Journal: Experimental & Molecular Medicine

Article Title: Functional and pathologic association of aminoacyl-tRNA synthetases with cancer

doi: 10.1038/s12276-022-00765-5

Figure Lengend Snippet: a The heatmap of cancer-associated ARS protein levels was generated with data extracted from The Human Protein Atlas (upper). The protein levels of each ARS are represented as a score that ranges from −2 to +2. The Human Protein Atlas provides information about protein levels based on the staining intensity in IHC images, which are classified into not detected, lowly detected, moderately detected and highly detected. We scored the staining intensities (not detected (−1), lowly detected (−1/3), moderately detected (+1/3) and highly detected (+1)) and averaged the score in normal and cancer tissues. Then, cancer-associated ARS protein levels were calculated by subtracting the normal score from the corresponding cancer score. A heatmap of the cancer-associated ARS mRNA levels was also generated with data extracted from TCGA (lower). The log2 of the fold change of each ARS mRNA in cancer tissue compared to normal tissue is displayed. Blue indicates low detection, red high detection, and white moderate detection in each cancer type. Cancer types and genes are hierarchically clustered based on the Pearson correlation score and average linkage (dendrogram shown for cancer types). b Correlation of the cancer-associated mRNA and protein levels of ARSs (top-left panel) and ribosome subunit proteins (top-right panel) is compared. The plot for ARSs is further divided into three different plots of MSC, non-MSC and mitochondrial ARSs (bottom panel). For analysis of ARSs, all 37 ARS types were investigated. For analysis of ribosome subunits, RPSA, RPS5, RPS6, RPS13, RPS20, RPLP0, RPL5, RLP8, RPL9, and RPL10A were investigated. Levels of protein and mRNA were calculated using the same method as in Fig. . Cancer types shared by both databases were utilized for the correlation plot. The coefficient of correlation (r-value) and the significance level (p-value) were calculated via GraphPad PrismX. The coefficient of correlation and significance level were only statistically significant for ARSs.

Article Snippet: The Human Protein Atlas provides information about protein levels based on the staining intensity in IHC images, which are classified into not detected, lowly detected, moderately detected and highly detected.

Techniques: Generated, Staining

Journal: Bioengineered

Article Title: Transcriptional factor 3 binds to sirtuin 1 to activate the Wnt/β-catenin signaling in cervical cancer

doi: 10.1080/21655979.2022.2076481

Figure Lengend Snippet: TCF3 is possibly linked to unfavorable prognosis of CC. A, expression of TCF3 in pan cancers; B, expression of TCF3 in GSE7803 and GSE9750 datasets; C, distribution of TCF3 in CC tissues and normal cervical tissues in The Human Protein Atlas system; D, TCF3 expression in TCGA-CESC; E, association of TCF3 expression with the patient survival in TCGA-CESC; F, TCF3 mRNA expression in CC cell lines (CaSki, C-33A, SiHa, SW756 and HeLa) and in normal End1/E6E7 cells detected by RT-qPCR (* p < 0.05; ** p < 0.01; one-way ANOVA). Data are expressed as the mean ± SD.

Article Snippet: The distribution image of TCF3 in CC tissues was downloaded from the Human Protein Atlas system ( https://www.proteinatlas.org/ ).

Techniques: Expressing, Quantitative RT-PCR

Journal: Bioengineered

Article Title: Transcriptional factor 3 binds to sirtuin 1 to activate the Wnt/β-catenin signaling in cervical cancer

doi: 10.1080/21655979.2022.2076481

Figure Lengend Snippet: TCF3 downregulation reduces proliferation, migration and invasiveness, and resistance to death of CC cells in vitro . A, TCF3 expression in HeLa and SiHa cells after si-TCF3 transfection detected by RT-qPCR (* p < 0.05, two-way ANOVA); B, proliferation activity of HeLa and SiHa cells examined by colony formation assay (* p < 0.05, two-way ANOVA); C, migration activity of HeLa and SiHa cells measured by Transwell assay (* p < 0.05, two-way ANOVA); D, invasiveness of HeLa and SiHa cells examined by Transwell assay (* p < 0.05, two-way ANOVA); E, HeLa and SiHa apoptosis examined by flow cytometry (* p < 0.05, two-way ANOVA). Data are expressed as the mean ± SD.

Article Snippet: The distribution image of TCF3 in CC tissues was downloaded from the Human Protein Atlas system ( https://www.proteinatlas.org/ ).

Techniques: Migration, In Vitro, Expressing, Transfection, Quantitative RT-PCR, Activity Assay, Colony Assay, Transwell Assay, Flow Cytometry

Journal: Bioengineered

Article Title: Transcriptional factor 3 binds to sirtuin 1 to activate the Wnt/β-catenin signaling in cervical cancer

doi: 10.1080/21655979.2022.2076481

Figure Lengend Snippet: TCF3 plays a transcriptional activation role in CC cells. A, the structural domain of TCF3 determined by protein sequencing; B, construction of pmir-GLO luciferase reporter vectors containing TCF3 and VP16; C, effect of TCF3 on the activity of the luciferase reporter examined by the luciferase assay (* p < 0.05, two-way ANOVA); D, construction of pGLO-TCF3 vector; E, transcriptional regulation activity of TCF3 validated via the luciferase assay (* p < 0.05, unpaired t test). Data are expressed as the mean ± SD.

Article Snippet: The distribution image of TCF3 in CC tissues was downloaded from the Human Protein Atlas system ( https://www.proteinatlas.org/ ).

Techniques: Activation Assay, Sequencing, Luciferase, Activity Assay, Plasmid Preparation

Journal: Bioengineered

Article Title: Transcriptional factor 3 binds to sirtuin 1 to activate the Wnt/β-catenin signaling in cervical cancer

doi: 10.1080/21655979.2022.2076481

Figure Lengend Snippet: TCF3 binds to the promoter of SIRT1. A, a PPI network of the TCF3-related gene clusters; B, GO and KEGG pathway enrichment analyses of the TCF3-related genes; C, volcano maps for the DEGs in the GSE7803 and GSE9750 datasets; D, a Venn diagram for common DEGs in two datasets; E, GO and KEGG pathway enrichment analyses based on the DEGs; F, putative binding site between TCF3 and the SIRT1 promoter; G, binding between TCF3 and the SIRT1 promoter validated by the ChIP-qPCR assay (* p < 0.05, two-way ANOVA). Data are expressed as the mean ± SD.

Article Snippet: The distribution image of TCF3 in CC tissues was downloaded from the Human Protein Atlas system ( https://www.proteinatlas.org/ ).

Techniques: Binding Assay, ChIP-qPCR

Journal: Bioengineered

Article Title: Transcriptional factor 3 binds to sirtuin 1 to activate the Wnt/β-catenin signaling in cervical cancer

doi: 10.1080/21655979.2022.2076481

Figure Lengend Snippet: TCF3 binds to SIRT1 to promote β-catenin nuclear accumulation. A, expression of SIRT1 in TCGA-CESC; B, prognostic value of SIRT1 in CC in TCGA-CESC; C, correlation between TCF3 and SIRT1 in CC tumor tissues in TCGA-CESC; D, expression of SIRT1 in CC tissues in GSE7803 and GSE9750 datasets; E, correlation between TCF3 and SIRT1 in CC in GSE7803 and GSE9750 datasets; F, binding relationship between SIRT1 and β-catenin examined by ChIP-qPCR (* p < 0.05, two-way ANOVA); G, acetylation and nuclear accumulation of β-catenin in CC cells (*# p < 0.05, two-way ANOVA; * compared to SIRT1-NC; # compared to DMSO). Data are expressed as the mean ± SD.

Article Snippet: The distribution image of TCF3 in CC tissues was downloaded from the Human Protein Atlas system ( https://www.proteinatlas.org/ ).

Techniques: Expressing, Binding Assay, ChIP-qPCR

Journal: Bioengineered

Article Title: Transcriptional factor 3 binds to sirtuin 1 to activate the Wnt/β-catenin signaling in cervical cancer

doi: 10.1080/21655979.2022.2076481

Figure Lengend Snippet: Interactions between TCF3/SIRT1/β-catenin in CC cells. A, SIRT1 expression and β-catenin nuclear accumulation in CC cell lines (CaSki, C-33A, SiHa, SW756 and HeLa) and normal End1/E6E7 cells examined by western blot analysis (* p < 0.05, two-way ANOVA); B, SIRT1 expression and β-catenin nuclear accumulation in HeLa and SiHa cells transfected with si-TCF3 determined by western blot assay (* p < 0.05, two-way ANOVA); C, expression of SIRT1 and nuclear accumulation of β-catenin in HeLa and SiHa cells after SIRT1-OE transfection and XAV-939 treatment examined by western blot assay (*# p < 0.05, two-way ANOVA, * compared to si-TCF3 + SIRT1-NC; # compared to SIRT1-OE + DMSO); D, cell proliferation determined by colony formation assay (*# p < 0.05, two-way ANOVA, * compared to si-TCF3 + SIRT1-NC; # compared to SIRT1-OE + DMSO); E, migration of cells determined by Transwell assay (*# p < 0.05, two-way ANOVA, * compared to si-TCF3 + SIRT1-NC; # compared to SIRT1-OE + DMSO); F, apoptosis rate in HeLa and SiHa cells detected by flow cytometry (*# p < 0.05, two-way ANOVA, * compared to si-TCF3 + SIRT1-NC; # compared to SIRT1-OE + DMSO). Data are expressed as the mean ± SD.

Article Snippet: The distribution image of TCF3 in CC tissues was downloaded from the Human Protein Atlas system ( https://www.proteinatlas.org/ ).

Techniques: Expressing, Western Blot, Transfection, Colony Assay, Migration, Transwell Assay, Flow Cytometry

Journal: Bioengineered

Article Title: Transcriptional factor 3 binds to sirtuin 1 to activate the Wnt/β-catenin signaling in cervical cancer

doi: 10.1080/21655979.2022.2076481

Figure Lengend Snippet: TCF3/SIRT1/β-catenin mediates CC development in vivo . A, growth rate of xenograft tumors induced by HeLa cells in nude mice (*#@ p < 0.05, two-way ANOVA; * compared to si-TCF3-NC; # compared to si-TCF3+ SIRT1-NC; @ compared to SIRT1 + DMSO); B, weight of the xenograft tumors on the 28 th day (*#@p < 0.05, one-way ANOVA; * compared to si-TCF3; # compared to si-TCF3 + SIRT1-NC; @ compared to SIRT1 + DMSO); C, expression of Ki-67 in xenograft tumors examined by IHC (*#@ p < 0.05, one-way ANOVA; * compared to si-TCF3; # compared to si-TCF3+ SIRT1-NC; @ compared to SIRT1 + DMSO). In each group, n = 5. Data are expressed as the mean ± SD.

Article Snippet: The distribution image of TCF3 in CC tissues was downloaded from the Human Protein Atlas system ( https://www.proteinatlas.org/ ).

Techniques: In Vivo, Expressing, Paraffin-embedded Immunohistochemistry

Journal: Journal of Inflammation Research

Article Title: Involvement of ICAM5 in Carcinostasis Effects on LUAD Based on the ROS1-Related Prognostic Model

doi: 10.2147/JIR.S475088

Figure Lengend Snippet: ( A ) Expression of ICAM5 in normal and tumor tissues of pan-cancer cohorts. ( B ) IHC staining images of ICAM5 in normal lung tissue and LUAD. ( C ) Differences in HLA genes expression in LUAD cohort. ( D ) Differences in immunostimulatory factors expression in LUAD cohort. ( E ) Differences in the results of the ESTIMATE algorithm in pan-cancer cohort. ( F ) Forest plot demonstrating the effect of ICAM5 expression in LUAD on OS, DSS, PFI and DFI. ( G ) KM survival analysis of OS in LUAD. ( H, I ) Enrichment plots from GSEA in the high- ICAM5 expression group and low- ICAM5 expression group. *0.01< p <0.05; **0.001< p <0.01; ***0.0001< p <0.001; **** p <0.0001; ns, not significant.

Article Snippet: Immunohistochemistry (IHC) staining images of ICAM5 from LUAD and healthy lung tissue were obtained from the Human Protein Atlas database ( https://www.proteinatlas.org/ ).

Techniques: Expressing, Immunohistochemistry