{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T14:56:26Z","timestamp":1792508186098,"version":"4.5.0"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T00:00:00Z","timestamp":1769040000000},"content-version":"vor","delay-in-days":752,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007915","name":"Baylor College of Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007915","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["HL149744"],"award-info":[{"award-number":["HL149744"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007856","name":"Baylor College of Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007856","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007856","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["HL149744"],"award-info":[{"award-number":["HL149744"]}],"id":[{"id":"10.13039\/100007856","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.atsjournals.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Rationale<\/jats:title>\n                    <jats:p>Within chronic obstructive pulmonary disease (COPD), emphysema is characterized by a significant yet partially understood B cell immune component.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To characterize the transcriptomic signatures from lymphoid follicles (LFs) in ever-smokers without COPD and patients with COPD with varying degrees of emphysema.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Lung sections from 40 patients with COPD and ever-smokers were used for LF proteomic and transcriptomic spatial profiling. Formalin- and O.C.T.-fixed lung samples obtained from biopsies or lung explants were assessed for LF presence. Emphysema measurements were obtained from clinical chest computed tomographic scans. High-confidence transcriptional target intersection analyses were conducted to resolve emphysema-induced transcriptional networks.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Measurements and Main Results<\/jats:title>\n                    <jats:p>Overall, 115 LFs from ever-smokers and Global Initiative for Chronic Obstructive Lung Disease (GOLD) 1\u20132 and GOLD 3\u20134 patients were analyzed. No LFs were found in never-smokers. Differential gene expression analysis revealed significantly increased expression of LF assembly and B cell marker genes in subjects with severe emphysema. High-confidence transcriptional analysis revealed activation of an abnormal B cell activity signature in LFs (q-value\u2009=\u20092.56E-111). LFs from patients with GOLD 1\u20132 COPD with emphysema showed significantly increased expression of genes associated with antigen presentation, inflammation, and B cell activation and proliferation. LFs from patients with GOLD 1\u20132 COPD without emphysema showed an antiinflammatory profile. The extent of centrilobular emphysema was significantly associated with genes involved in B cell maturation and antibody production. Protein-RNA network analysis showed that LFs in emphysema have a unique signature skewed toward chronic B cell activation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>An off-targeted B cell activation within LFs is associated with autoimmune-mediated emphysema pathogenesis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1164\/rccm.202303-0507le","type":"journal-article","created":{"date-parts":[[2023,11,7]],"date-time":"2023-11-07T12:51:34Z","timestamp":1699361494000},"page":"48-58","update-policy":"https:\/\/doi.org\/10.1164\/crossmarkpolicies","source":"Crossref","is-referenced-by-count":54,"title":["Spatial Transcriptomics Resolve an Emphysema-Specific Lymphoid Follicle B Cell Signature in Chronic Obstructive Pulmonary Disease"],"prefix":"10.1093","volume":"209","author":[{"given":"Joselyn","family":"Rojas-Quintero","sequence":"first","affiliation":[{"name":"Pulmonary Division, Department of Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott A.","family":"Ochsner","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felicia","family":"New","sequence":"additional","affiliation":[{"name":"Spatial Data Analysis Services, Nanostring Biotechnologies, Seattle, Washington"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prajan","family":"Divakar","sequence":"additional","affiliation":[{"name":"Spatial Data Analysis Services, Nanostring Biotechnologies, Seattle, Washington"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen Xi","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianshi David","family":"Wu","sequence":"additional","affiliation":[{"name":"Pulmonary Division, Department of Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerid","family":"Robinson","sequence":"additional","affiliation":[{"name":"Field Application Scientists, Nanostring Biotechnologies, Seattle, Washington"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Darshan Shimoga","family":"Chandrashekar","sequence":"additional","affiliation":[{"name":"Pathology, Division of Genomic Diagnostics & Bioinformatics, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas E.","family":"Banovich","sequence":"additional","affiliation":[{"name":"Translational Genomics Research Institute, Phoenix, Arizona"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan O.","family":"Rosas","sequence":"additional","affiliation":[{"name":"Pulmonary Division, Department of Medicine, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maor","family":"Sauler","sequence":"additional","affiliation":[{"name":"Pulmonary and Critical Care Medicine, Yale University, New Haven, Connecticut"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Farrah","family":"Kheradmand","sequence":"additional","affiliation":[{"name":"Pulmonary Division, Department of Medicine, and"},{"name":"Michael E. 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