Knockdown of Cdc25B in renal cell carcinoma is associated with decreased malignant features

Flow induces common and specific transcriptional changes in renal tubular epithelial cells involving the PI3K pathway

Flow-induced shear stress affects renal epithelial cells in the nephron tubule with potential implications for differential functionalities of the individual segments. Disruptions of cellular mechanosensation or flow conditions are associated with the development and progression of various renal diseases. This study investigates the effects of flow on the transcriptome of various renal tubular epithelial cell types. We analyzed the transcriptome of induced renal epithelial cells (iREC) cultured under physiological flow (0.57 ± 0.05 dyn/cm2 ) or in static conditions for 72 h. RNA sequencing showed 861 differentially expressed genes (DEGs), with 503 up- and 358 downregulated under flow. DEGs were linked to extracellular matrix (ECM) components (e.g. Col1a1, Col4a3, Col4a4, Fn1, Smoc2), junctions (Gja1, Tubb5), channel activities (Abcc4, Aqp1), and transcription factors (Foxq1, Lgr6). Next, we performed a meta-analysis comparing our data with three published datasets that subjected epithelial cell lines from distinct segments to flow, including proximal tubule and collecting duct cells. We found that TGF-ß, p53, MAPK, and PI3K are common flow-regulated pathways. Tfrc expression and thus the capability of iron uptake is commonly upregulated under flow. Many DEGs were related to kidney diseases, such as fibrosis (e.g. Tgfb1-3 and Serpine1). To obtain further mechanistic insights we investigated the role of the PI3K pathway in flow sensing. Applying flow and inhibition of PI3K showed significantly altered expression of transcripts related to ECM remodeling, angiogenesis, and ion transport. This suggests that the PI3K pathway is a critical mediator in flow-dependent cellular processes and gene expression, potentially influencing renal development and tissue remodeling. Finally, we derived a cross-cell-line summary of common as well as segment-specific transcriptomic effects, thus providing insights into the molecular mechanisms underlying flow sensing in the nephron tubule.

Knockdown of MAPK14 inhibits the proliferation and migration of clear cell renal cell carcinoma by downregulating the expression of CDC25B

Mitogen‐activated protein kinase 14 (MAPK14), which plays an important role in DNA damage and repair, is activated by various environmental stress and proinflammatory cytokines. It is highly active in a variety of tumors, acting as a tumor promoter or suppressor, but its role in clear cell renal cell carcinoma (ccRCC) has not been elucidated. Cell division cycle 25B (CDC25B) is involved in cell cycle regulation and is highly expressed in many malignant tumors. The transcription levels of MAPK14 and CDC25B in 72 pairs of ccRCC and adjacent healthy tissues from the cancer genome atlas database and the protein expression levels in 66 pairs of clinical samples were analyzed in this study. After MAPK14 was knocked down by small interfering RNA (siRNA), P‐MAPK14 and CDC25B protein levels decreased. Subsequently, Western blot and co‐immunoprecipitation demonstrated that P‐MAPK14 could bind to CDC25B, potentially maintaining its stability. The proliferation and migration of ccRCC cell lines were suppressed by siRNA knockdown of MAPK14, however, that could be partially reversed by the overexpression of CDC25B. These results suggest that downregulation of MAPK14 and P‐MAPK14 could inhibit the proliferation and migration of ccRCC by downregulating CDC25B.

IGF2 mRNA binding protein 3 (IMP3) mediated regulation of transcriptome and translatome in glioma cells

RNA binding proteins mediate global regulation at the level of transcriptome and translatome of a cell. We studied the global level expression changes regulated by IMP3 in transcriptome and translatome by performing microarray using total cellular RNA and heavy polysome derived RNA of IMP3 silenced glioma cells respectively. Differentially regulated transcripts at the transcriptome level (n = 2388) and at the level of translatome (n = 479) were identified. Further, these transcripts were classified as direct and indirect targets on the basis of presence of IMP3 binding site. Additional investigation revealed that direct targets at transcriptome level were found to be associated with processes related to cell cycle, whereas direct targets at the translatome level participated in apoptosis related pathways. Probable mechanism of indirect regulation at both the levels is also investigated. Collectively, our study reveals multi-level gene expression regulation imposed by IMP3 in glioma cells.

Identification of Biomarkers Correlated with the TNM Staging and Overall Survival of Patients with Bladder Cancer

Objective: To identify candidate biomarkers correlated with clinical prognosis of patients with bladder cancer (BC). Methods: Weighted gene co-expression network analysis was applied to build a co-expression network to identify hub genes correlated with tumor node metastasis (TNM) staging of BC patients. Functional enrichment analysis was conducted to functionally annotate the hub genes. Protein-protein interaction network analysis of hub genes was performed to identify the interactions among the hub genes. Survival analyses were conducted to characterize the role of hub genes on the survival of BC patients. Gene set enrichment analyses were conducted to find the potential mechanisms involved in the tumor proliferation promoted by hub genes. Results: Based on the results of topological overlap measure based clustering and the inclusion criteria, top 50 hub genes were identified. Hub genes were enriched in cell proliferation associated gene ontology terms (mitotic sister chromatid segregation, mitotic cell cycle and, cell cycle, etc.) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (cell cycle, Oocyte meiosis, etc.). 17 hub genes were found to interact with ≥5 of the hub genes. Survival analysis of hub genes suggested that lower expression of MMP11, COL5A2, CDC25B, TOP2A, CENPF, CDCA3, TK1, TPX2, CDCA8, AEBP1, and FOXM1were associated with better overall survival of BC patients. BC samples with higher expression of hub genes were enriched in gene sets associated with P53 pathway, apical junction, mitotic spindle, G2M checkpoint, and myogenesis, etc. Conclusions: We identified several candidate biomarkers correlated with the TNM staging and overall survival of BC patients. Accordingly, they might be used as potential diagnostic biomarkers and therapeutic targets with clinical utility.

Identification of genes associated with renal cell carcinoma using gene expression profiling analysis

Renal cell carcinoma (RCC) is the most common type of kidney cancer in adults and accounts for ~80% of all kidney cancer cases. However, the pathogenesis of RCC has not yet been fully elucidated. To interpret the pathogenesis of RCC at the molecular level, gene expression data and bio-informatics methods were used to identify RCC associated genes. Gene expression data was downloaded from Gene Expression Omnibus (GEO) database and identified differentially coexpressed genes (DCGs) and dysfunctional pathways in RCC patients compared with controls. In addition, a regulatory network was constructed using the known regulatory data between transcription factors (TFs) and target genes in the University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) and the regulatory impact factor of each TF was calculated. A total of 258,0427 pairs of DCGs were identified. The regulatory network contained 1,525 pairs of regulatory associations between 126 TFs and 1,259 target genes and these genes were mainly enriched in cancer pathways, ErbB and MAPK. In the regulatory network, the 10 most strongly associated TFs were FOXC1, GATA3, ESR1, FOXL1, PATZ1, MYB, STAT5A, EGR2, EGR3 and PELP1. GATA3, ERG and MYB serve important roles in RCC while FOXC1, ESR1, FOXL1, PATZ1, STAT5A and PELP1 may be potential genes associated with RCC. In conclusion, the present study constructed a regulatory network and screened out several TFs that may be used as molecular biomarkers of RCC. However, future studies are needed to confirm the findings of the present study.

Consensus reference gene(s) for gene expression studies in human cancers: end of the tunnel visible?

BACKGROUND

Gene expression studies are increasingly used to provide valuable information on the diagnosis and prognosis of human cancers. Also, for in vitro and in vivo experimental cancer models gene expression studies are widely used. The complex algorithms of differential gene expression analyses require normalization of data against a reference or normalizer gene, or a set of such genes. For this purpose, mostly invariant housekeeping genes are used. Unfortunately, however, there are no consensus (housekeeping) genes that serve as reference or normalizer for different human cancers. In fact, scientists have employed a wide range of reference genes across different types of cancer for normalization of gene expression data. As a consequence, comparisons of these data and/or data harmonizations are difficult to perform and challenging. In addition, an inadequate choice for a reference gene may obscure genuine changes and/or result in erroneous gene expression data comparisons.

METHODS

In our effort to highlight the importance of selecting the most appropriate reference gene(s), we have screened the literature for gene expression studies published since the turn of the century on thirteen of the most prevalent human cancers worldwide.

CONCLUSIONS

Based on the analysis of the data at hand, we firstly recommend that in each study the suitability of candidate reference gene(s) should carefully be evaluated in order to yield reliable differential gene expression data. Secondly, we recommend that a combination of PPIA and either GAPDH, ACTB, HPRT and TBP, or appropriate combinations of two or three of these genes, should be employed in future studies, to ensure that results from different studies on different human cancers can be harmonized. This approach will ultimately increase the depth of our understanding of gene expression signatures across human cancers.

The BET bromodomain inhibitor JQ1 suppresses growth of pancreatic ductal adenocarcinoma in patient-derived xenograft models

The primary aim of this study was to evaluate the antitumor efficacy of the bromodomain inhibitor JQ1 in pancreatic ductal adenocarcinoma (PDAC) patient-derived xenograft (tumorgraft) models. A secondary aim of the study was to evaluate whether JQ1 decreases expression of the oncogene c-Myc in PDAC tumors, as has been reported for other tumor types. We used five PDAC tumorgraft models that retain specific characteristics of tumors of origin to evaluate the antitumor efficacy of JQ1. Tumor-bearing mice were treated with JQ1 (50 mg/kg daily for 21 or 28 days). Expression analyses were performed with tumors harvested from host mice after treatment with JQ1 or vehicle control. An nCounter PanCancer Pathways Panel (NanoString Technologies) of 230 cancer-related genes was used to identify gene products affected by JQ1. Quantitative RT-PCR, immunohistochemistry and immunoblots were carried out to confirm that changes in RNA expression reflected changes in protein expression. JQ1 inhibited the growth of all five tumorgraft models (P<0.05), each of which harbors a KRAS mutation; but induced no consistent change in expression of c-Myc protein. Expression profiling identified CDC25B, a regulator of cell cycle progression, as one of the three RNA species (TIMP3, LMO2 and CDC25B) downregulated by JQ1 (P<0.05). Inhibition of tumor progression was more closely related to decreased expression of nuclear CDC25B than to changes in c-Myc expression. JQ1 and other agents that inhibit the function of proteins with bromodomains merit further investigation for treating PDAC tumors. Work is ongoing in our laboratory to identify effective drug combinations that include JQ1.

MicroRNA-211, a direct negative regulator of CDC25B expression, inhibits triple-negative breast cancer cells' growth and migration

The non-coding microRNAs (miRNAs) have tissue- and disease-specific expression patterns. Dysregulation of miRNAs has been associated with initiation and progression of oncogenesis in humans. The abnormal expression of CDC25B phosphatases detected in a number of tumors implies that their dysregulation is involved in malignant transformation. Using miRNA target prediction software, we found that miR-211 could target the 3'UTR sequence of CDC25B. To shed light on their roles of miR-211 in breast cancer, the expression of miR-211 was examined by real-time RT-PCR in breast cancer and normal tissues. MiR-211 is significantly downregulated in breast cancer. MiR-211 re-expression suppressed cell growth, cell cycle, migration, and invasion in triple-negative breast cancer (TNBC) cell line MDA-MB231. Luciferase expression from a reporter vector containing the CDC25B -3'UTR was decreased when this construct was transfected with miR-211. The over-expression of miR-211 suppressed the endogenous CDC25B protein level in TNBC cells. For the first time, we demonstrate that miRNA-211 is a direct negative regulator of CDC25B expression in TNBC cells, alters other related target proteins CCNB1 and FOXM1, and then inhibits breast cancer cells growth, migration, and invasion and lead G2/M arrest. The transcriptional loss of miR-211 and the resultant increase in CDC25B expression facilitate increased genomic instability at an early stage of tumor development.

High expression of Cdc25B and low expression of 14-3-3σ is associated with the development and poor prognosis in urothelial carcinoma of bladder

Cdc25 dual-specicity phosphatases are essential regulators at critical stages of cell cycle. Cdc25B is overexpressed in several human tumor types. The activity of Cdc25B is regulated by 14-3-3 dimer. To investigate the roles of Cdc25B and 14-3-3σ in bladder carcinoma, we examined expressions of Cdc25B and 14-3-3σ proteins in bladder carcinoma and cell lines and analyzed their roles in the development and prognosis of urinary bladder carcinoma. Immunohistochmistry was used to detect the expressions of Cdc25B and 14-3-3σ in 105 bladder carcinomas. Moreover, expressions of Cdc25B and 14-3-3σ were analyzed by real-time PCR and Western blot in 40 bladder carcinomas and 20 normal epithelial tissues. Specific siRNA was used to knockdown the expression of Cdc25B or 14-3-3σ. Wild-type plasmid was used to overexpress 14-3-3σ. MTT assay and Flow cytometry were used to examine proliferation and cell cycle of bladder cancer cells. There were higher Cdc25B expression and lower 14-3-3σ expression in carcinomas than in the adjacent normal tissues (P < 0.05), positive and negative correlations being noted with clinical stage and histopathologic grade. Cdc25B expression was positively correlated with recurrence and poor prognosis. Downregulation of Cdc25B resulted in slower growth, more G2/M cells and 14-3-3σ increasing. However, upregulation and downregulation of 14-3-3σ did not affect cell growth and Cdc25B expression. It showed that Cdc25B upregulation and 14-3-3σ downregulation might promote development of bladder cancer and suggested a poor prognosis. Moreover, Cdc25B could play an important role on the bladder cancer cell proliferation and cell cycle progression and regulate expression of 14-3-3σ.

The regulatory roles of phosphatases in cancer

The relevance of potentially reversible post-translational modifications required for controlling cellular processes in cancer is one of the most thriving arenas of cellular and molecular biology. Any alteration in the balanced equilibrium between kinases and phosphatases may result in development and progression of various diseases, including different types of cancer, though phosphatases are relatively under-studied. Loss of phosphatases such as PTEN (phosphatase and tensin homologue deleted on chromosome 10), a known tumour suppressor, across tumour types lends credence to the development of phosphatidylinositol 3-kinase inhibitors alongside the use of phosphatase expression as a biomarker, though phase 3 trial data are lacking. In this review, we give an updated report on phosphatase dysregulation linked to organ-specific malignancies.

MicroRNA-141 is downregulated in human renal cell carcinoma and regulates cell survival by targeting CDC25B

Background/objective

MicroRNAs (miRNAs) are small noncoding RNAs (ribonucleic acids), approximately 22 nucleotides in length, that function as regulators of gene expression. Dysregulation of miRNAs has been associated with the initiation and progression of oncogenesis in humans. The cell division cycle (CDC)25 phosphatases are important regulators of the cell cycle. Their abnormal expression detected in a number of tumors implies that their dysregulation is involved in malignant transformation.

Methods

Using miRNA target prediction software, we found that miR-141 could target the 3′ untranslated region (3′UTR) sequence of CDC25B. To shed light on the role of miR-141 in renal cell carcinogenesis, the expression of miR-141 was examined by real-time polymerase chain reaction (RT-PCR) in renal cell carcinoma and normal tissues. The impact of miR-141 re-expression on 769-P cells was analyzed using 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and colony-forming assay. A luciferase reporter assay was applied to prove the functionality of the miR-141 binding site.

Results

miR-141 is significantly downregulated in renal cell carcinoma. miR-141 re-expression suppressed cell growth in 769-P cells. Luciferase expression from a reporter vector containing the CDC25B-3′UTR was decreased when this construct was transfected with miR-141 in 769-P cells. The overexpression of miR-141 suppressed the endogenous CDC25B protein level in 769-P cells.

Conclusion

For the first time, we demonstrated that CDC25B is a direct target of miR-141 in renal cell carcinoma. The transcriptional loss of miR-141 and the resultant increase in CDC25B expression facilitates increased genomic instability at an early stage of renal cell carcinoma development.