Additional file 1 of Pancancer landscape analysis of the thymosin family identified TMSB10 as a potential prognostic biomarker and immunotherapy target in glioma
Creators: name: Xiong, Ye
name: Qi, Yanhua
name: Pan, Ziwen
name: Wang, Shaobo
name: Li, Boyan
name: Feng, Bowen
name: Xue, Hao
name: Zhao, Rongrong
name: Li, Gang
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: Additional file 1: Figure S1. The expression of TMSs in cancer cell lines in CCLE dataset. The expression of (A) TMSB10, (B)TMSB4X, (C) TMSB4Y, (D) TMSB15A, (E) TMSB15B, (F) PTMA and (G) PTMS in cancer cell lines in CCLE dataset. Figure S2. The expression of TMSs in normal tissues in GETx dataset. The expression of (A) TMSB10, (B)TMSB4X, (C) TMSB4Y, (D) TMSB15A, (E) TMSB15B, (F) PTMA and (G) PTMS in normal tissues in GETx dataset. Figure S3. The expression of TMSs between GTEx normal tissues and paired tumor tissues. The expression of (A)TMSB4X, (B) TMSB4Y, (C) TMSB15A, (D) TMSB15B, (E) PTMA and (F) PTMS between GTEx normal tissues and tumor tissues. The asterisks indicated a statistically significant p-value calculated using Mann-Whitney U test. The statistical significance is indicated as follows: ns&gt;0.05; *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001. Figure S4. Biological pathways and immunological characteristics of TMSB10 in glioma. A Kaplan–Meier curves for the OS of GBM patients with high TMSB10 expression and low TMSB10 expression in three GBM datasets; the log-rank test was used to calculate the p value. B Correlation between TMSB10 and the infiltration of 25 tumor-associated TME cells calculated with the ssGSEA algorithm. The color indicates the correlation coefficient. C Spearman correlation analysis of TMSB10 and classical signaling pathways in three glioma cohorts. Red indicates positive correlations, and the darkness of color is proportional to the correlation coefficient. The size of the circle represents the statistical P value, with larger circles representing greater statistical significance. Bar graph of (D) enriched terms, colored by p-values, and (E) summary of enrichmentanalysis in TRRUST across genes positively correlated with TMSB10 in CGGA glioma dataset. Figure S5. Multiomics regulatory profile of TMSB10 in glioma. A KEGG enrichment analysis of genes with significantly upregulated at both mRNA and protein levels in GBM samples with high TMSB10 expression. B Waterfall plot of the tumor somatic mutation landscape in the (upper) low-TMSB10 and (lower) high-TMSB10 samples in the wang GBM dataset. Dot plot of the log2FC (protein expression) versus the (C) log2FC (protein phosphorylation expression), and (D) log2FC (protein acylation expression), showing a positive correlation between the overall protein phosphorylation/acylation level and protein expression and the distribution of genes with significant changes in both the protein expression (|FC| &gt; 1.2, P &lt; 0.05) and corresponding protein phosphorylation/acylation expression (|FC| &gt; 1.2, P &lt; 0.05) in the high TMSB10 expression group compared with the low TMSB10 expression group. Figure S6. TMSB10 expression is associated with glioma pathological malignant progression and immune phenotype in the Qilu dataset. A GSVA enrichment analysis showing the activation status of biological pathways in the HSPA7-high and HSPA7-low groups. Heatmap was used to visualize these biological processes. Yellow represents activated pathways, black represents moderately activated pathways, and blue represents inhibited pathways. B GSEA showing the classical cancer-promoting pathways and immune-related pathways were signficantly enriched in the high TMSB10 expression glioma samples in Qilu dataset. C Abundances of immune/stromal score, tumorpurity and 25 immune cell types in TMSB10 high glioma samples versus low samples in Qilu dataset. The upper and lower ends of the boxes indicate the interquartile range of the values. The lines in the boxes represent the median values, and black dots show outliers. The significance of differences between the three clusters were determined by the Mann-Whitney U test. The statistical significance is indicated as follows: ns&gt;0.05; *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001. Bar graph of (D) enriched terms, colored by p-values, and (E) summary of enrichmentanalysis in TRRUST across genes positively correlated with TMSB10 in Qilu glioma dataset. Figure S7. TMSB10 promotes the proliferation, migration and invasion of glioma cells in vitro. A QRT-PCR assays showing the relative expression of TMSB10 in GBM cells and GSCs transfected with knocking down TMSB10 (sh-WEE2-AS1) or corresponding negative contorl (sh-NC). B Colony-forming assays showing the proliferation ability of GBM cells transfected with sh-NC or sh-TMSB10. C EDU assays showing the proliferation ability of GBM cells transfected with sh-NC or sh-TMSB10, scale bar, 50μm. Quantification histogram represented cell population. Data represented mean ± SD from at least three independent experiments. D QRT-PCR assays showing the relative expression of TMSB10 in GBM cells and GSCs overexpressing WEE2-AS1 (ov-WEE2-AS1) or corresponding negative control (ov-NC). E Wound Healing assays showing the migration ability of GBM cells transfected with sh-NC or sh-TMSB10. (F-G) Western blot assays showing the protein expression of MMP-9, N-cadherin, bcl2, bax, p21, CDK4 and cyclin D1 expression in GBM cells and mice tumor samples transfected with sh-NC or sh-TMSB10. Amounts of protein determined by densitometry of protein bands from three experiments. GAPDH was the loading control. Data represented mean ± SD from at least three independent experiments. The statistical significance is shown as: *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; ****P &lt; 0.0001. Figure S8. TMSB10 regulates the cell cycle and apoptosis of glioma cells in vitro. (A, B) Cell cycle analysis for U87MG and U251 cells transfected with sh-NC or sh-TMSB10. The percentage of cells arrested in the G1/S phase is analyzed in a histogram (right panels). C Representative flow cytometry plots of cell apoptosis and quantitative analysis are shown. D Western blot assays showing the protein expression of TMSB10 expression in GBM cells. E-H Western blot assays showing the protein expression of CD44, YAP1, LOX, as well as phosphorylation levels of AKT and ERK1/2 in GSCs transfected with sh-NC or sh-TMSB10 and ov-NC or ov-TMSB10 as indicated. Amounts of protein determined by densitometry of protein bands from three experiments. β-actin was the loading control. I Western blot assays showing the protein expression of SPP1 in THP-1 differentiated macrophages treated with CM from GSCs transfected with sh-NC or sh-TMSB10 and ov-NC or ov-TMSB10 as indicated. Amounts of protein determined by densitometry of protein bands from three experiments. β-actin was the loading control. Data represented mean ± SD from at least three independent experiments. The statistical significance is shown as: *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001; ****P &lt; 0.0001. Figure S9. TMSB10 promotes GBM MES transformation and facilitates macrophage infiltration. A Correlation between TMSB10 and suppressive immunomodulators in three GBM datasets. The color indicates the correlation coefficient. B Correlation between TMSB10 and suppressive immunomodulators in Qilu dataset. Angle of sector indicates the correlation coefficient. C Correlation between TMSB10 and CD44 in three GBM datasets. GSEA showing the (D) MES signature and (E) CORDENONSI_YAP_CONSERVED_SIGNATURE in the high TMSB10 expression group in the Lee Y and Wang GBM cohorts.