COVID-19

Auteurs: Nico Reusch, Elena De Domenico, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Kevin Baßler, Joachim L. Schultze, Anna C. Aschenbrenner
Publié dans: Frontiers in Immunology, Numéro 12, 2021, ISSN 1664-3224
Éditeur: Frontiers
DOI: 10.3389/fimmu.2021.652470

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

Auteurs: 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
Publié dans: International Journal of Molecular Sciences, Numéro 14220067, 2022, ISSN 1422-0067
Éditeur: 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

Auteurs: 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
Publié dans: Immunity, Numéro 00928674, 2021, ISSN 0092-8674
Éditeur: 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

Auteurs: 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
Publié dans: Epigenetics & Chromatin, Vol 14, Iss 1, Pp 1-17 (2021), Numéro 17568935, 2021, ISSN 1756-8935
Éditeur: BioMed Central
DOI: 10.17863/cam.77053

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

Auteurs: 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
Publié dans: eLife, Numéro 2050084X, 2022, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.78012

Swarm Learning for decentralized and confidential clinical machine learning

Auteurs: 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
Publié dans: Nature, Numéro 594/7862, 2021, Page(s) 265-270, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-021-03583-3

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

Auteurs: Elena De Domenico, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Matthias Becker, Kristian Händler, Joachim L. Schultze
Publié dans: STAR Protocols, Numéro 1/3, 2020, Page(s) 100233, ISSN 2666-1667
Éditeur: 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

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

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

Auteurs: Panagiotis Garantziotis, Dimitrios Nikolakis, Stavros Doumas, Eleni Frangou, George Sentis, Anastasia Filia, Antonis Fanouriakis, George Bertsias and Dimitrios T. Boumpas
Publié dans: Frontiers in Immunology, Numéro 16643224, 2022, ISSN 1664-3224
Éditeur: 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

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

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

Auteurs: 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
Publié dans: Frontiers in Mircrobiology, Numéro 1664302X, 2022, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2022.811922

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

Auteurs: 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,
Publié dans: Cell, Numéro 00928674, 2021, ISSN 0092-8674
Éditeur: 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

Auteurs: 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
Publié dans: Nature Genetics, Numéro 24, 2021, ISSN 1061-4036
Éditeur: 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

Auteurs: 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
Publié dans: Journal of Clinical Medicine, Numéro 7, 2020, Page(s) 127, ISSN 2077-0383
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.18154/rwth-2020-04417

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

Auteurs: 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
Publié dans: Genome Medicine, Numéro 13/1, 2021, ISSN 1756-994X
Éditeur: BioMed Central
DOI: 10.1186/s13073-020-00823-5

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

Auteurs: 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
Publié dans: Gut, 2022, ISSN 0017-5749
Éditeur: BMJ Publishing Group
DOI: 10.1136/gutjnl-2021-325373

Towards a European health research and innovation cloud (HRIC)

Auteurs: 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
Publié dans: Genome Medicine, Numéro 1756994X, 2020, ISSN 1756-994X
Éditeur: 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

Auteurs: 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
Publié dans: Gastroenterology, 2019, ISSN 0016-5085
Éditeur: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2019.07.025

Monocytes and Macrophages in COVID-19

Auteurs: Rainer Knoll, Joachim L. Schultze, Jonas Schulte-Schrepping
Publié dans: Frontiers in Immunology, Numéro 16624548, 2021, ISSN 1662-4548
Éditeur: 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

Auteurs: 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
Publié dans: Nutrients, Numéro 9/5, 2017, Page(s) 499, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu9050499

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 8/1, 2017, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-017-00453-3

Increased Tryptophan Metabolism Is Associated With Activity of Inflammatory Bowel Diseases

Auteurs: 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
Publié dans: Gastroenterology, Numéro 153/6, 2017, Page(s) 1504-1516.e2, ISSN 0016-5085
Éditeur: 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

Auteurs: 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
Publié dans: BMJ Open, Numéro 1, 2018, ISSN 2044-6055
Éditeur: BMJ Publishing Group
DOI: 10.1136/bmjopen-2017-018166

Overview of methodologies for T-cell receptor repertoire analysis

Auteurs: Elisa Rosati, C Marie Dowds, Evaggelia Liaskou, Eva Kristine Klemsdal Henriksen, Tom H Karlsen, Andre Franke
Publié dans: BMC Biotechnology, Numéro 17/1, 2017, ISSN 1472-6750
Éditeur: BioMed Central
DOI: 10.1186/s12896-017-0379-9

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 9/1, 2018, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-018-04365-8

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

Auteurs: 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,
Publié dans: Cell, Numéro 172/3, 2018, Page(s) 500-516.e16, ISSN 0092-8674
Éditeur: Cell Press
DOI: 10.1016/j.cell.2017.11.042

Systems Medicine in Chronic Inflammatory Diseases

Auteurs: Joachim L. Schultze, Philip Rosenstiel
Publié dans: Immunity, Numéro 48/4, 2018, Page(s) 608-613, ISSN 1074-7613
Éditeur: Cell Press
DOI: 10.1016/j.immuni.2018.03.022

The resilience of the intestinal microbiota influences health and disease

Auteurs: Felix Sommer, Jacqueline Moltzau Anderson, Richa Bharti, Jeroen Raes, Philip Rosenstiel
Publié dans: Nature Reviews Microbiology, Numéro 15/10, 2017, Page(s) 630-638, ISSN 1740-1526
Éditeur: Nature Publishing Group
DOI: 10.1038/nrmicro.2017.58

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

Auteurs: 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
Publié dans: Gastroenterology, Numéro 154/5, 2018, Page(s) 1320-1333.e10, ISSN 0016-5085
Éditeur: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2018.01.002

Profiling and genetic control of the murine immunoglobulin G glycome

Auteurs: 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
Publié dans: Nature Chemical Biology, Numéro 14/5, 2018, Page(s) 516-524, ISSN 1552-4450
Éditeur: 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

Auteurs: Ivan Gudelj, Perttu P. Salo, Irena Trbojević-Akmačić, Malena Albers, Dragan Primorac, Markus Perola, Gordan Lauc
Publié dans: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Numéro 1864/6, 2018, Page(s) 2034-2039, ISSN 0925-4439
Éditeur: 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

Auteurs: Marko Kosicek, Ivan Gudelj, Anita Horvatic, Tanja Jovic, Frano Vuckovic, Gordan Lauc, Silva Hecimovic
Publié dans: Molecular & Cellular Proteomics, Numéro 17/4, 2018, Page(s) 631-642, ISSN 1535-9476
Éditeur: 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

Auteurs: 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
Publié dans: Journal of Human Hypertension, 2018, ISSN 0950-9240
Éditeur: Nature Publishing Group
DOI: 10.1038/s41371-018-0071-0

Quantitative microbiome profiling links gut community variation to microbial load

Auteurs: 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
Publié dans: Nature, Numéro 551, 2017, Page(s) 507-511, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/nature24460

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

Auteurs: 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
Publié dans: Gut, 2018, ISSN 0017-5749
Éditeur: 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

Auteurs: 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
Publié dans: International Journal of Colorectal Disease, Numéro 33/7, 2018, Page(s) 927-936, ISSN 0179-1958
Éditeur: 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

Auteurs: 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
Publié dans: Gastroenterology, Numéro 154/3, 2018, Page(s) 585-598, ISSN 0016-5085
Éditeur: 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

Auteurs: 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
Publié dans: Human Molecular Genetics, Numéro 27/6, 2018, Page(s) 1106-1121, ISSN 0964-6906
Éditeur: 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

Auteurs: 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
Publié dans: Journal of Crohn's and Colitis, 2019, ISSN 1873-9946
Éditeur: Elsevier Science
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aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data

Auteurs: Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Publié dans: BMC Genomics, Numéro 20/1, 2019, ISSN 1471-2164
Éditeur: BioMed Central
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Biomarkers of Whole-Grain and Cereal-Fiber Intake in Human Studies: A Systematic Review of the Available Evidence and Perspectives

Auteurs: Mohamad Jawhara, Signe Bek Sørensen, Berit Lilienthal Heitmann, Vibeke Andersen
Publié dans: Nutrients, Numéro 11/12, 2019, Page(s) 2994, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
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Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 47/18, 2019, Page(s) 9637-9657, ISSN 0305-1048
Éditeur: Oxford University Press
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Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics

Auteurs: 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
Publié dans: iScience, Numéro 23/1, 2020, Page(s) 100780, ISSN 2589-0042
Éditeur: Cell Press
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Update on the pathogenesis of central nervous system lupus

Auteurs: Dionysis Nikolopoulos, Antonis Fanouriakis, Dimitrios T. Boumpas
Publié dans: Current Opinion in Rheumatology, Numéro 31/6, 2019, Page(s) 669-677, ISSN 1040-8711
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Increased central adiposity is associated with pro-inflammatory immunoglobulin G N-glycans

Auteurs: Alyce C. Russell, Agnieszka Kepka, Irena Trbojević-Akmačić, Ivo Ugrina, Manshu Song, Jennie Hui, Michael Hunter, Simon M. Laws, Gordan Lauc, Wei Wang
Publié dans: Immunobiology, Numéro 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

Auteurs: 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
Publié dans: Nature, Numéro 574/7776, 2019, Page(s) 122-126, ISSN 0028-0836
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ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS–STING

Auteurs: 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,
Publié dans: The Journal of Experimental Medicine, Numéro 215/11, 2018, Page(s) 2868-2886, ISSN 0022-1007
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Combined genetic and transcriptome analysis of patients with SLE: distinct, targetable signatures for susceptibility and severity

Auteurs: 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
Publié dans: Annals of the Rheumatic Diseases, Numéro 78/8, 2019, Page(s) 1079-1089, ISSN 0003-4967
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Transcriptional Signature Derived from Murine Tumor-Associated Macrophages Correlates with Poor Outcome in Breast Cancer Patients

Auteurs: 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
Publié dans: Cell Reports, Numéro 29/5, 2019, Page(s) 1221-1235.e5, ISSN 2211-1247
Éditeur: Cell Press
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NCX1 represents an ionic Na+ sensing mechanism in macrophages

Auteurs: 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
Publié dans: PLOS Biology, Numéro 18/6, 2020, Page(s) e3000722, ISSN 1545-7885
Éditeur: PLOS
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Regulatory T-cell Transcriptomic Reprogramming Characterizes Adverse Events by Checkpoint Inhibitors in Solid Tumors

Auteurs: 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
Publié dans: Cancer Immunology Research, Numéro 9/7, 2021, Page(s) 726-734, ISSN 2326-6066
Éditeur: American Association for Cancer Research Inc.
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Defining trained immunity and its role in health and disease

Auteurs: 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
Publié dans: Nature Reviews Immunology, Numéro 20/6, 2020, Page(s) 375-388, ISSN 1474-1733
Éditeur: Nature Publishing Group
DOI: 10.1038/s41577-020-0285-6

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

Auteurs: 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.
Publié dans: iScience, 2022, ISSN 2589-0042
Éditeur: 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

Auteurs: Thomas Sénard; Irini Flouri; Frano Vučković; Garyfalia Papadaki; Panagiota Goutakoli; Aggelos Banos; Maja Pučić-Baković; Marija Pezer; George Bertsias; Gordan Lauc; Prodromos Sidiropoulos
Publié dans: Arthritis Research & Therapy, Numéro 14786362, 2022, ISSN 1478-6362
Éditeur: Springer
DOI: 10.1186/s13075-022-02897-5

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

Auteurs: 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
Publié dans: Cell, Numéro 182/6, 2020, Page(s) 1419-1440.e23, ISSN 0092-8674
Éditeur: Cell Press
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Genetic and Environmental Influences of Dietary Indices in a UK Female Twin Cohort

Auteurs: Olatz Mompeo, Rachel Gibson, Paraskevi Christofidou, Tim D. Spector, Cristina Menni, Massimo Mangino
Publié dans: Twin Research and Human Genetics, Numéro 23/6, 2020, Page(s) 330-337, ISSN 1832-4274
Éditeur: Australian Academic Press Pty Ltd.
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Decreased Immunoglobulin G Core Fucosylation, A Player in Antibody-dependent Cell-mediated Cytotoxicity, is Associated with Autoimmune Thyroid Diseases

Auteurs: 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
Publié dans: Molecular & Cellular Proteomics, Numéro 19/5, 2020, Page(s) 774-792, ISSN 1535-9476
Éditeur: 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

Auteurs: 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
Publié dans: Immunity, Numéro 53/6, 2020, Page(s) 1296-1314.e9, ISSN 1074-7613
Éditeur: Cell Press
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A guide to systems-level immunomics

Auteurs: Lorenzo Bonaguro, Jonas Schulte-Schrepping, Thomas Ulas, Anna C. Aschenbrenner, Marc Beyer, Joachim L. Schultze
Publié dans: nature immunology, Numéro 15292908, 2022, ISSN 1529-2908
Éditeur: Nature Publishing Group
DOI: 10.1038/s41590-022-01309-9

COVID-19 and the human innate immune system

Auteurs: Joachim L. Schultze, Anna C. Aschenbrenner
Publié dans: Cell, Numéro 184/7, 2021, Page(s) 1671-1692, ISSN 0092-8674
Éditeur: Cell Press
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Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Auteurs: 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
Publié dans: Genome Medicine, Numéro 1756994X, 2022, ISSN 1756-994X
Éditeur: BioMed Central
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Temporal variability in quantitative human gut microbiome profiles and implications for clinical research

Auteurs: Doris Vandeputte, Lindsey De Commer, Raul Y Tito, Gunter Kathagen, João Sabino, Séverine Vermeire, Karoline Faust, Jeroen Raes
Publié dans: Nature communications, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
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Glycosylation of IgG Associates with Hypertension and Type 2 Diabetes Mellitus Comorbidity in the Chinese Muslim Ethnic Minorities and the Han Chinese

Auteurs: 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
Publié dans: Journal of Personalized Medicine, Numéro 11/7, 2021, Page(s) 614, ISSN 2075-4426
Éditeur: MDPI
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Impact of fibre and red/processed meat intake on treatment outcomes among patients with chronic inflammatory diseases initiating biological therapy: A prospective cohort study

Auteurs: 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
Publié dans: Frontiers in Nutrition, Numéro 2296861X, 2019, ISSN 2296-861X
Éditeur: Frontiers Media S.A.
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Therapeutic Interleukin-6 Trans-signaling Inhibition by Olamkicept (sgp130Fc) in Patients With Active Inflammatory Bowel Disease

Auteurs: 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
Publié dans: Gastroenterology, Numéro 160/7, 2021, Page(s) 2354-2366.e11, ISSN 0016-5085
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Crohn’s-associated invariant T cells (CAITs) recognise small sulfonate molecules on CD1d

Auteurs: Minervina, Anastasia A., Mikhail V. Pogorelyy, Steffen Paysen, Ulrich Luening, Frauke Degenhardt, Andre Franke, Paul G. Thomas, and Elisa Rosati
Publié dans: Gut, 2022, ISSN 0017-5749
Éditeur: BMJ Publishing Group
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An intrinsic role of IL-33 in Treg cell–mediated tumor immunoevasion

Auteurs: 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
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