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Comparing Gene Expression (comparing + gene_expression)
Selected AbstractsIdentification of prospective factors promoting osteotropism in breast cancer: a potential role for CITED2INTERNATIONAL JOURNAL OF CANCER, Issue 4 2010Wen Min Lau Abstract Breast cancer metastases develop in the bone more frequently than any other site and are a common cause of morbidity in the form of bone pain, pathological fractures, nerve compression and life-threatening hypercalcemia. Despite ongoing research efforts, the molecular and cellular mechanisms that regulate breast cancer cell homing to and colonization of the bone as well as resultant pathological bone alteration remain poorly understood. To identify key mediators promoting breast cancer metastasis to bone, we utilized an immunocompetent, syngeneic murine model of breast cancer metastasis employing the mammary tumor cell line NT2.5. Following intracardiac injection of NT2.5 cells in neu-N mice, metastases developed in the bone, liver and lung, closely mimicking the anatomical distribution of metastases in patients with breast cancer. Using an in vivo selection process, we established NT2.5 sublines demonstrating an enhanced ability to colonize the bone and liver. Genome-wide cDNA microarray analysis comparing gene expression between parental NT2.5 cells and established sublines revealed both known and novel mediators of bone metastasis and osteolysis, including the transcriptional co-activator CITED2. In further studies, we found that expression of CITED2 was elevated in human primary breast tumors and bone metastasis compared to normal mammary epithelium and was highest in breast cancer cell lines that cause osteolytic bone metastasis in animal models. In addition, reducing CITED2 expression in NT2.5 cells inhibited the establishment of bone metastasis and osteolysis in vivo, suggesting a potential role for CITED2 in promoting breast cancer bone metastasis. [source] Adipose tissue gene expression in obese dogs after weight lossJOURNAL OF ANIMAL PHYSIOLOGY AND NUTRITION, Issue 3 2008V. Leray Summary Body weight (BW) mainly depends on a balance between fat storage (lipogenesis) and fat mobilization (lipolysis) in adipocytes. BW changes play a role in insulin resistance (IR), the inability of insulin target tissue to respond to physiological levels of insulin. This results in inhibition of lipogenesis and stimulation of lipolysis. Weight gain leads to IR whereas, weight loss improves insulin sensitivity (IS). The aim of this study was to evaluate the effect of weight loss and recovery of IS on the expression of genes involved in lipogenesis and lipolysis in weight losing dogs. Gene expression was studied in both subcutaneous and visceral adipose tissue. Obese dogs received a hypoenergetic low fat high protein diet (0.6 × NRC recommendation). Before and after weight loss, IS was assessed using the euglycaemic hyperinsulinaemic clamp. Gene expression of IRS-2, SREBP, intracellular insulin effectors, ACC, FAS, FABP, ADRP, PEPCK, lipogenesis key proteins, perilipin and HSL, lipolysis key proteins were quantified using real-time RT-PCR in subcutaneous and visceral fat. BW decreased from 15.2 ± 0.5 to 11.4 ± 0.4 kg (p < 0.05) over 78 ± 8 days. When obese, dogs were insulin resistant. After weight loss, IS was improved. In the subcutaneous adipose tissue, the expression of only the IRS-2 was increased. In the visceral adipose tissue, the expression of the genes involved in the lipogenesis was decreased whereas one of the genes implied in the lipolysis did not change. The expression profile of genes involved in lipid metabolism, as measured after weight loss, is indicative for a lower lipogenesis after weight loss than in obese dogs. Our results also confirm dramatic differences in the lipid metabolism of visceral and subcutaneous fat. They should be completed by comparing gene expression during weight losing and normal weight steady state. [source] phorest: a web-based tool for comparative analyses of expressed sequence tag dataMOLECULAR ECOLOGY RESOURCES, Issue 2 2004Dag Ahren Abstract Comparative analysis of expressed sequence tags is becoming an important tool in molecular ecology for comparing gene expression in organisms grown in certain environments. Additionally, expressed sequence tag database information can be used for the construction of DNA microarrays and for the detection of single nucleotide polymorphisms. For such applications, we present phorest, a web-based tool for managing, analysing and comparing various collections of expressed sequence tags. It is written in PHP (PHP: Hypertext Preprocessor) and runs on UNIX, Microsoft Windows and Macintosh (Mac OS X) platforms. [source] A joint transcriptomic, proteomic and metabolic analysis of maize endosperm development and starch fillingPLANT BIOTECHNOLOGY JOURNAL, Issue 9 2008Jean Louis Prioul Summary The maize endosperm transcriptome was investigated through cDNA libraries developed at three characteristic stages: (i) lag phase [10 days after pollination (DAP)]; (ii) beginning of storage (14 DAP); and (iii) maximum starch accumulation rate (21 DAP). Expressed sequence tags for 711, 757 and 384 relevant clones, respectively, were obtained and checked manually. The proportion of sequences with no clear function decreased from 35% to 20%, and a large increase in storage protein sequences (i.e. 5% to 38%) was observed from stages (i) to (iii). The remaining major categories included metabolism (11%,13%), transcription,RNA processing,protein synthesis (13%,20%), protein destination (5%,9%), cellular communication (3%,9%) and cell rescue,defence (4%). Good agreement was generally found between category rank in the 10-DAP transcriptome and the recently reported 14-DAP proteome, except that kinases and proteins for RNA processing were not detected in the latter. In the metabolism category, the respiratory pathway transcripts represented the largest proportion (25%,37%), and showed a shift in favour of glycolysis at 21 DAP. At this stage, amino acid metabolism increased to 17%, whereas starch metabolism surprisingly decreased to 7%. A second experiment focused on carbohydrate metabolism by comparing gene expression at three levels (transcripts, proteins and enzyme activities) in relation to substrate or product from 10 to 40 DAP. Here, two distinct patterns were observed: invertases and hexoses were predominant at the beginning, whereas enzyme patterns in the starch pathway, at the three levels, anticipated and paralleled starch accumulation, suggesting that, in most cases, transcriptional control is responsible for the regulation of starch biosynthesis. [source] Nephritogenic Anti-DNA antibodies regulate gene expression in MRL/lpr mouse glomerular mesangial cellsARTHRITIS & RHEUMATISM, Issue 7 2006Xiaoping Qing Objective Lupus-associated IgG anti,double-stranded DNA antibodies are thought to be pathogenic in the kidney due to cross-reaction with glomerular antigens, leading subsequently to immune complex formation in situ and complement activation. We undertook this study to determine if pathogenic anti-DNA antibodies may also contribute to renal damage by directly influencing mesangial gene expression. Methods Complementary DNA microarray gene profiling was performed in primary mesangial cells (derived from lupus-prone MRL/lpr mice) treated with pathogenic, noncomplexed anti-DNA antibodies. Significant gene up-regulation induced by anti-DNA antibodies as determined by microarray analysis was further investigated by real-time polymerase chain reaction and methods to detect the relevant proteins. Induction of proinflammatory genes by pathogenic antibodies was confirmed by comparing gene expression in glomeruli of old versus young MRL/lpr mice, and by antibody injection in vivo. Results Pathogenic, but not nonpathogenic, antibodies significantly induced a number of transcripts, including CXCL1/KC, LCN2, iNOS, CX3CL1/fractalkine, SERPINA3G, and I,B, ("marker genes"). Blocking of Fc, receptors or using Fc, chain,knockout mesangial cells had no effect on the gene regulation effect of the pathogenic antibody R4A, indicating a non,Fc-dependent mechanism. The glomerular expression of these marker genes increased over time with the development of glomerular antibody deposition and active nephritis in MRL/lpr mice. Moreover, injection of R4A into SCID mice in vivo significantly up-regulated glomerular marker gene expression. Conclusion These findings indicate that the renal pathogenicity of anti-DNA antibodies may be attributed in part to their ability to directly modulate gene expression in kidney mesangial cells through both Fc-dependent and non,Fc-dependent mechanisms. [source] | |||||||||||||