Journal: Oncotarget

Article Title: Comparative evaluation of three proliferation markers, Ki-67, TOP2A, and RacGAP1, in bronchopulmonary neuroendocrine neoplasms: Issues and prospects

doi: 10.18632/oncotarget.9747

Figure Lengend Snippet: Overview of the patient population in terms of the investigated markers in the different evaluation methods. BP-NEN – bronchopulmonary neuroendocrine neoplasms; TC – typical carcinoids; AC – atypical carcinoids; SCLC – small cell lung cancer; LCNEC – large cell neuroendocrine lung carcinoma; FFPE – formalin-fixed, paraffin-embedded; TOP2A – Topoisomerase 2 alpha; RacGAP1 – Rac GTPase activating protein 1; IHC – immunohistochemistry.

Article Snippet: After dewaxing and microwaving of the sections in 10 mM citrate buffer (pH = 6.0) for 16 minutes at 600 W, the slices were incubated overnight at 4°C with the primary antibodies (Ki-67 (mouse monoclonal, 1:50, Dako Germany GmbH, Hamburg, GER), TOP2A (rabbit monoclonal, 1:100, Abcam, Cambridge, UK), RacGAP1 (rabbit polyclonal, 1:350, Atlas Antibodies, Stockholm, SWE)).

Techniques: Formalin-fixed Paraffin-Embedded, Immunohistochemistry

Journal: Oncotarget

Article Title: Comparative evaluation of three proliferation markers, Ki-67, TOP2A, and RacGAP1, in bronchopulmonary neuroendocrine neoplasms: Issues and prospects

doi: 10.18632/oncotarget.9747

Figure Lengend Snippet: The boxplots are depicting the TOP2A and RacGAP1 protein (left) and mRNA (right) levels in the different BP-NEN entities as evaluated by immunohistochemistry and RT-qPCR. To the right the respective Kaplan-Meier-Analyses of each marker in the IHC investigation are shown. Blue indicates low, green moderate and red high TOP2A/RacGAP1 expression levels, according to the cut-off limits of the ROC analysis between TC – AC and AC – SCLC. With both markers, high expression levels imply poor patient survival.

Article Snippet: After dewaxing and microwaving of the sections in 10 mM citrate buffer (pH = 6.0) for 16 minutes at 600 W, the slices were incubated overnight at 4°C with the primary antibodies (Ki-67 (mouse monoclonal, 1:50, Dako Germany GmbH, Hamburg, GER), TOP2A (rabbit monoclonal, 1:100, Abcam, Cambridge, UK), RacGAP1 (rabbit polyclonal, 1:350, Atlas Antibodies, Stockholm, SWE)).

Techniques: Immunohistochemistry, Quantitative RT-PCR, Marker, Expressing

Journal: Oncotarget

Article Title: Comparative evaluation of three proliferation markers, Ki-67, TOP2A, and RacGAP1, in bronchopulmonary neuroendocrine neoplasms: Issues and prospects

doi: 10.18632/oncotarget.9747

Figure Lengend Snippet: Spearman's rank correlations of Ki-67, TOP2A and RacGAP1 protein and mRNA levels with clinical data and extent of necrosis

Article Snippet: After dewaxing and microwaving of the sections in 10 mM citrate buffer (pH = 6.0) for 16 minutes at 600 W, the slices were incubated overnight at 4°C with the primary antibodies (Ki-67 (mouse monoclonal, 1:50, Dako Germany GmbH, Hamburg, GER), TOP2A (rabbit monoclonal, 1:100, Abcam, Cambridge, UK), RacGAP1 (rabbit polyclonal, 1:350, Atlas Antibodies, Stockholm, SWE)).

Techniques:

Journal: Oncotarget

Article Title: Comparative evaluation of three proliferation markers, Ki-67, TOP2A, and RacGAP1, in bronchopulmonary neuroendocrine neoplasms: Issues and prospects

doi: 10.18632/oncotarget.9747

Figure Lengend Snippet: Below two examples for a strong positivity of RacGAP1 protein expression at the invasive front are shown (magnification 10 × 10). The graph above depicts a Kaplan-Meier-Analysis with a high RacGAP1 protein expression (red line) and a weak/no RacGAP1 expression (blue line) at the invasive front. According to the Log-Rank Test the curves differ highly significantly: High RacGAP1 expression at the invasive front indicates poor patient prognosis.

Article Snippet: After dewaxing and microwaving of the sections in 10 mM citrate buffer (pH = 6.0) for 16 minutes at 600 W, the slices were incubated overnight at 4°C with the primary antibodies (Ki-67 (mouse monoclonal, 1:50, Dako Germany GmbH, Hamburg, GER), TOP2A (rabbit monoclonal, 1:100, Abcam, Cambridge, UK), RacGAP1 (rabbit polyclonal, 1:350, Atlas Antibodies, Stockholm, SWE)).

Techniques: Expressing

Journal: Oncotarget

Article Title: Comparative evaluation of three proliferation markers, Ki-67, TOP2A, and RacGAP1, in bronchopulmonary neuroendocrine neoplasms: Issues and prospects

doi: 10.18632/oncotarget.9747

Figure Lengend Snippet: Immunohistochemical staining of Ki-67, TOP2A and RacGAP1 at the same location of each one TC, AC, SCLC and LCNEC sample (magnification 40 × 10).

Article Snippet: After dewaxing and microwaving of the sections in 10 mM citrate buffer (pH = 6.0) for 16 minutes at 600 W, the slices were incubated overnight at 4°C with the primary antibodies (Ki-67 (mouse monoclonal, 1:50, Dako Germany GmbH, Hamburg, GER), TOP2A (rabbit monoclonal, 1:100, Abcam, Cambridge, UK), RacGAP1 (rabbit polyclonal, 1:350, Atlas Antibodies, Stockholm, SWE)).

Techniques: Immunohistochemical staining, Staining

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: Systematically profiling the expression of TRIP13 in glioma. ( A ) The expression profiles of TRIP13 mRNA in glioblastoma and normal brain tissues based on TCGA are represented. Quantification data shows the expression levels of TRIP13 in gliomas from the TCGA, GSE16011 datasets, and CGGA stratified by the IDH status ( B – D ) and WHO grade ( E – G ). ( H ) The Human Protein Atlas database shows that TRIP13 was colocalized with nucleoplasm or microtubules in the cytoplasm of A549 and U-2 OS cells. ( I , J ) Validation of TRIP13 mRNA expression and protein production in U87MG, LN229, GBM8401, U118MG, and LNZ308 glioma cell lines in comparison with normal brain tissues. ( K ) TRIP13 expression was detected in the different subcellular location of GBM in the IVY GBM dataset. * p < 0.05, *** p < 0.001, and **** p < 0.0001 compared to the normal brain tissue group. n.s: not significant.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Expressing, Biomarker Discovery, Comparison

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: TRIP13 mRNA expression was related to clinical outcome in lower-grade glioma (LGG) and glioblastoma (GBM). ( A – C ) Kaplan–Meier estimates of overall survival for ( A ) all grade, ( B ) LGG and ( C ) GBM patients in the GSE16011 data. ( D – F ) Kaplan–Meier estimates of overall survival for ( D ) all grade, ( E ) LGG and ( F ) GBM patients in the CGGA. ( G – I ) Kaplan–Meier estimates of overall survival for ( G ) all grade, ( H ) LGG and ( I ) GBM patients in the TCGA. ( J – L ) Kaplan–Meier estimates of progression-free survival for ( J ) all grade, ( K ) LGG and ( L ) GBM patients in the TCGA. ( M – O ) TRIP13 expression individual in two distinct clinical status including disease free and recurred in ( M ) all grade, ( N ) LGG and ( O ) GBM patients (TCGA, Firehose Legacy). The p -values were calculated using the log-rank test. OS, overall survival. PFS, progression-free survival.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Expressing

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: TRIP13 is preferentially expressed in recurrent glioblastoma and stem-like cell lines. ( A ) The expression profiles of TRIP13 mRNA in patients with or without radiotherapy based on TCGA lower-grade glioma (LGG) and glioblastoma (GBM) are represented. ( B ) Comparison of TRIP13 mRNA expression levels in primary and recurrent GBM in the TCGA dataset. ( C ) Comparison of TRIP13 mRNA expression levels in primary tumors ( n = 12), GS neurospheres ( n = 17) and glioblastoma stem-like cell lines ( n = 27) in the GDS3885 dataset. Correlation analysis between TRIP13 and ( D ) MKI67, ( E ) PAF, and ( F ) PROM1 mRNA expression levels in primary tumors, neurospheres and glioblastoma stem-like cell lines in the GDS3885 dataset. r, Pearson correlation coefficient. The p -value indicates the significance of the correlation.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Expressing, Comparison

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: Functional enrichment analysis associated with TRIP13 expression level in human gliomas based on three datasets (TCGA, CGGA301 and GSE16011). ( A ) Heatmaps of clinicopathological parameters, TRIP13 co-expressed genes (R > 0.6) expression based on TRIP13 expression in glioma from TCGA, CGGA301 and GSE16011 array data. ( B ) Venn analysis of TRIP13 co-expressed genes. There were 121 overlapping genes positively associated (R > 0.6) with TRIP13 in TCGA, CGGA301 and GSE16011 array data. ( C ) GO and ( D ) KEGG pathway analysis of 121 overlapping genes in TCGA, CGGA301 and GSE16011 array data. CGGA, Chinese Glioma Genome Atlas; TCGA, The Cancer Genome Atlas; GO, Gene Ontology; Mut, mutant; WT, wild type.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Functional Assay, Expressing, Mutagenesis

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: Identification of TRIP13 co-expressed genes functions and canonical pathway using IPA. ( A ) Ingenuity pathways analysis (IPA) Diseases and Functions Annotation. Bars with positive z-scores indicate that functional activity is increased (red color), whereas negative z-scores represent decreased activity (blue color). (|z-score| > 1.4, p -value < 0.0001). ( B ) Mitotic roles of polo-like kinases. TRIP13 co-expressed genes (in red) are highly expressed in all mitotic pathways involving polo-like kinases (Plks). ( C ) IPA shows canonical pathways most significantly ( p < 0.05) associated with TRIP13. The p -value for each pathway is representative of a blue bar and reported as the negative log of the p -value.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Functional Assay, Activity Assay

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: Network of interactions between the TRIP13 co-expressed genes and potential upstream regulators; confirmed relationships between TRIP13 and these regulators in TCGA-GBM database by correlation analysis. ( A ) The network was generated by the Path Designer tool of IPA. TP53, FOXM1, TCF1, E2F1 and E2F3 were the top regulators (different colors distinguish between them, with regulator–target gene connections by arrows/lines in the same colors), with high z-scores for activation. The circles represent proteins; squares indicate mRNA or genes. All mRNA for genes are displayed as expression values (low to high expression, light to dark red) from the TCGA database. ( B ) The scatter plot shows Pearson correlation (r) of TRIP13 expression with these transcription regulators.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Generated, Activation Assay, Expressing

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: GeneMANIA network of TRIP13 and its co-expressed genes. The red node is the TRIP13 gene, the yellow nodes are its co-expressed genes and the gray nodes are predicted interactors. The between-nodes edges indicate relationship types, including co-expression, co-localization, physical interaction, pathway, genetic interaction and predicted interaction, which are colored according to the legend. The thickness of edges represents interaction weight (i.e., strength of pairing relationships).

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Expressing

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: Associations among TRIP13 expression and DNA methylation and clinical characteristics in lower-grade glioma (LGG) and glioblastoma (GBM). ( A ) Visualization of the correlation between TRIP13 mRNA expression and DNA methylation in ( a ) TCGA-LGG and ( b ) TCGA-GBM cohort using the MEXPRESS program. The Pearson correlation coefficients (r) and p -value are indicated in the bottom panel. TSS, transcription start site; UTR, untranslated region. ( B ) The methylation status of TRIP13 expression in low-grade glioma ( n = 473) and GBM ( n = 106) samples in TCGA. ( C ) Correlation analysis between methylation and gene expression levels of TRIP13 of low-grade and high-grade glioma samples in TCGA. r, Pearson correlation coefficient of methylation and gene expression. P, p -value indicates the significance of the correlation. ( D , E ) Volcano plot of the distribution of all differentially expressed genes significantly associated with TRIP13 methylation of LGG and GBM samples in TCGA. The red nodes represent upregulated differentially expressed genes; the blue nodes represent downregulated differentially expressed genes. The orange nodes represent the downregulated TRIP13 co-expressed genes (LGG, n = 118; GBM, n = 14). The gray dashed line indicates the −Log 10 ( p -value) cutoff value of less than 1.30 (means p -value < 0.05). ( F ) KEGG pathway analysis in TRIP13 methylation using GSEA incorporated with LGG and GBM samples. Normalized enrichment scores and p -value corrected by FDR were calculated by GSEA. Only significantly enriched pathways (FDR adj. p -value < 0.05) are shown. Color represents the enrichment analysis results (blue, negative; red, positive). ( G , H ) Kaplan–Meier estimates of survival for LGG and GBM patients with hyper- or hypo-methylated TRIP13 in TCGA. TCGA, The Cancer Genome Atlas; GBM, glioblastoma; GSEA, gene set enrichment analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; FDR, false discovery rate.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Expressing, DNA Methylation Assay, Methylation, Gene Expression

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: The miRNAs predicted to regulate TRIP13 based on lower-grade glioma (LGG) miRNA- sequence analysis. ( A ) Venn analysis of selected miRNAs predicted interactive with TRIP13. There were 4 overlapping miRNAs significantly negatively associated (r > −0.2) with TRIP13 in LinkedOmics, miRanda and PITA datasets. ( B ) Heatmaps of miRNAs negatively correlated with TRIP13 mRNA expression in the TCGA-LGG dataset (LinkedOmics). The miR-29 family (29a, 29b, 29c) are shown significantly inversed with TRIP13 based on 512 lower-grade glioma samples. ( C ) The starBase program demonstrated that TRIP13 mRNA expression was negatively correlated with the expression of miR-29 family (522 lower-grade glioma samples). ( D ) The expression profiles of miR-29 family (29a, 29b, 29c) mRNA were validated in LGG and GBM samples, respectively, in the GSE112009 dataset.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Sequencing, Expressing

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: TRIP13 correlates with tumor aneuploidy and reduced immune expression signatures. ( A ) OncoPrint depicting somatic copy number alterations, aneuploidy score (reflecting the number of altered chromosome arms) ( a ) and overall survival time ( b , c ) using the cBioportal. The bottom-right “Kaplan–Meier curve” shows the overall survival time in TCGA-LGG ( n = 443) and GBM ( n = 458) cohorts stratified on the basis of high versus low aneuploidy score. ( B ) The plot shows the percentage of tumor samples in TCGA-LGG and GBM cohorts ( n = 507 and n = 566, respectively) versus corresponding aneuploidy score which is determined by ABSOLUTE algorithm. ( C , D ) TRIP13 expression in low and high aneuploidy levels in TCGA LGG ( n = 507) and GBM ( n = 153) samples. ( E ) The correlation analysis between the transcriptional levels of TRIP13 and aneuploidy score for GBM ( n = 153) and LGG ( n = 514) tumor samples. r, Pearson correlation coefficient. The p -value indicates the significance of the correlation. ( F ) Volcano plot of the distribution of all differentially expressed genes significantly associated with TRIP13 of ( a ) LGG and ( b ) GBM samples in TCGA. The red nodes indicate upregulated differentially expressed genes; the blue nodes indicate downregulated differentially expressed genes. Among them, the 948 genes in LGG and 402 genes in GBM are significantly negative correlated (r < −0.3) and highlighted in deep blue, and several immune-related genes (e.g., c5orf53, MAP3K5, SELL, CYLD, MAPK3 and PSTPIP1 ) are labeled on the plot. The gray dashed line indicates the –Log10 ( p -value) cutoff value of less than 1.3 (means p -value < 0.05). ( G ) The Reactome pathway analysis reveals significant enrichment of negatively correlated genes with TRIP13 involved in major immune pathways in ( a ) LGG and ( b ) GBM. The top significant term is “immune system”. ( H ) Heat map demonstrating expression (z-score in RNA-seq by Expectation-Maximization) of the top 20 genes in the “immune system” term of ( F ) based on the Pearson correlation coefficient r in ( a ) LGG and ( b ) GBM. TCGA LGG and GBM samples are ordered by TRIP13 expression level. ( I ) The expression of genes specific for distinct types of immune cells (see ) were evaluated in TCGA LGG and GBM with low or high TRIP13 levels. The legend illustrating gene symbols and expression pattern is obtained from the RNA-seq analysis (% dec., percent decrease). ( J ) The network of TRIP13 and immune-related genes based on ( I ). The blue node is TRIP13 gene, the other color nodes are immune-related genes, and the gray nodes are predicted interactors. The between-nodes edges indicate relationship types, including co-expression, co-localization, physical interaction and pathway which are colored according to the legend. The thickness of edges represents interaction weight (i.e., strength of pairing relationships).

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Expressing, Labeling, RNA Sequencing

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: Immune genes negatively correlated with TRIP13 expression in TCGA GBM and LGG samples.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Expressing

Journal: Cancers

Article Title: Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker

doi: 10.3390/cancers13102338

Figure Lengend Snippet: The ratio of immune cell type associated with TRIP13 expression and the corresponding Kaplan–Meier curves in lower-grade glioma (LGG) and glioblastoma (GBM) form TCGA. The boxplots displaying the gene expression ratio (RSEM normalization values) in LGG and GBM based on ( A , B ) CD8 + T cell-specific to Treg-specific genes, ( C , D ) anti-tumor to pro-tumor modulators specific genes and ( E , F ) M1 macrophage-specific genes to M2 macrophage-specific genes. Kaplan–Meier estimates of survival for high/low ratio of patients in TCGA LGG and GBM data based on ( G , H ) CD8 + T cell-specific to Treg-specific genes, ( I , J ) anti-tumor to pro-tumor modulators specific genes and ( K , L ) M1 macrophage-specific genes to M2 macrophage-specific genes.

Article Snippet: The primary antibodies for TRIP13 (Atlas Antibodies, STO, SWE) and GAPDH (Santa-Cruz, Dallas, TX, USA) were used.

Techniques: Expressing, Gene Expression