Journal: Cell reports

Article Title: Id2 levels determine the development of effector vs. exhausted tissue-resident memory CD8 + T cells during CNS chronic infection.

doi: 10.1016/j.celrep.2025.115861

Figure Lengend Snippet: Figure 1. Heterogeneity of Id2 expression across brain Trm subsets correlates with their functional heterogeneity during the chronic phase of T. gondii infection (A) scRNA-seq of CD8+ T cells isolated from the brain and the spleen of mice infected with Tg.GRA6-OVA at day 154 post-immunization. Uniform Manifold Approximation and Projection (UMAP) shows segregation between spleen and brain CD8+ T cells. (B) UMAP of SEURAT-generated clusters (left) and cluster frequencies (right). (C) Dot plot of gene expression for the indicated genes involved in CD8+ T cell differentiation and tissue residency. (D) GSEA for the indicated published gene signatures. Normalized enrichment score (NES) and adjusted p values are shown. (E) Violin plot shows Id2 expression in the two most abundant Trm clusters, cluster 2 and cluster 3. Statistical differences were assessed using Wilcoxon rank-sum test. (F) GSEA of DE genes decreased in Id2-deficient CD8+ T cells (Id2-induced gene signature) or increased in Id2-deficient CD8+ T cells (Id2-repressed gene signature) from Masson et al.24 in cluster 2 vs. cluster 3. (G) Dot plot of gene expression for the indicated genes involved in CD8+ T cell exhaustion and effector functions.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase D Roche Cat # 11088882001 DNase I Sigma Cat # DN25 Percoll GE Healthcare Cat # 17-0891-01 RetroNectin Takara Cat # T202 Polybrene R&D Cat # 7711 Human IL-2 Recombinant Peprotech Cat # 200-02 Mouse IL-7 Recombinant Peprotech Cat # 217-07 Mouse IL-15 Recombinant Peprotech Cat # 210-15 Mouse IL-12 p70 Recombinant Peprotech Cat # 210-12 Mouse IL-33 Recombinant Peprotech Cat # 210-33 Human TGF-beta 1 Recombinant Peprotech Cat # 100-21 OVA peptide Genescust N/A Critical commercial assays Dynabeads Untouched Mouse CD8 Cells Kit Invitrogen Cat # 11417D CD8α T Cell Isolation Kit Miltenyi Cat # 130-104-075 Cytofix/Cytoperm Kit BD Biosciences Cat # 554714 Foxp3/Transcription Factor Staining Buffer Set eBioscience Cat # 00-5523-00 Deposited data Single-cell RNA seq This paper GEO:GSE270492 Experimental models: Organisms/strains C57BL/6J (Ptprcb/b) mice Janvier-Labs N/A Id2 floxed x CD4Cre mice (Id2fl/flCD4Cre+, Id2fl/+CD4Cre-, or Id2+/+CD4Cre+) In house N/A C57BL/6 CD45.1 x CD45.2 mice (Ptprca/a or Ptprca/b) In house N/A OT-I x C57BL/6 CD45.1 mice (OT-ITg/+; Ptprca/a) In house N/A OT-I x Hobit-TdTomato-Cre-DTR x C57BL/6 CD45.1 mice (OT-ITg/+;Ptprca/a;HobitCre/+) In house N/A Oligonucleotides TOX 9 Sigma 5’-AGGAGAGATATCAGGACTGTAG TOX 11 Sigma 5’-GCGTCGTCTCGTCTAGATCG Recombinant DNA pMSCV-Id2-IRES-GFP Masson et al.24 N/A pMSCV-IRES-GFP Masson et al.24 N/A pMSCV-Tcfe2a-IRES-mCherry Masson et al.61 N/A pMSCV-IRES-mCherry Masson et al.61 N/A Software and algorithms CellRanger 10X Genomics Version 4.0.3 Seurat Satija Lab Version 4.2.1 FlowJo FlowJo LLC Version 10.9.0 Prism GraphPad Version 10.1.2 Inkscape Inkscape Version 1.4 Adobe Illustrator CC Adobe Version 21.1.0 Endnote Endnote Version 7 GSEA Mac App Broad Institute Version 4.4.0 18 Cell Reports 44, 115861, June 24, 2025

Techniques: Expressing, Functional Assay, Infection, Isolation, Generated, Gene Expression, Cell Differentiation