Down-Regulation of Fibroblast Growth Factor 2 (FGF2) Contributes to the Premature Senescence of Mouse Embryonic Fibroblast.

BACKGROUND Freshly isolated mouse embryonic fibroblasts (MEFs) have great proliferation capacity but quickly enter senescent state after several rounds of cell cycle, a process called premature senescence. Cellular senescence can be induced by various stresses such as telomere erosion, DNA damage, and oncogenic signaling. But the contribution of other molecules, such as growth factors, to cellular senescence is incompletely understood. This study aimed to compare the gene expression difference between non-senescent and senescent MEFs to identify the key molecule(s) involved in the spontaneous senescence of MEFs. MATERIAL AND METHODS Primary MEFs were isolated from E12.5 pregnant C57/BL6 mice. The cells were continuously cultured in Dulbecco's Modified Eagle Medium for 9 passages. SA-ß-Gal staining was used as an indicator of cell senescence. The supernatant from primary MEFs (P1 medium) or Passage 6 MEFs (P6 medium) were used to culture freshly isolated MEFs to observe the effects on cell senescence state. Gene expression profiles of primary and senescent MEFs were investigated by RNA-Seq to find the key genes involved in cell senescence. Adipocyte differentiation assay was used to evaluate the stemness of MEFs cultured in FGF2-stimulated medium. RESULTS The senescence of MEFs cultured in the P1 medium was alleviated when compared to the P6 medium. Downregulation of FGF2 expression was revealed by RNA-Seq and further confirmed by real-time quantitative polymerase chain reaction and western blot. FGF2-stimulated medium also had anti-senescence function and could maintain the differentiation ability of MEFs. CONCLUSIONS The premature senescence of MEFs was at least partially caused by FGF2 deficiency. Exogenous FGF2 could alleviate the senescent phenotype.

EBT: a statistic test identifying moderate size of significant features with balanced power and precision for genome-wide rate comparisons.

MOTIVATION: In genome-wide rate comparison studies, there is a big challenge for effective identification of an appropriate number of significant features objectively, since traditional statistical comparisons without multi-testing correction can generate a large number of false positives while multi-testing correction tremendously decreases the statistic power. RESULTS: In this study, we proposed a new exact test based on the translation of rate comparison to two binomial distributions. With modeling and real datasets, the exact binomial test (EBT) showed an advantage in balancing the statistical precision and power, by providing an appropriate size of significant features for further studies. Both correlation analysis and bootstrapping tests demonstrated that EBT is as robust as the typical rate-comparison methods, e.g. χ 2 test, Fisher's exact test and Binomial test. Performance comparison among machine learning models with features identified by different statistical tests further demonstrated the advantage of EBT. The new test was also applied to analyze the genome-wide somatic gene mutation rate difference between lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), two main lung cancer subtypes and a list of new markers were identified that could be lineage-specifically associated with carcinogenesis of LUAD and LUSC, respectively. Interestingly, three cilia genes were found selectively with high mutation rates in LUSC, possibly implying the importance of cilia dysfunction in the carcinogenesis. AVAILABILITY AND IMPLEMENTATION: An R package implementing EBT could be downloaded from the website freely: http://www.szu-bioinf.org/EBT . CONTACT: wangyj@szu.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Increased gene expression noise in human cancers is correlated with low p53 and immune activities as well as late stage cancer.

Gene expression in metazoans is delicately organized. As genetic information transmits from DNA to RNA and protein, expression noise is inevitably generated. Recent studies begin to unveil the mechanisms of gene expression noise control, but the changes of gene expression precision in pathologic conditions like cancers are unknown. Here we analyzed the transcriptomic data of human breast, liver, lung and colon cancers, and found that the expression noise of more than 74.9% genes was increased in cancer tissues as compared to adjacent normal tissues. This suggested that gene expression precision controlling collapsed during cancer development. A set of 269 genes with noise increased more than 2-fold were identified across different cancer types. These genes were involved in cell adhesion, catalytic and metabolic functions, implying the vulnerability of deregulation of these processes in cancers. We also observed a tendency of increased expression noise in patients with low p53 and immune activity in breast, liver and lung caners but not in colon cancers, which indicated the contributions of p53 signaling and host immune surveillance to gene expression noise in cancers. Moreover, more than 53.7% genes had increased noise in patients with late stage than early stage cancers, suggesting that gene expression precision was associated with cancer outcome. Together, these results provided genomic scale explorations of gene expression noise control in human cancers.

Upregulation of SOX4 antagonizes cellular senescence in esophageal squamous cell carcinoma.

Senescence, a terminal cell proliferation arrest that is caused by a variety of cellular stresses such as telomere erosion, DNA damage and oncogenic signaling, is classically considered a tumor defense barrier. However, the mechanism by which cancer cells overcome senescence is undetermined. In this study, the gene expression array data of esophageal squamous cell carcinoma (ESCC) was compared with paired normal tissues and showed that a cohort of genes, including proteinases, chemokines and inflammation factors, are upregulated in ESCC, which exhibits the senescence-associated secretory phenotype. In addition, reverse transcription-quantitative polymerase chain reaction was used to demonstrate that gender determining region Y-box 4 (SOX4) is upregulated in ESCC, and that its expression is inversely correlated with senescence markers. In addition, the knockdown of SOX4 expression by short hairpin RNA decreases ESCC cell proliferation and enhances doxorubicin-induced cell senescence. These results reveal the presence of a senescent microenvironment in ESCC, and suggest an important antisenescence role of SOX4 in ESCC progression.

Downregulation of serum brain specific microRNA is associated with inflammation and infarct volume in acute ischemic stroke.

Cerebral ischemic injury activates a robust inflammatory response, exacerbating neurological deficit. Several brain specific microRNA (miRNA) molecules have been reported to mediate functioning of the immune system, referred to as NeurimmiR. We aimed to explore possible associations between serum miRNA levels and stroke severity and their involvement in the regulation of inflammatory responses after stroke. Blood samples were obtained from 31 patients with acute ischemic stroke and 11 healthy controls. We evaluated infarct volume using diffusion weighted imaging and neurological deficit using the National Institutes of Health Stroke Scale. Serum levels of three NeurimmiR, miR-124, miR-9 and miR-219 were detected by real-time polymerase chain reaction and serum levels of metalloproteinase-9 (MMP-9), a proinflammation marker in brain injury, were examined by enzyme-linked immunosorbent assay. We found that serum miR-124 was significantly decreased within 24 hours after stroke onset and serum miR-9 was decreased in patients with larger stroke. There were no significant changes in serum miR-219. Both serum miR-124 and miR-9 levels within 24 hours were negatively correlated with infarct volume and plasma high-sensitivity C-reactive protein levels. All three NeurimmiR negatively correlated with MMP-9 levels. Our preliminary findings indicate that serum miR-124, miR-9 and miR-219 are suppressed in acute ischemic stroke thus facilitating neuroinflammation and brain injury.

Trichostatin A induces mesenchymal-like morphological change and gene expression but inhibits migration and colony formation in human cancer cells.

Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl from lysine residues in histones and other proteins, which results in gene transcriptional repression and subsequent changes in signaling events. HDACs inhibitors (HDACIs) have been used to reverse the aberrant epigenetic changes associated with cancer. However, the effects of HDACIs on epithelial-mesenchymal transition (EMT) in human cancer cells remain unclear. EMT is a fundamental process governing morphogenesis in multicellular organisms and promotes cancer invasion and metastasis. In this study, human cancer cells were treated with the HDACI trichostatin A (TSA). TSA was found to induce mesenchymal­like morphological changes in BGC-823 human gastric cancer and MCF-7 breast cancer cells, and increase the expression levels of the mesenchymal markers Vimentin and Twist. However, the expression levels of the epithelial cell marker E-cadherin were also increased in response to TSA treatment, while cell migration was reduced by TSA. Furthermore, TSA decreased cancer cell colony formation in BGC-823 and MCF-7 cells, and led to the deregulation of ß-catenin, a critical signaling molecule involved in EMT. In conclusion, the results suggested that TSA exhibits dual functions in EMT induction and inhibition in human cancer cells, but the detailed mechanisms require further investigation.

PEG10 plays a crucial role in human lung cancer proliferation, progression, prognosis and metastasis.

Paternally expressed gene 10 (PEG10) has been identified as a genetic imprinted gene, which is important for apoptosis resistance in cancer cells. Mounting evidence suggests that PEG10 is expressed in the majority of hepatocellular carcinoma (HCC) cells with growth-promoting activity. In the present study, we evaluated the correlation between PEG10 expression and the clinicopathological features of lung, breast and HCC tumors, and predicted the relationship between survival and expression levels of PEG10 in lung cancer patients. Furthermore, we chose non-small cell lung cancer cell line A549 as a model to analyze the function of PEG10 in proliferation and metastasis in vitro. Our results revealed that expression of PEG10 was closely correlated with clinical TNM grade and patient prognosis in lung cancer. PEG10 enhanced cell proliferation and promoted tumor cell migration and invasion by upregulating the expression of ß-catenin, MMP-2 and MMP-9, and decreased the expression of E-cadherin in the A549 cells. Our findings provide significant insight into the molecular mechanisms of lung cancer and offer novel ideas for designing new therapeutic targets for lung carcinoma.

An epigenetic mechanism underlying doxorubicin induced EMT in the human BGC-823 gastric cancer cell.

The epithelial to mesenchymal transition (EMT) is a key step during embryonic morphogenesis and plays an important role in drug resistance and metastasis in diverse solid tumors. We previously reported that 48 h treatment of anti-cancer drug doxorubicin could induce EMT in human gastric cancer BGC-823 cells. However, the long term effects of this transient drug treatment were unknown. In this study we found that after 48 h treatment with 0.1 µg/ml doxorubicin, most cells died during next week, while a minor population of cells survived and formed colonies. We propagated the surviving cells in drug free medium and found that these long term cultured drug survival cells (abbreviated as ltDSCs) retained a mesenchymal-like cell morphology, and expressed high levels of EMT-related molecules such as vimentin, twist and ß-catenin. The expression of chromatin reprogramming factors, Oct4 and c-myc, were also higher in ltDSCs than parental cells. We further demonstrated that the protein level of p300 was upregulated in ltDSCs, and inhibition of p300 by siRNA suppressed the expression of vimentin. Moreover, the ltDSCs had higher colony forming ability and were more drug resistant when compared to parental cells. Our results suggested that an epigenetic mechanism is involved in the EMT of ltDSCs.

Activation of ß-catenin signaling is critical for doxorubicin-induced epithelial-mesenchymal transition in BGC-823 gastric cancer cell line.

The epithelial-mesenchymal transition (EMT) is a fundamental process governing morphogenesis in multicellular organisms and has recently been implicated in promoting carcinoma invasion and metastasis. Besides their therapeutic effects, accumulating evidences suggest that chemotherapeutic agents also induced EMT and enhanced the malignancy of treated cancer cells; however, the mechanism(s) still remains unclear. Here, we investigated the role of ß-catenin signaling in doxorubicin (Dox)-induced EMT in human gastric cancer cell line BGC-823. We found that the transient treatment of Dox induced EMT and enhanced the in vitro migration ability of cancer cells. We also found that ß-catenin signaling was activated upon Dox treatment. Inhibition of ß-catenin by indomethacin (Indo) or siRNA suppressed Dox-induced EMT and decreased cancer cell migration ability. Our results showed that ß-catenin signaling was critical to Dox-induced EMT. Indo and other ß-catenin inhibitors may have a potential implication in prevention of gastric cancer metastasis.

Enhanced invasiveness in multidrug resistant leukemic cells is associated with overexpression of P-glycoprotein and cellular inhibitor of apoptosis protein.

Multidrug resistance (MDR) and multi-organ infiltration are the major obstacles to the successful treatment of leukemia. It is known that the drug efflux protein, P-glycoprotein (P-gp), and inhibitors of apoptosis proteins (IAPs) are involved in the MDR of leukemic cells, but their roles in leukemia infiltration have not been clearly elucidated. In this study, leukemic cell lines K562 and HL60 and their MDR variants K562R and HL60R have been used to analyze their infiltrative ability. MDR variants display enhanced invasion compared with parental cells. Results from xenografts in SCID (severe combined immunodeficiancy) mice are consistent with these in vitro observations. Furthermore, P-gp and cIAP are overexpressed and co-localize with protein kinase C-ε (PKC-ε) in MDR variants. Our study shows that overexpression of P-gp and cIAP may enhance the infiltration of leukemic cells.

Specific killing of CCR9 high-expressing acute T lymphocytic leukemia cells by CCL25 fused with PE38 toxin.

We have previously demonstrated that CCR9 plays a pivotal role in drug resistance and invasion in human acute T-lymphocytic leukemia (T-ALL). In this study, we investigated whether the MOLT4 cells, which naturally express CCR9 at high levels, can be successfully killed by the specific ligand, CCL25 fused to Pseudomonas exotoxin 38 (PE38) toxin. Our results demonstrated that CCL25-PE38 was able to specifically kill MOLT4 cells via apoptosis induction, and suppress the growth of CCR9(+) tumors. This work shows that CCR9 high-expressing human T-ALL cells can be successfully killed by delivering PE38 toxin fused to the ligand CCL25.