Fig 1.
Spatial transcriptomics analysis of 8 high grade serious ovarian cancer patients.
(A): Workflow of the study. (B): Uniform Manifold Approximation and Projection (UMAP) plot of clustering results of spatial transcriptomics (ST) data. (C): Cluster distributions in each patient. (D): UMAP plot of marker expression for tumor (blue) and stromal (pink) samples. (E): Heatmap of pathway activity in tumor and stromal clusters.
Fig 2.
Gene expression and pathway enrichment of tumor and stromal clusters.
(A): Spatial distribution of clusters in patients (From left to right: patient 1, patient 4, patient 8). (B): Visualization of clusters’ gene expression through dimensional reduction. (C): Heatmap of pathway activity in tumor clusters. (D): Heatmap of pathway activity in stromal clusters. (E): Heatmap of cell enrichment in two groups (divided by the different enrichment of Gene Set Variation Analysis (GSVA) signaling pathways) of stromal clusters.
Fig 3.
Depict tumor heterogeneity based on copy number variation.
(A - B): Clonal evolutionary tree (left) and spatial visualization (middle and right) of patient 4 (A) and patient 8 (B). (C): Heatmap of pathway activity of different clones in patient 8. (D): Changes in gene expression potentially affected by copy number variations (CNVs) in patient 8.
Fig 4.
Cellular meta-programs and cell-cell communication.
(A): Heatmap of expression programs in representative patients. (B): Shared meta-programs across different patients. (C): Sub-clustering of tumor cells. (D): Expression of meta-program signatures in tumor cell clusters. (E): Dot plot of cell-cell communication between tumor cells. (F): Chord plot of important ligand-receptor pairs in the communication of tumor cells.
Fig 5.
NCL overexpression promotes tumor cells’ proliferation.
(A): NCL overexpression activates the AKT pathway (B): Effect of NCL overexpression on SKOV3 cell proliferation (N = 3). SKOV3 cells were transfected with an NCL overexpression plasmid or the corresponding empty vector. Cell Counting Kit-8 (CCK8) assays were utilized to evaluate cells’ proliferation in each group at different time points. Results are presented as mean ± standard deviation (SD) from three independent experiments. ** indicates P < 0.01. (C - F): Effect of NCL overexpression on gene expression(N = 3). The gene expressions of NCL (C), phosphatase and tensin homolog (PTEN) (D), AKT1 (E), and Ki-67 (F) in each group of cells were examined using quantitative polymerase chain reaction (qPCR). Results represent the mean ± SD from three independent experiments. ** indicates P < 0.01. (G - L): The effect of NCL overexpression on protein level. The protein expression levels of NCL (G, H), PTEN (G, I), AKT (G, J), p-AKT (S473) (G, K), and Ki67 (G, L) in the cells from each group were detected by Western Blot. Results are presented as mean ± SD from three independent experiments. **P < 0.01.
Fig 6.
Cell type enrichments in different patients.
(A): Heatmap of copy number variations (CNVs) in patient 8 (B-C): Enrichment of cell type(B) and tumor score(C). Normalized enrichment of different cell types and tumor score (blue and black) in patient 8 (left). Hematoxylin and Eosin (H&E) staining image (right).(D): Tumor score in patients 1–8.
Fig 7.
Analysis of macrophages in patients.
(A): Sub-clustering of macrophages. (B): Dot plot illustrating the expression of signatures. (C): Enrichment of different meta-programs across patients. (D): Enrichment of different groups of tumor cells and macrophages across patients. (E): Chord plot depicting important ligand-receptor pairs in cellular communication. (F): Dot plot visualizing cell-cell communication between tumor cells and macrophages.
Fig 8.
Potential signaling pathways regulated by enriched MDK-NCL.
The potential pathways contribute to tumor progression regulated by the AKT pathway when MDK-NCL is highly enriched. Red represents up-regulate/activated, and blue represents down-regulated.