{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T14:13:15Z","timestamp":1789827195331,"version":"4.0.1"},"reference-count":47,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T00:00:00Z","timestamp":1740787200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100009592","name":"Beijing Municipal Science and Technology Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009592","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100019018","name":"Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100019018","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.fr","clinicalkey.jp","clinicalkey.es","clinicalkey.com.au","clinicalkey.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Clinical Immunology"],"published-print":{"date-parts":[[2025,3]]},"DOI":"10.1016\/j.clim.2025.110430","type":"journal-article","created":{"date-parts":[[2025,1,26]],"date-time":"2025-01-26T17:43:21Z","timestamp":1737913401000},"page":"110430","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":5,"special_numbering":"C","title":["Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease"],"prefix":"10.1016","volume":"272","author":[{"given":"Minghua","family":"Zhan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyao","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianing","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanling","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhou","family":"Bai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Binghuai","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongbin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yudong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.clim.2025.110430_bb0005","doi-asserted-by":"crossref","first-page":"1730","DOI":"10.1002\/art.42961","article-title":"The risk of lung cancer in rheumatoid arthritis and rheumatoid arthritis-associated interstitial lung disease","volume":"76","author":"Brooks","year":"2024","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.clim.2025.110430_bb0010","doi-asserted-by":"crossref","first-page":"1700","DOI":"10.1136\/annrheumdis-2017-211138","article-title":"A population-based cohort study of rheumatoid arthritis-associated interstitial lung disease: comorbidity and mortality","volume":"76","author":"Hyldgaard","year":"2017","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.clim.2025.110430_bb0015","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1002\/art.42812","article-title":"Plasma matrix metalloproteinase concentrations and risk of interstitial lung disease in a prospective rheumatoid arthritis cohort","volume":"76","author":"Luedders","year":"2024","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.clim.2025.110430_bb0020","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1002\/art.42640","article-title":"Identification, monitoring, and management of rheumatoid arthritis-associated interstitial lung disease","volume":"75","author":"Koduri","year":"2023","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.clim.2025.110430_bb0025","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2024.1341321","article-title":"Rate of severe and fatal infections in a cohort of patients with interstitial lung disease associated with rheumatoid arthritis: a multicenter prospective study","volume":"15","author":"Mena-Vazquez","year":"2024","journal-title":"Front. Immunol."},{"key":"10.1016\/j.clim.2025.110430_bb0030","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1038\/s41590-019-0451-9","article-title":"The influence of the microbiome on respiratory health","volume":"20","author":"Wypych","year":"2019","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.clim.2025.110430_bb0035","doi-asserted-by":"crossref","first-page":"525","DOI":"10.7861\/clinmedicine.17-6-525","article-title":"The lung microbiome in health and disease","volume":"17","author":"Moffatt","year":"2017","journal-title":"Clin. Med. (Lond.)"},{"key":"10.1016\/j.clim.2025.110430_bb0040","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1007\/s00296-019-04460-z","article-title":"Periodontal disease and influence of periodontal treatment on disease activity in patients with rheumatoid arthritis and spondyloarthritis","volume":"40","author":"Bialowas","year":"2020","journal-title":"Rheumatol. Int."},{"key":"10.1016\/j.clim.2025.110430_bb0045","article-title":"The relationship between Porphyromonas Gingivalis and rheumatoid arthritis: a Meta-analysis","volume":"12","author":"Li","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.clim.2025.110430_bb0050","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1002\/JPER.20-0295","article-title":"Novel and known periodontal pathogens residing in gingival crevicular fluid are associated with rheumatoid arthritis","volume":"92","author":"Manoil","year":"2021","journal-title":"J. Periodontol."},{"key":"10.1016\/j.clim.2025.110430_bb0055","doi-asserted-by":"crossref","first-page":"1756","DOI":"10.1002\/art.34344","article-title":"Brief report: airways abnormalities and rheumatoid arthritis-related autoantibodies in subjects without arthritis: early injury or initiating site of autoimmunity?","volume":"64","author":"Demoruelle","year":"2012","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.clim.2025.110430_bb0060","doi-asserted-by":"crossref","first-page":"2545","DOI":"10.1002\/art.38066","article-title":"Sputum autoantibodies in patients with established rheumatoid arthritis and subjects at risk of future clinically apparent disease","volume":"65","author":"Willis","year":"2013","journal-title":"Arthritis Rheum."},{"key":"10.1016\/j.clim.2025.110430_bb0065","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/s40168-016-0206-x","article-title":"The lung microbiota in early rheumatoid arthritis and autoimmunity","volume":"4","author":"Scher","year":"2016","journal-title":"Microbiome"},{"key":"10.1016\/j.clim.2025.110430_bb0070","doi-asserted-by":"crossref","DOI":"10.3390\/ijms25063386","article-title":"Infectious and commensal Bacteria in rheumatoid arthritis-role in the outset and progression of the disease","volume":"25","author":"Korzeniowska","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.clim.2025.110430_bb0075","doi-asserted-by":"crossref","DOI":"10.3390\/cells10123291","article-title":"COVID-19 and rheumatoid arthritis crosstalk: emerging association, therapeutic options and challenges","volume":"10","author":"Dewanjee","year":"2021","journal-title":"Cells"},{"key":"10.1016\/j.clim.2025.110430_bb0080","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01777-21","article-title":"Signatures of COVID-19 severity and immune response in the respiratory tract microbiome","volume":"12","author":"Merenstein","year":"2021","journal-title":"mBio"},{"key":"10.1016\/j.clim.2025.110430_bb0085","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1007\/s00134-023-07033-8","article-title":"ERS\/ESICM\/ESCMID\/ALAT guidelines for the management of severe community-acquired pneumonia","volume":"49","author":"Martin-Loeches","year":"2023","journal-title":"Intensive Care Med."},{"key":"10.1016\/j.clim.2025.110430_bb0090","article-title":"Serum human epididymis protein 4 as a novel biomarker in identifying patients with interstitial lung disease in rheumatoid arthritis","volume":"8","author":"Liang","year":"2021","journal-title":"Front. Med. (Lausanne)"},{"issue":"2010","key":"10.1016\/j.clim.2025.110430_bb0095","doi-asserted-by":"crossref","first-page":"1580","DOI":"10.1136\/ard.2010.138461","article-title":"Rheumatoid arthritis classification criteria: an American College of Rheumatology\/European league against rheumatism collaborative initiative","volume":"69","author":"Aletaha","year":"2010","journal-title":"Ann. Rheum. Dis."},{"key":"10.1016\/j.clim.2025.110430_bb0100","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.clim.2025.110430_bb0105","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1038\/s41596-022-00738-y","article-title":"Metagenome analysis using the kraken software suite","volume":"17","author":"Lu","year":"2022","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.clim.2025.110430_bb0110","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009442","article-title":"Multivariable association discovery in population-scale meta-omics studies","volume":"17","author":"Mallick","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.clim.2025.110430_bb0115","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.clim.2025.110430_bb0120","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"Genome project data processing, the sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.clim.2025.110430_bb0125","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"10.1016\/j.clim.2025.110430_bb0130","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.clim.2025.110430_bb0135","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.clim.2025.110430_bb0140","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.687975","article-title":"IOBR: multi-omics Immuno-oncology biological Research to decode tumor microenvironment and signatures","volume":"12","author":"Zeng","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.clim.2025.110430_bb0145","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/s13059-016-1070-5","article-title":"Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression","volume":"17","author":"Becht","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.clim.2025.110430_bb0150","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s13073-019-0638-6","article-title":"Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data","volume":"11","author":"Finotello","year":"2019","journal-title":"Genome Med."},{"key":"10.1016\/j.clim.2025.110430_bb0155","doi-asserted-by":"crossref","first-page":"5361","DOI":"10.1038\/s41467-018-07767-w","article-title":"Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer","volume":"9","author":"Jia","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.clim.2025.110430_bb0160","doi-asserted-by":"crossref","DOI":"10.3390\/metabo10040135","article-title":"\u201cnotame\u201d: workflow for non-targeted LC-MS metabolic profiling","volume":"10","author":"Klavus","year":"2020","journal-title":"Metabolites"},{"key":"10.1016\/j.clim.2025.110430_bb0165","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1186\/s12859-017-1579-y","article-title":"metaX: a flexible and comprehensive software for processing metabolomics data","volume":"18","author":"Wen","year":"2017","journal-title":"BMC Bioinforma."},{"key":"10.1016\/j.clim.2025.110430_bb0170","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.3389\/fimmu.2018.01680","article-title":"Myeloid-specific deletion of Peptidylarginine deiminase 4 mitigates atherosclerosis","volume":"9","author":"Liu","year":"2018","journal-title":"Front. Immunol."},{"key":"10.1016\/j.clim.2025.110430_bb0175","doi-asserted-by":"crossref","DOI":"10.1016\/j.clim.2023.109297","article-title":"Antibodies against neutrophil extracellular traps (NETs) potentiate clinical performance of anti-double-stranded DNA antibodies in systemic lupus erythematosus","volume":"249","author":"Zhan","year":"2023","journal-title":"Clin. Immunol."},{"key":"10.1016\/j.clim.2025.110430_bb0180","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-0716-3682-4","article-title":"Role of STING deficiency in amelioration of mouse models of lupus and atherosclerosis","author":"Liu","year":"2024","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.clim.2025.110430_bb0185","doi-asserted-by":"crossref","DOI":"10.1016\/j.clim.2023.109836","article-title":"Enoxaparin improves COVID-19 by reducing neutrophils extracellular traps (NETs) production","volume":"257","author":"Corneo","year":"2023","journal-title":"Clin. Immunol."},{"key":"10.1016\/j.clim.2025.110430_bb0190","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.02692-23","article-title":"Can our microbiome break our hearts? Collaborative production of p-cresol sulfate and indoxyl sulfate by commensal microbes increases susceptibility to thrombosis","volume":"15","author":"Machado Ribeiro","year":"2024","journal-title":"mBio"},{"key":"10.1016\/j.clim.2025.110430_bb0195","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.yjmcc.2023.03.011","article-title":"Indoxyl-sulfate activation of the AhR- NF-kappaB pathway promotes interleukin-6 secretion and the subsequent osteogenic differentiation of human valvular interstitial cells from the aortic valve","volume":"179","author":"Candellier","year":"2023","journal-title":"J. Mol. Cell. Cardiol."},{"key":"10.1016\/j.clim.2025.110430_bb0200","doi-asserted-by":"crossref","DOI":"10.3390\/biom13071086","article-title":"Quantitative, targeted analysis of gut microbiota derived metabolites provides novel biomarkers of early diabetic kidney disease in type 2 diabetes mellitus patients","volume":"13","author":"Balint","year":"2023","journal-title":"Biomolecules"},{"key":"10.1016\/j.clim.2025.110430_bb0205","doi-asserted-by":"crossref","first-page":"370","DOI":"10.3389\/fphar.2017.00370","article-title":"Indoxyl sulfate affects glial function increasing oxidative stress and Neuroinflammation in chronic kidney disease: interaction between astrocytes and microglia","volume":"8","author":"Adesso","year":"2017","journal-title":"Front. Pharmacol."},{"key":"10.1016\/j.clim.2025.110430_bb0210","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1186\/s12879-021-06095-7","article-title":"Carnobacterium inhibens isolated in blood culture of an immunocompromised, metastatic cancer patient: a case report and literature review","volume":"21","author":"Lo","year":"2021","journal-title":"BMC Infect. Dis."},{"key":"10.1016\/j.clim.2025.110430_bb0215","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1111\/apt.15675","article-title":"Gastric mucosal microbiota in a Mongolian population with gastric cancer and precursor conditions","volume":"51","author":"Gantuya","year":"2020","journal-title":"Aliment. Pharmacol. Ther."},{"key":"10.1016\/j.clim.2025.110430_bb0220","doi-asserted-by":"crossref","DOI":"10.1016\/j.ccell.2023.06.011","article-title":"Carnobacterium maltaromaticum boosts intestinal vitamin D production to suppress colorectal cancer in female mice","volume":"41","author":"Li","year":"2023","journal-title":"Cancer Cell"},{"key":"10.1016\/j.clim.2025.110430_bb0225","article-title":"Neutrophils in Bronchoalveolar lavage fluid indicating the severity and relapse of pulmonary sarcoidosis","volume":"8","author":"Feng","year":"2021","journal-title":"Front. Med. (Lausanne)"},{"key":"10.1016\/j.clim.2025.110430_bb0230","doi-asserted-by":"crossref","first-page":"2190","DOI":"10.3389\/fimmu.2020.02190","article-title":"Identification of a novel HIF-1alpha-alpha(M)beta(2) integrin-NET Axis in fibrotic interstitial lung disease","volume":"11","author":"Khawaja","year":"2020","journal-title":"Front. Immunol."},{"key":"10.1016\/j.clim.2025.110430_bb0235","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1038\/s41591-020-0901-9","article-title":"Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19","volume":"26","author":"Liao","year":"2020","journal-title":"Nat. Med."}],"container-title":["Clinical Immunology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1521661625000051?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1521661625000051?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,2,26]],"date-time":"2025-02-26T17:58:59Z","timestamp":1740592739000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1521661625000051"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":47,"alternative-id":["S1521661625000051"],"URL":"https:\/\/doi.org\/10.1016\/j.clim.2025.110430","relation":{},"ISSN":["1521-6616"],"issn-type":[{"value":"1521-6616","type":"print"}],"subject":[],"published":{"date-parts":[[2025,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease","name":"articletitle","label":"Article Title"},{"value":"Clinical Immunology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.clim.2025.110430","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"110430"}}