{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Liu M"],"funding":["MOH | National Medical Research Council (NMRC)","Fondazione Italiana per la Ricerca sul Cancro (Italian Foundation for Cancer Research)","China Scholarship Council (CSC)"],"pagination":["2113"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10923916"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["15(1)"],"pubmed_abstract":["Macrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Macrophage estimation by immunohistochemistry shows varying prognostic significance across studies in DLBCL, and does not provide a comprehensive analysis of macrophage subtypes. Here, using digital spatial profiling with whole transcriptome analysis of CD68+ cells, we characterize macrophages in distinct spatial niches of reactive lymphoid tissues (RLTs) and DLBCL. We reveal transcriptomic differences between macrophages within RLTs (light zone /dark zone, germinal center/ interfollicular), and between disease states (RLTs/ DLBCL), which we then use to generate six spatially-derived macrophage signatures (MacroSigs). We proceed to interrogate these MacroSigs in macrophage and DLBCL single-cell RNA-sequencing datasets, and in gene-expression data from multiple DLBCL cohorts. We show that specific MacroSigs are associated with cell-of-origin subtypes and overall survival in DLBCL. This study provides a spatially-resolved whole-transcriptome atlas of macrophages in reactive and malignant lymphoid tissues, showing biological and clinical significance."],"journal":["Nature communications"],"pubmed_title":["Spatially-resolved transcriptomics reveal macrophage heterogeneity and prognostic significance in diffuse large B-cell lymphoma."],"pmcid":["PMC10923916"],"funding_grant_id":["22759","202006940018","22145","MOH-000715-00"],"pubmed_authors":["Jaynes P","Peng Y","Chan EHL","Sridhar S","De Mel S","Liu M","Chua R","Lee J","Ng SB","Ye X","Jeyasekharan AD","Jayalakshmi","Lee RX","Hue SS","Chang ST","Chandy KG","Chee YL","Syn N","Bertolazzi G","Chuang SS","Tripodo C","Fan S","Ginhoux F","Thng J","Mulder K","Poon L","Batumalai Y","Pan-Hammarstrom Q","Hoppe MM"],"additional_accession":[]},"is_claimable":false,"name":"Spatially-resolved transcriptomics reveal macrophage heterogeneity and prognostic significance in diffuse large B-cell lymphoma.","description":"Macrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Macrophage estimation by immunohistochemistry shows varying prognostic significance across studies in DLBCL, and does not provide a comprehensive analysis of macrophage subtypes. Here, using digital spatial profiling with whole transcriptome analysis of CD68+ cells, we characterize macrophages in distinct spatial niches of reactive lymphoid tissues (RLTs) and DLBCL. We reveal transcriptomic differences between macrophages within RLTs (light zone /dark zone, germinal center/ interfollicular), and between disease states (RLTs/ DLBCL), which we then use to generate six spatially-derived macrophage signatures (MacroSigs). We proceed to interrogate these MacroSigs in macrophage and DLBCL single-cell RNA-sequencing datasets, and in gene-expression data from multiple DLBCL cohorts. We show that specific MacroSigs are associated with cell-of-origin subtypes and overall survival in DLBCL. This study provides a spatially-resolved whole-transcriptome atlas of macrophages in reactive and malignant lymphoid tissues, showing biological and clinical significance.","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Mar","modification":"2026-06-15T06:35:29.934Z","creation":"2026-06-15T03:08:52.477Z"},"accession":"S-EPMC10923916","cross_references":{"pubmed":["38459052"],"doi":["10.1038/s41467-024-46220-z"]}}