Journal: Cancers
Article Title: The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer
doi: 10.3390/cancers12051122
Figure Lengend Snippet: Increase in p53 levels and downregulation of cell cycle and DNA repair control genes following TAPIR-2 knockdown. ( A ) Differential mRNA expression following TAPIR-2 knockdown. A microarray analysis was performed 24 h after TAPIR-2 knockdowns. Data were analyzed and visualized using ReactomePA software to identify regulated target genes and cellular processes. ReactomePA is a pathway database tool used for the visualization, interpretation, and analysis of regulated pathways. A table shows all cell cycle, mitosis, and checkpoint regulated genes 24 h after TAPIR-2 knockdown. Notably, this table includes 117 of the total 276 significantly regulated genes. Adjusted p -values are given as p ≤ 0.01 (**) and p ≤ 0.001 (***). Regulatory interactions are visualized using the function cnetplot of the ReactomePA package. An enlarged version of the graph is provided as . Downregulated genes are shown in green, upregulated genes in red. Shown are the identified regulated genes of the four most regulated cellular processes: cell cycle, mitotic, m-phase, and cell cycle checkpoints. Interactions of molecules are indicated by black lines. ( B ) Heatmap of differentially up- and down-regulated TAPIR-2 target genes 24 h post siRNA transfection, determined using microarray analysis (performed in quadruplicates). Significant upregulated genes are shown in red, downregulated genes in green. Note that ~95% of the targets are downregulated. ( C ) Microarray signaling pathway impact analysis (SPIA). Transcriptome wide RNA expression patterns of siRNA treated LNCaP cells (each experiment was performed in quadruplicates) were measured using custom expression microarrays 24 h after transfection. The biological pathways extraction was done using the Kyoto Encyclopedia of Genes and Genomes (KEGG) PATHWAY database. Downregulation of cell cycle and Fanconi anemia pathway genes (left red boxes) and upregulation of the p53 signaling pathway (right red box) is shown. The false discovery rate-adjusted global probability (pGFdr) is given. ( D ) Validation of the microarray-determined expression patterns of cell cycle regulating target RNAs after TAPIR knockdown using qPCR. Total RNA was isolated from LNCaP cells 48 h post siRNA transfection and reverse transcribed into cDNA. qPCR was performed to quantify p21 CIP1 /CDKN1A, CCNB1 , CCNB2 , KIF23 , MYBL2 , CDC25C , AURKA , HISTH1B , E2F1 , and Survivin/ BIRC5 . The ∆Ct values were determined by subtracting the Ct value of the housekeeper Ct value (GAPDH). Each qPCR reaction was performed in triplicate with at least three independent biological replicates. Data are shown as means ± s.d.; Significance p ≤ 0.001 (***); two-sided student- t test. Similar data are obtained for TAPIR-1 knockdown, shown in .
Article Snippet: RNA was hybridized to Agilent Sureprint G3 Custom Exon 4 × 180k microarray (Design-ID: 058029, GEO platform ID GPL26898).
Techniques: Expressing, Microarray, Software, Transfection, RNA Expression, Isolation
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![Expression analysis of the lncRNAs TAPIR-1 and -2 shows significant overexpression in prostate cancer tissue. ( A ) Schematic representation of the chromosomal location of the TAPIR-1 and TAPIR-2 gene locus and intron exon transcript structure. Exons are represented by numbered black boxes, introns by black lines. ( B , C ) Box plot analysis for the lncRNAs TAPIR-1 ( B ), TAPIR-2 ( C ), measured by Agilent custom expression microarrays of the validation cohort only (tumor tissues from 124 PCa patients and control tissues from 39 BPH patients). The results of the exploratory cohort are shown in . ( D ) Expression patterns of TAPIR-1 ( D ), and TAPIR-2 ( B ) determined using <t>microarray</t> analyses are shown related to clinical risk classification. Normalized expression intensity [log2] was plotted against subgroups based on clinical data sets: patient risk factor (none, very low, low, and high); Gleason Score (none, =7, ≤7, >7); tumor tissue (−/+), verified tumor cell content >60% for tumor tissue (denoted with *; −/+); matched tumor adjacent tissue (−/+), verified tumor cell content 0–5% for matched tumor surrounding tissue (denoted with **; −/+); lymph node metastases (−/+), died of disease (−/+). Groups are defined as follows: BPH, PCa-risk groups: V = very low; L = low; Ms = medium, with lymph node metastases; Md = medium, with lymph node metastases and death because of disease (DoD); tumor tissue (t): H-st = high, without metastases; H-dt = high, without metastases and DoD; H+st = high with lymph node metastases; and H+dt = high, with metastases and DoD; matched tumor (free) adjacent tissue (f): H-sf = high, without metastases; H-df = high, without metastases and DoD; H+sf = high with lymph node. ***: FDR (false discovery rate) ≤0.001; #: tumor cell content 0–5%; ##: tumor cell content >60%.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_0983/pmc07280983/pmc07280983__cancers-12-01122-g001.jpg)
![Expression pattern of TAPIR-1 and -2 showing potent diagnostic properties as prostate cancer biomarker in tissue analysis. ( A ) ROC curve analysis for the lncRNAs TAPIR-1 , TAPIR-2 and the clinical PCa biomarker prostate cancer antigen 3 (PCA3) measured using Agilent custom expression microarray analysis of tissue specimens of the validation cohort (tumor tissues from 124 PCa patients and control tissues from 39 BPH patients). All three RNA markers, TAPIR-1 , TAPIR-2 , and PCA3 , revealed high PCa diagnostic AUC values of 0.94 [CI:0.91–0.97] measured by two specific custom probes; FDR (false discovery rate) ≤ 0.001, of 0.94 [CI:0.91–0.97] measured by three specific custom probes; FDR ≤ 0.001, and of 0.9 [CI:0.86–0.95] measured by three specific custom probes; FDR ≤ 0.01, respectively. ( B ) The validation cohort was stratified into patients who died of the tumor (DoD, n = 25) and patients who survived or died of other causes (alive/DoC, n = 139). Patients with benign prostate hyperplasia (BPH, n = 39) served as control group. Expression patterns of TAPIR-1 , TAPIR-2 , and PCA3 , determined using microarray analyses, are shown related to clinical classification. Normalized expression intensity [log2] was plotted against subgroups. TAPIR-lncRNAs show high expression and a high diagnostic potential even for the DoD patient group (AUC 0.98 [CI:0.96–1] and AUC 0.98 [CI:0.95–1] for TAPIR-1 and -2 , respectively) in contrast to PCA3, where the expression was significantly lowered in DoD (AUC 0.80 [CI:0.68–0.91]). ( C ) ROC curve analysis for the mRNA PCa biomarker DLX1 and HOXC6 (SelectMDx) measured by Agilent custom expression microarray analysis of tissue specimens of the validation cohort (tumor tissues from 124 PCa patients and control tissues from 39 BPH patients). DLX1 and HOXC6 revealed high PCa diagnostic AUC values of 0.94 [CI:0.91–0.97] and 0.97 [CI:0.94–0.99], respectively. These results indicate that the AUCs of lncRNA TAPIR-1 and -2 are in the same range as those mRNA PCa markers and have the potential to serve as highly sensitive and specific diagnostic markers. ( D ) ROC curve analysis of the prostate specific antigen (clinical PSA blood test) revealed an AUC value of 0.837 [CI:0.75–0.92]; FDR ≤ 0.01 in our validation cohort. ( D ) ROC curve analysis of the prostate specific antigen (clinical PSA blood test) revealed an AUC value of 0.837 [CI:0.75–0.92]; FDR ≤ 0.01 in our validation cohort.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_0983/pmc07280983/pmc07280983__cancers-12-01122-g002.jpg)
