sFRP-1: A functional prognostic marker for gastric cancer?

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Background: Despite being a leading cause of cancer-related death world wide, gastric adenocarcinoma (GA) lacks distinctive biomarkers and targeted therapies. Underexpression of the E-cadherin gene in GA is associated with an aggressive phenotype and a poor prognosis but the mechanisms of this difference are poorly understood. Developing effective therapies for GA requires identification of critical functional markers and deeper understanding of its pathophysiology.

Methods: Unsupervised hierarchical clustering analysis of a publicly available 230-sample GA microarray dataset identified a prominent cluster (21.7%) associated with underexpression of E-cadherin and overexpression of a Wnt-family protein: secreted frizzled-related protein 1 (sFRP-1). Archival GA specimens were then assessed for the expression of sFRP-1 by immunohistochemistry. Prognostic significance was assessed using univariate and multivariate analyses. GA cell lines transfected with sFRP-1 were used to determine the role of sFRP-1 in gastric cancer.

Results: 85 patients with GA underwent surgery with curative intent; 39 stained positive for sFRP-1 (46%). In this positive group, sFRP-1 staining was focal; was commonly found on the leading edge of the infiltrating tumor mass; and was not restricted to one histopathologic group, grade, or clinical stage. On univariate analysis T stage, nodal involvement, pathologic stage, nuclear grade, E-cadherin status and sFRP-1 status were predictive of overall survival. In a multivariate model, T stage (p < 0.001), nuclear grade (p < 0.001), E-cadherin status (p = 0.031) and sFRP-1 status (p = 0.0097) were predictive of overall survival. Overexpression of sFRP-1 in GA cell lines induced mesenchymal phenotype, enhanced growth and stem cell-like properties. sFRP-1 also attenuated Wnt signaling and E-cadherin expression, but potentiated Notch and Hedgehog signaling known to be involved in GA progression. These findings suggest a Wnt-independent mechanism mediated by sFRP-1.

Conclusions: The aggressive biological subtype of gastric cancer may be linked to overexpression of sFRP-1. Our findings identify sFRP-1 as a functional prognostic biomarker for gastric cancer, which may serve as a potential therapeutic target.

No significant financial relationships to disclose.

Clustering Scatter Plots Using Data Depth Measures

Clustering is rapidly becoming a powerful data mining technique, and has been broadly applied to many domains such as bioinformatics and text mining. However, the existing methods can only deal with a data matrix of scalars. In this paper, we introduce a hierarchical clustering procedure that can handle a data matrix of scatter plots. To more accurately reflect the nature of data, we introduce a dissimilarity statistic based on “data depth” to measure the discrepancy between two bivariate distributions without oversimplifying the nature of the underlying pattern. We then combine hypothesis testing with hierarchical clustering to simultaneously cluster the rows and columns of the data matrix of scatter plots. We also propose novel painting metrics and construct heat maps to allow visualization of the clusters. We demonstrate the utility and power of our new clustering method through simulation studies and application to a microbe-host-interaction study.

Single feature polymorphism detection using recombinant inbred line microarray expression data

MOTIVATION

The Affymetrix GeneChip microarray is currently providing a high-density and economical platform for discovery of genetic polymorphisms. Microarray data for single feature polymorphism (SFP) detection in recombinant inbred lines (RILs) can capitalize on the high level of replication available for each locus in the RIL population. It was suggested that the binding affinities from all of the RILs would form a multimodal distribution for a SFP. This motivated us to estimate the binding affinities from the robust multi-array analysis (RMA) method and formulate the SFP detection problem as a hypothesis testing problem, i.e. testing whether the underlying distribution of the estimated binding affinity (EBA) values of a probe is unimodal or multimodal.

RESULTS

We developed a bootstrap-based hypothesis testing procedure using the 'dip' statistic. Our simulation studies show that the proposed procedure can reach satisfactory detection power with false discovery rate controlled at a desired level and is robust to the unimodal distribution assumption, which facilitates wide application of the proposed procedure. Our analysis of the real data identified more than four times the SFPs compared to the previous studies, covering 96% of their findings. The constructed genetic map using the SFP markers predicted from our procedure shows over 99% concordance of the genetic orders of these markers with their known physical locations on the genome sequence.

AVAILABILITY

The R package 'dipSFP' can be downloaded from http://sites.google.com/a/bioinformatics.ucr.edu/xinping-cui/home/software.

The protein kinase Pak4 disrupts mammary acinar architecture and promotes mammary tumorigenesis

The Pak4 serine/threonine kinase is highly expressed in many cancer cell lines and human tumors. While several studies have addressed the role for Pak4 in transformation of fibroblasts, most human cancers are epithelial in origin. Epithelial cancers are associated not only with changes in cell growth, but also with changes in the cellular organization within the three dimensional (3D) architecture of the affected tissues. Here we used immortalized mouse mammary epithelial cells (iMMECs) as a model system to study the role for Pak4 in mammary tumorigenesis. iMMECs are an excellent model system for studying breast cancer they can grow in 3D-epithelial cell culture, where they form acinar structures that recapitulate in vivo mammary morphogenesis. While Pak4 is expressed at low levels in wild type iMMECs, it is overexpressed in response to oncogenes, such as oncogenic Ras and Her2/neu. Here we found that overexpression of Pak4 in iMMECs leads to changes in 3D acinar architecture that are consistent with oncogenic transformation. These include decreased central acinar cell death, abrogation of lumen formation, cell polarity alterations, and deregulation of acinar size and cell number. Furthermore, iMMECs overexpressing Pak4 form tumors when implanted into the fat pads of athymic mice. Our results suggest that overexpression of Pak4 triggers events that are important for the transformation of mammary epithelial cells. This is likely to be due to the ability of Pak4 to inhibit apoptosis and promote cell survival, and thus subsequent uncontrolled proliferation, and to its ability to deregulate cell shape and polarity.

A cellulose synthase-like protein is required for osmotic stress tolerance in Arabidopsis

Osmotic stress imposed by soil salinity and drought stress significantly affects plant growth and development, but osmotic stress sensing and tolerance mechanisms are not well understood. Forward genetic screens using a root-bending assay have previously identified salt overly sensitive (sos) mutants of Arabidopsis that fall into five loci, SOS1 to SOS5. These loci are required for the regulation of ion homeostasis or cell expansion under salt stress, but do not play a major role in plant tolerance to the osmotic stress component of soil salinity or drought. Here we report an additional sos mutant, sos6-1, which defines a locus essential for osmotic stress tolerance. sos6-1 plants are hypersensitive to salt stress and osmotic stress imposed by mannitol or polyethylene glycol in culture media or by water deficit in the soil. SOS6 encodes a cellulose synthase-like protein, AtCSLD5. Only modest differences in cell wall chemical composition could be detected, but we found that sos6-1 mutant plants accumulate high levels of reactive oxygen species (ROS) under osmotic stress and are hypersensitive to the oxidative stress reagent methyl viologen. The results suggest that SOS6/AtCSLD5 is not required for normal plant growth and development but has a critical role in osmotic stress tolerance and this function likely involves its regulation of ROS under stress.

RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis

Soil salinity limits agricultural production and is a major obstacle for feeding the growing world population. We used natural genetic variation in salt tolerance among different Arabidopsis accessions to map a major quantitative trait locus (QTL) for salt tolerance and abscisic acid (ABA) sensitivity during seed germination and early seedling growth. A recombinant inbred population derived from Landsberg erecta (Ler; salt and ABA sensitive) x Shakdara (Sha; salt and ABA resistant) was used for QTL mapping. High-resolution mapping and cloning of this QTL, Response to ABA and Salt 1 (RAS1), revealed that it is an ABA- and salt stress-inducible gene and encodes a previously undescribed plant-specific protein. A premature stop codon results in a truncated RAS1 protein in Sha. Reducing the expression of RAS1 by transfer-DNA insertion in Col or RNA interference in Ler leads to decreased salt and ABA sensitivity, whereas overexpression of the Ler allele but not the Sha allele causes increased salt and ABA sensitivity. Our results suggest that RAS1 functions as a negative regulator of salt tolerance during seed germination and early seedling growth by enhancing ABA sensitivity and that its loss of function contributes to the increased salt tolerance of Sha.

Optimized ranking and selection methods for feature selection with application in microarray experiments

In microarray experiments, the goal is often to examine many genes, and select some of them for additional investigation. Traditionally, such a selection problem has been formulated as a multiple testing problem. When the genes of interest are genes with unequal distribution of gene expression under different conditions, multiple testing methods provide an appropriate framework for addressing the selection problems. However, when the genes of interest are a set of genes with the largest difference in gene expression under different conditions, multiple testing methods do not directly address the selection goal and sometimes lead to biased conclusions. For such cases, we propose two methods based on the statistical ranking and selection framework to directly address the selection goal. The proposed methods have an inherent optimization nature in that the selection is optimized according to either a prespecified minimum correct selection ratio (r* selection) or probability of making a correct selection (P* selection). These methods are compared with the multiple testing method that controls the tail probability of the proportion of false positives. Both simulation studies and real data applications provide insight into the fundamental difference between the multiple testing methods and the proposed methods in the way of addressing different selection goals. It has been shown that the proposed methods provide a clear advantage over the multiple testing methods when the goal is to select the most significant genes (not all the significant genes). When the goal is to select all the significant genes, the proposed methods perform equally well as the current multiple testing methods. Another advantage provided by the proposed methods is their ability to detect noisy data and therefore suggest no sensible selection can be made.

Effects of surfactant replacement on alveolar overdistension and plasma cytokines in ventilator-induced lung injury

BACKGROUND

Overdistension of the lung causes ventilator-induced lung injury (VILI) accompanied by surfactant abnormalities and inflammatory changes. We investigated the effects of surfactant replacement on overdistension of the terminal airspaces and plasma cytokine levels in VILI.

METHODS

VILI was induced by high-pressure ventilation (HPV) in rats anesthetized with pentobarbital, followed by ventilation for 2 h in the maintenance mode (tidal volume=10 ml/kg, positive end-expiratory pressure = 7.5 cmH(2)O) with or without surfactant replacement. The sizes of the terminal airspaces were determined after fixing the lungs at an airway pressure of 10 cmH(2)O on deflation. Cytokine levels were assessed by enzyme-linked immunosorbent assay.

RESULTS

The mean ratio of the largest terminal airspace size class (> or = 64,000 microm(2)) was increased from 13.4% to 32.0% by HPV (P<0.05). After maintenance-mode ventilation, the ratio decreased to 16.1% with surfactant replacement (P<0.05), but increased to 44.6% without surfactant replacement (P<0.05). Mean macrophage inflammatory protein-2 (MIP-2) levels in the plasma increased from <0.02 to 6.9 ng/ml with HPV (P<0.05), and further increased to > or = 11.8 ng/ml, regardless of surfactant replacement after maintenance-mode ventilation. Similar tendencies were observed in the interleukin (IL)-6 and IL-10 levels. Tumor necrosis factor-alpha levels were almost negligible during the experiment.

CONCLUSION

In rats with VILI, surfactant replacement reversed overdistension of the terminal airspaces that may induce barotrauma, but not upregulation of MIP-2, IL-6, and IL-10 within 2 h.

Erythropoietin promotes spinal cord-derived neural progenitor cell proliferation by regulating cell cycle

Erythropoietin (EPO) regulates the proliferation and differentiation of erythroid cells by binding to its specific transmembrane receptor (EPOR). The presence of EPO and its receptor in the CNS suggests a different function for EPO other than erythropoiesis. The purpose of the present study was to examine EPOR expression and the role of EPO in the proliferation of neonatal spinal cord-derived neural progenitor cells. The effect of EPO on cell cycle progression was also examined, as well as the signaling cascades involved in this process. Our results showed that EPOR was present in the neural progenitor cells and EPO significantly enhanced their proliferation. Cell cycle analysis of EPO-treated neural progenitor cells indicated a reduced percentage of cells in G0/G1 phase, whereas the cell proliferation index (S phase plus G2/M phase) was increased. EPO also increased the proportion of 5-bromo-2-deoxyuridine (BrdU)-positive cells. With respect to the cell cycle signaling, we examined the cyclin-dependent kinases D1, D2 and E, and cyclin-dependent kinase inhibitors, p21cip1, p27kip1 and p57kip2. No significant differences were observed in the expression of these transcripts after EPO administration. Interestingly, the anti-apoptotic factors, mcl-1 and bcl-2 were significantly increased twofold. Moreover, these specific effects of EPO were eliminated by incubation of the progenitor cells with anti-EPO neutralizing antibody. Those observations suggested that EPO may play a role in normal spinal cord development by regulating cell proliferation and apoptosis.

Positive inotropic effect of PHR0007 (2-(4-(4-(Benzyloxy)-3-methoxybenzyl)piperazin-1-)-N-(1-methyl-4,5-dihydro[1,2,4]triazolo[4,3-a]quinolin-7-yl)acetamide) on atrial dynamics in beating rabbit atria

The aim of the present study was to examine the positive inotropic effects and mechanism of action of PHR0007 (2-(4-(4-(Benzyloxy)-3-methoxybenzyl)piperazin-1-)-N-(1-methyl-4,5-dihydro[1,2,4]triazolo[4,3-a]quinolin-7-yl)acetamide) on beating rabbit atria. Atria were obtained from New Zealand white rabbits, and experiments performed using a perfused beating atrial model. The effects of PHR0007 (1, 30, or 100 μmol/L), and of the protein kinase inhibitors, staurosporine (1.0 μmol/L) or H-89 (10 μmol/L), plus PHR0007 (30 μmol/L), on atrial pulse pressure and stroke volume were analyzed. PHR0007 significantly increased atrial pulse pressure and atrial stroke volume in beating rabbit atria compared with control baseline levels. These effects of PHR0007 were completely blocked by pretreatment with either staurosporine (a nonspecific protein kinase inhibitor) or H-89 (a cAMP-dependent protein kinase A inhibitor). In addition, 3-isobutyl-1-methylxanthine (IBMX), a non-specific inhibitor of phosphodiesterases (PDEs), completely blocked the positive inotropic effect of PHR0007 on atrial dynamics, but forskolin, an activator of adenylyl cyclases (AC), failed to modulate PHR0007-induced increases in atrial pulse pressure and stroke volume. In conclusion, these data suggest that PHR0007 produces a positive inotropic effect in rabbit atria via the PDE-cAMP-PKA signaling pathway.

A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development

RNA-directed DNA methylation (RdDM) is a conserved mechanism for epigenetic silencing of transposons and other repetitive elements. We report that the rdm4 (RNA-directed DNA Methylation4) mutation not only impairs RdDM, but also causes pleiotropic developmental defects in Arabidopsis. Both RNA polymerase II (Pol II)- and Pol V-dependent transcripts are affected in the rdm4 mutant. RDM4 encodes a novel protein that is conserved from yeast to humans and interacts with Pol II and Pol V in plants. Our results suggest that RDM4 functions in epigenetic regulation and plant development by serving as a transcriptional regulator for RNA Pol V and Pol II, respectively.

Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress

Background

Rice and barley are both members of Poaceae (grass family) but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley.

Results

A hierarchical clustering approach identified several interesting expression trajectories among rice and barley genotypes. There were no major conserved expression patterns between the two species in response to salt stress. A wheat salt-stress dataset was queried for comparison with rice and barley. Roughly one-third of the salt-stress responses of barley were conserved with wheat while overlap between wheat and rice was minimal. These results demonstrate that, at transcriptome level, rice is strikingly different compared to the more closely related barley and wheat. This apparent lack of analogous transcriptional programs in response to salt stress is further highlighted through close examination of genes associated with root growth and development.

Conclusion

The analysis provides support for the hypothesis that conservation of transcriptional signatures in response to environmental cues depends on the genetic similarity among the genotypes within a species, and on the phylogenetic distance between the species.

Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

BACKGROUND

A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent.

RESULTS

Expression data obtained by hybridizing RNA to an oligonucleotide array were analyzed using a statistical method called robustified projection pursuit (RPP). By applying the RPP method, a total of 1208 SFP probes were detected between two presumed parental genotypes (Pokkali and IR29) of a RIL population segregating for salt tolerance. We focused on the Saltol region, a major salt tolerance QTL. Analysis of FL478, a salt tolerant RIL, revealed a small (< 1 Mb) region carrying alleles from the presumed salt tolerant parent, flanked by alleles matching the salt sensitive parent IR29. Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.

CONCLUSION

Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the Saltol region. The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.

Role of FOXC1 in regulation of basal-like/triple-negative breast cancer

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Background: Class identification studies have proposed 3 prognostically relevant molecular subtypes of breast cancer: luminal, HER2 and basal-like. The latter is associated with poor prognosis but its molecular basis is not clear. We hypothesized a direct correlation between FOXC1 expression and basal-like breast cancer. Methods: Expression of FOXC1, CK5, CK14, EGFR, c-Kit, αB-crystallin, ITGB4 and FOXC2 in basal-like breast cancer was examined using publicly available microarray datasets. A molecular signature of 40 genes sharing co-ordinate up or down regulation with FOXC1 was identified on one microarray (49 patients) and validated on 5 other microarrays (1,232 patients). The clinical significance of FOXC1 gene expression and the FOXC1 gene signature was evaluated using censored survival data. FOXC1 protein expression was assessed by immunohistochemistry (IHC) of a 96-sample breast cancer tissue microarray. Normal breast epithelial, luminal and basal breast cancer cells transfected with FOXC1 vectors were evaluated for cell proliferation, migration and invasion. Results: FOXC1 was found to be consistently and exclusively upregulated in basal-like triple negative breast cancer and was associated with poor overall survival (p<0.0001). The FOXC1 gene signature accurately predicted the basal-like phenotype. IHC analysis of FOXC1 protein expression in human breast cancers confirmed its potential to be used as a clinical biomarker of basal-like breast cancer. Normal breast epithelial cells and luminal breast cancer cells with low or no FOXC1 expression underwent epithelial-to-mesenchymal transition and displayed increased cellular proliferation, migration, invasion, and expression of basal cell markers when FOXC1 was overexpressed. In contrast, knockdown of FOXC1 by shRNA in basal-like breast cancer cells conferred luminal phenotype. Breast cancer progression-linked signaling pathways like NF-κB and p38MAPK were significantly stimulated in basal-like breast cancer as well as by in vitro FOXC1 overexpression. Conclusions: FOXC1 is a dominant determinant of the basal-like phenotype of breast cancer. We propose FOXC1 to be the single best molecular marker of and a potential therapeutic target for basal-like / triple negative breast cancer.

No significant financial relationships to disclose.

Genetic mapping by single sperm typing

The polymerase chain reaction makes it possible to analyse DNA sequences in a single cell and has led to a new approach for constructing genetic maps. We describe a procedure called 'sperm typing' which can accurately classify individual meiotic products as recombinant of non-recombinant. This permits the linkage relationships among DNA polymorphisms to be determined without pedigree analysis.

Improved statistics for contrasting means of two samples under non-normality

This paper presents the asymptotic expansions of the distributions of the two-sample t-statistic and the Welch statistic, for testing the equality of the means of two independent populations under non-normality. Unlike other approaches, we obtain the null distributions in terms of the distribution and density functions of the standard normal variable up to n(-1), where n is the pooled sample size. Based on these expansions, monotone transformations are employed to remove the higher-order cumulant effect. We show that the new statistics can improve the precision of statistical inference to the level of o (n(-1)). Numerical studies are carried out to demonstrate the performance of the improved statistics. Some general rules for practitioners are also recommended.

Role of endothelial nitric oxide synthetase in arteriogenesis after stroke in mice

Arteriogenesis supports restored perfusion in the ischemic brain and improves long-term functional outcome after stroke. We investigate the role of endothelial nitric oxide synthetase (eNOS) and a nitric oxide (NO) donor, (Z)-1-[N-(2-aminoethyl)-N-(2-ammonioethyl) amino] diazen-1-ium-1, 2-diolate (DETA-NONOate), in promoting arteriogenesis after stroke. Adult wild-type (WT, n=18) and eNOS-knockout (eNOS(-/-), n=36) mice were subjected to transient (2.5 h) right middle cerebral artery occlusion (MCAo) and were treated with or without DETA-NONOate (0.4 mg/kg) 24 h after MCAo. Functional evaluation was performed. Animals were sacrificed 3 days after MCAo for arterial cell culture studies, or 14 days for immunohistochemical analysis. Consistent with previous studies, eNOS(-/-) mice exhibited a higher mortality rate (P<0.05, n=18/group) and more severe neurological functional deficit after MCAo than WT mice (P<0.05, n=12/group). Decreased arteriogenesis, was evident in eNOS(-/-) mice compared with WT mice, as demonstrated by reduced vascular smooth muscle cell (VSMC) proliferation, arterial density and diameter in the ischemic brain. eNOS(-/-) mice treated with DETA-NONOate had a significantly decreased mortality rate and improved functional recovery, and exhibited enhanced arteriogenesis identified by increased VSMC proliferation, and upregulated arterial density and diameter compared to eNOS(-/-) mice after stroke (P<0.05, n=12/group). To elucidate the mechanisms underlying eNOS/NO mediated arteriogenesis, VSMC migration was measured in vitro. Arterial cell migration significantly decreased in the cultured common carotid artery (CCA) derived from eNOS(-/-) mice 3 days after MCAo compared to WT arterial cells. DETA-NONOate-treatment significantly attenuated eNOS(-/-)-induced decrease of arterial cell migration compared to eNOS(-/-) control artery (P<0.05; n=6/group). Using VSMC culture, DETA-NONOate significantly increased VSMC migration, while inhibition of NOS significantly decreased VSMC migration (P<0.05; n=6/group). Our data indicated that eNOS not only promotes vascular dilation but also increases VSMC proliferation and migration, and thereby enhances arteriogenesis after stroke. Therefore, increase eNOS may play an important role in regulating of arteriogenesis after stroke.

Developmental Vitamin D Deficiency (DVD) and Brain Dopamine Ontogeny

Our group has pioneered research indicating that Developmental vitamin D (DVD) deficiency (a candidate risk factor for schizophrenia) alters both brain development and function. We have convergent evidence indicating a disturbance in dopamine signalling in this model. 1stly the superior colliculus (the proto-basal ganglia) is the initial site where the vitamin D receptor is expressed in foetal brain; 2ndly we show a reduction in Catechol-O-methyl transferase (a major metabolic enzyme for dopamine) in these foetal brains; 3rdly dopamine metabolites in the DVD deplete neonatal brain reflect this enzymatic change. When we allow these animals to mature under vitamin D normal conditions we repeatedly observe alterations in both spontaneous and psychomimetic enhanced locomotion. Consistent with the theme of persistent changes in dopamine signalling in this model we now present new data showing that dopamine transporter density and/or affinity are altered in DVD deplete female offspring whilst DA 1 receptor density and dopamine cell number are reduced in DVD deplete male offspring (all P< 0.05 n>8).

Our most recent studies indicate that Nurr-1, a nuclear transcription regulator important in both bone and dopamine neuron development and survival may be a molecular mediator of these processes. Nurr-1 is upregulated by parathyroid hormone (PTH). PTH levels are 2-3 fold greater in vitamin D deficient Dams across gestation. Most importantly we have just shown that Nurr-1 is dose-dependently upregulated by parathyroid hormone (PTH) in a neuroblastoma cell line.

Conclusions:

Our findings strongly suggest that vitamin D directly (or indirectly via PTH) mediates dopamine neuron development.