{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T14:18:39Z","timestamp":1793974719328,"version":"4.8.0"},"reference-count":85,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2022,10,25]],"date-time":"2022-10-25T00:00:00Z","timestamp":1666656000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,10,25]],"date-time":"2022-10-25T00:00:00Z","timestamp":1666656000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 1160 IMPATH project A04"],"award-info":[{"award-number":["SFB 1160 IMPATH project A04"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 1160 IMPATH project B05"],"award-info":[{"award-number":["SFB 1160 IMPATH project B05"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 1160 IMPATH project Z01"],"award-info":[{"award-number":["SFB 1160 IMPATH project Z01"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 1160 IMPATH project Z02N"],"award-info":[{"award-number":["SFB 1160 IMPATH project Z02N"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["TRR167"],"award-info":[{"award-number":["TRR167"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["project Z01"],"award-info":[{"award-number":["project Z01"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["GR1617\/14-1\/iPAD"],"award-info":[{"award-number":["GR1617\/14-1\/iPAD"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["RESIST\u2013EXC 2155\u2013Project ID 517 390874280"],"award-info":[{"award-number":["RESIST\u2013EXC 2155\u2013Project ID 517 390874280"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CIBSS\u2013EXC-2189\u2013Project ID 390939984"],"award-info":[{"award-number":["CIBSS\u2013EXC-2189\u2013Project ID 390939984"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CRC 850 subprojects C9"],"award-info":[{"award-number":["CRC 850 subprojects C9"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["Z1"],"award-info":[{"award-number":["Z1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CRC1479 (Project ID: 441891347- S1)"],"award-info":[{"award-number":["CRC1479 (Project ID: 441891347- S1)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CRC1453 (Project ID 431984000 - S1)"],"award-info":[{"award-number":["CRC1453 (Project ID 431984000 - S1)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["GAIN 748 01GM1910A"],"award-info":[{"award-number":["GAIN 748 01GM1910A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["GAIN 748 01GM1910A"],"award-info":[{"award-number":["GAIN 748 01GM1910A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["FKZ 01ZZ1801B"],"award-info":[{"award-number":["FKZ 01ZZ1801B"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009553","name":"Agentura Pro Zdravotnick\u00fd V\u00fdzkum \u010cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["NV18-05\u201300162"],"award-info":[{"award-number":["NV18-05\u201300162"]}],"id":[{"id":"10.13039\/501100009553","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009553","name":"Agentura Pro Zdravotnick\u00fd V\u00fdzkum \u010cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["NU20-05\u201300282"],"award-info":[{"award-number":["NU20-05\u201300282"]}],"id":[{"id":"10.13039\/501100009553","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["FAPESP grant 2020\/01688-0"],"award-info":[{"award-number":["FAPESP grant 2020\/01688-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Universit\u00e4tsklinikum Freiburg"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Clin Immunol"],"published-print":{"date-parts":[[2023,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Purpose<\/jats:title>\n                    <jats:p>About 15% of patients with common variable immunodeficiency (CVID) develop a small intestinal enteropathy, which resembles celiac disease with regard to histopathology but evolves from a distinct, poorly defined pathogenesis that has been linked in some cases to chronic norovirus (NV) infection. Interferon-driven inflammation is a prominent feature of CVID enteropathy, but it remains unknown how NV infection may contribute.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Duodenal biopsies of CVID patients, stratified according to the presence of villous atrophy (VA), IgA plasma cells (PCs), and chronic NV infection, were investigated by flow cytometry, multi-epitope-ligand cartography, bulk RNA-sequencing, and RT-qPCR of genes of interest.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      VA development was connected to the lack of intestinal (IgA\n                      <jats:sup>+<\/jats:sup>\n                      ) PC, a T helper 1\/T helper 17 cell imbalance, and increased recruitment of granzyme\n                      <jats:sup>+<\/jats:sup>\n                      CD8\n                      <jats:sup>+<\/jats:sup>\n                      T cells and pro-inflammatory macrophages to the affected site. A mixed interferon type I\/III and II signature occurred already in the absence of histopathological changes and increased with the severity of the disease and in the absence of (IgA\n                      <jats:sup>+<\/jats:sup>\n                      ) PCs. Chronic NV infection exacerbated this signature when compared to stage-matched NV-negative samples.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our study suggests that increased IFN signaling and T-cell cytotoxicity are present already in mild and are aggravated in severe stages (VA) of CVID enteropathy. NV infection preempts local high IFN-driven inflammation, usually only seen in VA, at milder disease stages. Thus, revealing the impact of different drivers of the pathological mixed IFN type I\/III and II signature may allow for more targeted treatment strategies in CVID enteropathy and supports the goal of viral elimination.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Graphical abstract<\/jats:title>\n                  <\/jats:sec>","DOI":"10.1007\/s10875-022-01379-2","type":"journal-article","created":{"date-parts":[[2022,10,25]],"date-time":"2022-10-25T05:02:56Z","timestamp":1666674176000},"page":"371-390","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Interferon-Driven Immune Dysregulation in Common Variable Immunodeficiency\u2013Associated Villous Atrophy and Norovirus Infection"],"prefix":"10.1007","volume":"43","author":[{"given":"Valentina","family":"Strohmeier","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geoffroy","family":"Andrieux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne","family":"Unger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Pascual-Reguant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Klocperk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximilian","family":"Seidl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Otavio Cabral","family":"Marques","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marleen","family":"Eckert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katja","family":"Gr\u00e4we","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"Shabani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"von Spee-Mayer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Friedmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ina","family":"Harder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvia","family":"Gutenberger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baerbel","family":"Keller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele","family":"Proietti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alla","family":"Bulashevska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bodo","family":"Grimbacher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Provaznik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir","family":"Benes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sigune","family":"Goldacker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Schell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja E.","family":"Hauser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie","family":"Boerries","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Hasselblatt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1172-865X","authenticated-orcid":false,"given":"Klaus","family":"Warnatz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,10,25]]},"reference":[{"issue":"1","key":"1379_CR1","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.jaip.2015.07.025","volume":"4","author":"FA Bonilla","year":"2016","unstructured":"Bonilla FA, Barlan I, Chapel H, Costa-Carvalho BT, Cunningham-Rundles C, de la Morena MT, et al. International Consensus Document (ICON): common variable immunodeficiency disorders. J Allergy Clin Immunol Pract. 2016;4(1):38\u201359.","journal-title":"J Allergy Clin Immunol Pract"},{"issue":"7","key":"1379_CR2","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1182\/blood-2011-09-377945","volume":"119","author":"ES Resnick","year":"2012","unstructured":"Resnick ES, Moshier EL, Godbold JH, Cunningham-Rundles C. Morbidity and mortality in common variable immune deficiency over 4 decades. Blood. 2012;119(7):1650\u20137.","journal-title":"Blood"},{"issue":"1","key":"1379_CR3","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1016\/j.jaci.2013.12.1077","volume":"134","author":"B Gathmann","year":"2014","unstructured":"Gathmann B, Mahlaoui N, G\u00e9rard L, Oksenhendler E, Warnatz K, Schulze I, et al. Clinical picture and treatment of 2212 patients with common variable immunodeficiency. J Allergy Clin Immunol. 2014;134(1):116\u201326.","journal-title":"J Allergy Clin Immunol"},{"issue":"5","key":"1379_CR4","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1016\/j.jaci.2016.12.978","volume":"140","author":"A Fischer","year":"2017","unstructured":"Fischer A, Provot J, Jais JP, Alcais A, Mahlaoui N. Autoimmune and inflammatory manifestations occur frequently in patients with primary immunodeficiencies. J Allergy Clin Immunol. 2017;140(5):1388-93.e8.","journal-title":"J Allergy Clin Immunol"},{"issue":"2","key":"1379_CR5","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1182\/blood-2007-11-124545","volume":"112","author":"H Chapel","year":"2008","unstructured":"Chapel H, Lucas M, Lee M, Bjorkander J, Webster D, Grimbacher B, et al. Common variable immunodeficiency disorders: division into distinct clinical phenotypes. Blood. 2008;112(2):277\u201386.","journal-title":"Blood"},{"issue":"11","key":"1379_CR6","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.3109\/00365521.2014.962605","volume":"49","author":"R Hein","year":"2014","unstructured":"Hein R, K\u00f6ster I, Bollschweiler E, Schubert I. Prevalence of inflammatory bowel disease: estimates for 2010 and trends in Germany from a large insurance-based regional cohort. Scand J Gastroenterol. 2014;49(11):1325\u201335.","journal-title":"Scand J Gastroenterol"},{"issue":"5","key":"1379_CR7","doi-asserted-by":"publisher","first-page":"746","DOI":"10.1007\/s10875-010-9424-3","volume":"30","author":"G Mouillot","year":"2010","unstructured":"Mouillot G, Carmagnat M, G\u00e9rard L, Garnier JL, Fieschi C, Vince N, et al. B-cell and T-cell phenotypes in CVID patients correlate with the clinical phenotype of the disease. J Clin Immunol. 2010;30(5):746\u201355.","journal-title":"J Clin Immunol"},{"issue":"10","key":"1379_CR8","doi-asserted-by":"publisher","first-page":"2262","DOI":"10.1038\/ajg.2010.214","volume":"105","author":"G Malamut","year":"2010","unstructured":"Malamut G, Verkarre V, Suarez F, Viallard JF, Lascaux AS, Cosnes J, et al. The enteropathy associated with common variable immunodeficiency: the delineated frontiers with celiac disease. Am J Gastroenterol. 2010;105(10):2262\u201375.","journal-title":"Am J Gastroenterol"},{"issue":"9573","key":"1379_CR9","doi-asserted-by":"publisher","first-page":"1627","DOI":"10.1016\/S0140-6736(07)60750-8","volume":"369","author":"DC Baumgart","year":"2007","unstructured":"Baumgart DC, Carding SR. Inflammatory bowel disease: cause and immunobiology. Lancet (London, England). 2007;369(9573):1627\u201340.","journal-title":"Lancet (London, England)"},{"issue":"12","key":"1379_CR10","doi-asserted-by":"publisher","first-page":"1800","DOI":"10.1097\/PAS.0b013e3180cab60c","volume":"31","author":"JA Daniels","year":"2007","unstructured":"Daniels JA, Lederman HM, Maitra A, Montgomery EA. Gastrointestinal tract pathology in patients with common variable immunodeficiency (CVID): a clinicopathologic study and review. Am J Surg Pathol. 2007;31(12):1800\u201312.","journal-title":"Am J Surg Pathol"},{"issue":"9","key":"1379_CR11","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1016\/j.cgh.2013.02.024","volume":"11","author":"S Agarwal","year":"2013","unstructured":"Agarwal S, Mayer L. Diagnosis and treatment of gastrointestinal disorders in patients with primary immunodeficiency. Clin Gastroenterol Hepatol. 2013;11(9):1050\u201363.","journal-title":"Clin Gastroenterol Hepatol"},{"issue":"5","key":"1379_CR12","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1016\/j.anai.2019.07.014","volume":"123","author":"S Agarwal","year":"2019","unstructured":"Agarwal S, Cunningham-Rundles C. Autoimmunity in common variable immunodeficiency. Ann Allergy Asthma Immunol: off Pub Am Coll Allergy Asthma Immunol. 2019;123(5):454\u201360.","journal-title":"Ann Allergy Asthma Immunol: off Pub Am Coll Allergy Asthma Immunol"},{"issue":"5","key":"1379_CR13","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1007\/s10875-013-9892-3","volume":"33","author":"N Venhoff","year":"2013","unstructured":"Venhoff N, Emmerich F, Neagu M, Salzer U, Koehn C, Driever S, et al. The role of HLA DQ2 and DQ8 in dissecting celiac-like disease in common variable immunodeficiency. J Clin Immunol. 2013;33(5):909\u201316.","journal-title":"J Clin Immunol"},{"issue":"2","key":"1379_CR14","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1111\/j.1365-2249.1994.tb06513.x","volume":"95","author":"EW Herbst","year":"1994","unstructured":"Herbst EW, Armbruster M, Rump J-A, Buscher H-P, Peter H-H. Intestinal B cell defects in common variable immunodeficiency. Clin Exp Immunol. 1994;95(2):215\u201321.","journal-title":"Clin Exp Immunol"},{"issue":"3","key":"1379_CR15","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1111\/cei.12884","volume":"188","author":"J Woodward","year":"2017","unstructured":"Woodward J, Gkrania-Klotsas E, Kumararatne D. Chronic norovirus infection and common variable immunodeficiency. Clin Exp Immunol. 2017;188(3):363\u201370.","journal-title":"Clin Exp Immunol"},{"key":"1379_CR16","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.clim.2018.09.008","volume":"197","author":"N Shulzhenko","year":"2018","unstructured":"Shulzhenko N, Dong X, Vyshenska D, Greer RL, Gurung M, Vasquez-Perez S, et al. CVID enteropathy is characterized by exceeding low mucosal IgA levels and interferon-driven inflammation possibly related to the presence of a pathobiont. Clin Immunol. 2018;197:139\u201353.","journal-title":"Clin Immunol"},{"issue":"12","key":"1379_CR17","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1038\/nm.2505","volume":"17","author":"N Shulzhenko","year":"2011","unstructured":"Shulzhenko N, Morgun A, Hsiao W, Battle M, Yao M, Gavrilova O, et al. Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nat Med. 2011;17(12):1585\u201393.","journal-title":"Nat Med"},{"issue":"5","key":"1379_CR18","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1136\/jcp.55.5.393","volume":"55","author":"M Hayat","year":"2002","unstructured":"Hayat M, Cairns A, Dixon MF, O\u2019Mahony S. Quantitation of intraepithelial lymphocytes in human duodenum: what is normal? J Clin Pathol. 2002;55(5):393\u20134.","journal-title":"J Clin Pathol"},{"issue":"2","key":"1379_CR19","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/0950-3528(95)90032-2","volume":"9","author":"MN Marsh","year":"1995","unstructured":"Marsh MN, Crowe PT. Morphology of the mucosal lesion in gluten sensitivity. Bailliere\u2019s Clin Gastroenterol. 1995;9(2):273\u201393.","journal-title":"Bailliere\u2019s Clin Gastroenterol"},{"issue":"10","key":"1379_CR20","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1097\/00042737-199910000-00019","volume":"11","author":"G Oberhuber","year":"1999","unstructured":"Oberhuber G, Granditsch G, Vogelsang H. The histopathology of coeliac disease: time for a standardized report scheme for pathologists. Eur J Gastroenterol Hepatol. 1999;11(10):1185\u201394.","journal-title":"Eur J Gastroenterol Hepatol"},{"issue":"9","key":"1379_CR21","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1002\/cyto.a.23526","volume":"93","author":"K Holzwarth","year":"2018","unstructured":"Holzwarth K, K\u00f6hler R, Philipsen L, Tokoyoda K, Ladyhina V, W\u00e4hlby C, et al. Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections. Cytometry A. 2018;93(9):876\u201388.","journal-title":"Cytometry A"},{"issue":"1","key":"1379_CR22","doi-asserted-by":"publisher","first-page":"1737","DOI":"10.1038\/s41467-021-21994-8","volume":"12","author":"A Pascual-Reguant","year":"2021","unstructured":"Pascual-Reguant A, K\u00f6hler R, Mothes R, Bauherr S, Hern\u00e1ndez DC, Uecker R, et al. Multiplexed histology analyses for the phenotypic and spatial characterization of human innate lymphoid cells. Nat Commun. 2021;12(1):1737.","journal-title":"Nat Commun"},{"issue":"10","key":"1379_CR23","doi-asserted-by":"publisher","first-page":"1270","DOI":"10.1038\/nbt1250","volume":"24","author":"W Schubert","year":"2006","unstructured":"Schubert W, Bonnekoh B, Pommer AJ, Philipsen L, B\u00f6ckelmann R, Malykh Y, et al. Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nat Biotechnol. 2006;24(10):1270\u20138.","journal-title":"Nat Biotechnol"},{"issue":"3","key":"1379_CR24","doi-asserted-by":"publisher","first-page":"1242","DOI":"10.1109\/TIP.2012.2231087","volume":"22","author":"S Pertuz","year":"2013","unstructured":"Pertuz S, Puig D, Garcia MA, Fusiello A. Generation of all-in-focus images by noise-robust selective fusion of limited depth-of-field images. IEEE Trans Image Process. 2013;22(3):1242\u201351.","journal-title":"IEEE Trans Image Process"},{"issue":"7","key":"1379_CR25","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9(7):676\u201382.","journal-title":"Nat Methods"},{"issue":"12","key":"1379_CR26","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1038\/s41592-019-0582-9","volume":"16","author":"S Berg","year":"2019","unstructured":"Berg S, Kutra D, Kroeger T, Straehle CN, Kausler BX, Haubold C, et al. ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 2019;16(12):1226\u201332.","journal-title":"Nat Methods"},{"issue":"10","key":"1379_CR27","doi-asserted-by":"publisher","first-page":"R100","DOI":"10.1186\/gb-2006-7-10-r100","volume":"7","author":"AE Carpenter","year":"2006","unstructured":"Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, et al. Cell Profiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7(10):R100.","journal-title":"Genome Biol"},{"key":"1379_CR28","doi-asserted-by":"crossref","unstructured":"Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 2007;35:W71\u2013W4.","DOI":"10.1093\/nar\/gkm306"},{"issue":"15","key":"1379_CR29","first-page":"2114","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (Oxford, England). 2014;30(15):2114\u201320.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"1379_CR30","first-page":"15","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England). 2013;29(1):15\u201321.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"12","key":"1379_CR31","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.","journal-title":"Genome Biol"},{"issue":"43","key":"1379_CR32","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102(43):15545\u201350.","journal-title":"Proc Natl Acad Sci"},{"issue":"14","key":"1379_CR33","doi-asserted-by":"publisher","first-page":"i436","DOI":"10.1093\/bioinformatics\/btz363","volume":"35","author":"G Sturm","year":"2019","unstructured":"Sturm G, Finotello F, Petitprez F, Zhang JD, Baumbach J, Fridman WH, et al. Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Bioinformatics (Oxford, England). 2019;35(14):i436\u201345.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"5","key":"1379_CR34","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/nmeth.3337","volume":"12","author":"AM Newman","year":"2015","unstructured":"Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453\u20137.","journal-title":"Nat Methods"},{"issue":"22","key":"1379_CR35","doi-asserted-by":"publisher","first-page":"12306","DOI":"10.1073\/pnas.1915681117","volume":"117","author":"EC Reilly","year":"2020","unstructured":"Reilly EC, Lambert Emo K, Buckley PM, Reilly NS, Smith I, Chaves FA, et al. TRM integrins CD103 and CD49a differentially support adherence and motility after resolution of influenza virus infection. Proc Natl Acad Sci. 2020;117(22):12306\u201314.","journal-title":"Proc Natl Acad Sci"},{"issue":"11","key":"1379_CR36","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1038\/nri1490","volume":"4","author":"LH Glimcher","year":"2004","unstructured":"Glimcher LH, Townsend MJ, Sullivan BM, Lord GM. Recent developments in the transcriptional regulation of cytolytic effector cells. Nat Rev Immunol. 2004;4(11):900\u201311.","journal-title":"Nat Rev Immunol"},{"issue":"5","key":"1379_CR37","doi-asserted-by":"publisher","first-page":"1267","DOI":"10.1016\/j.jcmgh.2020.12.012","volume":"11","author":"A Pattekar","year":"2021","unstructured":"Pattekar A, Mayer LS, Lau CW, Liu C, Palko O, Bewtra M, et al. Norovirus-specific CD8(+) T cell responses in human blood and tissues. Cell Mol Gastroenterol Hepatol. 2021;11(5):1267\u201389.","journal-title":"Cell Mol Gastroenterol Hepatol"},{"issue":"4","key":"1379_CR38","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1038\/s41385-018-0030-7","volume":"11","author":"D Bernardo","year":"2018","unstructured":"Bernardo D, Marin AC, Fern\u00e1ndez-Tom\u00e9 S, Montalban-Arques A, Carrasco A, Trist\u00e1n E, et al. Human intestinal pro-inflammatory CD11chighCCR2+CX3CR1+ macrophages, but not their tolerogenic CD11c\u2212CCR2\u2212CX3CR1\u2212 counterparts, are expanded in inflammatory bowel disease. Mucosal Immunol. 2018;11(4):1114\u201326.","journal-title":"Mucosal Immunol"},{"issue":"3","key":"1379_CR39","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1136\/gut.38.3.414","volume":"38","author":"BS Nielsen","year":"1996","unstructured":"Nielsen BS, Borregaard N, Bundgaard JR, Timshel S, Sehested M, Kjeldsen L. Induction of NGAL synthesis in epithelial cells of human colorectal neoplasia and inflammatory bowel diseases. Gut. 1996;38(3):414\u201320.","journal-title":"Gut"},{"issue":"1","key":"1379_CR40","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0086844","volume":"9","author":"C Thelemann","year":"2014","unstructured":"Thelemann C, Eren RO, Coutaz M, Brasseit J, Bouzourene H, Rosa M, et al. Interferon-\u03b3 induces expression of MHC class II on intestinal epithelial cells and protects mice from colitis. PLoS ONE. 2014;9(1): e86844.","journal-title":"PLoS ONE"},{"issue":"5","key":"1379_CR41","doi-asserted-by":"publisher","first-page":"1206","DOI":"10.1016\/S0016-5085(86)80018-X","volume":"91","author":"F Arnaud-Battandier","year":"1986","unstructured":"Arnaud-Battandier F, Cerf-Bensussan N, Amsellem R, Schmitz J. Increased HLA-DR expression by enterocytes in children with celiac disease. Gastroenterology. 1986;91(5):1206\u201312.","journal-title":"Gastroenterology"},{"issue":"6","key":"1379_CR42","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1038\/s41385-019-0199-4","volume":"12","author":"E Hassan","year":"2019","unstructured":"Hassan E, Baldridge MT. Norovirus encounters in the gut: multifaceted interactions and disease outcomes. Mucosal Immunol. 2019;12(6):1259\u201367.","journal-title":"Mucosal Immunol"},{"issue":"2","key":"1379_CR43","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1038\/ajg.2014.432","volume":"110","author":"JM Woodward","year":"2015","unstructured":"Woodward JM, Gkrania-Klotsas E, Cordero-Ng AY, Aravinthan A, Bandoh BN, Liu H, et al. The role of chronic norovirus infection in the enteropathy associated with common variable immunodeficiency. Offic J Am Coll Gastroenterol ACG . 2015;110(2):320\u20137.","journal-title":"Offic J Am Coll Gastroenterol ACG ."},{"issue":"3","key":"1379_CR44","doi-asserted-by":"publisher","first-page":"748","DOI":"10.1053\/j.gastro.2006.06.022","volume":"131","author":"PJ Mannon","year":"2006","unstructured":"Mannon PJ, Fuss IJ, Dill S, Friend J, Groden C, Hornung R, et al. Excess IL-12 but not IL-23 accompanies the inflammatory bowel disease associated with common variable immunodeficiency. Gastroenterology. 2006;131(3):748\u201356.","journal-title":"Gastroenterology"},{"issue":"6","key":"1379_CR45","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1038\/mi.2010.36","volume":"3","author":"M Bodd","year":"2010","unstructured":"Bodd M, R\u00e1ki M, Tollefsen S, Fallang LE, Bergseng E, Lundin KE, et al. HLA-DQ2-restricted gluten-reactive T cells produce IL-21 but not IL-17 or IL-22. Mucosal Immunol. 2010;3(6):594\u2013601.","journal-title":"Mucosal Immunol"},{"key":"1379_CR46","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1136\/gut.37.6.766","volume":"37","author":"E Nilsen","year":"1995","unstructured":"Nilsen E, Lundin K, Krajci P, Scott H, Sollid L, Brandtzaeg P. Gluten specific, HLA-DQ restricted T cells from coeliac mucosa produce cytokines with Th1 or Th0 profile dominated by interferon gamma. Gut. 1995;37:766\u201376.","journal-title":"Gut"},{"issue":"3","key":"1379_CR47","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.4049\/jimmunol.1001723","volume":"186","author":"M Lochner","year":"2011","unstructured":"Lochner M, B\u00e9rard M, Sawa S, Hauer S, Gaboriau-Routhiau V, Fernandez TD, et al. Restricted microbiota and absence of cognate TCR antigen leads to an unbalanced generation of Th17 cells. J Immunol (Baltimore, Md: 1950). 2011;186(3):1531\u20137.","journal-title":"J Immunol (Baltimore, Md: 1950)"},{"key":"1379_CR48","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/518483","volume":"2013","author":"P Nijeboer","year":"2013","unstructured":"Nijeboer P, van Wanrooij RL, Tack GJ, Mulder CJ, Bouma G. Update on the diagnosis and management of refractory coeliac disease. Gastroenterol Res Pract. 2013;2013: 518483.","journal-title":"Gastroenterol Res Pract"},{"issue":"3","key":"1379_CR49","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","volume":"139","author":"II Ivanov","year":"2009","unstructured":"Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009;139(3):485\u201398.","journal-title":"Cell"},{"issue":"4","key":"1379_CR50","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1038\/ni.2552","volume":"14","author":"K Hirota","year":"2013","unstructured":"Hirota K, Turner JE, Villa M, Duarte JH, Demengeot J, Steinmetz OM, et al. Plasticity of Th17 cells in Peyer\u2019s patches is responsible for the induction of T cell-dependent IgA responses. Nat Immunol. 2013;14(4):372\u20139.","journal-title":"Nat Immunol"},{"issue":"9","key":"1379_CR51","doi-asserted-by":"publisher","first-page":"4666","DOI":"10.4049\/jimmunol.1200955","volume":"189","author":"AT Cao","year":"2012","unstructured":"Cao AT, Yao S, Gong B, Elson CO, Cong Y. Th17 cells upregulate polymeric Ig receptor and intestinal IgA and contribute to intestinal homeostasis. J Immunol (Baltimore, Md: 1950). 2012;189(9):4666\u201373.","journal-title":"J Immunol (Baltimore, Md: 1950)"},{"key":"1379_CR52","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.exppara.2015.06.003","volume":"156","author":"SM Dann","year":"2015","unstructured":"Dann SM, Manthey CF, Le C, Miyamoto Y, Gima L, Abrahim A, et al. IL-17A promotes protective IgA responses and expression of other potential effectors against the lumen-dwelling enteric parasite Giardia. Exp Parasitol. 2015;156:68\u201378.","journal-title":"Exp Parasitol"},{"issue":"8","key":"1379_CR53","doi-asserted-by":"publisher","first-page":"4507","DOI":"10.4049\/jimmunol.0900237","volume":"182","author":"Z Jaffar","year":"2009","unstructured":"Jaffar Z, Ferrini ME, Herritt LA, Roberts K. Cutting edge: lung mucosal Th17-mediated responses induce polymeric Ig receptor expression by the airway epithelium and elevate secretory IgA levels. J Immunol (Baltimore, Md: 1950). 2009;182(8):4507\u201311.","journal-title":"J Immunol (Baltimore, Md: 1950)"},{"issue":"1","key":"1379_CR54","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1038\/mi.2016.28","volume":"10","author":"D Christensen","year":"2017","unstructured":"Christensen D, Mortensen R, Rosenkrands I, Dietrich J, Andersen P. Vaccine-induced Th17 cells are established as resident memory cells in the lung and promote local IgA responses. Mucosal Immunol. 2017;10(1):260\u201370.","journal-title":"Mucosal Immunol"},{"issue":"1","key":"1379_CR55","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/j.immuni.2008.11.005","volume":"30","author":"YK Lee","year":"2009","unstructured":"Lee YK, Turner H, Maynard CL, Oliver JR, Chen D, Elson CO, et al. Late developmental plasticity in the T helper 17 lineage. Immunity. 2009;30(1):92\u2013107.","journal-title":"Immunity"},{"issue":"7","key":"1379_CR56","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1007\/s10875-021-01084-6","volume":"41","author":"R-M Berbers","year":"2021","unstructured":"Berbers R-M, van der Wal MM, van Montfrans JM, Ellerbroek PM, Dalm VASH, van Hagen PM, et al. Chronically activated T-cells retain their inflammatory properties in common variable immunodeficiency. J Clin Immunol. 2021;41(7):1621\u201332.","journal-title":"J Clin Immunol"},{"issue":"10","key":"1379_CR57","doi-asserted-by":"publisher","first-page":"4866","DOI":"10.4049\/jimmunol.1200402","volume":"188","author":"KA Casey","year":"2012","unstructured":"Casey KA, Fraser KA, Schenkel JM, Moran A, Abt MC, Beura LK, et al. Antigen-independent differentiation and maintenance of effector-like resident memory T cells in tissues. J Immunol (Baltimore, Md: 1950). 2012;188(10):4866\u201375.","journal-title":"J Immunol (Baltimore, Md: 1950)"},{"issue":"11","key":"1379_CR58","doi-asserted-by":"publisher","first-page":"6641","DOI":"10.4049\/jimmunol.162.11.6641","volume":"162","author":"MP Sch\u00f6n","year":"1999","unstructured":"Sch\u00f6n MP, Arya A, Murphy EA, Adams CM, Strauch UG, Agace WW, et al. Mucosal T lymphocyte numbers are selectively reduced in integrin \u03b1E (CD103)-deficient mice. J Immunol. 1999;162(11):6641\u20139.","journal-title":"J Immunol"},{"issue":"6","key":"1379_CR59","doi-asserted-by":"publisher","first-page":"798","DOI":"10.1016\/j.immuni.2007.04.010","volume":"26","author":"TA Fehniger","year":"2007","unstructured":"Fehniger TA, Cai SF, Cao X, Bredemeyer AJ, Presti RM, French AR, et al. Acquisition of murine NK cell cytotoxicity requires the translation of a pre-existing pool of granzyme B and perforin mRNAs. Immunity. 2007;26(6):798\u2013811.","journal-title":"Immunity"},{"issue":"1","key":"1379_CR60","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1073\/pnas.0405979102","volume":"102","author":"SL Pull","year":"2005","unstructured":"Pull SL, Doherty JM, Mills JC, Gordon JI, Stappenbeck TS. Activated macrophages are an adaptive element of the colonic epithelial progenitor niche necessary for regenerative responses to injury. Proc Natl Acad Sci USA. 2005;102(1):99\u2013104.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"1379_CR61","doi-asserted-by":"publisher","first-page":"3229","DOI":"10.1038\/s41467-019-11148-2","volume":"10","author":"G Desalegn","year":"2019","unstructured":"Desalegn G, Pabst O. Inflammation triggers immediate rather than progressive changes in monocyte differentiation in the small intestine. Nat Commun. 2019;10(1):3229.","journal-title":"Nat Commun"},{"issue":"7630","key":"1379_CR62","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1038\/nature20138","volume":"539","author":"RJ Cummings","year":"2016","unstructured":"Cummings RJ, Barbet G, Bongers G, Hartmann BM, Gettler K, Muniz L, et al. Different tissue phagocytes sample apoptotic cells to direct distinct homeostasis programs. Nature. 2016;539(7630):565\u20139.","journal-title":"Nature"},{"issue":"3","key":"1379_CR63","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1038\/mi.2012.89","volume":"6","author":"CC Bain","year":"2013","unstructured":"Bain CC, Scott CL, Uronen-Hansson H, Gudjonsson S, Jansson O, Grip O, et al. Resident and pro-inflammatory macrophages in the colon represent alternative context-dependent fates of the same Ly6Chi monocyte precursors. Mucosal Immunol. 2013;6(3):498\u2013510.","journal-title":"Mucosal Immunol"},{"issue":"2","key":"1379_CR64","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1084\/jem.20170057","volume":"215","author":"A Bujko","year":"2018","unstructured":"Bujko A, Atlasy N, Landsverk OJB, Richter L, Yaqub S, Horneland R, et al. Transcriptional and functional profiling defines human small intestinal macrophage subsets. J Exp Med. 2018;215(2):441\u201358.","journal-title":"J Exp Med"},{"issue":"3","key":"1379_CR65","doi-asserted-by":"publisher","first-page":"e33556-e","DOI":"10.1371\/journal.pone.0033556","volume":"7","author":"A-CR Beitnes","year":"2012","unstructured":"Beitnes A-CR, R\u00e1ki M, Brottveit M, Lundin KEA, Jahnsen FL, Sollid LM. Rapid accumulation of CD14+CD11c+ dendritic cells in gut mucosa of celiac disease after in vivo gluten challenge. PLoS One. 2012;7(3):e33556-e.","journal-title":"PLoS One"},{"key":"1379_CR66","doi-asserted-by":"crossref","unstructured":"Atlasy N, Bujko A, B\u00e6kkevold ES, Brazda P, Janssen-Megens E, Lundin KEA, et al. Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease. Nat Commun. 2022;13(1):4920.","DOI":"10.1038\/s41467-022-32691-5"},{"issue":"12","key":"1379_CR67","doi-asserted-by":"publisher","first-page":"6843","DOI":"10.4049\/jimmunol.0903987","volume":"184","author":"AM Platt","year":"2010","unstructured":"Platt AM, Bain CC, Bordon Y, Sester DP, Mowat AM. An independent subset of TLR expressing CCR2-dependent macrophages promotes colonic inflammation. J Immunol. 2010;184(12):6843\u201354.","journal-title":"J Immunol"},{"issue":"8","key":"1379_CR68","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1084\/jem.20102101","volume":"208","author":"M Kurachi","year":"2011","unstructured":"Kurachi M, Kurachi J, Suenaga F, Tsukui T, Abe J, Ueha S, et al. Chemokine receptor CXCR3 facilitates CD8+ T cell differentiation into short-lived effector cells leading to memory degeneration. J Exp Med. 2011;208(8):1605\u201320.","journal-title":"J Exp Med"},{"issue":"1","key":"1379_CR69","doi-asserted-by":"publisher","first-page":"4987","DOI":"10.1038\/s41467-019-12980-2","volume":"10","author":"NJ Maurice","year":"2019","unstructured":"Maurice NJ, McElrath MJ, Andersen-Nissen E, Frahm N, Prlic M. CXCR3 enables recruitment and site-specific bystander activation of memory CD8+ T cells. Nat Commun. 2019;10(1):4987.","journal-title":"Nat Commun"},{"issue":"5","key":"1379_CR70","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1016\/j.yexcr.2010.12.017","volume":"317","author":"JR Groom","year":"2011","unstructured":"Groom JR, Luster AD. CXCR3 in T cell function. Exp Cell Res. 2011;317(5):620\u201331.","journal-title":"Exp Cell Res"},{"issue":"2","key":"1379_CR71","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1158\/1078-0432.CCR-19-1868","volume":"26","author":"IG House","year":"2020","unstructured":"House IG, Savas P, Lai J, Chen AXY, Oliver AJ, Teo ZL, et al. Macrophage-derived CXCL9 and CXCL10 are required for antitumor immune responses following immune checkpoint blockade. Clin Cancer Res: Offic J Am Assoc Cancer Res. 2020;26(2):487\u2013504.","journal-title":"Clin Cancer Res: Offic J Am Assoc Cancer Res"},{"issue":"12","key":"1379_CR72","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1016\/j.it.2004.09.015","volume":"25","author":"A Mantovani","year":"2004","unstructured":"Mantovani A, Sica A, Sozzani S, Allavena P, Vecchi A, Locati M. The chemokine system in diverse forms of macrophage activation and polarization. Trends Immunol. 2004;25(12):677\u201386.","journal-title":"Trends Immunol"},{"issue":"2","key":"1379_CR73","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1172\/JCI112815","volume":"79","author":"CF Nathan","year":"1987","unstructured":"Nathan CF. Secretory products of macrophages. J Clin Investig. 1987;79(2):319\u201326.","journal-title":"J Clin Investig"},{"issue":"23","key":"1379_CR74","doi-asserted-by":"publisher","first-page":"4385","DOI":"10.1007\/s00018-018-2898-5","volume":"75","author":"H Bragde","year":"2018","unstructured":"Bragde H, Jansson U, Fredrikson M, Grodzinsky E, S\u00f6derman J. Celiac disease biomarkers identified by transcriptome analysis of small intestinal biopsies. Cell Mol Life Sci. 2018;75(23):4385\u2013401.","journal-title":"Cell Mol Life Sci"},{"issue":"11","key":"1379_CR75","doi-asserted-by":"publisher","first-page":"e111-e","DOI":"10.1038\/cti.2016.59","volume":"5","author":"Y Fujiwara","year":"2016","unstructured":"Fujiwara Y, Hizukuri Y, Yamashiro K, Makita N, Ohnishi K, Takeya M, et al. Guanylate-binding protein 5 is a marker of interferon-\u03b3-induced classically activated macrophages. Clin Transl Immunology. 2016;5(11):e111-e.","journal-title":"Clin Transl Immunology."},{"issue":"4","key":"1379_CR76","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1016\/j.chom.2016.02.019","volume":"19","author":"C Krapp","year":"2016","unstructured":"Krapp C, Hotter D, Gawanbacht A, McLaren Paul J, Kluge Silvia F, St\u00fcrzel Christina M, et al. Guanylate binding protein (GBP) 5 is an interferon-inducible inhibitor of HIV-1 infectivity. Cell Host Microbe. 2016;19(4):504\u201314.","journal-title":"Cell Host Microbe"},{"key":"1379_CR77","doi-asserted-by":"crossref","unstructured":"Li Y, Lin X, Wang W, Wang W, Cheng S, Huang Y, et al. The Proinflammatory Role of Guanylate-Binding Protein 5 in Inflammatory Bowel Diseases. Frontiers in microbiology. 2022;13:926915.","DOI":"10.3389\/fmicb.2022.926915"},{"issue":"3","key":"1379_CR78","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1203\/01.PDR.0000079184.70237.9C","volume":"54","author":"VM Salvati","year":"2003","unstructured":"Salvati VM, MacDonald TT, del Vecchio BG, Mazzarella G, Monteleone I, Vavassori P, et al. Enhanced expression of interferon regulatory factor-1 in the mucosa of children with celiac disease. Pediatr Res. 2003;54(3):312\u20138.","journal-title":"Pediatr Res"},{"issue":"6","key":"1379_CR79","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1016\/S1074-7613(00)80443-4","volume":"6","author":"S Taki","year":"1997","unstructured":"Taki S, Sato T, Ogasawara K, Fukuda T, Sato M, Hida S, et al. Multistage regulation of Th1-type immune responses by the transcription factor IRF-1. Immunity. 1997;6(6):673\u20139.","journal-title":"Immunity"},{"issue":"1","key":"1379_CR80","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1038\/mi.2009.124","volume":"3","author":"EC Lavelle","year":"2010","unstructured":"Lavelle EC, Murphy C, O\u2019Neill LAJ, Creagh EM. The role of TLRs, NLRs, and RLRs in mucosal innate immunity and homeostasis. Mucosal Immunol. 2010;3(1):17\u201328.","journal-title":"Mucosal Immunol"},{"issue":"3","key":"1379_CR81","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1016\/j.immuni.2007.08.007","volume":"27","author":"SM Kaech","year":"2007","unstructured":"Kaech SM, Wherry EJ. Heterogeneity and cell-fate decisions in effector and memory CD8+ T cell differentiation during viral infection. Immunity. 2007;27(3):393\u2013405.","journal-title":"Immunity"},{"issue":"17","key":"1379_CR82","doi-asserted-by":"publisher","first-page":"1793","DOI":"10.1093\/hmg\/10.17.1793","volume":"10","author":"AM Bowcock","year":"2001","unstructured":"Bowcock AM, Shannon W, Du F, Duncan J, Cao K, Aftergut K, et al. Insights into psoriasis and other inflammatory diseases from large-scale gene expression studies. Hum Mol Genet. 2001;10(17):1793\u2013805.","journal-title":"Hum Mol Genet"},{"issue":"3","key":"1379_CR83","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1111\/j.0022-202X.2004.22322.x","volume":"122","author":"S Suomela","year":"2004","unstructured":"Suomela S, Cao L, Bowcock A, Saarialho-Kere U. Interferon \u03b1-inducible protein 27 (IFI27) is upregulated in psoriatic skin and certain epithelial cancers. J Investig Dermatol. 2004;122(3):717\u201321.","journal-title":"J Investig Dermatol"},{"issue":"1","key":"1379_CR84","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1097\/00054725-200401000-00001","volume":"10","author":"TP Dooley","year":"2004","unstructured":"Dooley TP, Curto EV, Reddy SP, Davis RL, Lambert GW, Wilborn TW, et al. Regulation of gene expression in inflammatory bowel disease and correlation with IBD drugs: screening by DNA microarrays. Inflamm Bowel Dis. 2004;10(1):1\u201314.","journal-title":"Inflamm Bowel Dis"},{"key":"1379_CR85","doi-asserted-by":"crossref","unstructured":"Hosmillo M, Chaudhry Y, Nayak K, Sorgeloos F, Koo BK, Merenda A, et al. Norovirus replication in human intestinal epithelial cells is restricted by the interferon-induced JAK\/STAT signaling pathway and RNA polymerase II-mediated transcriptional responses. mBio. 2020;11(2):e00215\u201320.","DOI":"10.1128\/mBio.00215-20"}],"container-title":["Journal of Clinical Immunology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10875-022-01379-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10875-022-01379-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10875-022-01379-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T12:45:03Z","timestamp":1675428303000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10875-022-01379-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,25]]},"references-count":85,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2023,2]]}},"alternative-id":["1379"],"URL":"https:\/\/doi.org\/10.1007\/s10875-022-01379-2","relation":{},"ISSN":["0271-9142","1573-2592"],"issn-type":[{"value":"0271-9142","type":"print"},{"value":"1573-2592","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,10,25]]},"assertion":[{"value":"23 February 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 October 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 October 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All procedures performed in this study were in accordance with the ethical standards of the institutional and national research committee and with the 1964 Helsinki Declaration and its later amendments. The study was approved by local authorities (Freiburg 526\/14 and amendment 26\/14_170104).Written informed consent was obtained from all individual participants (patients and controls) included in this study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics Approval and Consent to Participate"}},{"value":"No identifiable information is published within this study.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for Publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of Interest"}}]}}