Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

/pdf/gene-set-enrichment-analysis-a-knowledge-based-approach-for-mbpti6qljw.pdf

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.

/pdf/limma-powers-differential-expression-analyses-for-rna-4yl7ae3arh.pdf

limma powers differential expression analyses for RNA-sequencing and microarray studies

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

http://www.klinikaikozpont.u-szeged.hu/pedia/images/pdf/CME_TEL/Full-Text/25.pdf

The Hallmarks of Aging

Obesity alters adipose tissue metabolic and endocrine function and leads to an increased release of fatty acids, hormones, and proinflammatory molecules that contribute to obesity associated complications. To further characterize the changes that occur in adipose tissue with increasing adiposity, we profiled transcript expression in perigonadal adipose tissue from groups of mice in which adiposity varied due to sex, diet, and the obesity-related mutations agouti (Ay) and obese (Lepob). We found that the expression of 1,304 transcripts correlated significantly with body mass. Of the 100 most significantly correlated genes, 30% encoded proteins that are characteristic of macrophages and are positively correlated with body mass. Immunohistochemical analysis of perigonadal, perirenal, mesenteric, and subcutaneous adipose tissue revealed that the percentage of cells expressing the macrophage marker F4/80 (F4/80+) was significantly and positively correlated with both adipocyte size and body mass. Similar relationships were found in human subcutaneous adipose tissue stained for the macrophage antigen CD68. Bone marrow transplant studies and quantitation of macrophage number in adipose tissue from macrophage-deficient (Csf1op/op) mice suggest that these F4/80+ cells are CSF-1 dependent, bone marrow-derived adipose tissue macrophages. Expression analysis of macrophage and nonmacrophage cell populations isolated from adipose tissue demonstrates that adipose tissue macrophages are responsible for almost all adipose tissue TNF-alpha expression and significant amounts of iNOS and IL-6 expression. Adipose tissue macrophage numbers increase in obesity and participate in inflammatory pathways that are activated in adipose tissues of obese individuals.

/pdf/obesity-is-associated-with-macrophage-accumulation-in-130af7ivca.pdf

Obesity is associated with macrophage accumulation in adipose tissue

Nature, 413, 179–183 (2001). In the third sentence, “hyperglycaemia” should have read “hypoglycaemia”. The corrected sentence is: "Here we show that mice carrying a targeted disruption of the cyclic AMP (cAMP) response element binding (CREB) protein gene, or overexpressing a dominant-negative CREB inhibitor, exhibit fasting hypoglycaemia and reduced expression of gluconeogenic enzymes."

/pdf/correction-creb-regulates-hepatic-gluconeogenesis-through-t44lhgtjwt.pdf

Correction: CREB regulates hepatic gluconeogenesis through the coactivator PGC-1

ELLULAR development occurs in several stages in higher eukaryotic organisms. This process is generally characterized by the loss of pluripotency and restriction of possible cell fates, leading to a highly "determined" cell that can either proliferate or differentiate into a defined end-type cell. The process of cell differentiation can be studied in many cell types, some of which offer convenient culture systems. We are particularly interested in the development of fat cells. In our studies we have had two objectives. First, to use adipocyte differentiation as a model for the process of signal transduction in cellular development, whereby extracellular stimulation leads to the ultimate expression of end-product genes, extinction of genes characteristic of the precursor cells, and phenotypic differentiation. In addition, because the adipose cell is centrally involved in certain pathological syndromes of systemic energy balance, most notably obesity, obesity-linked diabetes, and cachexia (fat and muscle wasting), we are interested in using studies of gene control to improve our understanding of these disorders. Because cancer is a disease involving loss of cellular growth control and disruption of the usual pattern of cell differentiation, there has been much interest in the role of oncogenes and their normal cellular counterparts (protooncogenes) in controlling patterns of gene expression during differentiation. Many studies using the expression of oncogenes introduced into cells have shown profound effects, either promoting or inhibiting differentiation depending on the oncogene and cellular system being analyzed (4, 5, 8, 13, 17, 19, 21, 24). One difficulty with this approach has been that the connection between the oncoprotein and the ultimate alterations in gene expression is usually not clear. We have recently approached the same goals through a different method. By studying in detail the cis- and trans-acting components involved in activating a particular gene during adipocyte differentiation, we have identified the first gene product related to an oncogene (fos) which appears to play a direct role in controlling gene expression during differentiation. This will be the major subject discussed below. Adipose Differentiation in Cultured Cell Lines The study of adipocyte development became much simpler with the isolation of preadipocyte cell lines that differentiate in culture, initially by Green and Kehinde (16) and later by many others. These lines typically resemble fibroblasts when kept in a growing state but undergo morphological and biochemical changes characteristic of fat cells when they stop growing under appropriate culture conditions. Many or most of the key enzymes of fatty acid and triglyceride synthesis are greatly increased during this process. The striking change in cell shape during adipocyte differentiation is independent of lipid accumulation; blocking triglyceride formation by depriving cells of biotin has little or no effect on the alterations in cell morphology (20). The gross changes in cell morphology are accompanied by alterations in the synthesis and assembly of cytoskeletal proteins (28). Experiments which interfered with morphological conversion using exogenous extracellular matrix components suggest that changes in cellular structure may be necessary for the programmed alterations in gene expression (29). The differentiation of adipocytes is accelerated by a number of defined or undefined factors including FCS, insulin, growth hormone, glucocorticoids, sex steroids, thyroid hormones, and indomethacin. Differentiation is inhibited by interferon, retinoic acid, interleukin-1, tumor promoters, and tumor necrosis factor. It is likely that at least some of these factors play a physiological role in adipocyte differentiation in vivo but this remains to be proven.

fos Protooncogene and the Regulation of Gene Expression in Adipocyte Differentiation

Increasing energy expenditure is an attractive approach to fighting the worldwide epidemic in obesity and type 2 diabetes. Exercise is an important component of good health and represents the first line of therapy for humans with a variety of metabolic disorders: obesity, diabetes, and nonalcoholic hepatic steatosis. Recent data has shown that exercise, besides using calories to do physical work, also causes an increase in energy expenditure through augmentation in brown fat and the browning of white fat (Fig. 1) (1,2). Indeed, these effects on brown fat could represent part of the longer-lasting benefits of exercise.



Figure 1 
Recombinant irisin regulates the thermogenic program in fat through ERK and p38 pathways. Recombinant irisin produced in yeast is glycosylated and active. It induces the thermogenic gene program in 3T3-L1 cells and primary subcutaneous adipocytes. In vivo treatments of this recombinant protein in mice show strong anti-obesity effects and improve systematic glucose homeostasis.



That brown fat, in all of its dimensions, can improve type 2 diabetes and metabolic health seems to be settled science, at least in experimental animals (3). These cells express UCP1 and have a high mitochondrial content, thereby dissipating chemical energy …

https://diabetes.diabetesjournals.org/content/diabetes/63/2/381.full.pdf

Irisin ERKs the Fat

Adipsin gene expression is greatly diminished in certain forms of genetic and acquired obesity. In the present study we evaluate the time course for the development of adipsin deficiency in obesity and its regulation by the sympathomimeticthermogenic drug mixture ephedrine and caffeine. Previously, it was unknown whether adipsin deficiency occurred before or after the development of massive obesity. In the first series of experiments in which mice were treated with monosodium glutamate (MSG) for the first week of life, we demonstrate that adipsin deficiency occurs early in the development of MSG-induced obesity as evidenced by decreased circulating adipsin concentrations by 1 week of age and deficient adipsin mRNA levels in white adipose tissue (WAT) by 2 weeks. In db/db mice, diminished circulating adipsin was noted at 2 weeks of age. In both models, decreased adipsin gene expression precedes the development of marked obesity. Little is known about the factors which regulate adipsin gene expression in ob...

Reduced adipsin expression in murine obesity: effect of age and treatment with the sympathomimetic-thermogenic drug mixture ephedrine and caffeine.

The recent recognition that humans possess active depots of brown adipose tissue has boosted the interest in this tissue as a potential target for the prevention and treatment of obesity and related metabolic disorders. Furthermore, it was also revealed that brown adipose tissue (BAT) in humans may consist of so-called beige or brite adipocytes. So far, cold exposure is recognised as the strongest activator of BAT in humans, but there is much ongoing research focused on finding alternative activators of BAT. The consequences of long-term BAT activation and/or cold exposure on metabolic health are still unknown, and this represents an area of intensive research. This is one of a series of commentaries under the banner '50 years forward', giving personal opinions on future perspectives in diabetes, to celebrate the 50th anniversary of Diabetologia (1965-2015).

/pdf/the-future-of-brown-adipose-tissues-in-the-treatment-of-type-3njdtxmnna.pdf

Bruce M. Spiegelman

Papers

Correction: CREB regulates hepatic gluconeogenesis through the coactivator PGC-1

fos Protooncogene and the Regulation of Gene Expression in Adipocyte Differentiation

Irisin ERKs the Fat

Reduced adipsin expression in murine obesity: effect of age and treatment with the sympathomimetic-thermogenic drug mixture ephedrine and caffeine.

The future of brown adipose tissues in the treatment of type 2 diabetes