Journal: World Journal of Hepatology
Article Title: Chromatin accessibility module identified by single-cell sequencing underlies the diagnosis and prognosis of hepatocellular carcinoma
doi: 10.4254/wjh.v17.i6.107329
Figure Lengend Snippet: Epigenetic coordination between malignant and stromal cells. A: Co-accessible chromatin peaks between tumor and non-tumor cells (log10 transformed counts); B: Ligand-receptor interactions initiated by malignant cells in tumor microenvironments, quantified via CellChat; C: A bar plot showing the log10 of co-accessible peaks number among tumor cells and non-tumor cells across differentiated tumors and nondifferentiated tumors; D: A bar plot showing the number of ligand-receptor interactions when setting malignant cells as source among tumor cells and non-tumor cells across differentiated tumors and nondifferentiated tumors; E: Gene ontology enrichment for genes linked to malignant co-accessible regions. The score indicated normalized enrichment scores and q value denote Benjamini-Hochberg-adjusted P values; F: A circle network plot showing communication networks of the three common signaling pathways, Collagen, midkine (MDK) and peptidylprolyl isomerase A across differentiated tumors and nondifferentiated tumors. Line width indicates interaction strength; G: Expression of MDK pathway ligands (MDK, orange) and receptors (green) across differentiation states. Undifferentiated tumors exhibit upregulated MDK; H: MDK and nucleolin expression was lowest in well-differentiated samples grouped by Hoshida subtypes; I: Western blot of MDK, NCL and H3K27Ac expression in SNU449 cells transfected with 1 μmol/L A485 (CREB-binding protein/P300 inhibitor) for 48 hours. glyceraldehyde-3-phosphate dehydrogenaseserved as a loading control; J: Quantification of MDK, NCL and H3K27Ac levels normalized to glyceraldehyde-3-phosphate dehydrogenase ( n = 3). scRNA-seq: Single-cell RNA-sequencing; MK: Midkine related pathway; CypA: Peptidylprolyl isomerase A; MDK: Midkine; SDC: Syndecan; LRP: LDL Receptor Related Protein; NCL: Nucleolin; H3K27Ac: Histone 3 lysine 27 acetylation; CBP: CREB-binding protein; GAPDH: Glyceraldehyde-3-phosphate dehydrogenase.
Article Snippet: Gene expression of midkine (MDK) (1:1000; Proteintech #11009-1-AP) and nucleolin (NCL) (1:1000; Proteintech #83380-1-RR) was further identified in biological triplicates with statistical significance assessed by student’s t -test ( P < 0.05). siRNA transfection: siRNA was designed using the DharmaconTM siRNA Design Tool.
Techniques: Transformation Assay, Protein-Protein interactions, Expressing, Western Blot, Transfection, Binding Assay, Control, RNA Sequencing
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