spatial transcriptome datasets  (10X Genomics)

Journal: Cell Reports Medicine

Article Title: Spleen-targeted neoantigen mRNA vaccine induces ISG15 + CD8 + T cell-mediated tertiary lymphoid structure formation in hepatocellular carcinoma

doi: 10.1016/j.xcrm.2026.102754

Figure Lengend Snippet: STNvac induces antigen-specific tumor killing (A) UMAP visualization of single-cell transcriptomes from STNvac- and PBS-treated tumors showing nine major cell populations and a bar plot of their relative proportion. (B) Identification of tumor cells using SCEVAN. (C) Distribution changes of neoantigen expression after STNvac treatment. (D) Changes in the proportion of tumor cells expressing specific neoantigens after STNvac treatment. Subclones carrying highly immunogenic neoantigens ( Ptpn2_I383T and Traf7_C403W ) were significantly eliminated, whereas weakly immunogenic ones ( Samd91_K752M , Dtnb_K40T ) showed minimal change. (E) Bar plot showing the proportion changes in tumor cells expressing various numbers of neoantigens after STNvac treatment. (F) Bubble plot of cell-cell interaction showing ligand-receptor pairs between tumor cells and immune cells (T cells, NK cells, macrophages, DCs, and B cells).

Article Snippet: Spatial transcriptome dataset from Liu’s research , Mendeley Data , http://www.doi.org/10.17632/skrx2fz79n.1 , https://data.mendeley.com/datasets/skrx2fz79n/1.

Techniques: Single Cell, Expressing, Immunopeptidomics

Journal: Cell Reports Medicine

Article Title: Spleen-targeted neoantigen mRNA vaccine induces ISG15 + CD8 + T cell-mediated tertiary lymphoid structure formation in hepatocellular carcinoma

doi: 10.1016/j.xcrm.2026.102754

Figure Lengend Snippet: STNvac-induced enhancement of tumor infiltration, antigen-presenting capacity, and cytotoxic activity of ISG15 + CD8 + T cells (A) UMAP visualization of single-cell transcriptomes from CD45 + immune cells. (B) Relative proportions of major immune cell populations in PBS and STNvac groups. (C) UMAP visualization of T cell clusters from PBS and STNvac groups. (D) Relative proportions of different T cell clusters in PBS and STNvac groups. (E) Violin plots showing expression levels of T cell function markers across T cell clusters. (F) Representative multicolor immunofluorescence images of tumor sections showing co-localization of ISG15 + CD8 + T cells with GZMB and IFN-γ in PBS and STNvac groups. Scale bars, 50 μm. (G) Quantification of ISG15 + CD8 + T cell density co-expressing GZMB and IFN-γ, corresponding to (F). Unpaired two-tailed t test; ∗p < 0.05. Mean ± SD ( n = 3 biological replicates). (H) Comparative GO and KEGG pathway enrichment analyses of ISG15 + CD8 + T cells between PBS and STNvac groups. (I) Kaplan-Meier curves showing 5-year overall survival (OS) and progression-free survival (PFI) for HCC patients in TCGA: LIHC cohort stratified by ISG15 + CD8 + T cell signatures. See also and .

Article Snippet: Spatial transcriptome dataset from Liu’s research , Mendeley Data , http://www.doi.org/10.17632/skrx2fz79n.1 , https://data.mendeley.com/datasets/skrx2fz79n/1.

Techniques: Activity Assay, Single Cell, Expressing, Cell Function Assay, Immunofluorescence, Two Tailed Test

Journal: Cell Reports Medicine

Article Title: Spleen-targeted neoantigen mRNA vaccine induces ISG15 + CD8 + T cell-mediated tertiary lymphoid structure formation in hepatocellular carcinoma

doi: 10.1016/j.xcrm.2026.102754

Figure Lengend Snippet: Spatial localization of ISG15 + CD8 + T cells and APCs and the formation of TLS following STNvac treatment (A–D) Spatial transcriptomics analysis of tumor samples isolated from PBS- and STNvac-treated mice. (A) H&E staining and corresponding spatial clustering of transcriptome spots; 19 clusters were identified, with clusters 4 and 7 showing marked enrichment of immune cells (CD45 + ). (B) Spatial expression of Ptprc (CD45) mapped on H&E-stained tissues, highlighting immune-cell-dense regions. (C) Region of interest annotation based on TESLA, illustrating colocalization of ISG15 + CD8 + T cells (approximated by Pclaf / Birc5 ), B cells, DCs, and CD4 + T cells; CXCL13 expression overlapped with these immune clusters, and TLS-like regions were identified using a TLS score (co-localization of B cells, CD4 + T cells, DCs, and CXCL13). (D) Magnified views of regions I and II from (A), showing compact lymphoid aggregates (white arrows) and smaller, loosely organized foci (black arrows) at the tumor margin corresponding to TLS. (E–G) Multicolor immunofluorescence staining analysis of TLSs and ISG15 + CD8 + T cells in tumors from different groups. (E) Representative images showing CD20 + B cells and CD23 + follicular regions within TLSs, together with ISG15 + CD8 + T cells localized around TLS structures. Scale bars: 500 μm; inset, 50 μm. (F) Magnified views of Region I from (E), including H&E and additional multicolor staining for CD20, CD21, CD23, and CD34, highlighting organized FDC networks and HEV-like microvessels within TLS boundaries. Scale bars, 100 μm (left) and 50 μm (right). (G) Quantitative analysis of TLS density in tumors from different treatment groups ( n = 3 biological replicates). (H) Spatial transcriptomic mapping of human HCC tissues from Liu et al.’s study showing ISG15 + CD8 + T cells located near or within TLS-like regions in immune-inflamed tumors. See also .

Article Snippet: Spatial transcriptome dataset from Liu’s research , Mendeley Data , http://www.doi.org/10.17632/skrx2fz79n.1 , https://data.mendeley.com/datasets/skrx2fz79n/1.

Techniques: Spatial Transcriptomics, Isolation, Staining, Expressing, Multicolor Immunofluorescence Staining

Journal: Cell Reports Medicine

Article Title: Spleen-targeted neoantigen mRNA vaccine induces ISG15 + CD8 + T cell-mediated tertiary lymphoid structure formation in hepatocellular carcinoma

doi: 10.1016/j.xcrm.2026.102754

Figure Lengend Snippet: STNvac induces antigen-specific tumor killing (A) UMAP visualization of single-cell transcriptomes from STNvac- and PBS-treated tumors showing nine major cell populations and a bar plot of their relative proportion. (B) Identification of tumor cells using SCEVAN. (C) Distribution changes of neoantigen expression after STNvac treatment. (D) Changes in the proportion of tumor cells expressing specific neoantigens after STNvac treatment. Subclones carrying highly immunogenic neoantigens ( Ptpn2_I383T and Traf7_C403W ) were significantly eliminated, whereas weakly immunogenic ones ( Samd91_K752M , Dtnb_K40T ) showed minimal change. (E) Bar plot showing the proportion changes in tumor cells expressing various numbers of neoantigens after STNvac treatment. (F) Bubble plot of cell-cell interaction showing ligand-receptor pairs between tumor cells and immune cells (T cells, NK cells, macrophages, DCs, and B cells).

Article Snippet: TCGA: LIHC dataset was obtained from GDC Data Portal and patients were stratified according to the ssGSEA scores of the signature containing CD8A, CD8B and ISG15, the survival analysis was then further conducted using survival packages in R. Mendeley Data: http://www.doi.org/10.17632/skrx2fz79n.1 (the spatial transcriptome dataset from Liu’s research ) was downloaded with the link provided in that publication.

Techniques: Single Cell, Expressing, Immunopeptidomics

Journal: Cell Reports Medicine

Article Title: Spleen-targeted neoantigen mRNA vaccine induces ISG15 + CD8 + T cell-mediated tertiary lymphoid structure formation in hepatocellular carcinoma

doi: 10.1016/j.xcrm.2026.102754

Figure Lengend Snippet: STNvac-induced enhancement of tumor infiltration, antigen-presenting capacity, and cytotoxic activity of ISG15 + CD8 + T cells (A) UMAP visualization of single-cell transcriptomes from CD45 + immune cells. (B) Relative proportions of major immune cell populations in PBS and STNvac groups. (C) UMAP visualization of T cell clusters from PBS and STNvac groups. (D) Relative proportions of different T cell clusters in PBS and STNvac groups. (E) Violin plots showing expression levels of T cell function markers across T cell clusters. (F) Representative multicolor immunofluorescence images of tumor sections showing co-localization of ISG15 + CD8 + T cells with GZMB and IFN-γ in PBS and STNvac groups. Scale bars, 50 μm. (G) Quantification of ISG15 + CD8 + T cell density co-expressing GZMB and IFN-γ, corresponding to (F). Unpaired two-tailed t test; ∗p < 0.05. Mean ± SD ( n = 3 biological replicates). (H) Comparative GO and KEGG pathway enrichment analyses of ISG15 + CD8 + T cells between PBS and STNvac groups. (I) Kaplan-Meier curves showing 5-year overall survival (OS) and progression-free survival (PFI) for HCC patients in TCGA: LIHC cohort stratified by ISG15 + CD8 + T cell signatures. See also and .

Article Snippet: TCGA: LIHC dataset was obtained from GDC Data Portal and patients were stratified according to the ssGSEA scores of the signature containing CD8A, CD8B and ISG15, the survival analysis was then further conducted using survival packages in R. Mendeley Data: http://www.doi.org/10.17632/skrx2fz79n.1 (the spatial transcriptome dataset from Liu’s research ) was downloaded with the link provided in that publication.

Techniques: Activity Assay, Single Cell, Expressing, Cell Function Assay, Immunofluorescence, Two Tailed Test

Journal: Cell Reports Medicine

Article Title: Spleen-targeted neoantigen mRNA vaccine induces ISG15 + CD8 + T cell-mediated tertiary lymphoid structure formation in hepatocellular carcinoma

doi: 10.1016/j.xcrm.2026.102754

Figure Lengend Snippet: Spatial localization of ISG15 + CD8 + T cells and APCs and the formation of TLS following STNvac treatment (A–D) Spatial transcriptomics analysis of tumor samples isolated from PBS- and STNvac-treated mice. (A) H&E staining and corresponding spatial clustering of transcriptome spots; 19 clusters were identified, with clusters 4 and 7 showing marked enrichment of immune cells (CD45 + ). (B) Spatial expression of Ptprc (CD45) mapped on H&E-stained tissues, highlighting immune-cell-dense regions. (C) Region of interest annotation based on TESLA, illustrating colocalization of ISG15 + CD8 + T cells (approximated by Pclaf / Birc5 ), B cells, DCs, and CD4 + T cells; CXCL13 expression overlapped with these immune clusters, and TLS-like regions were identified using a TLS score (co-localization of B cells, CD4 + T cells, DCs, and CXCL13). (D) Magnified views of regions I and II from (A), showing compact lymphoid aggregates (white arrows) and smaller, loosely organized foci (black arrows) at the tumor margin corresponding to TLS. (E–G) Multicolor immunofluorescence staining analysis of TLSs and ISG15 + CD8 + T cells in tumors from different groups. (E) Representative images showing CD20 + B cells and CD23 + follicular regions within TLSs, together with ISG15 + CD8 + T cells localized around TLS structures. Scale bars: 500 μm; inset, 50 μm. (F) Magnified views of Region I from (E), including H&E and additional multicolor staining for CD20, CD21, CD23, and CD34, highlighting organized FDC networks and HEV-like microvessels within TLS boundaries. Scale bars, 100 μm (left) and 50 μm (right). (G) Quantitative analysis of TLS density in tumors from different treatment groups ( n = 3 biological replicates). (H) Spatial transcriptomic mapping of human HCC tissues from Liu et al.’s study showing ISG15 + CD8 + T cells located near or within TLS-like regions in immune-inflamed tumors. See also .

Article Snippet: TCGA: LIHC dataset was obtained from GDC Data Portal and patients were stratified according to the ssGSEA scores of the signature containing CD8A, CD8B and ISG15, the survival analysis was then further conducted using survival packages in R. Mendeley Data: http://www.doi.org/10.17632/skrx2fz79n.1 (the spatial transcriptome dataset from Liu’s research ) was downloaded with the link provided in that publication.

Techniques: Spatial Transcriptomics, Isolation, Staining, Expressing, Multicolor Immunofluorescence Staining

Journal: Nature Communications

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma

doi: 10.1038/s41467-025-68156-8

Figure Lengend Snippet: a Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). b Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders ( n = 7 patients) and non-responders ( n = 12 patients) (scale bars, 100 μm). c A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. d , e Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated DEN/CCl4-induced HCC model. f A schematic representation of the treatment strategy in the AKT/NRasV12 -induced HCC model. g , h Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. i A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. j , k Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden ( n = 6 mice) from the indicated Hepa1-6-induced HCC model. l , m Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days ( n = 6 mice); a , b , e , h , k , m P values were calculated using an unpaired t test (two-tailed). The box plots show data distribution with the overlaid box plot indicating the median, first (Q1) and third (Q3) quartiles, and the whiskers extending to the 1.5× interquartile range (IQR). Source data are provided as a file.

Article Snippet: Fig. 8 Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. a Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). b Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders ( n = 7 patients) and non-responders ( n = 12 patients) (scale bars, 100 μm). c A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. d , e Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated DEN/CCl4-induced HCC model. f A schematic representation of the treatment strategy in the AKT/NRasV12 -induced HCC model. g , h Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. i A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. j , k Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden ( n = 6 mice) from the indicated Hepa1-6-induced HCC model. l , m Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days ( n = 6 mice); a , b , e , h , k , m P values were calculated using an unpaired t test (two-tailed).

Techniques: Expressing, Immunohistochemistry, Staining, Two Tailed Test