Fig. 5

Involvement of LINC00461 in HDAC6-mediated cell division and survival in GBM cells. A Volcano plot visualizing the differentially expressed genes between si-NC and si-LINC00461 (si461) treatment. Green and red dots represent genes with significant downregulation and upregulation (p-value < 0.01), respectively, in si-LINC00461 compared with si-NC. B Venn diagram illustrating overlaps between the number of genes that were significantly altered in MPT0B291-treated and si-LINC00461-treated cells. C Top five molecular and cellular functions of genes altered in si-LINC00461-treated (334 genes), MPT0B291-treated (1709 genes), and intersection subset (88 genes) by IPA. The number of genes involved in the biological process is shown on the right side of the bar chart. D Heatmap representation of the top 20 predicted influential biological functions after treatment by IPA. Positive activation Z-score (red) represents activated pathways, and negative activation Z-score (green) represents inhibited pathways. E Relationships between si-LINC00461-treated NGS data (in horizontal) and TCGA-GBM NGS data (in vertical) by Pearson’s correlation coefficient (PCC). Each dot represents the expression value of a cell-division-related gene that existed in the intersection subset. F Forest plots showing hazard ratios for risk of mortality in high-grade glioma patients with higher expressions of the indicated genes. Circles represent the hazard ratio, and bars on both sides denote their corresponding 95% confidence intervals (CI). The original survival curves were obtained from PROGgeneV2 (Fig. S4). Log-rank test. G Individual cells suspended/isolated directly from patient’s fresh GBM sample were used for single-cell RNA sequencing. Each dot denotes one cell with the expression of LINC00461, and the depth of blue represents the amount of LINC00461 expression. The red dashed circle indicates cluster 5. H Expression profiles of LINC00461 and cell-division-related genes in cell clusters from the single-cell RNA sequencing dataset. Dot size reflects the percent of cells expressing the gene, and dot color indicates average gene expression