Application of genomic technologies:

Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees

This article focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from brain tissue to the original locations within the brain that they are derived from using digital atlas mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we highlight studies that have mined biochemical and molecular information from the hypothalamus and then lay out a strategy for how these data can be linked spatially to the mapped locations in a canonical brain atlas where the data come from, thereby allowing researchers to integrate these data with other datasets across multiple scales. A key methodology that enables atlas-based mapping of extracted datasets-laser-capture microdissection-is discussed in detail, with a view of how this technology is a bridge between systems biology and systems neuroscience.

Adipose Gene Expression Patterns of Weight Gain Suggest Counteracting Steroid Hormone Synthesis

OBJECTIVE

To identify early molecular changes in weight gain, using analysis of gene expression changes in adipose tissue of mice fed well-defined humanized (Western) high-fat and low-fat (control) diets during a short (3- to 5-week) time interval.

RESEARCH METHODS AND PROCEDURES

An adipose-enriched cDNA microarray was constructed and used for the expression analyses of visceral adipose tissues of wildtype young adult C57BL/6J male mice on different diets.

RESULTS

Mice on a high-fat diet had significantly higher body weight (at most, 9.6% greater) and adipose tissue weights compared with mice on a control diet. Gene expression analyses revealed 31 transcripts significantly differentially expressed in visceral adipose tissue between the diet groups. Most of these genes were expressed more on the high-fat diet. They mainly encode proteins involved in cellular structure (e.g., myosin, procollagen, vimentin) and lipid metabolism (e.g., leptin, lipoprotein lipase, carbonic anhydrase 3). This increase in gene expression was accompanied by a decrease in oxidative phosphorylation and carbohydrate metabolism (ATP citrate lyase). Importantly, genes belonging to steroid hormone biosynthesis (3beta-hydroxysteroid dehydrogenase-1, cholesterol side-chain cleavage cytochrome P450, and steroid-11beta-hydroxylase) were all expressed less in mice on a high-fat diet.

DISCUSSION

A short time period of 3 to 5 weeks of high-fat feeding altered gene expression patterns in visceral adipose tissue in male mice. Gene expression changes indicate initiation of adipose tissue enlargement and the down-regulation of adipose steroid hormone biosynthesis. The latter suggests a mechanism by which initial progression toward weight gain is counteracted.

Biological assessment of robust noise models in microarray data analysis

Motivation: Although several recently proposed analysis packages for microarray data can cope with heavy-tailed noise, many applications rely on Gaussian assumptions. Gaussian noise models foster computational efficiency. This comes, however, at the expense of increased sensitivity to outlying observations. Assessing potential insufficiencies of Gaussian noise in microarray data analysis is thus important and of general interest.

Results: We propose to this end assessing different noise models on a large number of microarray experiments. The goodness of fit of noise models is quantified by a hierarchical Bayesian analysis of variance model, which predicts normalized expression values as a mixture of a Gaussian density and t-distributions with adjustable degrees of freedom. Inference of differentially expressed genes is taken into consideration at a second mixing level. For attaining far reaching validity, our investigations cover a wide range of analysis platforms and experimental settings. As the most striking result, we find irrespective of the chosen preprocessing and normalization method in all experiments that a heavy-tailed noise model is a better fit than a simple Gaussian. Further investigations revealed that an appropriate choice of noise model has a considerable influence on biological interpretations drawn at the level of inferred genes and gene ontology terms. We conclude from our investigation that neglecting the over dispersed noise in microarray data can mislead scientific discovery and suggest that the convenience of Gaussian-based modelling should be replaced by non-parametric approaches or other methods that account for heavy-tailed noise.

Contact:peter.sykacek@boku.ac.at

Availability:http://bioinf.boku.ac.at/alexp/robmca.html.

DNA microarrays to define and search for genes associated with obesity

One of the major goals of this review was to identify obesity-specific gene profiles in animal models to help comprehend the pathogenic mechanisms and the prediction of the phenotypic outcomes of obesity and its associated metabolic diseases. The genomic examination of insulin-sensitive tissues, such as the adipose and hepatic tissues, has provided a wealth of information about the changes in gene expression in obesity and its associated metabolic diseases. The overexpression of genes related to inflammation, immune response, adhesion molecules, and lipid metabolism is a major characteristic of white adipose tissue, while the overexpression of the genes related to lipid metabolism, adipocyte differentiation, defense, and stress responses is noticeable in the non-alcoholic fatty liver of obese rodents. The hepatic-gene expression profiles led us to hypothesize that in obese rodents, the livers are supplied with large amounts of free fatty acids under conditions associated with obesity either through increased fatty acid biosynthesis or through decreased fatty acid oxidation, which may lead to increased mitochondrial respiratory activity. The wide list of genes that were identified in previous studies could be a source of potential therapeutic targets because most of these genes are involved in the key mechanisms of obesity development, from adipocyte differentiation to the disturbance of metabolism.

Obesity: genes, brain, gut, and environment

Obesity, which is assuming alarming proportions, has been attributed to genetic factors, hypothalamic dysfunction, and intestinal gut bacteria and an increase in the consumption of energy-dense food. Obesity predisposes to the development of type 2 diabetes mellitus, hypertension, coronary heart disease, and certain forms of cancer. Recent studies have shown that the intestinal bacteria in obese humans and mice differ from those in lean that could trigger a low-grade systemic inflammation. Consumption of a calorie-dense diet that initiates and perpetuates obesity could be due to failure of homeostatic mechanisms that regulate appetite, food consumption, and energy balance. Hypothalamic factors that regulate energy needs of the body, control appetite and satiety, and gut bacteria that participate in food digestion play a critical role in the onset of obesity. Incretins, cholecystokinin, brain-derived neurotrophic factor, leptin, long-chain fatty acid coenzyme A, endocannabinoids and vagal neurotransmitter acetylcholine play a role in the regulation of energy intake, glucose homeostasis, insulin secretion, and pathobiology of obesity and type 2 diabetes mellitus. Thus, there is a cross-talk among the gut, liver, pancreas, adipose tissue, and hypothalamus. Based on these evidences, it is clear that management of obesity needs a multifactorial approach.

Effect of high-fat feeding on expression of genes controlling availability of dopamine in mouse hypothalamus

Objective

Hypothalamic centers integrate external signals of nutrient availability and energy status and initiate responses to maintain homeostasis. Quantifying changes in hypothalamic gene expression in the presence of nutrient excess may identify novel responsive elements.

Methods

Affymetrix Mouse Genome 430 2.0 oligonucleotide microarrays containing 45 102 probe sets were used to interrogate differential expression of genes in dietary-induced obesity model C57BL6 inbred mice fed a high-fat (35% fat; n = 8) or standard (4% fat; n = 6) diet from 3 to 15 wk of age. Ontologies of regulated genes were examined and expression of selected genes was validated by quantitative real-time polymerase chain reaction.

Results

One thousand two hundred twelve unique gene transcripts showed altered expression on the microarrays. Gene ontology analysis revealed changes in neuropeptide genes responding to leptin, Pomc, Cart, Npy, and Agrp, compatible with a homeostatic response to high-fat intake, although mean weight increased 2.3-fold compared with standard fed mice (P < 0.001). Neurotransmitter system ontologies revealed upregulation of five genes controlling availability of dopamine. Changes in Th tyrosine hydroxylase (2.1-fold) and Slc18a2 solute carrier family 18 (vesicular monoamine), member 2 (4.4-fold) controlling synthesis and release, and Slc6a3 solute carrier family 6 (neurotransmitter transporter, dopamine), member 3 (4.8-fold), Snca α-synuclein (1.3-fold), and Maoa monoamine oxidase (1.9-fold) limiting availability were confirmed by quantitative real-time polymerase chain reaction.

Conclusion

Expression of five genes involved in availability of dopamine was increased after a high-fat diet. Failure to reduce dopamine availability sufficiently, to counter the feeding reward effect, could contribute to diet-induced obesity in these mice.

Advances in Nutrigenomics research: novel and future analytical approaches to investigate the biological activity of natural compounds and food functions

In recent years, nutrition research has moved from classical epidemiology and physiology to molecular biology and genetics. Following this trend, Nutrigenomics has emerged as a novel and multidisciplinary research field in nutritional science that aims to elucidate how diet can influence human health. It is already well known that bioactive food compounds can interact with genes affecting transcription factors, protein expression and metabolite production. The study of these complex interactions requires the development of advanced analytical approaches combined with bioinformatics. Thus, to carry out these studies Transcriptomics, Proteomics and Metabolomics approaches are employed together with an adequate integration of the information that they provide. In this article, an overview of the current methodologies and a thorough revision of the advances in analytical technologies and their possibilities for future developments and applications in the field of Nutrigenomics is provided.

Weight regain after Roux-en-Y: a significant 20% complication related to PYY

OBJECTIVE

Roux-en-Y gastric bypass (RYGB) produces rapid and dramatic weight loss in very heavy obese patients. Up to 20% cannot sustain their weight loss beyond 2 to 3 y after surgery.

METHODS

To identify putative etiologic factors producing post-RYGB weight regain, a literature survey of metabolic changes in very obese and a review of our diet-induced obese RYGB rat model data was done.

RESULTS

Weight regain suggests an imbalance in physiologic mechanisms regulating appetite and metabolic rate. Weight regain occurred in 25% of our rats, produced by return to presurgical energy intake levels. The 75% of rats that sustained weight loss secreted a significantly larger amount of peptide YY (PYY) while suppressing leptin secretion; those that failed were unable to develop or sustain a sufficiently large plasma PYY:leptin ratio. Metabolic consequences of this failure included reversal of initial postsurgical increases in peripheral fatty acid oxidation, anorexigenic activity in the hypothalamic arcuate nucleus and paraventricular nucleus, and the expression of uncoupling protein-2 in adipose tissues, and decreases in hepatic lipogenesis, free tri-iodothyronine secretion, expression of orexigenic activity in the arcuate nucleus and paraventricular nucleus, expression of adenosine monophosphate kinase in adipose tissues, skeletal muscle mitochondrial mass, and endocannabinoid content and appetite.

CONCLUSION

Weight regain after RYGB occurs in approximately 20% of patients and constitutes a serious complication. Weight regain-promoting consequences are attributed to a failure to sustain elevated plasma PYY concentrations, indicating that combining RYGB with pharmacologic stimulation of PYY secretion in patients after RYGB who exhibit inadequate PYY concentration may increase long-term success of surgical weight reduction in morbidly obese adults.

Short-term oleoyl-estrone treatment affects capacity to manage lipids in rat adipose tissue

BACKGROUND

Short-term OE (oleoyl-estrone) treatment causes significant decreases in rat weight mainly due to adipose tissue loss. The aim of this work was to determine if OE treatment affects the expression of genes that regulate lipid metabolism in white adipose tissue.

RESULTS

Gene expression in adipose tissue from female treated rats (48 hours) was analysed by hybridization to cDNA arrays and levels of specific mRNAs were determined by real-time PCR. Treatment with OE decreased the expression of 232 genes and up-regulated 75 other genes in mesenteric white adipose tissue. The use of real-time PCR validate that, in mesenteric white adipose tissue, mRNA levels for Lipoprotein Lipase (LPL) were decreased by 52%, those of Fatty Acid Synthase (FAS) by 95%, those of Hormone Sensible Lipase (HSL) by 32%, those of Acetyl CoA Carboxylase (ACC) by 92%, those of Carnitine Palmitoyltransferase 1b (CPT1b) by 45%, and those of Fatty Acid Transport Protein 1 (FATP1) and Adipocyte Fatty Acid Binding Protein (FABP4) by 52% and 49%, respectively. Conversely, Tumour Necrosis Factor (TNFalpha) values showed overexpression (198%).

CONCLUSION

Short-term treatment with OE affects adipose tissue capacity to extract fatty acids from lipoproteins and to deal with fatty acid transport and metabolism.

Is a model useful in exploring the catabolic mechanisms of weight loss after gastric bypass in humans?

PURPOSE OF REVIEW

In the USA, approximately 3% of adults are morbidly obese, in whom behavior modification and drug therapy is ineffective in inducing major weight loss. Surgery is their only reliable option. The Roux-en-Y gastric bypass accounts for 90% of all bariatric surgeries because it achieves the best weight loss results. Many studies describe weight loss and changes in metabolic blood parameters after Roux-en-Y gastric bypass. We compare recent human data with the findings in our rats to validate the versatility of using a Roux-en-Y gastric bypass rat model to explore the multifactorial molecular and physiological dimensions of weight loss and weight regain.

RECENT FINDINGS

Not only mechanical factors but also changes in gastrointestinal and adipose hormones and hypothalamic neuropeptides contribute to Roux-en-Y gastric bypass induced weight loss by promoting catabolic processes. Nevertheless, the exact mechanisms of weight loss remain unknown.

SUMMARY

To investigate these catabolic mechanisms we used our Roux-en-Y gastric bypass rat model in diet induced obese rats. We found clear morphometric, physiological and biochemical parallelisms between humans and our rats. It is likely that Roux-en-Y gastric bypass induces similar changes in hypothalamic neuropeptides which can only be studied using the rat model. It therefore provides a useful research tool for exploring and studying the development of adjuvant antiobesity therapies.

Application of DNA Microarrays in the Study of Human Obesity and Type 2 Diabetes

DNA microarrays have provided medical researchers with a powerful tool to study the mechanisms of complex diseases, including obesity and type 2 diabetes (T2D). The technology has been used to dissect virtually every aspect of the genetic and molecular basis of these two diseases. Gene expression profiling is the major application of DNA microarrays so far. Subcutaneous fat, visceral fat, adipocyte and preadipocyte, muscle, liver, pancreas and specific nuclei in the hypothalamus under normal and disease conditions are used in addressing the profile of gene expression in obesity and T2D. Comparisons of fat depots in humans and animal models - including ob/ob and db/db mice, diet-induced obese mice, fa/fa Zucker rats, gene knockout (plin (-/-), GLUT4 (-/-)) and transgenic mice (GLUT4-Tg) - have been employed in microarray experiments. The effects of various interventions, such as hormonal and drug treatments, exercise, and surgery, have been studied to determine the expression profile of different developmental stages in cells and the effect of treatment on the two diseases. In this review, the application of microarrays in elucidating the role of retinol binding protein 4 as a link between obesity and T2D is discussed. The possible role in obesity of a common genetic variant near the INSIG2 gene and the discovery of the BBS9 gene are also discussed. The problems and challenges are summarized under eight categories and suggestions for the future direction of research in this area are proposed.

OMICS-driven biomarker discovery in nutrition and health

While traditional nutrition research has dealt with providing nutrients to nourish populations, it nowadays focuses on improving health of individuals through diet. Modern nutritional research is aiming at health promotion and disease prevention and on performance improvement. As a consequence of these ambitious objectives, the disciplines "nutrigenetics" and "nutrigenomics" have evolved. Nutrigenetics asks the question how individual genetic disposition, manifesting as single nucleotide polymorphisms, copy-number polymorphisms and epigenetic phenomena, affects susceptibility to diet. Nutrigenomics addresses the inverse relationship, that is how diet influences gene transcription, protein expression and metabolism. A major methodological challenge and first pre-requisite of nutrigenomics is integrating genomics (gene analysis), transcriptomics (gene expression analysis), proteomics (protein expression analysis) and metabonomics (metabolite profiling) to define a "healthy" phenotype. The long-term deliverable of nutrigenomics is personalised nutrition for maintenance of individual health and prevention of disease. Transcriptomics serves to put proteomic and metabolomic markers into a larger biological perspective and is suitable for a first "round of discovery" in regulatory networks. Metabonomics is a diagnostic tool for metabolic classification of individuals. The great asset of this platform is the quantitative, non-invasive analysis of easily accessible human body fluids like urine, blood and saliva. This feature also holds true to some extent for proteomics, with the constraint that proteomics is more complex in terms of absolute number, chemical properties and dynamic range of compounds present. Apart from addressing the most complex "-ome", proteomics represents the only platform that delivers not only markers for disposition and efficacy but also targets of intervention. The Omics disciplines applied in the context of nutrition and health have the potential to deliver biomarkers for health and comfort, reveal early indicators for disease disposition, assist in differentiating dietary responders from non-responders, and, last but not least, discover bioactive, beneficial food components. This paper reviews the state-of-the-art of the three Omics platforms, discusses their implication in nutrigenomics and elaborates on applications in nutrition and health such as digestive health, allergy, diabetes and obesity, nutritional intervention and nutrient bioavailability. Proteomic developments, applications and potential in the field of nutrition have been specifically addressed in another review issued by our group.

Catabolic effects of gastric bypass in a diet-induced obese rat model

PURPOSE OF REVIEW

In the USA, 8-10 million people are morbidly obese, which is associated with a high frequency of comorbidities. The most effective treatment is surgery. Of around 180,000 bariatric operations performed in 2005, 80% were Roux-en-Y gastric bypass, consisting of a small gastric pouch to minimize food intake and a Roux-en-Y of distal small bowel bypassing the upper gastrointestinal tract. The precise mechanisms whereby Roux-en-Y gastric bypass achieves sustained weight loss remain unknown. To gain insight into the catabolic events of sustained weight loss we developed a diet-induced obese Roux-en-Y gastric bypass rat model. We review our rat model data from the novel viewpoint of the catabolic state, comparing it with the limited human data available and the catabolic events occurring in cancer anorexia/cachexia syndrome.

RECENT FINDINGS

Current data suggest the involvement of mechanisms other than restrictive and malabsorptive factors of the Roux-en-Y gastric bypass, classically thought of as the mechanisms responsible for weight loss. Based on available data, gastrointestinal hormones and cytokines play a key role in reducing food intake and regulating energy homeostasis. Because of the cross talk between peripheral modulators and the hypothalamus, a critical role for their interaction in the outcome of Roux-en-Y gastric bypass is emerging.

SUMMARY

In our Roux-en-Y gastric bypass rat model many of the changes in gastrointestinal hormones, adipokines and cytokines as well as in hypothalamic neuropeptides and neurotransmitters resemble the changes observed in the anorexia/cachexia rat model, suggesting that Roux-en-Y gastric bypass triggers a catabolic state responsible for loss of appetite and prolonged body weight reduction.

Isolation and confirmation of a calcium excretion quantitative trait locus on chromosome 1 in genetic hypercalciuric stone-forming congenic rats

Hypercalciuria is the most common risk factor for kidney stones and has a substantial genetic component. The genetic hypercalciuric stone-forming (GHS) rat model displays complex changes in physiology involving intestine, bone, and kidney and overexpression of the vitamin D receptor, thereby reproducing the human phenotype of idiopathic hypercalciuria. Through quantitative trait locus (QTL) mapping of rats that were bred from GHS female rats and normocalciuric Wistar Kyoto (WKY) male rats, loci that are linked to hypercalciuria and account for a 6 to eight-fold phenotypic difference between the GHS and WKY progenitors were mapped. GHS x WKY rats were backcrossed to breed for congenic rats with the chromosome 1 QTL HC1 on a normocalciuric WKY background. Ten generations of backcrosses produced N10F1 rats, which were intercrossed to produce rats that were homozygous for GHS loci in the HC1 region between markers D1Mit2 and D1Mit32. On a high-calcium diet (1.2% calcium), significantly different levels of calcium excretion were found between male congenic (1.67 +/- 0.71 mg/24 h) and male WKY control rats (0.78 +/- 0.19 mg/24 h) and between female congenic (3.11 +/- 0.90 mg/24 h) and female WKY controls (2.11 +/- 0.50 mg/24 h); the congenics preserve the calcium excretion phenotype of the GHS parent strain. Microarray expression analyses of the congenic rats, compared with WKY rats, showed that of the top 100 most changed genes, twice as many as were statistically expected mapped to chromosome 1. Of these, there is a clear bias in gene expression change for genes in the region of the HC1. Of >1100 gene groups analyzed, one third of the 50 most differentially expressed gene groups have direct or secondary action on calcium metabolism or transport. This is the first QTL for hypercalciuria to be isolated in a congenic animal.

Metabolomics reviewed: a new "omics" platform technology for systems biology and implications for natural products research

Metabolomics is the study of global metabolite profiles in a system (cell, tissue, or organism) under a given set of conditions. The analysis of the metabolome is particularly challenging due to the diverse chemical nature of metabolites. Metabolites are the result of the interaction of the system's genome with its environment and are not merely the end product of gene expression but also form part of the regulatory system in an integrated manner. Metabolomics has its roots in early metabolite profiling studies but is now a rapidly expanding area of scientific research in its own right. Metabolomics (or metabonomics) has been labeled one of the new "omics", joining genomics, transcriptomics, and proteomics as a science employed toward the understanding of global systems biology. Metabolomics is fast becoming one of the platform sciences of the "omics", with the majority of the papers in this field having been published only in the last two years. In this review metabolomic methodologies are discussed briefly followed by a more detailed review of the use of metabolomics in integrated applications where metabolomics information has been combined with other "omic" data sets (proteomics, transcriptomics) to enable greater understanding of a biological system. The potential of metabolomics for natural product drug discovery and functional food analysis, primarily as incorporated into broader "omic" data sets, is discussed.

Changes in GI hormones and their effect on gastric emptying and transit times after Roux-en-Y gastric bypass in rat model

BACKGROUND

We determined whether Roux-en-Y gastric bypass (RYGB)-induced protracted weight loss is associated with an increase in anorectic peptide YY (PYY) and decreased gastrointestinal (GI) motility.

METHODS

RYGB and control sham-operated GI intact obese (SO Obese) and sham-operated GI intact pair-fed (PF) rats were studied. Postoperatively, body weight (BW) and food intake were measured for 90 days. Rats were killed to measure PYY, ghrelin, cholecystokinin (CCK), and glucagonlike peptide-1 (GLP-1). Ninety-day food intake trends were examined by quadratic trend analysis. On the basis of a 28-day weight loss rate, PYY also was measured at 14 and 28 days. Peak 28-day PYY results corresponded with peak BW loss rate; thus, gastric emptying (GE) and intestinal transit time were measured. Data were analyzed by analysis of variance and Tukey's pairwise multiple comparison.

RESULTS

At 90 days, BW in SO Obese versus PF versus RYGB rats was 801 +/- 15 g versus 661 +/- 24 g versus 538 +/- 32 g respectively (P < .05). Concentrations of plasma PYY were increased, while plasma ghrelin was decreased in RYGB versus SO Obese and PF (P < .05). CCK and GLP-1 were unchanged. In RYGB versus controls, PYY was increased at 14 and 28 days but was most elevated at 28 days. In RYGB versus controls, GE was delayed (P < .05) and intestinal transit time was longer (P < .05).

CONCLUSIONS

After RYGB, an increase in PYY and a decrease in ghrelin occurred, probably explaining the decrease in food intake, the slower GE and transit time, which contributed to weight loss. Longitudinal studies can be performed with the use of our RYGB model, providing insight into weight loss mechanisms by generating long-term follow-up data currently not available in human studies.

Transcriptional analysis of multiple brain regions in Parkinson's disease supports the involvement of specific protein processing, energy metabolism, and signaling pathways, and suggests novel disease mechanisms

In both genetic and idiopathic forms of Parkinson's disease (PD), considerable evidence supports the involvement of alpha-synuclein, electron transport chain complex I, protein aggregation, and the ubiquitin-proteasome system. To investigate alterations in the transcription of genes that comprise these pathways, we performed gene expression profiling and functional gene group analysis of three brain regions (the substantia nigra, putamen, and area 9) in postmortem tissue from matched groups of PD or control subjects (n = 15/group). Verification of selected changes was performed using RT-PCR, and visualization of selected changes in expression was accomplished using in situ hybridization (ISH). Our results provide strong support for the impairment of multiple electron transport chain complexes and the ubiquitin-proteasomal system in PD, along with a robust induction of heat shock proteins and some anti-apoptotic gene groups. Several novel gene and gene group findings were also obtained that offer new insight into the pathogenesis and potential treatment of PD.

Gene expression analysis of peripheral blood leukocytes from discordant sib-pairs with schizophrenia and bipolar disorder reveals points of convergence between genetic and functional genomic approaches

We performed global RNA transcript analysis and comprehensive gene group analysis of peripheral blood leukocyte (PBL) RNA from two groups of matched sib-pairs that were discordant for either schizophrenia (n = 33 sib-pairs) or bipolar disorder (n = 5 sib-pairs). The pairs chosen for these analyses were selected from families with known patterns of genetic linkage (5q for schizophrenia and 6q for bipolar disorder). At the single gene level, we obtained lists of the transcripts with the most significant changes in expression and from these lists determined those with the highest degree of predictive power for classifying subjects according to diagnosis in these samples. At the gene group level, we comprehensively analyzed pairwise expression changes of more than 4,000 functional groups and cytogenetic locations, and present a novel method of displaying these data that we term "cytogenomic" mapping. Verification of selected changes in expression was performed using quantitative real-time RT-PCR. Our results provide compelling evidence for the utility of analyzing PBL RNA for changes in expression in neuropsychiatric disorders.

Gene expression profiles post Roux-en-Y gastric bypass

BACKGROUND

The hypothalamus is involved in regulation of food intake (FI) and fat deposition. Molecular mechanisms of weight loss after Roux-en-Y gastric bypass (RYGB) were studied by correlating changes in gene expression profiles in hypothalamic arcuate nucleus (ARC) and subcutaneous abdominal fat (SAF).

METHOD

Diet-induced obese rats were divided into RYGB, sham-operated (SO-Obese), and sham-operated pair-fed (PF) groups. A non-obese group on a regular chow diet served as control. Body weight (BW) and FI were measured. Rats were killed 10 days after the operation. Plasma was analyzed for biochemical indices, ARC and SAF were analyzed for gene expression profiles. Body SAF was also weighed. Data were analyzed by ANOVA and factor analysis.

RESULTS

BW and FI decreased in RYGB versus SO-Obese, as reflected by decreased SAF (53%). Genes similarly expressed in ARC and SAF after RYGB were limited to several genes that predominantly related to metabolic pathways of carbohydrate, fat, neuropeptide, and cytokines. These expression profiles were similar to those seen in chow control and to those seen in a comparison of PF and SO-Obese.

CONCLUSIONS

RYGB-induced weight loss is associated with changes in gene profile expressions that could influence metabolic changes, contributing to weight loss.