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: Cell reports

Article Title: Altered hepatic metabolism in Down syndrome

doi: 10.1016/j.celrep.2025.116835

Figure Lengend Snippet: (A) Volcano plot summarizing results of whole liver transcriptome analysis of wild-type ( n = 6, 3 females) versus Dp16 ( n = 6, 3 females) mice. Significantly differentially expressed (q < 0.1) genes are colored in red. (B) Bar plot summarizing the results of gene set enrichment analysis of gene expression changes data in (A). (C) Heatmap showing the median Z score of the top 10 leading-edge genes from the epithelial-mesenchymal transition gene set. (D) Sina plots displaying the normalized relative expression (RPKM) of Col1a1 and Eln in wild-type and Dp16 mice. (E) Uniform manifold approximation and projection (UMAP) plot of single-cell RNA sequencing (scRNA-seq) analysis of mouse liver, color coded by cell clusters identified using Seurat. (F) UMAP plot displaying differential cellular abundance of clusters from scRNA-seq analysis of mouse liver. Significant (false discovery rate [FDR] <0.1) clusters are colored by mean fold-change. (G) Sina plots showing the Dp16 versus wild-type abundance of hepatocyte cluster 1 and endothelial cell cluster 2 from scRNA-seq analysis of mouse liver. (H) UMAP plot displaying the epithelial-mesenchymal transition gene set normalized enrichment score (NES) for each cluster. (I) Bubble plot summarizing Col1a1 single-cell expression across clusters and animals, with color representing mean expression and size representing percent of cells with expression. (J) Sina plot displaying the normalized pseudobulk counts of Col1a1 expression within the stellate cell cluster in wild-type and Dp16 animals. (K) Representative images of multiplexed stained liver sections from wild-type and Dp16 mice where DAPI is stained in blue, desmin in red, and smooth muscle actin (SMA) in yellow. Sina plot showing number of desmin+ and SMA+ cells as a percentage of total cells in wild-type mice ( n = 6, 3 females) and Dp16 mice ( n = 6, 3 females). (L) Representative images of picrosirius-red-stained (PSR) liver sections from wild-type ( n = 8, 4 females) and Dp16 ( n = 7, 4 females) mice, imaged under polarized light. Sina plot shows the total percent positive PSR staining in wild-type and Dp16 liver. For (K and L), individual data are presented with a bar at the median, and the p value, as determined by a Mann-Whitney U test, is shown. Scale bars, 100 μm.

Article Snippet: Fixed liver single cell suspensions were hybridized with the Next GEM Single Cell Fixed RNA Mouse Transcriptome Probe Kit (10X Genomics), according to manufacturer instructions, and loaded into a Chromium X (10X Genomics) microfluidics instrument to generate an oil emulsion with partitioned nanoliter-scale droplets, each ideally containing a barcoded gel bead and a single cell, along with enzyme Master Mix (10X Genomics) for probe pair ligation and gel bead primer barcode extension.

Techniques: Gene Expression, Expressing, Single Cell, RNA Sequencing, Staining, MANN-WHITNEY

Journal: Cell reports

Article Title: Altered hepatic metabolism in Down syndrome

doi: 10.1016/j.celrep.2025.116835

Figure Lengend Snippet: (A) Heatmap showing the median Z score of the leading-edge genes from the IFN gamma response gene set from wild-type and Dp16 liver bulk transcriptome analysis. (B) Sina plot displaying relative expression (RPKM) of Cxcl9 in wild-type and Dp16 liver bulk transcriptome analysis. (C) UMAP plot displaying the IFN gamma response gene set normalized enrichment score (NES) for each cluster. (D) Bubble plot displaying the mean expression and the percent of cells per cluster expressing Cxcl9 in wild-type and Dp16 mice. (E) Sina plot displaying the log 2 of the normalized counts of Cxcl9 expression within endothelial cell cluster 1 in wild-type and Dp16 animals. (F) Representative images of H&E-stained liver sections from adult wild-type, Dp16, and Dp16 2xIFNRs mice. Scale bars, 100 μm. (G) Sina plots showing liver pathology scoring from adult wild-type ( n = 13, 6 females), Dp16 ( n = 12, 5 females), and Dp16 2xIFNRs ( n = 13, 7 females) mice. p values, determined by a Mann-Whitney U test, are shown. (H) Sina plot displaying the grams/deciliter of plasma albumin from adult wild-type ( n = 6, 4 females), Dp16 ( n = 6, 2 females), and Dp16 2xIFNRs ( n = 8, 1 female) mice. p values, as determined by a Mann-Whitney U test, are shown. (I) Heatmap displaying the median Z score of plasma bile acids in adult wild-type ( n = 9, 4 females), Dp16 ( n = 13, 6 females), and Dp16 2xIFNRs ( n = 10, 5 females) mice. For (B and E), Benjamini-Hochberg adjusted p value ( q value) are indicated. For (B, E, and G), individual data are presented with a bar at the median.

Article Snippet: Fixed liver single cell suspensions were hybridized with the Next GEM Single Cell Fixed RNA Mouse Transcriptome Probe Kit (10X Genomics), according to manufacturer instructions, and loaded into a Chromium X (10X Genomics) microfluidics instrument to generate an oil emulsion with partitioned nanoliter-scale droplets, each ideally containing a barcoded gel bead and a single cell, along with enzyme Master Mix (10X Genomics) for probe pair ligation and gel bead primer barcode extension.

Techniques: Expressing, Staining, MANN-WHITNEY, Clinical Proteomics

Journal: Cell reports

Article Title: Altered hepatic metabolism in Down syndrome

doi: 10.1016/j.celrep.2025.116835

Figure Lengend Snippet: (A) Volcano plots summarizing the results of transcriptome analysis of livers from Dp16 versus wild-type mice fed a low-fat diet (LFD) and from Dp16 mice versus wild-type fed a high-fat diet (HFD) (wild-type LFD n = 10, 4 females, Dp16 LFD n = 8, 4 females, wild-type HFD n = 14, 4 females, Dp16 HFD n = 13, 4 females). Points in blue are in the MMU16 region triplicated in Dp16 mice. (B) Venn diagrams displaying the overlap in the significant differentially expressed genes in the Dp16 triplicated region between HFD fed mice and LFD mice (top) or in the differentially expressed genes that are not triplicated in Dp16 mice (bottom). (C) Scatterplot comparing GSEA NES values for signatures in the livers of Dp16 versus wild-type mice on LFD ( x axis) and Dp16 versus wild-type mice on HFD diet ( y axis). (D) Scatterplots comparing the fold changes of leading-edge genes from the cholesterol homeostasis, fatty acid metabolism, and adipogenesis hallmark gene sets for Dp16 versus wild-type mice on LFD ( x axis) and Dp16 versus wild-type on HFD ( y axis). (E) Sina plots displaying the log 2 (RPKM) of various genes. Horizontal bars indicate median values. Benjamini-Hochberg adjusted p -values ( q values) are indicated. For (C–E), points are colored according to significant in both groups (red), significant in the LFD group only (green), significant in the HFD group only (yellow), or not significant in any group (gray). Significance is defined as q < 0.1 using GSEA or DESeq2.

Article Snippet: Fixed liver single cell suspensions were hybridized with the Next GEM Single Cell Fixed RNA Mouse Transcriptome Probe Kit (10X Genomics), according to manufacturer instructions, and loaded into a Chromium X (10X Genomics) microfluidics instrument to generate an oil emulsion with partitioned nanoliter-scale droplets, each ideally containing a barcoded gel bead and a single cell, along with enzyme Master Mix (10X Genomics) for probe pair ligation and gel bead primer barcode extension.

Techniques:

Journal: Cell reports

Article Title: Pten regulates endocytic trafficking of cell adhesion and Wnt signaling molecules to pattern the retina

doi: 10.1016/j.celrep.2024.114005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Cell suspensions of 1X 10^6 cells/ml were prepared and loaded into GEM Chip K for an expected recovery of 10,000 cells using Chromium Next GEM Single Cell 5′ Reagent Kit v2 (10X genomics, Cat #1000263).

Techniques: Control, Affinity Purification, Recombinant, Bicinchoninic Acid Protein Assay, Western Blot, Electron Microscopy, RNAscope, Multiplex Assay, Mass Spectrometry, Mutagenesis, Software, Microscopy