Changes In Target Gene Expression Research Articles

Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer.

Prostate cancer (PCa) is the second most common solid tumor for cancer related deaths in American men. Genome wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with the increased risk of PCa. Because most of the susceptibility SNPs are located in noncoding regions, little is known about their functional mechanisms. We hypothesize that functional SNPs reside in cell type-specific regulatory elements that mediate the binding of critical transcription factors (TFs), which in turn result in changes in target gene expression. Using PCa-specific functional genomics data, here we identify 38 regulatory candidate SNPs and their target genes in PCa. Through risk analysis by incorporating gene expression and clinical data, we identify 6 target genes (ZG16B, ANKRD5, RERE, FAM96B, NAALADL2 and GTPBP10) as significant predictors of PCa biochemical recurrence. In addition, 5 SNPs (rs2659051, rs10936845, rs9925556, rs6057110 and rs2742624) are selected for experimental validation using Chromatin immunoprecipitation (ChIP), dual-luciferase reporter assay in LNCaP cells, showing allele-specific enhancer activity. Furthermore, we delete the rs2742624-containing region using CRISPR/Cas9 genome editing and observe the drastic downregulation of its target gene UPK3A. Taken together, our results illustrate that this new methodology can be applied to identify regulatory SNPs and their target genes that likely impact PCa risk. We suggest that similar studies can be performed to characterize regulatory variants in other diseases.

Abstract LB-305: A computational approach to identify recurrent somatic driver events in noncoding regions in human cancers

Abstract SNVs in non-coding regions can be relevant for cancer making it promising to search for driver somatic events within non-coding regions. For example, a number of recent studies have described the first known recurrent non-coding event in the promoter region of the TERT gene in melanoma and other cancer types (Horn et al., 2013; Huang et al., 2013; Vinagre et al., 2013). Other candidate regions (PLEKHS1, WDR74 and SDHD) were recently identified using a computational approach for which the code is not available (Weinhold et al., 2014). Currently available approaches require narrowing down the list of genomic regions by filtering by particular categories of genomic elements like promoters, enhancers or DNAse-hypersensitive sites or by proximity to TSS (Fredriksson et al., 2014). We aimed to develop a computational approach to identify somatic events in non-coding regions that are both recurrent and functionally relevant in cancer in an unbiased, genome-wide scale. Somatic mutational density in cancer is known to correlate with various genetic and epigenetic features, including replication timing, gene expression levels and chromatin states (Lawrence et al., 2013; Schuster-Böckler & Lehner, 2012; Supek et al., 2014). We made use of this prior knowledge in our approach to correct for background mutational rates and to identify recurrently mutated regions in cancer genome. Our approach uses genomic windows and employs a list of covariates to select regions with comparable genomic background mutational rates. Among these, regions that are recurrently mutated in tumors are identified, functionally annotated and tested for potential mechanisms of oncogenesis (i.e. follow-up on target gene expression changes). We performed our initial analysis on a cohort of 698 cancer genomes (Alexandrov et al., 2013; unpublished). Our computational validations on a list of 209 unpublished medulloblastoma samples demonstrate that our findings are consistent with the previous knowledge on medulloblastoma biology. For example, we identified in an unbiased way recurrent mutations in: 1) WNT signaling pathway genes (CTNNB1, SMARCA4, PTCH1) as candidates in medulloblastoma of WNT subtype; 2) previously-described TERT promoter mutations. Additionally, we identified a promising novel candidate region on chromosome 11 in lung adenocarcinoma patients. We are currently developing and extending our pipeline to test for effects of parameters choice, including those recently published, on recurrent non-coding mutations identification: for example genomic window sizes (ranging between 50 bp and 10 mb), genetic and epigenetic features correlating with recurrent somatic mutations in cancer alone and in a combination. Citation Format: Vasilisa Rudneva, Simon Anders, Wolfgang Huber, Jan Korbel. A computational approach to identify recurrent somatic driver events in noncoding regions in human cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-305. doi:10.1158/1538-7445.AM2015-LB-305

Selection of reliable reference genes for gene expression studies in Clonostachys rosea 67-1 under sclerotial induction

Reference genes are important to precisely quantify gene expression by real-time PCR. In order to identify stable and reliable expressed genes in mycoparasite Clonostachys rosea in different modes of nutrition, seven commonly used housekeeping genes, 18S rRNA, actin, β-tubulin, elongation factor 1, ubiquitin, ubiquitin-conjugating enzyme and glyceraldehyde-3-phosphate dehydrogenase, from the effective biocontrol isolate C. rosea 67-1 were tested for their expression under sclerotial induction and during vegetative growth on PDA medium. Analysis by three software programs showed that differences existed among the candidates. Elongation factor 1 was most stable; the M value in geNorm, SD value in Bestkeeper and stability value in Normfinder analysis were 0.405, 0.450 and 0.442, respectively, indicating that the gene elongation factor 1 could be used to normalize gene expression in C. rosea in both vegetative growth and parasitic process. By using elongation factor 1, the expression of a serine protease gene, sep, in different conditions was assessed, which was consistent with the transcriptomic data. This research provides an effective method to quantitate expression changes of target genes in C. rosea, and will assist in further investigation of parasitism-related genes of this fungus.

Human Gene-Centered Transcription Factor Networks for Enhancers and Disease Variants

Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions of the genome. As current GRN mapping methods test one TF at a time and require the use of cells harboring the mutation(s) of interest, they are not suitable to identify TFs that bind to wild-type and mutant loci. Here, we use gene-centered yeast one-hybrid (eY1H) assays to interrogate binding of 1,086 human TFs to 246 enhancers, as well as to 109 non-coding disease mutations. We detect both loss and gain of TF interactions with mutant loci that are concordant with target gene expression changes. This work establishes eY1H assays as a powerful addition to the toolkit of mapping human GRNs and for the high-throughput characterization of genomic variants that are rapidly being identified by genome-wide association studies.

Promoter-proximal transcription factor binding is transcriptionally active when coupled with nucleosome repositioning in immediate vicinity.

Previous studies have analyzed patterns of transcription, transcription factor (TF) binding or mapped nucleosome occupancy across the genome. These suggest that the three aspects are genetically connected but the cause and effect relationships are still unknown. For example, physiologic TF binding studies involve many TFs, consequently, it is difficult to assign nucleosome reorganization to the binding site occupancy of any particular TF. Therefore, several aspects remain unclear: does TF binding influence nucleosome (re)organizations locally or impact the chromatin landscape at a more global level; are all or only a fraction of TF binding a result of reorganization in nucleosome occupancy and do all TF binding and associated changes in nucleosome occupancy result in altered gene expression? With these in mind, following characterization of two states (before and after induction of a single TF of choice) we determined: (i) genomic binding sites of the TF, (ii) promoter nucleosome occupancy and (iii) transcriptome profiles. Results demonstrated that promoter-proximal TF binding influenced expression of the target gene when it was coupled to nucleosome repositioning at or close to its binding site in most cases. In contrast, only in few cases change in target gene expression was found when TF binding occurred without local nucleosome reorganization.

Hydrogen Sulfide Improves Drought Tolerance in Arabidopsis thaliana by MicroRNA Expressions

Hydrogen sulfide (H2S) is a gasotransmitter and plays an important role in many physiological processes in mammals. Studies of its functions in plants are attracting ever growing interest, for example, its ability to enhance drought resistance in Arabidopsis. A general role of microRNAs (miRNAs) in plant adaptive responses to drought stress has thereby increased our interest to delve into the possible interplay between H2S and miRNAs. Our results showed that treating wild type (WT) Arabidopsis seedlings with polyethylene glycol 8000 (PEG8000) to simulate drought stress caused an increase in production rate of endogenous H2S; and a significant transcriptional reformation of relevant miRNAs, which were also triggered by exogenous H2S in WT. When lcd mutants (with lower H2S production rate than WT) were treated with PEG8000, they showed lower levels of miRNA expression changes than WT. In addition, we detected significant changes in target gene expression of those miRNAs and the corresponding phenotypes in lcd, including less roots, retardation of leaf growth and development and greater superoxide dismutase (SOD) activity under drought stress. We thereby conclude that H2S can improve drought resistance through regulating drought associated miRNAs in Arabidopsis.

Gene batteries and synexpression groups applied in a multivariate statistical approach to dose–response analysis of toxicogenomic data

Univariate statistical analyses have limited strength when employed in low-dose toxicogenomic studies, due to diminished magnitudes and frequencies of gene expression responses, compounded by high data dimensionality. Analysis using co-regulated gene sets and a multivariate statistical test based upon ranks of expression were explored as means to improve statistical confidence and biological insight at low-doses. Sixteen gene regulatory groups were selected in order to investigate murine hepatic gene expression changes following low-dose oral exposure to the beta-adrenergic agonist, isoproterenol (IPR). Gene sets in this focussed analysis included well-defined gene batteries and synexpression groups with co-regulated responses to toxin exposures and linkage of chronic responses to adverse outcomes. Significant changes of target gene expression within Nfkb, Stat3 and 5′ terminal oligopryrimidine (5′TOP) batteries, as well as the acute phase and angiogenesis synexpression groups, were detected at IPR doses 100-fold lower than doses producing significant individual gene expression values. IPR-induced changes in these target gene groups were confirmed using a similar analysis of rat toxicogenomic data from published IPR-induced cardiotoxicity studies. Cumulative expression differences within gene sets were useful as aggregated metrics for benchmark dose calculations. The results supported the conclusion that toxicologically-relevant, co-regulated genes provide an effective means to reduce microarray dimensionality, thereby providing substantial statistical and interpretive power for quantitative analysis of low-dose, toxin-induced gene expression changes.

A M-MLV reverse transcriptase with reduced RNaseH activity allows greater sensitivity of gene expression detection in formalin fixed and paraffin embedded prostate cancer samples

Formalin fixed and paraffin embedded (FFPE) human tissue collections are an invaluable resource for retrospective gene expression studies. However formalin fixation results in chemical modification of RNA and increased RNA degradation. This can affect RNA yield and quality. A critical step when analysing gene expression is the conversion of RNA to complementary DNA (cDNA) using a reverse transcriptase (RT) enzyme. FFPE derived RNA may affect the performance and efficiency of the RT enzyme and cDNA synthesis. We directly compared three commonly used FFPE RNA isolation methods and measured RNA yield, purity and integrity. We also assessed the effectiveness of three commercially available Moloney Murine Leukemia Virus (M-MLV) RTs on cDNA synthesis and gene expression sensitivity when using FFPE RNA as a template. Our results show that gene detection sensitivity is dependent on the isolation method, RT and length of the PCR amplicon (<200bp) when using FFPE RNA. The use of an M-MLV RT enzyme with reduced RNaseH activity gave significantly increased qRT-PCR sensitivity when using FFPE RNA derived from prostate tissue. The choice of RT can also affect perceived changes in target gene expression and thus the same RT should be used when attempting to reproduce results from different studies. This study highlights the need to optimise and evaluate RNA isolation methods and RTs when using FFPE RNA as a template in order to maximise a successful outcome in PCR applications.

Effects of BPA and E2 on expression profiles of genes related to hypothalamic-pituitary-gonadal axis of half-smooth tongue sole Cynoglossus semilaevis

Endocrine disrupting chemicals (EDCs) are increasingly viewed as persistent pollutants, similar to natural hormones in function. This paper describes the expression profiles of 7 genes (DMRT, VTG GnRHR FSHR CYP17A CYP19A, and CYP19B) involved in sex steroid synthesis and action as well as sexual development in adult male and female Cynoglossus semilaevis, after exposure to different concentrations of Bisphenol A (BPA) and 17β-estradiol (E2). Both BPA (1, 10, 50, 125, and 250 mg/kg) and E2 (0.5, 5, and 10 mg/kg) induced changes in target gene expression, although the estrogenic effects of E2 as a model estrogen were stronger. Among the 7 genes, VTG CYP17A and CYP19 responded strongly to BPA or E2 exposure and can thus serve as reference biomarkers for estrogenic EDCs exposure in marine teleosts. These data will provide a window to establish a hypothalamic-pituitary-gonadal model in C. semilaevis to better understand the effect pathways of EDCs.

MicroRNA regulate immunological pathways in T-cells in immune thrombocytopenia (ITP)

AbstractMicroRNA are small noncoding RNA molecules that regulate gene expression. To investigate the role of microRNA in immune thrombocytopenia (ITP), we performed genome-wide expression analyses of mRNA and microRNA in T cells from ITP patients and controls. We identified 1915 regulated genes and 22 regulated microRNA that differed between ITP patients and controls. Seventeen of the 22 regulated microRNA were linked to changes in target gene expression; 57 of these target genes were associated with the immune system, eg, T-cell activation and regulation of immunoglobulin production. CXCL13 and IL-21 were two microRNA target genes significantly increased in ITP. We could demonstrate increased plasma levels of CXCL13 and others have reported increased plasma levels of interleukin-21 in ITP. Thus, regulated microRNA were significantly associated with both gene and protein expression of molecules in immunological pathways. We suggest that microRNA may be important regulatory molecules involved in the loss of tolerance in ITP.

Molecular Mechanisms of Antitumor Activity of the Selective Inhibitor of Nuclear Export (SINE) CRM1 Antagonist KPT-185 in Mantle Cell Lymphoma.

Abstract 2438CRM1, a member of the importin b super family of nuclear transport receptors, functions as a major nuclear export factor by shuttling transcription factors including p53, p21, I-kB, and FOXO3a from nucleus to cytoplasm, thereby preventing their activity. CRM1 is also involved in the transport of rRNA and a certain subset of mRNAs including Cyclin D1. Upregulated CRM1 expression has been reported to correlate with poor prognosis in various hematopoietic malignancies. MCL is a subtype of B-cell lymphoma which is frequently resistant to standard chemotherapy. The t(11,14)(q13;32) translocation of MCL juxtaposes the cyclin D1 gene, and constitutively overexpressed cyclin D1 is believed to be associated with oncogenesis. Additional genetic events such as mutation/overexpression of TP53 have been reported as adverse prognostic indicators. TP53 mutations are rare in typical MCL, although about 30% of aggressive blastoid MCL have mt-TP53. Because of the multiple signaling pathways that are dysregulated in MCL, a novel strategy aimed at restoring multiple anti-oncogenetic pathways, especially targeting p53-independent signaling pathways, is of considerable interest.In this study, we investigated the antitumor effects and molecular mechanisms of the SINE CRM1 antagonist KPT-185 (Karyopharm Therapeutics) in 4 MCL cells with known TP53 mutation status (wt-TP53: JVM2, Z138; mt-TP53: MINO, Jeko-1).Treatment with KPT-185 resulted in reduction of cell proliferation in a concentration-dependent manner without significant differences between wt- and mt-TP53 cells (IC50 at 72hrs by trypan blue exclusion method; 35nM for Z138, 92 nM for JVM2, 96 nM for MINO, 103 nM for Jeko-1). KPT-185 exhibited limited pro- apoptotic activity in the tested MCL cells except Z138 (ED50 at 48hrs by Annexin V positivity; 62 nM for Z138, 910 nM for JVM2, 665 nM for MINO, 618 nM for Jeko-1).We then investigated KPT-185-induced TP53 target gene expression changes (24 genes) by TaqMan low density arrays (TLDA) (Applied Biosystems). In wt-TP53 JVM2 and Z138 cells, KPT-185 (100nM for Z138, MINO, and 500nM for JVM2, Jeko-1) upregulated classical p53 targets such as p21 and MDM2 mRNA (>2.0 fold), while there was no increase in mt-TP53 MINO and Jeko-1 cells. Of note, in both wt- and mt-TP53 cells, KPT-185 upregulated gene expression of PUMA which is a target of FOXO3a, p73 and p53 (3.3 fold for JVM2, 2.5 fold for Z138, 3.3 fold for MINO, 4.8 fold for Jeko-1).Recently, CRM1 has been reported to positively modulate the nuclear export of Cyclin D1 mRNA in a eIF4E-dependent manner. We therefore examined Cyclin D1 protein levels by western blot analysis, and observed significantly high baseline expression of Cyclin D1 in Z-138 cells which are highly sensitive to KPT-185, as compared to less sensitive MCL cells. KPT-185 treatment decreased Cyclin D1 expression in a dose-dependent manner (50nM and 100nM) after 12hrs of treatment accompanied by p21 induction and decreased p-Rb.These findings demonstrate that KPT-185 successfully inhibits CRM1 activity in MCL resulting in inhibition of Cyclin D1 and cell proliferation, and in the p-53-independent upregulation of pro-apoptotic PUMA. In conclusion, CRM1 inhibition by KPT-185 results in cell growth inhibition and in moderate cell death in a TP-53 independent manner. Results also suggest that the sensitivity to KPT-185 in MCL may be dependent on Cyclin D1 expression. Therefore, KPT-185may be an effective agent for the treatment of MCL. Disclosures:Shacham:Karyopharm Therapeutics: Employment. Kauffman:Karyopharm Therapeutics Inc: Employment.

Dorsal-Ventral Gene Expression in the Drosophila Embryo Reflects the Dynamics and Precision of the Dorsal Nuclear Gradient

Patterning of the dorsal-ventral axis in the early Drosophila embryo depends on the nuclear distribution of the Dorsal transcription factor. Using live two-photon light-sheet microscopy, we quantified the nuclear Dorsal gradient in space and time and found that its amplitude and basal levels display oscillations throughout early embryonic development. These dynamics raise questions regarding how cells can reproducibly establish patterns of gene expression from a rapidly varying signal. We therefore quantified domains of Dorsal target genes, discovering their expression patterns are also dynamic. Computational modeling of this system reveals a correlation between Dorsal gradient dynamics and changes in target gene expression and suggests that these dynamics, together with time averaging of noise, results in the formation of graded gene expression borders in regions where the gradient is nearly flat. We propose that mRNA levels remain plastic during transient signaling events, allowing tissues to refine patterns in the face of genetic or environmental variation.

Hepatic reference gene selection in adult and juvenile female Atlantic salmon at normal and elevated temperatures

The use of quantitative real-time polymerase chain reaction (qPCR) has become widespread due to its specificity, sensitivity and apparent ease of use. However, experimental error can be introduced at many stages during sample processing and analysis, and for this reason qPCR data are often normalised to an internal reference gene. The present study used three freely available algorithms (GeNorm, NormFinder and BestKeeper) to assess the stability of hepatically expressed candidate reference genes (Hprt1, Tbp, Ef1α and β-tubulin) in two experiments. In the first, female Atlantic salmon (Salmo salar) broodstock of different ages were reared at either 14 or 22 °C for an entire reproductive season, therefore a reference gene that does not respond to thermal challenge or reproductive condition was sought. In the second, estrogen treated juvenile salmon were maintained at the same temperatures for 14 days and a reference gene that does not respond to temperature or estrogen was required. Additionally, we performed independent statistic analysis to validate the outputs obtained from the program based analysis. Based on the independent statistical analysis performed the stability of the genes tested was Tbp > Ef1α > Hprt1 > β-tubulin for the temperature/reproductive development experiment and Ef1α > Hprt1 > Tbp for the estrogen administration experiment (β-tubulin was not analysed). Results from the algorithms tested were quite ambiguous for both experiments; however all programs consistently identified the least stable candidate gene. BestKeeper provided rankings that were consistent with the independent analysis for both experiments. When an inappropriate candidate reference gene was used to normalise the expression of a hepatically expressed target gene, the ability to detect treatment-dependent changes in target gene expression was lost for multiple groups in both experiments. We have highlighted the need to independently validate the results of reference gene selection programs. In addition, we have provided a reference point for those wishing to study the effects of thermal challenge and/or hormonal treatment on gene stability in Atlantic salmon and other teleost species.

Structural features and bioavailability of four flavonoids and their implications for lifespan-extending and antioxidant actions in C. elegans

Various studies have demonstrated longevity effects of flavonoids, a major sub-group of plant polyphenolic compounds, in Caenorhabditis elegans. To better understand their structure–activity relationship in vivo we have used a comparative approach by exposing C. elegans to the structurally related flavonoids myricetin, quercetin, kaempferol and naringenin, and assessed their impact on lifespan and on putative modes of action. The bioavailability of the tested flavonoids was demonstrated by high-performance liquid chromatography with diode-array detection (HPLC/DAD) and a 2-aminoethyl diphenyl borate-based in vivo approach. While all flavonols increased lifespan in wild-type, only myricetin elongated the mev-1(kn1) lifespan, suggesting that the flavonols antioxidant action alone is not sufficient for longevity. Structural prerequisites of high antioxidant action in vitro were also essential to reduce the reactive oxygen species (ROS) load in vivo in C. elegans and were tested in isolated mouse muscle mitochondria. Since the insulin/IGF-like signaling (IIS) cascade is a key regulator of lifespan, all compounds were tested for the ability to cause nuclear translocation of the FOXO transcription factor DAF-16 and changes in target gene expression. An increased DAF-16 translocation and sod-3 promoter activity were observed with all flavonoids but was independent of their ROS scavenging capability and their effects on lifespan.

Identification of aryl hydrocarbon receptor binding targets in mouse hepatic tissue treated with 2,3,7,8-tetrachlorodibenzo- p-dioxin

Genome-wide, promoter-focused ChIP-chip analysis of hepatic aryl hydrocarbon receptor (AHR) binding sites was conducted in 8-week old female C57BL/6 treated with 30 μg/kg/body weight 2,3,7,8-tetrachlorodibenzo- p-dioxin (TCDD) for 2 h and 24 h. These studies identified 1642 and 508 AHR-bound regions at 2 h and 24 h, respectively. A total of 430 AHR-bound regions were common between the two time points, corresponding to 403 unique genes. Comparison with previous AHR ChIP-chip studies in mouse hepatoma cells revealed that only 62 of the putative target genes overlapped with the 2 h AHR-bound regions in vivo. Transcription factor binding site analysis revealed an over-representation of aryl hydrocarbon response elements (AHREs) in AHR-bound regions with 53% (2 h) and 68% (24 h) of them containing at least one AHRE. In addition to AHREs, E2f-Myc activator motifs previously implicated in AHR function, as well as a number of other motifs, including Sp1, nuclear receptor subfamily 2 factor, and early growth response factor motifs were also identified. Expression microarray studies identified 133 unique genes differentially regulated after 4 h treatment with TCDD. Of which, 39 were identified as AHR-bound genes at 2 h. Ingenuity Pathway Analysis on the 39 AHR-bound TCDD responsive genes identified potential perturbation in biological processes such as lipid metabolism, drug metabolism, and endocrine system development as a result of TCDD-mediated AHR activation. Our findings identify direct AHR target genes in vivo, highlight in vitro and in vivo differences in AHR signaling and show that AHR recruitment does not necessarily result in changes in target gene expression.

HMGA2 Overexpression-Induced Ovarian Surface Epithelial Transformation Is Mediated Through Regulation of EMT Genes

The AT-hook transcription factor HMGA2 is an oncogene involved in the tumorigenesis of many malignant neoplasms. HMGA2 overexpression is common in both early and late-stage high-grade ovarian serous papillary carcinoma. To test whether HMGA2 participates in the initiation of ovarian cancer and promotion of aggressive tumor growth, we examined the oncogenic properties of HMGA2 in ovarian surface epithelial (OSE) cell lines. We found that introduction of HMGA2 overexpression was sufficient to induce OSE transformation in vitro. HMGA2-mediated OSE transformation resulted in tumor formation in the xenografts of nude mice. By silencing HMGA2 in HMGA2-overexpressing OSE and ovarian cancer cell lines, the aggressiveness of tumor cell growth behaviors was partially suppressed. Global gene profiling analyses revealed that HMGA2-mediated tumorigenesis was associated with expression changes of target genes and microRNAs that are involved in epithelial-to-mesenchymal transition (EMT). Lumican, a tumor suppressor that inhibits EMT, was found to be transcriptionally repressed by HMGA2 and was frequently lost in human high-grade serous papillary carcinoma. Our findings show that HMGA2 overexpression confers a powerful oncogenic signal in ovarian cancers through the modulation of EMT genes.

Consequences of PPARαInvalidation on Glutathione Synthesis: Interactions with Dietary Fatty Acids

Glutathione (GSH) derives from cysteine and plays a key role in redox status. GSH synthesis is determined mainly by cysteine availability and γ-glutamate cysteine ligase (γGCL) activity. Because PPARα activation is known to control the metabolism of certain amino acids, GSH synthesis from cysteine and related metabolisms were explored in wild-type (WT) and PPARα-null (KO) mice, fed diets containing either saturated (COCO diet) or 18 : 3 n-3, LIN diet. In mice fed the COCO diet, but not in those fed the LIN diet, PPARα deficiency enhanced hepatic GSH content and γGCL activity, superoxide dismutase 2 mRNA levels, and plasma uric acid concentration, suggesting an oxidative stress. In addition, in WT mice, the LIN diet increased the hepatic GSH pool, without effect on γGCL activity, or change in target gene expression, which rules out a direct effect of PPARα. This suggests that dietary 18 : 3 n-3 may regulate GSH metabolism and thus mitigate the deleterious effects of PPARα deficiency on redox status, without direct PPARα activation.

ß-Catenin and its relation to VEGF and cyclin D1 expression in pT3 rectosigmoid cancers

β-Catenin is a critical component of the Wnt signaling pathway that regulates cell proliferation and differentiation. Wnt signaling leads to the stabilization of cytosolic β-catenin and to translocation to the nucleus, where it binds with T-cell factor and promotes the transcription and changes in target gene expression, including vascular endothelial growth factor and cyclin D1. The aim of this study was to assess the expression of cyclin D1 and vascular endothelial growth factor and to correlate them with β-catenin expression and some clinicopathologic parameters. In this study, we analyzed paraffin-embedded specimens from 42 patients with pT3 rectosigmoid cancer for β-catenin, vascular endothelial growth factor and cyclin D1 expression using immunohistochemistry. Thirty-six (85.7%) and 24 (57.1%) tumors expressed vascular endothelial growth factor and cyclin D1, respectively. Nuclear expression of β-catenin was detected in only 26.1% of tumors. It was revealed that cytoplasmic β-catenin expression was significantly related to vascular endothelial growth factor expression (p=0.011). No association was found between nuclear or cytoplasmic β-catenin and cyclin D1 expression. No significant association was seen between β-catenin, vascular endothelial growth factor or cyclin D1 expression and some investigated clinicopathologic features. Our results may contribute to knowledge regarding the functional interaction between β-catenin and vascular endothelial growth factor. We suggest that the overexpression of cyclin D1 in rectosigmoid cancers may be more complicated than purely upregulation by β-catenin. Further larger studies on Wnt/β-catenin and target gene activity and protein expression are necessary to better understand and define their roles in the pathogenesis of colorectal carcinoma.

Mechanisms associated with mitochondrial-generated reactive oxygen species in cancerThis article is one of a selection of papers published in a Special Issue on Oxidative Stress in Health and Disease.

The mitochondria are unique cellular organelles that contain their own genome and, in conjunction with the nucleus, are able to transcribe and translate genes encoding components of the electron transport chain (ETC). To do so, the mitochondria must communicate with the nucleus via the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), which are produced as a byproduct of aerobic respiration within the mitochondria. Mitochondrial signaling is proposed to be altered in cancer cells, where the mitochondria are frequently found to harbor mutations within their genome and display altered functional characteristics leading to increased glycolysis. As signaling molecules, ROS oxidize and inhibit MAPK phosphatases resulting in enhanced proliferation and survival, an effect particularly advantageous to cancer cells. In terms of transcriptional regulation, ROS affect the phosphorylation, activation, oxidation, and DNA binding of transcription factors such as AP-1, NF-kappaB, p53, and HIF-1alpha, leading to changes in target gene expression. Increased ROS production by defective cancer cell mitochondria also results in the upregulation of the transcription factor Ets-1, a factor that has been increasingly associated with aggressive cancers.

E-cadherin, β-catenin adhesion complex and relation to matrilysin expression in pT3 rectosigmoid cancers

E-cadherin/ β-catenin complex has a critical role in cell–cell adhesion. β-Catenin is a critical component of the highly conserved Wnt signaling pathway that regulates cell proliferation and differentiation. Wnt signaling leads to the stabilization of cytosolic β-catenin and to translocation to the nucleus, where it binds with T-cell factor and promotes the transcription and changes in target gene expression, including matrix metalloproteinases. In this study, we analyzed paraffin-embedded specimens from 42 patients with pT3 rectosigmoid cancer for E-cadherin, β-catenin, and matrix metalloproteinase-7(MMP-7, matrilysin) expression using immunohistochemistry. Seventy-four and 79% of tumors expressed β-catenin and E-cadherin, respectively. Nuclear expression of β-catenin was detected only in 26.1% of tumors. Forty-five percent of the rectosigmoid cancers showed strong expression of MMP-7. It was revealed that membranous or cytoplasmic β-catenin expression was significantly related to E-cadherin and MMP-7 expression. No significant association was seen between E-cadherin, β-catenin, or MMP-7 expression and some clinicopathologic features. Our results may contribute to the functional interaction between β-catenin and MMP-7. Further studies on Wnt/ β-catenin and MMP-7 gene activity and protein expression are necessary to better understand the pathogenesis of colorectal carcinoma.