C2ORF40 suppresses breast cancer cell proliferation and invasion through modulating expression of M phase cell cycle genes

Recently, it has been suggested that C2ORF40 is a candidate tumor suppressor gene in breast cancer. However, the mechanism for reduced expression of C2ORF40 and its functional role in breast cancers remain unclear. Here we show that C2ORF40 is frequently silenced in human primary breast cancers and cell lines through promoter hypermethylation. C2ORF40 mRNA level is significantly associated with patient disease-free survival and distant cancer metastasis. Overexpression of C2ORF40 inhibits breast cancer cell proliferation, migration and invasion. By contrast, silencing C2ORF40 expression promotes these biological phenotypes. Bioinformatics and FACS analysis reveal C2ORF40 functions at G2/M phase by downregulation of mitotic genes expression, including UBE2C. Our results suggest that C2ORF40 acts as a tumor suppressor gene in breast cancer pathogenesis and progression and is a candidate prognostic marker for this disease.     

Expression of genes related to the hypothalamic-pituitary-adrenal axis in murine fetal lungs in late gestation

Background  

Lung maturation is modulated by several factors, including glucocorticoids. Expression of hypothalamic-pituitary-adrenal (HPA) axis-related components, with proposed or described local regulatory systems analogous to the HPA axis, was reported in peripheral tissues. Here, HPA axis-related genes were studied in the mouse developing lung during a period overlapping the surge of surfactant production.     

Effect of protein or energy restriction during late gestation on hormonal and metabolic status in pregnant goats and postnatal male offspring

The objective of this study was to investigate the effects of maternal protein or energy restriction on hormonal and metabolic status of pregnant goats during late gestation and their postnatal male kids. Forty-five pregnant goats were fed a control (CON), 40% protein-restricted (PR) or 40% energy-restricted (ER) diet from 90 days of gestation until parturition. Plasma of mothers (90, 125 and 145 days of gestation) and kids (6 weeks of age) were sampled to determine metabolites and hormones. Glucose concentration for pregnant goats subjected to PR or ER was less (P<0.001) than that of CON goats at 125 and 145 days of gestation. However, plasma nonesterified fatty acids concentration was greater (P<0.01) at 125 and 145 days for PR and ER than CON. Protein restriction increased (P<0.01) maternal cortisol concentration by 145 days of gestation, and ER decreased (P<0.01) maternal insulin concentration at 125 days of gestation. Moreover, maternal amino acid (AA) concentrations were affected by nutritional restriction, with greater (P<0.05) total AA (TAA) and nonessential AA (NEAA) for PR goats but less (P<0.05) TAA and NEAA for ER goats at 125 days of gestation. After 6 weeks of nutritional recovery, plasma concentrations of most metabolic and hormonal parameters in restricted kids were similar to CON kids, except for reduced (P<0.05) insulin concentration in ER, and reduced (P<0.05) Asp concentration in PR and ER kids. These results provide information on potential metabolic mechanisms responsible for fetal programming.     

辛伐他汀对动脉粥样硬化大鼠凋亡相关基因Fas及FasL蛋白表达的影响

目的通过研究辛伐他汀对动脉粥样硬化大鼠血管壁中细胞凋亡相关基因Fas及FasL蛋白表达产物的影响,探讨其在预防动脉粥样硬化发生中的可能机制。方法复制动脉粥样硬化大鼠模型,以辛伐他汀干预,取胸主动脉,观察其斑块变化,采用免疫组化Elivision法测定动脉粥样硬化血管壁中Fas、FasL蛋白表达。结果Fas蛋白表达在实验组明显高于对照组及干预组(P<0.01,P<0.05),实验组FasL蛋白表达也明显高于对照组及干预组(P<0.05)。结论Fas及FasL基因通过促进细胞凋亡作用而诱发动脉粥样硬化过程,辛伐他汀可通过调节细胞凋亡过程发挥抗动脉粥样硬化作用。     

A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data

Background

Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics.

Results

We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling.

Conclusion

The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field.     

Effect of regulated expression of the fragile histidine traid gene on cell cycle and proliferation

The mechanism of tumor suppressor action of the fragile histidine triad (FHIT) gene is unknown. Disruption of cell cycle regulation leads to the tumor formation and many tumor suppressor genes suppress tumorigenesis through their effect on cell cycle regulation. We examined the expression of FHIT during the cell cycle, and determined whether overexpression of FHIT affects cell cycle kinetics and apoptosis. The FHIT cDNA was cloned into the ecdysone-inducible expression vector in both the sense and antisense orientations. Overexpression of the sense or antisense construct did not affect cell proliferation, cell cycle distribution or apoptosis in human 293T cells. Analysis of the FHIT expression in 293T cells collected at various cell cycle phases showed that the expression of FHIT is not under cell cycle regulation. These results indicate that the tumor suppressor activity of the FHIT gene may be independent of an effect on the cell cycle and apoptosis mechanisms.     

Effect of interleukin-2 on the expression of cell cycle genes in human T lymphocytes

We have studied the expression of seven cell cycle-dependent genes in phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells, in macrophage-depleted cultures and in macrophage-depleted cultures plus Interleukin-2 (IL-2). The expression of all seven genes is increased in PHA stimulated peripheral cells. Only two (2F1 and the IL-2 receptor) are increased in PHA-stimulated macrophage depleted cultures. Addition of IL-2 to these cultures increased the RNA levels of four genes (KC-1, c-myc, beta-actin and IL-2R), but has no effect on three others (4F1, 2F1, and JE-3). The results indicate that the expression of these cell cycle genes is regulated by different components of the mitogenic stimulus.     

Nucleolar silver-staining patterns related to cell cycle phase and cell generation of PHA-stimulated human lymphocytes

Silver staining (Ag-I) was used to investigate changes in the nucleolar structure of PHA-stimulated human lymphocytes through the phases of the cell cycle, G1, S and G2. Ag-I patterns and cell cycle phases of individual cells were assessed by sequential silver staining, Feulgen staining, DNA microdensitometry and 3H-thymidine autoradiography. The morphology and number of Ag-I nucleoli in a particular cell depended upon the phase of the cell cycle reached and on the number of generations the cell had passed through in culture. Resting, unstimulated cells usually had one small silver positive nucleolus. During blast transformation, the silver stained nucleoli increased in number and size, and then fused to form one very large, rounded or irregular-shaped nucleolus which was present through all cell cycle phases of the first reproductive cycle. Many lymphocytes developed a band-shaped nucleolus during their first S phase in culture. Lymphocytes at all cell cycle stages of the second and third generations after PHA-stimulation had multiple nucleoli whose combined areas approximated that of the single large nucleolus observed in first generation cells.     

Responses of intestinal morphology and function in offspring to heat stress in primiparous sows during late gestation

Late gestation is a key period for intestinal development. Maternal heat exposure may induce intestinal dysfunction of offspring. To investigate the responses of intestinal morphology and function of offspring to the maternal heat stress (HS), twelve first-parity Landrace × Large White sows were assigned to thermoneutral (TN) (18-22 °C; n = 6) or HS (28-32 °C; n = 6) treatment groups at 85 d of gestation until natural farrowing. Twenty-four newborn piglets (two piglets at medium body weight from each litter) were randomly selected and divided into in utero thermoneutral (IUTN, n = 12) and heat-stressed (IUHS, n = 12) groups according to the sow’s treatment. Blood and intestinal samples were harvested to evaluate stress hormone levels, intestinal morphology, integrity and barrier function in the newborn piglets. Our results showed that maternal HS piglets exhibited increased serum adrenocorticotropic hormone (ACTH) concentration compared with that observed in the IUTN group. IUHS piglets showed lower lactase activities in the jejunum and ileum, whereas no significant differences were found between the two groups in the length of intestine, villus length or crypt depth. Serum diamine oxidase (DAO) activity was increased in IUHS piglets. IUHS piglets also exhibited decreased ZO-1, ZO-2 and MUC2 mRNA expression in the jejunum, while the protein levels were not affected. Additionally, IUHS piglets had a lower apoptotic percentage and FAS mRNA expression in the jejunum than those in the IUTN group. Taken together, these results demonstrate that high ambient temperature during late gestation of primiparous sows causes stress response in neonatal piglets, compromising intestinal permeability and mucosal barrier function, which may be partly mediated by inducing intestinal apoptosis.     

Differing expression of genes involved in non-transferrin iron transport across plasma membrane in various cell types under iron deficiency and excess

We studied the effect of iron deficiency, i.e., 24-h preincubation in iron-free medium, and the effect of high level of non-transferrin iron, i.e., the preincubation in ferric citrate medium containing 500 muM ferric citrate, on the expression of DMT1, Dcytb, ferroportin, hephaestin, and ceruloplasmin in various functional types of human cells. The expression of these proteins potentially involved in non-transferrin iron transport across cell membranes was tested on mRNA level by quantitative real-time PCR as well as on protein level by western blot analysis in Caco-2 (colorectal carcinoma), K562 (erythroleukemia), and HEP-G2 (hepatocellular carcinoma) cells. We found that changes in non-transferrin iron availability, i.e., iron deficiency and high level of non-transferrin iron, affect the expression of tested proteins in a cell type-specific manner. We also demonstrated that changes in the expression on mRNA level do not often correlate with relevant changes on protein level.     

Chronic maternal calcium and 25-hydroxyvitamin D deficiency in Wistar rats programs abnormal hepatic gene expression leading to hepatic steatosis in female offspring

Importance of calcium and vitamin D deficiency is well established in adult dyslipidemia. We hypothesized that maternal calcium and vitamin D deficiency could alter offspring's lipid metabolism. Our objective was to investigate the effect of maternal dietary calcium and vitamin D deficiency on lipid metabolism and liver function of the F1 generation offspring. intergenerational calcium-deficient (CaD) and vitamin D-deficient (VDD) models were developed by mating normal male rats with deficient females and continuing maternal-deficient diets through pregnancy and lactation. Offspring were fed on control diet post-weaning and studied till 30 weeks. Lipid profile, serum glutamate pyruvate transaminase (SGPT), calcium and vitamin D levels were analyzed. Liver fat deposition, omega-3 fatty acids level and mRNA expression levels of peroxisome proliferator-activated receptor-alpha (PPAR-α), sterol regulatory element-binding protein 1c (SREBP-1c), interleukin 6 (IL-6), superoxide dismutase 1 (SOD-1) and uncoupling protein 2 (UCP2) were determined. Low serum vitamin D levels with an increase in SGPT and TG levels in CaD and VDD female offspring were observed. Severe liver steatosis with down-regulation of PPAR-α and UCP2 and up-regulation of SREBP-1c, IL-6 and SOD-1 was observed in the female offspring born to deficient dams. CaD and VDD male offspring showed mild steatosis and down-regulation of UCP2 and SOD-1. We conclude that maternal calcium and vitamin D deficiency programs abnormal lipid metabolism and hepatic gene expression in the F1 generation female offspring leading to hepatic steatosis, despite feeding them on control diet post-weaning.     

Differential expression of genes related to levels of mucosal cell proliferation among multiple rat strains by using oligonucleotide microarrays

Induction levels of cell proliferation, in response to gastric mucosal damage by N-methyl-N-nitro-N-nitrosoguanidine (MNNG), are different among rat strains and correlate with susceptibility to MNNG-induced gastric carcinogenesis. Here, we used oligonucleotide microarrays to search for genes that show expression levels accordant with the extents of cell proliferation among six rat strains. Expression levels of 8,800 probe sets were analyzed in the pylorus of ACI, LEW, WKY (strains with strong cell proliferation), F344, (ACI × BUF)F₁, and BUF rats (strains with weak cell proliferation) after 2-week MNNG treatment. No genes showed complete accordance, and 22 genes showed accordance with one or two exceptions. After confirmation by quantitative RT-PCR, four genes—cellular retinoic acid-binding protein II (Crabp2), fatty acid binding protein 1 (Fabp1), progastricsin (pepsinogen C, Pgc), and UDP-glucuronosyltransferase 2 family member 5 (Ugt2b5)—were found to show good accordance with only one exception. Crabp2, Fabp1, and Ugt2b5 were differentially expressed between ACI and BUF rats both before and after MNNG treatment. Although Crabp2 had been identified as one of the 16 genes differentially expressed between ACI and BUF rats with cDNA-RDA, Fabp1 and Ugt2b5 were newly identified in this study. All three genes are known to be involved in retinoic acid-mediated signaling and could be involved in the control of differential induction of cell proliferation.