Article ; Online: CaSSiDI: novel single-cell "Cluster Similarity Scoring and Distinction Index" reveals critical functions for PirB and context-dependent Cebpb repression.
Cell death and differentiation
2024 Volume 31, Issue 3, Page(s) 265–279
Abstract: PirB is an inhibitory cell surface receptor particularly prominent on myeloid cells. PirB curtails the phenotypes of activated macrophages during inflammation or tumorigenesis, but its functions in macrophage homeostasis are obscure. To elucidate PirB- ... ...
| Abstract | PirB is an inhibitory cell surface receptor particularly prominent on myeloid cells. PirB curtails the phenotypes of activated macrophages during inflammation or tumorigenesis, but its functions in macrophage homeostasis are obscure. To elucidate PirB-related functions in macrophages at steady-state, we generated and compared single-cell RNA-sequencing (scRNAseq) datasets obtained from myeloid cell subsets of wild type (WT) and PirB-deficient knockout (PirB KO) mice. To facilitate this analysis, we developed a novel approach to clustering parameter optimization called "Cluster Similarity Scoring and Distinction Index" (CaSSiDI). We demonstrate that CaSSiDI is an adaptable computational framework that facilitates tandem analysis of two scRNAseq datasets by optimizing clustering parameters. We further show that CaSSiDI offers more advantages than a standard Seurat analysis because it allows direct comparison of two or more independently clustered datasets, thereby alleviating the need for batch-correction while identifying the most similar and different clusters. Using CaSSiDI, we found that PirB is a novel regulator of Cebpb expression that controls the generation of Ly6C |
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| MeSH term(s) | Animals ; Mice ; Macrophages/metabolism ; Monocytes/metabolism ; Myeloid Cells/metabolism ; Receptors, Cell Surface ; Receptors, Immunologic/metabolism ; Single-Cell Analysis/methods ; CCAAT-Enhancer-Binding Protein-beta/metabolism |
| Chemical Substances | Receptors, Cell Surface ; Receptors, Immunologic ; Pirb protein, mouse ; Cebpb protein, mouse ; CCAAT-Enhancer-Binding Protein-beta |
| Language | English |
| Publishing date | 2024-02-21 |
| Publishing country | England |
| Document type | Journal Article ; Research Support, Non-U.S. Gov't |
| ZDB-ID | 1225672-9 |
| ISSN | 1476-5403 ; 1350-9047 |
| ISSN (online) | 1476-5403 |
| ISSN | 1350-9047 |
| DOI | 10.1038/s41418-024-01268-8 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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