Journal: Materials Today Bio

Article Title: Three-dimensional (3D) culture-primed placental mesenchymal stem cells decrease cellular heterogeneity, significantly enhancing osteogenesis via improving mitochondrial function

doi: 10.1016/j.mtbio.2026.103012

Figure Lengend Snippet: 3D culture decreases transcriptomic heterogeneity of PMSCs and enhances both mitochondrial and osteogenic processes. (A) Uniform Manifold Approximation and Projection (UMAP) analysis of cells from PMSC 2D and PMSC 3D as assessed using single-cell RNA sequencing data (National Center for Biotechnology Information-Gene Expression Omnibus or NCBI-GEO database: GSE268973 ). N = 6857 for 2D conditions; n = 10,705 for 3D conditions. (B) Cluster analysis of cells from PMSC 2D and PMSC 3D as visualized by UMAP. (C) Cluster analysis of cells from PMSC 2D as visualized by UMAP. (D) Cluster analysis of cells from PMSC 3D as visualized by UMAP. (E) Frequency analyses of clusters for PMSC 2D and PMSC 3D as assessed. (F) Mitochondrial transcription factor A ( TFM ), NADH:Ubiquinone oxidoreductase core subunit S1 ( NDUFS1 ), ubiquinol-cytochrome C reductase core protein 1 ( UQCRC1 ), cytochrome C oxidase subunit 6C ( COX6C ), and ATP synthase F1 subunit alpha ( ATP5F1A ) expression levels as visualized in cells from 2D- and 3D-preconditioned PMSCs by UMAP. (G) RUNX2, sirtuin1 ( SIRT1 ), alkaline phosphatase ( ALP ), bone sialoprotein ( IBSP ), and OPG expression levels as visualized in cells from PMSC 2D and PMSC 3D by UMAP. (H) Mitochondria- and bone-related GOBP pathways as enriched in cells from PMSC 3D vs. PMSC 2D by bubble plot analysis based on DEGs (fold change ≥1.5) and enrichment factor in Metascape. Bubble sizes represents the counts of genes associated with each GOBP pathway, while color gradient indicates p -values. (I) Mitochondria- and bone-related GOBP pathways as enriched in cells from PMSC 3D vs. PMSC 2D by bubble plot network analysis in Cytoscape. Bubble sizes represents the counts of genes associated with each GOBP pathway, while color gradient indicates NES. (J) Experimental design for the assessment of osteogenesis in 3D-preconditioned PMSCs: PMSCs were cultured under 2D or 3D conditions at a density of 1 × 10 5 cells/1 mL/cm 2 for one day. After preconditioning, both 2D- and 3D-cultured PMSCs were reseeded on 2D conditions with or without culture medium (CM) or osteogenic medium (OM). After 4 weeks, extracellular mineralization was assessed by staining calcium deposition with Alizarin Red (AR). (K) and (L) Representative and pooled data of extracellular mineralization in cells preconditioned from PMSC 2D and PMSC 3D as assessed with AR staining. Scale bar, 50 μm. N = 3 for each group. Data are shown as mean ± SD. One-way ANOVA: ∗∗, p < 0.01; ∗∗∗, p < 0.001. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: 3D culture decreases transcriptomic heterogeneity of PMSCs and enhances both mitochondrial and osteogenic processes. (A) Uniform Manifold Approximation and Projection (UMAP) analysis of cells from PMSC 2D and PMSC 3D as assessed using single-cell RNA sequencing data (National Center for Biotechnology Information-Gene Expression Omnibus or NCBI-GEO database: GSE268973 ).

Techniques: Single Cell, RNA Sequencing, Gene Expression, Expressing, Cell Culture, Staining

Journal: Cell Reports Medicine

Article Title: Valrubicin-loaded immunoliposomes targeting antigens on immunosuppressive cells to circumvent resistance to cancer immunotherapy

doi: 10.1016/j.xcrm.2026.102632

Figure Lengend Snippet: Val-ILs affect immunosuppressive cells and T lymphoma growth C57BL/6 mice were s.c. injected with 10 6 EL4 cells into the body side. When tumors reached 50 mm 3 , mice were i.v. injected with Val-ILs (10 12 NPs) on days 6 and 9. Analyses were performed on day 12 (excepted for L). (A) UMAP data frame and heatmap following FC showing expression levels of the different populations of immune cells in the TME of T lymphoma-bearing mice. Mean normalized data of n = 7 untreated mice. (B) UMAP data frame and heatmap following FC showing expression levels of the nine antigens targeted by Val-ILs-Combo among immune cells detected in the TME, mean normalized data of n = 7 untreated mice. (C) Treatment with NPs reduced the tumor volumes measured in vivo. Image of tumors isolated ex vivo. (D) NPs affected the repartition of immune cells in the TME. (E) NPs reduced the number of immunosuppressive cells in the TME. (F) NPs affected the repartition of immune cells in the spleen. (G) NPs reduced the number of immunosuppressive cells in the spleen. (H) MFI measured by FC on TAMs in the TME and macrophages in the spleen, to identify M1-like and M2-like phenotypes. (I) FC on tDCs in the TME and DCs in the spleen, to identify the percentage of activated MHC II + DCs. (J) FC on T-Ly in the TDLNs showing an increase in these populations. (K) Val-ILs-Combo affected the amount of Th17 and Tregs in the TDLNs. (L) Tumor growth volumes measured in vivo , following i.v. injection of Val-ILs-Combo and/or αPD-1 (200 μg), n = 8 mice per group. (M) FC plots and heatmaps showing the expression levels of the nine antigens targeted by Val-ILs-Combo on immunosuppressive cells, in the TME; mean normalized data of n = 5 mice. (N) Histogram showing the number of antigens targeted by the NPs and found repressed ( p < 0.05) on various immune cell populations. The number of mice used per group is indicated on the figure; data are shown as means ± SD, p values are compared to Val-ILs-IgG and are calculated using two-tailed unpaired Student’s t test. See also .

Article Snippet: UMAP plugin , Tree Star , https://www.flowjo.com.

Techniques: Injection, Expressing, In Vivo, Isolation, Ex Vivo, Two Tailed Test

Journal: Cell Reports Medicine

Article Title: Valrubicin-loaded immunoliposomes targeting antigens on immunosuppressive cells to circumvent resistance to cancer immunotherapy

doi: 10.1016/j.xcrm.2026.102632

Figure Lengend Snippet: Val-ILs affect immunosuppressive cells and B lymphoma growth BALB/c mice were s.c. injected with 10 6 A20 cells. When tumors reached 50 mm 3 , mice were i.v. injected with Val-ILs (10 12 NPs) on days 6, 9, and 12. Analyses were performed on day 15. (A) UMAP data frame and heatmap following FC showing the expression levels of the nine antigens targeted by Val-ILs-Combo among immune cells detected in the TME. Mean normalized data of n = 8 untreated mice. (B) NPs reduced the tumor volumes measured in vivo. Image of tumors isolated ex vivo , n = 8 mice per group, four did not develop tumors (black cross). (C) UMAP data showing that Val-ILs-Combo affected the repartition of immune cells in the TME. (D) NPs affected the repartition of immune cells in the spleen. (E and F) Val-ILs-Combo reduced the amount of Th17, Tregs, MDSCs, TAMs, or macrophages, in the TME (E) and the spleen (F). (G) Histogram showing the number of antigens targeted by the NPs and found repressed on the cell surface of various immune cell populations. (H) FC on TAMs in the TME and macrophages in the spleen, to identify M1-like and M2-like phenotypes. (I) FC on tDCs in the TME and DCs in the spleen, to identify the percentage of activated MHC II + DCs. (J) FC on CD4 + and CD8 + T-Ly in the TDLNs showing an increase in these populations. (K) FC showing that Val-ILs-Combo reduced the amount of Th17 and Tregs in the TDLNs. (L) Tumor growth volumes measured in vivo following the injection of Val-ILs-Combo and/or αPD-1 (200 μg). Image of tumors isolated ex vivo , n = 8 mice per group. The number of mice used per group is indicated on the figure, data are shown as means ± SD, and p values are compared to Val-ILs-IgG and are calculated using a two-tailed unpaired Student’s t test. See also .

Article Snippet: UMAP plugin , Tree Star , https://www.flowjo.com.

Techniques: Injection, Expressing, In Vivo, Isolation, Ex Vivo, Two Tailed Test

Journal: Cell Reports Medicine

Article Title: Valrubicin-loaded immunoliposomes targeting antigens on immunosuppressive cells to circumvent resistance to cancer immunotherapy

doi: 10.1016/j.xcrm.2026.102632

Figure Lengend Snippet: Val-ILs affect immunosuppressive cells in a mouse model of breast cancer 10 6 4T1 cells were transplanted through i.d. injection into the mammary gland of female BALB/c mice. When tumors reached 50 mm 3 , mice were i.v. injected with Val-ILs (10 12 NPs) on days 6, 9, and 12. Analyses were performed on day 15. (A) UMAP data frame and heatmap following FC showing the expression levels of the nine antigens targeted by the NPs among immune cells detected in the TME. Mean normalized data of n = 5 untreated mice. (B) NPs reduced the tumor volumes measured in vivo. Image of tumors isolated ex vivo , four did not develop tumors (black cross). (C) UMAP data showing that Val-ILs-Combo affected the repartition of immune cells in the TME. (D) NPs affected the repartition of immune cells in the spleen. (E and F) Val-ILs-Combo reduced the amount of Th17, Tregs, MDSCs, TAMs, or macrophages, in the TME (E) and the spleen (F). (G) Antigens targeted by the NPs found repressed on the cell surface of various immune cell populations. (H) FC on TAMs in the TME and macrophages in the spleen, to identify M1-like and M2-like phenotypes. (I) FC on tDCs in the TME and DCs in the spleen, to identify the percentage of activated MHC II + DCs. (J) FC on CD4 + and CD8 + T-Ly in the TDLNs showing an increase in these populations. (K) FC showing that Val-ILs-Combo affected the amount of Th17 and Tregs in the TDLNs. The number of mice used per group is indicated on the figure, data are shown as means ± SD, and p values are compared to Val-ILs-IgG and are calculated using two-tailed unpaired Student’s t test. See also .

Article Snippet: UMAP plugin , Tree Star , https://www.flowjo.com.

Techniques: Injection, Expressing, In Vivo, Isolation, Ex Vivo, Two Tailed Test

Journal: Cell Reports Medicine

Article Title: Valrubicin-loaded immunoliposomes targeting antigens on immunosuppressive cells to circumvent resistance to cancer immunotherapy

doi: 10.1016/j.xcrm.2026.102632

Figure Lengend Snippet: Val-ILs and αPD-1 affect immunosuppressive cells in the lung LLC1 tumor model Mice were i.v. injected with 10 6 LLC1 cells (day 0), i.v. injected with Val-ILs (10 12 NPs), and i.p. injected with αPD-1 (200 μg) on days 6, 9, 12, and 15. Analyses were performed on day 28. (A) UMAP data frame and heatmap following FC showing expression levels of the nine antigens targeted by Val-ILs-Combo among immune cells detected in the lung TME. Mean normalized data of n = 6 untreated mice. (B) NPs affected the number of immune cells in the lung TME. (C) NPs affected the repartition of immune cells in the spleen. (D and E) Val-ILs-Combo reduced the amount of Th17, Tregs, MDSCs, TAMs, or macrophages, in the TME (D) and the spleen (E). (F) Histogram showing the number of antigens targeted by the NPs and found repressed on the cell surface of various immune cell populations. (G) FC on TAMs in the TME and macrophages in the spleen, to identify M1-like and M2-like phenotypes. (H) FC on tDCs in the TME and DCs in the spleen, to identify the percentage of activated MHC II + DCs. (I) FC on CD4 + and CD8 + T-Ly in the TDLNs showing an increase in these populations. (J) FC data showing that NPs reduced the amount of Th17 and Tregs in the TDLNs. The number of mice used per group is indicated on the figure, data are shown as means ± SD, and p values are compared to Val-ILs-IgG + αIgG and are calculated using one-way ANOVA with Tukey’s multiple comparisons test. See also .

Article Snippet: UMAP plugin , Tree Star , https://www.flowjo.com.

Techniques: Injection, Expressing

Journal: bioRxiv

Article Title: Comparative transcriptomics analysis of histone deacetylases, transcription factors, and ion channel genes in human iPSC-cardiomyocytes vs. the adult human heart

doi: 10.64898/2026.01.16.700033

Figure Lengend Snippet: (A) Results for targeting HDAC classes I, II, and IV (B) Results for targeting HDAC class III. UMAP embedding performed after univariate data imputation and scaling. Samples color-coded by HDAC class. N1 and N2 are negative controls treated by scramble siRNA on Plate 1 and Plate 2 respectively. U1 and U2 are untreated controls on Plate 1 and Plate 2 respectively. Dotted lines mark samples that clustered relatively tight and far away from the control groups. For U1 group, n=4; for all other treatment groups, n=3. Bi-clustering heatmaps display log2 transformed expression values, sorted by their adjusted p-value for top 30 differentially expressed genes between the HDAC9 knockdown group and corresponding negative control ( C ) and between the SIRT3 knockdown group and corresponding negative control ( D ). Volcano plots display global transcriptional change across HDAC9 knockdown group and negative control ( E ) and across SIRT3 knockdown group and negative control ( F ). Each dot represents one gene. Genes with adjusted p-value < 0.05 and log2 fold change > 1 are colored red and are considered up-regulated. Genes with adjusted p-value < 0.05 and log2 fold change < −1 are colored green and are considered downregulated in the knockdown group compared to the control.

Article Snippet: Whole-transcriptome analysis of the HDAC/SIRT knockdowns in hiPSC-CM samples included our own UMAP clustering and differentially expressed gene (DEG) analysis performed by and provided by GENEWIZ/Azenta (South Plainfield, NJ).

Techniques: Control, Transformation Assay, Expressing, Knockdown, Negative Control

Journal: Bioinformatics

Article Title: Capturing gene–cell duality in a cat’s cradle

doi: 10.1093/bioinformatics/btaf681

Figure Lengend Snippet: (A) A UMAP of cells. Cells are colored according to cell type. Reproduced from Progatzky et al. (2021) . (B) A UMAP of genes. Here we use the 2000 most variable genes and cluster them using the Louvain algorithm. (C) As in B with genes encoding transcription factors highlighted. (D) Gene UMAPs with genes from selected Hallmark gene sets highlighted. (E) Sankey diagram showing relationships between selected gene clusters and cell clusters. (F) Gene UMAP coloured by mean z -score for expression of each of the 2000 most variable genes in selected cell types. (G) Gene UMAP coloured by absolute value of difference of mean z -score for TCells1 and TCells2. (H) Gene UMAP coloured by mean z-score for expression of each of the 2000 most variable genes in different conditions. Here WT and KO refer to control mice Sox10CreERT2; Ifngr2fl/+ (Ifngr2CTRL) and Sox10CreERT 2; Ifngr2fl/fl (Ifngr2 Δ EGC) mice respectively. (I) Violin plot showing observed UMAP distances between ligand-receptor pairs (red), randomized ligand-receptor pairs (green), and random gene pairs (blue). (J) Violin plot showing observed UMAP distances between pairs of genes encoding members of actual IntAct complexes, in comparison to randomized distances: the UMAP distance of permuted pairs, the UMAP distance for the first gene of each pair to a randomly chosen gene, and the UMAP distance between pairs derived from randomly chosen gene sets of the same size as our subset complexes.

Article Snippet: Relationships between genes can be displayed on a gene UMAP (this idea was independently arrived at and exploited in The Human Protein Atlas—proteinatlas.org).

Techniques: Expressing, Control, Comparison, Derivative Assay