BRB-ArrayTools is an integrated software system for the comprehensive analysis of DNA microarray experiments. It was developed by professional biostatisticians experienced in the design and analysis of DNA microarray studies and incorporates methods developed by leading statistical laboratories. The software is designed for use by biomedical scientists who wish to have access to state-of-the-art statistical methods for the analysis of gene expression data and to receive training in the statistical analysis of high dimensional data. The software provides the most extensive set of tools available for predictive classifi er development and complete cross-validation. It offers extensive links to genomic websites for gene annotation and analysis tools for pathway analysis. An archive of over 100 datasets of published microarray data with associated clinical data is provided and BRB-ArrayTools automatically imports data from the Gene Expression Omnibus public archive at the National Center for Biotechnology Information.

MicroRNAs (miRNAs) have been used as cancer-related biomarkers. Hepatocellular carcinoma (HCC) is an aggressive cancer with a dismal outcome largely due to metastasis and postsurgical recurrence. We investigated whether the expression of certain miRNAs are associated with HCC metastasis. We examined the miRNA expression profiles of 482 cancerous and noncancerous specimens from radical resection of 241 patients with HCC. Using a supervised algorithm and a clinically well-defined cohort of 131 cases, we built a unique 20-miRNA metastasis signature that could significantly predict (P < 0.001) primary HCC tissues with venous metastases from metastasis-free solitary tumors with 10-fold crossvalidation. However, significant miRNAs could not be identified from the corresponding noncancerous hepatic tissues. A survival risk prediction analysis revealed that a majority of the metastasis-related miRNAs were associated with survival. Furthermore, the 20-miRNA tumor signature was validated in 110 additional cases as a significant independent predictor of survival (P ‫؍‬ 0.009) and was significantly associated with both survival and relapse in 89 cases of early stage HCC (P ‫؍‬ 0.022 and 0.002, respectively). These 20 miRNAs may provide a simple profiling method to assist in identifying patients with HCC who are likely to develop metastases/recurrence. In addition, functional analysis of these miRNAs may enhance our biological understanding of HCC metastasis. (HEPATOLOGY 2008;47:897-907.) H epatocellular carcinoma (HCC) represents an extremely poor prognostic cancer that remains one of the most common and aggressive human malignancies worldwide. 1,2 The dismal outcome has been attributed to the major hallmarks of HCC, intrahepatic metastases or postsurgical recurrence. New tumor colonies frequently invade into the major branches of the portal vein and possibly other parts of the liver. 3-6 Resection or liver transplantation are the best options for a potential cure; however, only about 10%-20% of patients with HCC, defined by parameters of relatively normal liver function and a manageable tumor lesion as determined by the available clinical staging systems, are currently eligible for surgical intervention. Moreover, patients who were resected often have a high frequency of metastasis/recurrence, and postoperative 5-year survival is only 30%-40%.Metastasis is a complex process that involves multiple alterations. 7,8 Our understanding of such complexity has been improved by the advent of global microarray technology which allows for the molecular profiling of changes in gene expression that are associated with particular phenotypes, such as metastasis. In fact, several arraybased metastasis markers have also been demonstrated to be useful as prognostic molecular biomarkers, potentially offering additional tools for advanced diagnosis of HCC. For example, using complementary DNA (cDNA) microarray technology, we developed a unique tumor messenger RNA (mRNA) gene expression signature to predict prognosis and metastasis in pati...

When cells are challenged by hyperosmotic stress, one of the crucial adaptive responses is the expression of osmoprotective genes that are responsible for raising the intracellular level of compatible osmolytes such as sorbitol, betaine, and myo-inositol. This is achieved by the activation of the transcription factor called OREBP (also known as TonEBP or NFAT5) that specifically binds to the osmotic response element (ORE) or tonicity-responsive enhancer that enhances the transcription of these genes. Here we show that p38, a subgroup of the mitogen-activated kinases activated by hypertonic stress, and Fyn, a shrinkageactivated tyrosine kinase, are both involved in the hypertonic activation of OREBP/TonEBP. Inhibition of p38 by SB203580 or by the dominant negative p38 mutant partially blocked the hypertonic induction of ORE reporter (reporter gene regulated by ORE). Similarly, hypertonic activation of ORE reporter was partially blocked by pharmacological inhibition of Fyn or by a dominant negative Fyn and was attenuated in Fyn-deficient cells. Importantly, inhibiting p38 in Fyn-deficient cells almost completely abolished the hypertonic induction of ORE reporter activity, indicating that p38 and Fyn are the major signaling pathways for the hypertonic activation of OREBP/TonEBP. Further we show that the transactivation domain of OREBP/TonEBP is the target of p38-and Fyn-mediated hypertonic activation. These results indicate a dual control in regulating the expression of the osmoprotective genes in mammalian cells.

Aquaporin 2 (AQP2) is responsible for regulating the concentration of urine in the collecting tubules of the kidney under the control of vasopressin (Vp). Studies using Vp-deficient Brattleboro rats, however, indicated the existence of substantial Vp-independent mechanisms for membrane insertion, as well as transcriptional regulation, of this water channel. The Vp-independent mechanism(s) is clinically relevant to patients with X-linked nephrogenic diabetes insipidus (NDI) by therapeutically bypassing the dysfunctional Vp receptor. On the basis of studies with secretin receptor-null (SCTR ؊/؊ ) mice, we report here for the first time that mutation of the SCTR gene could lead to mild polydipsia and polyuria. Additionally, SCTR ؊/؊ mice were shown to have reduced renal expression of AQP2 and AQP4, as well as altered glomerular and tubular morphology, suggesting possible disturbances in the filtration and/or water reabsorption process in these animals. By using SCTR ؊/؊ mice as controls and comparing them with wild-type animals, we performed both in vivo and in vitro studies that demonstrated a role for secretin in stimulating (i) AQP2 translocation from intracellular vesicles to the plasma membrane in renal medullary tubules and (ii) expression of this water channel under hyperosmotic conditions. The present study therefore provides information for at least one of the Vp-independent mechanisms that modulate the process of renal water reabsorption. Future investigations in this direction should be important in developing therapeutic means for treating NDI patients.Secretin was originally isolated from upper intestinal mucosal extract, injection of which into the jugular vein of an anesthetized dog resulted in elevation of pancreatic and hepatic bile flow (4). The primary function of secretin in releasing bicarbonate, electrolytes, and water from pancreatic ductal epithelial cells is firmly established. Additionally, it can also stimulate electrolyte and water secretion in the epididymis, as well as bicarbonate-rich ductal bile secretion from cholangiocytes (1, 9). In cholangiocytes, a secretin-induced choleretic effect is associated with microtubule-dependent exocytotic insertion of cytoplasmic vesicles containing the water channel aquaporin 1 (AQP1) onto the apical plasma membrane (PM), leading to osmotic water movement (28). Interestingly, this type of regulated translocation of water channels has also been demonstrated in other cell types (5). For example, vasoactive intestinal polypeptide-induced translocation of AQP5 in Brunner's gland of the duodenum is associated with bicarbonate and mucin secretion, which is essential for mucosal protection (38), while Vp-and oxytocin-triggered translocation of AQP2 to and from the PM in renal collecting tubules (19, 36) is critical for renal water reabsorption. As there is considerable evidence indicating the involvement of Vp-independent mechanisms in the regulation of renal water reabsorption (19,21,25,44) and some of these mechanisms are associated with cyclic-AMP (cAMP...

Previously, exchange protein directly activated by cAMP 2 (Epac2) and PKA were known to play a role in glucose-stimulated insulin secretion (GSIS) by pancreatic β cells. The present study shows that Epac1 mRNA is also expressed by β cells. Therefore, we generated mice and embryonic stem (ES) cells with deletion of the Epac1 gene to define its role in β-cell biology and metabolism. The homozygous Epac1-knockout (Epac1(-/-)) mice developed impaired glucose tolerance and GSIS with deranged islet cytoarchitecture, which was confirmed by isolated islets from adult Epac1(-/-) mice. Moreover, Epac1(-/-) mice developed more severe hyperglycemia with increased β-cell apoptosis and insulitis after multiple low-dose streptozotocin (MLDS; 40 mg/kg) treatment than Epac1(+/+) mice. Interestingly, Epac1(-/-) mice also showed metabolic defects, including increased respiratory exchange ratio (RER) and plasma triglyceride (TG), and more severe diet-induced obesity with insulin resistance, which may contributed to β-cell dysfunction. However, islets differentiated from Epac1(-/-) ES cells showed insulin secretion defect, reduced Glut2 and PDX-1 expression, and abolished GLP-1-stimulated PCNA induction, suggesting a role of Epac1 in β-cell function. The current study provides in vitro and in vivo evidence that Epac1 has an important role in GSIS of β cells and phenotype resembling metabolic syndrome.

DLC2 (deleted in liver cancer 2), a Rho GTPase-activating protein, was previously shown to be underexpressed in human hepatocellular carcinoma and has tumor suppressor functions in cell culture models. We generated DLC2-deficient mice to investigate the tumor suppressor role of DLC2 in hepatocarcinogenesis and the function of DLC2 in vivo. In this study, we found that, unlike homologous DLC1, which is essential for embryonic development, DLC2 was dispensable for embryonic development and DLC2-deficient mice could survive to adulthood. We also did not observe a higher incidence of liver tumor formation or diethylnitrosamine (DEN)-induced hepatocarcinogenesis in DLC2-deficient mice. However, we observed that DLC2-deficient mice were smaller and had less adipose tissue than the wild type mice. These phenotypes were not due to reduction of cell size or defect in adipogenesis, as observed in the 190B RhoGAP-deficient mouse model. Together, these results suggest that deficiency in DLC2 alone does not enhance hepatocarcinogenesis.

Aim: To investigate early insulin release (EIR) and late insulin release (LIR) upon glucose challenge as well as important insulin signaling factors in differentiated insulin-producing cells from embryonic stem cells (ESCs). Methods: A recently published protocol was modified by increasing the concentration of Exendin-4 (from 0.1 nmol/L to 10 nmol/L) together with an additional 5-day culture in low glucose (5.5 mmol/L) medium after differentiation. Gene expression profile, insulin content, C-peptide, EIR and LIR were determined. Results: Compared to a lower concentration of Exendin-4 (0.1 nmol/L), a higher concentration of Exendin-4 (10 nmol/L) increased glucose-responsive insulin secretion, especially EIR. Moreover, 10 nmol/L Exendin-4 increased the expression of the following genes: insulin 1, Pdx-1 (an important transcription factor, newly recognized insulin signaling factors), Epac1 and Epac2 (exchange proteins directly activated by cAMP 1 and 2), and sulfonylurea receptor 1 (SUR1, the subunit of the K ATP channel). Conclusion: According to current knowledge, our modified protocol with a higher concentration of Exendin-4 (10 nmol/L) together with an additional 5-day 5.5 mmol/L glucose culture after differentiation improved the efficiency of differentiation toward the beta cell phenotype, which was possibly the result of stimulated expression of Pdx-1, Epac 1, and Epac 2, which in turn inhibited the K(ATP) channel through combination with SUR1, leading to increased EIR upon glucose challenge.

The sodium-dependent dicarboxylate cotransporter (NaDC1) has a proposed function of reabsorbing various Krebs cycle intermediates in the kidney and the small intestine. Since Krebs cycle intermediates have been suggested to be important for renal cell survival and recovery after hypoxia and reoxygenation, the transporter may play a role in the recovery of the kidney. Additionally, mutations in the transporter homolog in Drosophila led to fly longevity which was thought to be similar to that induced by caloric restriction (CR). To clarify the role of the sodium dicarboxylate cotransporter in vivo we generated cotransporter-deficient mice. These knockout mice excreted significantly higher amounts of various Krebs cycle intermediates in their urine; thus confirming the proposed function to reabsorb these metabolic intermediates in the kidney. No other phenotypic change was identified in these mice, however. Transporter deficiency did not affect renal function under normal physiological conditions, nor did it have an effect on renal damage and recovery from ischemic injury. Additionally, the absence of the transporter did not lead to metabolic or physiological changes associated with CR. Our results suggest that although the sodium dicarboxylate cotransporter is involved in regulating levels of various Krebs cycle intermediates in the kidney, impaired uptake of these intermediates does not significantly affect renal function under normal or ischemic stress.