Journal: Nature

Article Title: The type 2 cytokine Fc–IL-4 revitalizes exhausted CD8 + T cells against cancer

doi: 10.1038/s41586-024-07962-4

Figure Lengend Snippet: a , b , Real-time ECAR analysis ( a ) and average basal glycolysis, glycolytic capacity and reserve ( b ) of ex vivo-induced CD8 + T TE cells ( n = 5 biological replicates). mpH, milli-pH. c , Volcano plot of altered metabolites in ex vivo-induced CD8 + T TE cells treated with Fc–IL-4 ( n = 4 biological replicates) versus PBS ( n = 3 biological replicates). d – f , Experimental setting as described in Fig. . Shown are unsupervised UMAP clustering of PMEL CD8 + TILs based on the 1,667 genes involved in KEGG-defining metabolic pathways ( d ), cell proportion in each cluster ( e ) and systematic expression comparison of carbohydrate metabolisms among top four clusters ( f ). g , h , T cell counts ( g ) and frequencies of granzyme B + IFNγ + ( h ) among ex vivo-induced CD8 + T TE cells with or without 2-DG ( n = 4 biological replicates). i , j , Schematic illustration of single-cell ATAC and gene coprofiling of IL-4 versus PBS-treated ex vivo-induced CD8 + T TE cells and a joint ATAC–gene UMAP ( i ), and volcano plot showing differentially active motifs ( j ). k , l , Experimental setting as described in Fig. . Shown are signalling pathways regulated by DEGs ( k ) and top 20 ranked upstream regulators predicted from DEGs ( l ) in PMEL CD8 + TILs. m , Western blot analysis of indicated proteins in ex vivo-induced CD8 + T TE cells ( n = 3 biological replicates). n – p , Relative basal glycolysis ( n ) ( n = 5 biological replicates), T cell counts ( o ) and granzyme B MFI ( p ) ( n = 3 biological replicates) in Fc–IL-4-treated ex vivo-induced OT1 and OT1 STAT6-KO CD8 + T TE cells (normalized by that in the PBS group) with or without indicated inhibitors. All data represent mean ± s.e.m. and are analysed by two-sided unpaired Student’s t -test ( b and g , h ), two-tailed Mann–Whitney test ( j ), right-tailed Fisher’s exact test ( k ) or one-way ANOVA and Tukey’s test ( n – p ). Schematics in i created using BioRender ( https://Biorender.com ).

Article Snippet: Single-cell coprofiling of epigenomic landscape and gene expression in the same single nuclei was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics).

Techniques: Ex Vivo, Expressing, Comparison, Western Blot, Two Tailed Test, MANN-WHITNEY

Journal: Nature

Article Title: The type 2 cytokine Fc–IL-4 revitalizes exhausted CD8 + T cells against cancer

doi: 10.1038/s41586-024-07962-4

Figure Lengend Snippet: a , Quality assessment of sequenced data from IL-4 or PBS conditions, featuring TSS enrichment score, insert size distribution, unsupervised clustering analysis of ATAC and gene datasets, and corresponding count distribution. Consistent performance is observed with negligible batch effect. b , Gene or ATAC expression UMAP of all the single cells color-coded by their respective conditions. c , d , Expression of functional cytotoxicity ( c ) and survival ( d ) gene markers on the joint UMAP in Fig. , along with comparisons of corresponding accessible peaks between conditions. Statistical analyses were performed using two-sided unpaired Student’s t-test. e , Experimental setting was described in Fig. . Shown is the mechanistic networks associated with the significant activation of selected upstream regulators in Fc–IL-4 treated PMEL CD8 + TILs relative to the PBS condition. z score is computed and used to reflect the predicted activation level (z > 0, activated/upregulated; z < 0, inhibited/downregulated; z ≥ 2 or z ≤ −2 can be considered significant). Statistical analyses are performed using right-tailed Fisher’s Exact Test.

Article Snippet: Single-cell coprofiling of epigenomic landscape and gene expression in the same single nuclei was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics).

Techniques: Expressing, Functional Assay, Activation Assay

Journal: Journal of hepatology

Article Title: Adipose tissue macrophage dysfunction is associated with a breach of vascular integrity in NASH.

doi: 10.1016/j.jhep.2023.10.039

Figure Lengend Snippet: Fig. 1. Single-cell map of human VAT macrophages. (A) Workflow of the experimental pipeline. Human visceral adipose tissue was collected from patients undergoing cholecystectomy and bariatric surgery, NAFLD-stratified based on liver histology, and the stromal vascular fraction enzymatically isolated. The cells were sorted based on CD45, CD11b, and HLA-DR positivity and analyzed using 10X Genomics Chromium droplet single-cell RNA sequencing. The cells were then clustered based on marker genes and downstream analysis was performed. (B) Annotated UMAP map of 35,405 myeloid cells from the VAT of lean (n = 3) and obese patients with normal liver histology (n = 4), NAFL (n = 4) and NASH (n = 5), showing ResVAMs, MMacs, TransMacs, preInfMacs, Mon, ncMon and cDCs. (C) Heatmap showing the top 20 marker genes for the myeloid populations. Indicated are individual cluster markers and the total number of genes characterized. The expression is indicated by color saturation, the cluster and disease identity are marked by individual coloring. (D) Violin plots showing the expression of selected marker genes in myeloid cells,

Article Snippet: The cells were sorted based on CD45, CD11b, and HLA-DR positivity and analyzed using 10X Genomics Chromium droplet single-cell RNA sequencing.

Techniques: Isolation, RNA Sequencing, Marker, Expressing