Integration of Heterogeneous Expression Data Sets Extends the Role of the Retinol Pathway in Diabetes and Insulin Resistance

Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project (DGAP) was launched to profile gene expression in a variety of related animal models and human subjects. We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance. Results: We perform integrative analysis of the 16 DGAP data sets that span multiple tissues, conditions, array types, laboratories, species, genetic backgrounds and study designs. For each data set, we identify differentially expressed genes compared with control. Then, for the combined data, we rank genes according to the frequency with which they were found to be statistically significant across data sets. This analysis reveals RetSat as a widely shared component of mechanisms involved in insulin resistance and sensitivity and adds to the growing importance of the retinol pathway in diabetes, adipogenesis and insulin resistance. Top candidates obtained from our analysis have been confirmed in recent laboratory studies. Contact: [email protected]

Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance

Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project (DGAP) was launched to profile gene expression in a variety of related animal models and human subjects. We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance. Results: We perform integrative analysis of the 16 DGAP data sets that span multiple tissues, conditions, array types, laboratories, species, genetic backgrounds and study designs. For each data set, we identify differentially expressed genes compared with control. Then, for the combined data, we rank genes according to the frequency with which they were found to be statistically significant across data sets. This analysis reveals RetSat as a widely shared component of mechanisms involved in insulin resistance and sensitivity and adds to the growing importance of the retinol pathway in diabetes, adipogenesis and insulin resistance. Top candidates obtained from our analysis have been confirmed in recent laboratory studies.National Institutes of Health (U.S.) (Roadmap for Medical Research, grant U54LM008748

Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance

Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project (DGAP) was launched to profile gene expression in a variety of related animal models and human subjects. We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance

Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance

Motivation: Type 2 diabetes is a chronic metabolic disease that involves both environmental and genetic factors. To understand the genetics of type 2 diabetes and insulin resistance, the DIabetes Genome Anatomy Project (DGAP) was launched to profile gene expression in a variety of related animal models and human subjects. We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance

Eicosapentaenoic and docosahexaenoic acid-enriched high fat diet delays the development of fatty liver in mice

BACKGROUND: Low hepatic content of n-3 PUFA has been associated with NAFLD in humans. Whether this is associated with reduced dietary intake or increased turnover of these FA is not clear. We have here investigated the effects of dietary fat quality on hepatic lipid storage and transcriptomics over time. AIM: To investigate the effects of quality of fat in a high fat diet (HFD) over time on hepatic lipid storage and liver transcriptomics. METHODS AND RESULTS: Male C57BL/6J mice were fed control, HFD-eicosapentaenoic acid (EPA)/ docosahexaenoic acid (DHA) or HFD-corn oil diet for 8 or 12 weeks. Body weight, body composition, plasma and hepatic triglyceride contents were measured. Hepatic transcriptomes were analysed by microarray followed by gene-set enrichment analyses. At 8 weeks, the HFD-corn oil mice had higher body weight and adipose depot mass than the HFD-EPA/DHA but there were no differences at 12 weeks. Hepatic triglyceride content was lower in HFD-EPA/DHA fed compared with the HFD-corn oil fed mice at both time-points. Enrichment analyses of the hepatic transcriptomes showed that lipid/fatty acid biosynthesis; transport and homeostasis were lower in the HFD-EPA/DHA fed compared with the HFD-corn oil fed mice. Genes encoding proteins associated to cytoplasmic lipid droplets were expressed at higher levels in livers from the HFD-corn oil compared to HFD-EPA/DHA mice. CONCLUSIONS: Dietary EPA and DHA counteracted development of HFD-induced fatty liver. The liver transcriptome data implicate that the quality of dietary fat could modulate Ppar-related gene expression that in turn affects hepatic lipid storage and maintenance of metabolic health

Network strategies to understand the aging process and help age-related drug design

Recent studies have demonstrated that network approaches are highly appropriate tools to understand the extreme complexity of the aging process. The generality of the network concept helps to define and study the aging of technological, social networks and ecosystems, which may give novel concepts to cure age-related diseases. The current review focuses on the role of protein-protein interaction networks (interactomes) in aging. Hubs and inter-modular elements of both interactomes and signaling networks are key regulators of the aging process. Aging induces an increase in the permeability of several cellular compartments, such as the cell nucleus, introducing gross changes in the representation of network structures. The large overlap between aging genes and genes of age-related major diseases makes drugs which aid healthy aging promising candidates for the prevention and treatment of age-related diseases, such as cancer, atherosclerosis, diabetes and neurodegenerative disorders. We also discuss a number of possible research options to further explore the potential of the network concept in this important field, and show that multi-target drugs (representing "magic-buckshots" instead of the traditional "magic bullets") may become an especially useful class of age-related future drugs.Comment: an invited paper to Genome Medicine with 8 pages, 2 figures, 1 table and 46 reference

Métabolisme des rétinoïdes et facteurs d’influence dans l’obésité, la résistance à l’insuline et le diabète de type 2 : études chez l’animal et chez l’homme

Introduction: La vitamine A et ses métabolites actifs (acide rétinoïque tout-trans et 9-cis), qui activent les récepteurs nucléaires (RARs et RXRs), sont essentiels pour la différentiation cellulaire, l’embryogénèse, la fonction immunitaire, la croissance et la prévention de maladies tel que le cancer et le diabète. La différentiation des adipocytes est largement dépendante des rétinoïdes. La RBP4, transporteur sérique du rétinol (ROL), est aussi une adipokine inversement corrélée à la sensibilité à l’insuline. L’obésité et le diabète de type 2 (T2DM) sont des conditions métaboliques ayant pris des proportions alarmantes à travers le monde. Plusieurs études se font dans ces domaines, mais il reste beaucoup à faire. Le syndrome métabolique et le T2DM corrèlent avec une plus grande proportion de gras viscéral versus gras sous-cutané et perturbent l’homéostasie des rétinoïdes. Les rétinoïdes et les molécules connexes (RBP4, TTR), de par leurs implications dans les processus métaboliques, peuvent constituer des cibles de choix dans l’étude et le traitement de ces troubles métaboliques. Hypothèses: Dans ce contexte, nous postulons que le métabolisme des rétinoïdes diffère entre les gras sous-cutané et viscéral à un stade précoce, et que les niveaux de ROL, de RBP4 et de TTR corrèlent avec les composants déclarés de l’obésité, résistance à l’insuline (RI) et T2DM et peuvent servir comme indicateurs physiologiques précoces de l’obésité, la RI et du T2DM. Objectifs: L’objectif général de cette étude est de caractériser l’homéostasie des rétinoïdes dans différents types de gras et d’établir les relations qui existent entre les rétinoïdes et les molécules connexes avec l’obésité, la RI et le T2DM dans une étude fondamentale et une clinique. Tout d’abord nous avons eu comme objectifs spécifiques: (1.1). La caractérisation des enzymes RALDHs 1-4 impliquées dans la formation d’AR dans les tissus adipeux viscéral et sous-cutané de souris C57BL/6; (1.2) L’identification et la mesure des isomères de la vitamine A dans les tissus adipeux viscéral et sous-cutané de souris C57BL/6; (1.3) La comparaison de l’expression des gènes du métabolisme des rétinoïdes dans le gras souscutané versus le gras viscéral. Nous avons poursuivi en : (2.1) Évaluant le ROL circulant, le taux de RBP4, le ratio ROL/RBP4 et d’autres molécules reliés aux rétinoïdes et nous avons évalué leur potentiel en tant que marqueurs physiologiques prédictifs de la RI dans une étude clinique et (2.2) par l’évaluation des corrélations existantes entre ces changements physiologiques et les facteurs traditionnels de la RI et du T2DM. Méthodologie : Pour atteindre ces objectifs, nous avons utilisé ces approches expérimentaux : 1. L’identification et la mesure de l’activité des RALDHs par des essais enzymatiques; 2. Mesure des isomères du ROL par HPLC; 3. Comparaison de l’expression des gènes du métabolisme de rétinoïdes par RT-q-PCR; 4. Étude clinique chez l’humain sur 4 groupes de sujets: groupe A, témoins minces et en santé; groupe B et C, diabétiques obèses avec diabète mal- et bien-contrôlé; groupe D, obèses non-diabétiques. Chez ces sujets, nous avons pris des mesures anthropométriques et biochimiques: IMC, tour de taille (TT), FSC, profil lipidique, biochimie générale, ACR, TSH, HbA1c, glycémies à jeun, insulinémie, TTR, vitamine E et D, ROL sérique par HPLC, RBP4 sérique par WB/ImageQuant; 5. Évaluation du potentiel du RBP4, ROL, et ratios ROL/RBP4 comme marqueurs physiologiques précoces dans la clinique de la RI et T2DM (corrélations avec marqueurs T2DM traditionnels) Conclusions: Notre étude montre une relation directe entre le type de gras et l’homéostasie des rétinoïdes et des corrélations entre le niveau de RBP4 et l’obésité, la RI, et le T2DM, ainsi qu’une corrélation entre le ROL et l’intolérance au glucose et le T2DM. On observe chez la souris mince et en santé des niveaux plus grands d’ARNm de l’adipokine RBP4 dans le gras viscéral par rapport au gras sous-cutané, ce qui suggère une contribution précoce du gras viscéral à la future résistance à l’insuline qui s’installe avec l’obésité. Globalement on peut conclure que la RBP4 est impliquée dans le développement de la RI et le diabète et que son niveau circulant influence et est influencé par la RI, tandis que le ROL augmente seulement dans des conditions de décompensation pancréatique et d’intolérance au glucose. Une RBP4 sérique élevée contribue à la diminution du HDL cholestérol et pourrait également refléter une dysfonction rénale précoce. On peut proposer ces molécules, impliquées dans le métabolisme des rétinoïdes, comme marqueurs biologiques précoces de la résistance à l’insuline et du diabète chez les sujets obèses. Nos résultats apportent une lumière nouvelle dans l’étude de l’obésité et le T2DM de par son approche novatrice qui implique les rétinoïdes. Plusieurs études, sur de plus larges cohortes, sont nécessaires pour déterminer le rôle précis de la RBP4 et du ROL dans l’obésité et le T2DM, ainsi que pour explorer des voies thérapeutiques ciblées.Introduction: Vitamin A and its active metabolites (all-trans and 9-cis retinoic acid), which activate nuclear receptors (RARs and RXRs), are essential for cell differentiation, embryogenesis, growth and disease prevention such as cancer and diabetes. Differentiation of adipocytes is largely dependent on retinoid. Serum retinol (ROL) transporter, the RBP4, is also an adipokine inversely correlated with insulin sensitivity. Obesity and type 2 diabetes (T2DM) are diseases that have reached epidemic proportion worldwide. Many studies have tried to find a solution, but a clear cut treatment still strives to be found. Metabolic syndrome and T2DM are correlated with a higher proportion of visceral versus subcutaneous fat and disrupt retinoid homeostasis. The link between visceral fat, insulin resistance (IRe) and T2DM has been clearly established. Retinoid and related molecules (RBP4, TTR), may serve as metabolic targets in the study and treatment of these disorders. There is much to be done in this area, the links between these molecules and these pathologies being emergent. Hypothesis: In this context, we postulate that retinoid metabolism differs between subcutaneous and visceral fat and the levels of circulating ROL, RBP4, and TTR correlates with clinical descriptors of obesity, IRe and T2DM, as early physiological indicators of these conditions. Goals: The global goal of this study is to investigate retinoid homeostasis in visceral and subcutaneous fat and to establish the relationships between retinoid and related molecules with obesity, IRe and T2DM in a fundamental and in a clinical study. Our specific goals are: (1.1). The characterization of RALDHs 1-4 enzymes involved in RA formation in visceral and subcutaneous fat of C57BL/6 mice; (1.2) The identification and quantification of ROL isomers in visceral and subcutaneous fat of C57BL/6 mice; (1.3) A parallel in the expression levels (mRNA) for retinoid metabolism genes, in subcutaneous and visceral fat. Second step: (2.1) A clinical study, to evaluate serum ROL, RBP4, ROL/RBP4 and other retinoid-related molecules regarding their potential as physiological markers predicting IRe and (2.2) to assess the eventual correlations between these markers and clinical descriptors of IRe and T2DM. Methodology: Experimental approaches used to reach these goals are: 1. Identification and measurement of RALDH activity by enzymatic assays; 2. Measurement of ROL isomers by HPLC; 3. Evaluation of retinoid metabolism gene expressions by RT-q-PCR; 4. Clinical pilot study in humans using four groups of subjects: group A, normal weight and healthy controls; group B, obese diabetics with poorly-controlled diabetes; group C, well-controlled obese diabetics; and group D, non-diabetic obese. In this study we did anthropometric and biochemical measurements: BMI, waist circumference (WC), blood pressure, blood complete formula, lipids profile, general biochemistry, albumin-creatinine ratio, TSH, HbA1c, fasting glucose, insulinemia, TTR, vitamins E and D, serum ROL by HPLC, serum RBP4 by Western Blot/ImageQuant; 5.Evaluation of RBP4, ROL and ratio correlations with traditional IRe and T2DM markers. Conclusions: Our study shows a direct relationship of fat topography with retinoid homeostasis and correlations between RBP4 level and obesity, IRe, and T2DM, as well as between ROL, glucose intolerance and T2DM. In healthy and normal weight mice, higher levels of adipokine RBP4 (mRNA) are present in visceral versus subcutaneous fat, suggesting an early contribution of the visceral fat to future insulin resistance, which sets up with obesity. Overall it can be concluded that RBP4 is involved in the development of IRe and diabetes and that its circulating level influences and is influenced by IRe, whereas ROL only increases under conditions of pancreatic failure with glucose intolerance. High serum RBP4 contributes to decrease of HDL cholesterol and may also reflect early renal dysfunction. These molecules (RBP4 and ROL), originating from retinoid metabolism, can be proposed as early biological markers of insulin resistance and glucose intolerance respectively. Our findings highlight the retinoid innovative role in the study of obesity and T2DM. Several studies across larger cohorts are needed to determine the precise role of RBP4 and ROL in obesity, IRe and T2DM, as well as to explore targeted therapeutic pathways

The HLA-B associated transcript 1 (BAT1) expression in human adipose tissue : BAT1 modulation with increasing adiposity and diabetes

Obesity and type 2 diabetes (T2DM) are both inflammatory disorders with parallel escalating epidemics. Novel insights provided by the new biology suggest common pathways by which several pathogenic components of obesity affect glucose metabolism and cellular responsiveness to insulin leading eventually to the development of T2DM; inflammation is considered critical for the development of the above metabolic disorders and is directly influenced by weight gain. Adipose tissue (AT), particularly the abdominal fat depot is currently considered source of inflammatory agents that fuel whole body’s low grade inflammatory state. The HLA-B Associated Transcript 1 (BAT1) is a cellular member of the DExD/H-box RNA-helicases with essential role for cellular mRNA export, that also attains anti-inflammatory properties, as it was shown by studies investigating monocytes and T-cell lines. Furthermore, BAT1 polymorphisms were linked to predisposition to immunopathologic disorders including type 1 diabetes. These findings suggest a potential protective role of BAT1 against the obesity-associated lowgrade inflammatory state that contributes to T2DM development. The role of BAT1 in the adipocytes has not been investigated so far. Therefore, this thesis examined BAT1 expression and regulation within specific human AT depots and the adipocyte itself. Initial studies indicated BAT1 expression in ex vivo human AT but also the repressing effect of increasing adiposity and T2DM on BAT 1 expression. Remarkably, there was no difference in BAT1 expression between obese subjects and patients with T2DM indicating that BAT1 becomes suppressed with increasing adiposity and remains suppressed through to the development of T2DM and thereafter; this could in turn reduce the capacity to response to the inflammatory insults. As human AT contains many different types of cells besides adipocytes, including fibroblasts, macrophages, lymphocytes, pre-adipocytes and endothelial cells, some of which actually increase with increasing adiposity (e.g. macrophages and lymphocytes) subsequent studies determined the expression of BAT1 particularly in isolated human primary pre-adipocytes and mature adipocytes; the human pre adipocyte cell line Chub- S7 was used for this purpose. It was shown that BAT1 (mRNA and protein) was expressed in both cell types with maximum expression in mature (lipid accumulating) adipocytes. At the stage of complete maturation, the effects of nutrients and inflammatory factors on BAT1 expression were examined. Both glucose and non-esterified fatty acids (NEFA) were shown to repress BAT 1; these findings were in keeping with the ex vivo data determined in terms of AT from obese and T2DM subjects. Furthermore, these studies indicated a synergistic action of both JNK and NFκB when used in combination to reduce BAT1 expression, indicating interconnectivity between JNK and NFκB pathways, as noted in other human AT studies examining other molecules. Regarding NEFA however, the JNK pathway seemed to mediate its repressing effect on BAT1. These studies also showed that the potent inflammatory agent lipopolysacharide (LPS) also significantly reduced BAT1 expression which was again in keeping with the previous ex vivo AT data since LPS is raised in conditions of metabolic disease. Finally, the investigation of the paracrine influences of leptin and resistin on differentiated primary adipocytes highlighted BAT 1 repression whilst adiponectin appeared to have no significant effect alone to alter BAT 1 expression or inhibit LPS-induced BAT1 repression. Taken together, BAT1 was more susceptible to the repressing effects of nutritional factors (glucose and NEFA) in excess than paracrine inflammatory or antiinflammatory adipokines. The fact that several factors modulate BAT1 expression may suggest that BAT1 represents a first line, non-selective, cellular protective agent, which is therefore influenced by several different factors through common inflammatory pathways. Thus, BAT1 suppression may be an early key event in the pathogenesis of a low chronic inflammatory state. As such BAT1 could represent an important target to manipulate to combat the low chronic inflammatory state observed in both obese and T2DM patients

A Role for Adiponectin in Trophoblast Function

As the ultimate mediator of fetal growth and well-being, the placenta is inundated with a number of molecular cues from both the maternal and fetal systems. Successful integration of these signals is critical to the ongoing health of the pregnancy, and may have important implications for the future health of both mother and child. Maternal adipose tissue releases a variety of adipokines, whose primary aim is to regulate energy metabolism. Given this, and the importance of this process in the placenta, it follows that adipokines may have profound effects on the trophoblast cells of the placenta. However, the influence of most of these adipokines on the placenta remains poorly understood. We examined the role the adipokine, adiponectin, has on the human placenta using isolated trophoblasts collected from healthy term pregnancies. Treatment of these cells with adiponectin in culture inhibited the production of human chorionic gonadotropin (hCG), placental lactogen and progesterone, all hormones produced by the placenta that play a key role in the continued health and viability of the pregnancy. In addition, adiponectin induced a pro-inflammatory environment in trophoblast cells, with increases in production of both interleukin (IL)-1β and IL-8. We have gone on to show that adiponectin can mediate its actions on trophoblast cells through the adaptor protein APPL1, the signaling molecules mitogen-activated protein kinases (MAPKs), and the epidermal growth factor (EGF) receptor. Finally, we examined the effects of adiponectin on gene expression by term trophoblasts. These data have highlighted a number of additional processes influenced by adiponectin, including insulin-like growth factor bioavailability and cortisol metabolism. The implications for these effects at the maternal-fetal interface are great. From these data, we hypothesize that adiponectin works to maintain the balance between the energy demands of the fetus and the needs of the mother, with specific functions at the placenta that appear to favor the mother. Such a role is increasingly critical as gestation progresses and fetal demands continue to increase. With the continued prevalence of metabolic health diseases, such as obesity, it is especially important to understand the influences hormones such as adiponectin have on the placenta