Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development

Direct Effects of Mifepristone on Mice Embryogenesis: An In Vitro Evaluation by Single-Embryo RNA Sequencing Analysis

The clinical use of mifepristone for medical abortions has been established in 1987 in France and since 2000 in the United States. Mifepristone has a limited medical period that lasts <9 weeks of gestation, and the incidence of mifepristone treatment failure increases with gestation time. Mifepristone functions as an antagonist for progesterone and glucocorticoid receptors. Studies have confirmed that mifepristone treatments can directly contribute to endometrium disability by interfering with the endometrial receptivity of the embryo, thus causing decidual endometrial degeneration. However, whether mifepristone efficacy directly affects embryo survival and growth is still an open question. Some women choose to continue their pregnancy after mifepristone treatment fails, and some women express regret and seek medically unapproved mifepristone antagonization with high doses of progesterone. These unapproved treatments raise the potential risk of embryonic fatality and developmental anomalies. Accordingly, in the present study, we collected mouse blastocysts ex vivo and treated implanted blastocysts with mifepristone for 24 h. The embryos were further cultured to day 8 in vitro to finish their growth in the early somite stage, and the embryos were then collected for RNA sequencing (control n = 3, mifepristone n = 3). When we performed a gene set enrichment analysis, our data indicated that mifepristone treatment considerably altered the cellular pathways of embryos in terms of viability, proliferation, and development. The data indicated that mifepristone was involved in hallmark gene sets of protein secretion, mTORC1, fatty acid metabolism, IL-2-STAT5 signaling, adipogenesis, peroxisome, glycolysis, E2F targets, and heme metabolism. The data further revealed that mifepristone interfered with normal embryonic development. In sum, our data suggest that continuing a pregnancy after mifepristone treatment fails is inappropriate and infeasible. The results of our study reveal a high risk of fetus fatality and developmental problems when pregnancies are continued after mifepristone treatment fails.

Can Exercise Training Alter Human Skeletal Muscle DNA Methylation?

Skeletal muscle is highly plastic and dynamically regulated by the body’s physical demands. This study aimed to determine the plasticity of skeletal muscle DNA methylation in response to 8 weeks of supervised exercise training in volunteers with a range of insulin sensitivities. We studied 13 sedentary participants and performed euglycemic hyperinsulinemic clamps with basal vastus lateralis muscle biopsies and peak aerobic activity (VO2 peak) tests before and after training. We extracted DNA from the muscle biopsies and performed global methylation using Illumina’s Methylation EPIC 850K BeadChip. Training significantly increased peak aerobic capacity and insulin-stimulated glucose disposal. Fasting serum insulin and insulin levels during the steady state of the clamp were significantly lower post-training. Insulin clearance rates during the clamp increased following the training. We identified 13 increased and 90 decreased differentially methylated cytosines (DMCs) in response to 8 weeks of training. Of the 13 increased DMCs, 2 were within the following genes, FSTL3, and RP11-624M8.1. Of the 90 decreased DMCs, 9 were within the genes CNGA1, FCGR2A, KIF21A, MEIS1, NT5DC1, OR4D1, PRPF4B, SLC26A7, and ZNF280C. Moreover, pathway analysis showed an enrichment in metabolic and actin-cytoskeleton pathways for the decreased DMCs, and for the increased DMCs, an enrichment in signal-dependent regulation of myogenesis, NOTCH2 activation and transmission, and SMAD2/3: SMAD4 transcriptional activity pathways. Our findings showed that 8 weeks of exercise training alters skeletal muscle DNA methylation of specific genes and pathways in people with varying degrees of insulin sensitivity.

Embryonic developmental process and clinical anatomy of the preperitoneal fascia and its clinical significance

PURPOSE

Many researchers have different views on the origin and anatomy of the preperitoneal fascia. The purpose of this study is to review studies on the anatomy related to the preperitoneal fascia and to investigate the origin, structure, and clinical significance of the preperitoneal fascia in conjunction with previous anatomical findings of the genitourinary fascia, using the embryogenesis of the genitourinary system as a guide.

METHODS

Publications on the preperitoneal and genitourinary fascia are reviewed, with emphasis on the anatomy of the preperitoneal fascia and its relationship to the embryonic development of the genitourinary organs. We also describe previous anatomical studies of the genitourinary fascia in the inguinal region through the fixation of formalin-fixed cadavers.

RESULTS

Published literature on the origin, structure, and distribution of the preperitoneal fascia is sometimes inconsistent. However, studies on the urogenital fascia provide more than sufficient evidence that the formation of the preperitoneal fascia is closely related to the embryonic development of the urogenital fascia and its tegument. Combined with previous anatomical studies of the genitourinary fascia in the inguinal region of formalin-fixed cadavers showed that there is a complete fascial system. This fascial system moves from the retroperitoneum to the anterior peritoneum as the preperitoneal fascia.

CONCLUSIONS

We can assume that the preperitoneal fascia (PPF) is continuous with the retroperitoneal renal fascia, ureter and its accessory vessels, lymphatic vessels, peritoneum of the bladder, internal spermatic fascia, and other peritoneal and pelvic urogenital organ surfaces, which means that the urogenital fascia (UGF) is a complete fascial system, which migrates into PPF in the preperitoneal space and the internal spermatic fascia in the inguinal canal.

Association of KCTD15 gene with fat deposition in pigs

KCTD15 is associated with body mass index and fat deposition in humans, mice and chickens. However, the function of KCTD15 in pig fat deposition remains unclear. In this study, we cloned and analysed the cDNA sequence of porcine KCTD15. The full length of the mRNA sequence of KCTD15 is 4,091 bp, encoding 283 amino acids. The protein is hydrophilic, it has a relative molecular mass of about 31.9 kDa and an isoelectric point of 7.09 with no signal peptide sequence or transmembrane structure. Expression analysis showed that KCTD15 expression level was significantly higher in the tissues of Large White pigs (LW) than in those of Tibetan pigs (TP) and Diannan Small-ear pigs (DN) at 6 months of age, whereas its expression level in embryonic tissues of LW at 60 days was lower than that in tissues of TP and Wujin pigs (WJ). In pig primary adipocytes, the expression level of KCTD15 is high in the early stage of differentiation and gradually decreases in later stages. Additionally, the single-nucleotide polymorphism (SNP) site T-2030C (T/C mutation, located 2,030 bp upstream of the start codon) showed a dominant allele T with high promoter activity in the LW population and a dominant allele C in the TP and WJ populations. Our results indicate that KCTD15 is involved in pig fat deposition and that T-2030C is an important regulatory site for transcriptional activity, affecting fat deposition.

Dynamics of HOX gene expression and regulation in adipocyte development

HOX proteins are homeodomain-containing transcription factors that play a central role in development. We have applied genome-wide approaches to develop time-dependent profile of differentially expressed genes in early and mature adipocytes. The list of differentially expressed HOX genes were developed by analyzing the microarray datasets of murine adipocyte samples at different time points of development. Since these datasets were obtained from Gene Expression Omnibus (GEO), we were able to find a new HOX gene, HOXC13 in adipogenesis. To investigate whether these members of the homeobox gene family are expressed and regulated in preadipocytes or mature adipocytes, RNA was isolated from 3T3-L1 preadipocyte cells at different time point's through-out the preadipocyte and adipocyte state. A reverse transcriptase-polymerase chain reaction strategy was applied for the analysis of gene expression. We have observed that HOXA5 and HOXC13 were differentially expressed in preadipocytes and HOXD4 and HOXD8 in mature adipocytes. To understand this difference in expression pattern, we have considered to investigate the role of the major regulators of adipogenesis in HOX gene regulation. Since Retinoic acid receptor (RAR) was reported previously as a regulator of Hox genes, we chose the combination of Peroxisome proliferator-activated receptor gamma (PPARγ) and Retinoic X receptor (RXR) which are modulated by the presence of RAR. To provide a detailed analysis of retinoic acid (RA) and/or PPARγ induced transcriptional and epigenetic changes within the homeotic clusters of mouse fibroblast cells (3T3-L1), we have performed a promoter mapping of HOX genes and observed an enriched binding site for PPARγ and RXR in their promoter regions. We further confirmed this PPARγ and RXR binding to HOX gene promoters by re-analyzing the anti-PPARγ/anti-RXR ChIP-Seq data. Based on the results, we modulated the PPARγ expression at the transcriptional and translational levels by using 5 different pharmacological molecules (TSA, GW9662, ATRA, FH535, and Pioglitazone) to elucidate their effect on the HOX gene transcription. These pharmacological molecules had a direct or indirect regulatory effect on the PPARγ activity. We observed that PPARγ suppression alone is enough for the upregulation of HOXA5 and HOXD4 genes. In addition, HOXD8 regulation was mediated by RAR activation in mature adipocytes but the regulation of HOXC13 gene expression was not clear. We suggest that it might be partially mediated through suppressing PPARγ activation. Further insights are required to provide a mechanistic detail about HOX gene regulation through PPARγ. In this study, we have reported a time-dependent expression analysis of HOXA5, HOXD4, HOXD8, and HOXC13 in preadipocytes and mature adipocytes. Also, we have suggested PPARγ/RAR dependent regulation for these genes during adipogenesis.

Murine in vitro cellular models to better understand adipogenesis and its potential applications

Adipogenesis has been extensively studied using in vitro models of cellular differentiation, enabling long-term regulation of fat cell metabolism in human adipose tissue (AT) material. Many studies promote the idea that manipulation of this process could potentially reduce the prevalence of obesity and its related diseases. It has now become essential to understand the molecular basis of fat cell development to tackle this pandemic disease, by identifying therapeutic targets and new biomarkers. This review explores murine cell models and their applications for study of the adipogenic differentiation process in vitro. We focus on the benefits and limitations of different cell line models to aid in interpreting data and selecting a good cell line model for successful understanding of adipose biology.

Human Pluripotent Stem Cells: A Relevant Model to Identify Pathways Governing Thermogenic Adipocyte Generation

Brown and brown-like adipocytes (BAs) are promising cell targets to counteract obesity thanks to their potential to drain and oxidize circulating glucose and triglycerides. However, the scarcity of BAs in human adults is a major limitation for energy expenditure based therapies. Enhanced characterization of BA progenitor cells (BAPs) and identification of critical pathways regulating their generation and differentiation into mature BAs would be an effective way to increase the BA mass. The identification of molecular mechanisms involved in the generation of thermogenic adipocytes is progressing substantially in mice. Much less is known in humans, thus highlighting the need for an in vitro model of human adipocyte development. Pluripotent stem cells (PSCs), i.e., embryonic stem cells and induced pluripotent stem cells, help gain insight into the different phases in the development of multiple cell types. We will discuss the capacity of human PSCs to differentiate into BAs in this review. Several groups, including ours, have reported low spontaneous adipocyte generation from PSCs. However, factors governing the differentiation of induced pluripotent stem cell-derived BA progenitors cells were recently identified, and the TGFβ signaling pathway has a pivotal role. The development of new relevant methods, such as the differentiation of hPSC-BAPs into 3D adipospheres to better mimick the lobular structure of human adipose tissue, will also be discussed. Differentiation of human PSCs into thermogenic adipocytes at high frequency provides an opportunity to characterize new targets for anti-obesity therapy.

Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans

Curtailed sleep promotes weight gain and loss of lean mass in humans, although the underlying molecular mechanisms are poorly understood. We investigated the genomic and physiological impact of acute sleep loss in peripheral tissues by obtaining adipose tissue and skeletal muscle after one night of sleep loss and after one full night of sleep. We find that acute sleep loss alters genome-wide DNA methylation in adipose tissue, and unbiased transcriptome-, protein-, and metabolite-level analyses also reveal highly tissue-specific changes that are partially reflected by altered metabolite levels in blood. We observe transcriptomic signatures of inflammation in both tissues following acute sleep loss, but changes involving the circadian clock are evident only in skeletal muscle, and we uncover molecular signatures suggestive of muscle breakdown that contrast with an anabolic adipose tissue signature. Our findings provide insight into how disruption of sleep and circadian rhythms may promote weight gain and sarcopenia.

Amplification of Adipogenic Commitment by VSTM2A

Despite progress in our comprehension of the mechanisms regulating adipose tissue development, the nature of the factors that functionally characterize adipose precursors is still elusive. Defining the early steps regulating adipocyte development is needed for the generation of tools to control adipose tissue size and function. Here, we report the discovery of V-set and transmembrane domain containing 2A (VSTM2A) as a protein expressed and secreted by committed preadipocytes. VSTM2A expression is elevated in the early phases of adipogenesis in vitro and adipose tissue development in vivo. We show that VSTM2A-producing cells associate with the vasculature and express the common surface markers of adipocyte progenitors. Overexpression of VSTM2A induces adipogenesis, whereas its depletion impairs this process. VSTM2A controls preadipocyte determination at least in part by modulating BMP signaling and PPARγ2 activation. We propose a model in which VSTM2A is produced to preserve and amplify the adipogenic capability of adipose precursors.

Identification of transcription factors potentially involved in human adipogenesis in vitro

BACKGROUND

Increased adiposity in humans leads to obesity, which is a major risk factor for cardiovascular disease, type 2 diabetes, and cancer. We previously conducted an extensive unbiased in vitro transcriptomic analysis of adipogenesis, using human adipose-derived stromal cells (ASCs). Here, we have applied computational methods to these data to identify transcription factors (TFs) that constitute the upstream gene regulatory networks potentially, driving adipocyte formation in human ASCs.

METHODS

We used Affymetrix Transcription Analysis Console™ v3.0 for calculating differentially expressed genes. MATCH™ and F-MATCH™ algorithms for TF identification. STRING v10 to predict protein-protein interactions between TFs.

RESULTS

A number of TFs that were reported to have a significant role in adipogenesis, as well as novel TFs that have not previously been described in this context, were identified. Thus, 32 upstream TFs were identified, with most belonging to the C2H2-type zinc finger and HOX families, which are potentially involved in regulating most of the differentially expressed genes observed during adipocyte differentiation. Furthermore, 17 important upstream TFs were found to have increased regulatory effects on their downstream target genes and were consistently up-regulated during the differentiation process. A strong hypothetical functional interaction was observed among these TFs, which supports their common role in the downstream regulation of gene expression during adipogenesis.

CONCLUSION

Our results support several previous findings on TFs involved in adipogenesis and thereby validate the comprehensive and systematic in silico approach described in this study. In silico analysis also allowed for the identification of novel regulators of adipocyte differentiation.

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals both local and trans expression Quantitative Trait Loci (eQTLs) demonstrating 2 trans eQTL 'hotspots' associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provide a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation.

DOI:http://dx.doi.org/10.7554/eLife.15614.001

Metabolism is a term that describes all the chemical reactions that are involved in keeping a living organism alive. Diseases related to metabolism – such as obesity, heart disease and diabetes – are a major health problem in the Western world. The causes of these diseases are complex and include both environmental factors, such as diet and exercise, and genetics. Indeed, many genetic variants that contribute to obesity have been uncovered in both humans and mice. However, it is only dimly understood how these genetic variants affect the underlying networks of interacting genes that cause metabolic disorders.

Measuring gene activity or expression, and tracing how genetic instructions are carried from DNA into RNA and proteins, can reliably identify groups of genes that correlate with metabolic traits in specific organs. This strategy was successfully used in previous studies to reveal new information about abnormalities linked to obesity in specific tissues such as the liver and fat tissues. It was also shown that this approach might suggest new molecules that could be targeted to treat metabolic disorders.

A brain region called the hypothalamus is key to the control of metabolism, including feeding behavior and obesity. Hasin-Brumshtein et al. set out to explore gene expression in the hypothalamus of 99 different strains of mice, in the hope that the data will help identify new connections between gene expression and metabolism.

This approach showed that thousands of new and known genes are expressed in the mouse hypothalamus, some of which coded for proteins, and some of which did not. Hasin-Brumshtein et al. uncovered two genetic variants that controlled the expression of hundreds of other genes. Further analysis then revealed thousands of genetic variants that regulated the expression of, and type of RNA (so-called "spliceforms") produced from neighboring genes. Also, the expression of many individual genes showed significant similarities with about 150 metabolic measurements that had been evaluated previously in the mice.

This new dataset is a unique resource that can be coupled with different approaches to test existing ideas and develop new ones about the role of particular genes or genetic mechanisms in obesity. Future studies will likely focus on new genes that show strong associations with attributes that are relevant to metabolic disorders, such as insulin levels, weight and fat mass.

DOI:http://dx.doi.org/10.7554/eLife.15614.002

Obesity and diabetes: the link between adipose tissue dysfunction and glucose homeostasis

Obesity and type 2 diabetes mellitus (T2DM) epidemics, which have already spread, imply the possibility of both conditions being closely related. Thus, the goal of the present review was to draw a parallel between obesity, adipose tissue (AT) changes, and T2DM development. To this end, a search was conducted in PubMed, MEDLINE and SciELO databases, using the following key words and their combinations: obesity; diabetes; insulin resistance; diet; weight loss; adipocin; inflammation markers; and interleukins. Based on a literature review, AT dysfunction observed in obesity is characterised by adipocyte hypertrophy, macrophage infiltration, impaired insulin signalling and insulin resistance. In addition, there is release of inflammatory adipokines and an excessive amount of NEFA promoting ectopic fat deposition and lipotoxicity in muscle, liver and pancreas. Recent evidence supports the hypothesis that the conception of AT as a passive energy storage organ should be replaced by a dynamic endocrine organ, which regulates metabolism through a complex adipocyte communication with the surrounding microenvironment. The present review demonstrates how glucose homeostasis is changed by AT dysfunction. A better understanding of this relationship enables performing nutritional intervention strategies with the goal of preventing T2DM.

Role of developmental transcription factors in white, brown and beige adipose tissues

In this review we discuss the role of developmental transcription factors in adipose tissue biology with a focus on how these developmental genes may contribute to regional variation in adipose tissue distribution and function. Regional, depot-specific, differences in lipid handling and signalling (lipolysis, lipid storage and adipokine/lipokine signalling) are important determinants of metabolic health. At a cellular level, preadipocytes removed from their original depot and cultured in vitro retain depot-specific functional properties, implying that these are intrinsic to the cells and not a function of their environment in situ. High throughput screening has identified a number of developmental transcription factors involved in embryological development, including members of the Homeobox and T-Box gene families, that are strongly differentially expressed between regional white adipose tissue depots and also between brown and white adipose tissue. However, the significance of depot-specific developmental signatures remains unclear. Developmental transcription factors determine body patterning during embryogenesis. The divergent developmental origins of regional adipose tissue depots may explain their differing functional characteristics. There is evidence from human genetics that developmental genes determine adipose tissue distribution: in GWAS studies a number of developmental genes have been identified as being correlated with anthropometric measures of adiposity and fat distribution. Additionally, compelling functional studies have recently implicated developmental genes in both white adipogenesis and the so-called 'browning' of white adipose tissue. Understanding the genetic and developmental pathways in adipose tissue may help uncover novel ways to intervene with the function of adipose tissue in order to promote health.

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network

Adipose tissue is a key determinant of whole body metabolism and energy homeostasis. Unraveling the regulatory mechanisms underlying adipogenesis is therefore highly relevant from a biomedical perspective. Our current understanding of fat cell differentiation is centered on the transcriptional cascades driven by the C/EBP protein family and the master regulator PPARγ. To elucidate further components of the adipogenic gene regulatory network, we performed a large-scale transcription factor (TF) screen overexpressing 734 TFs in mouse pre-adipocytes and probed their effect on differentiation. We identified 22 novel pro-adipogenic TFs and characterized the top ranking TF, ZEB1, as being essential for adipogenesis both in vitro and in vivo. Moreover, its expression levels correlate with fat cell differentiation potential in humans. Genomic profiling further revealed that this TF directly targets and controls the expression of most early and late adipogenic regulators, identifying ZEB1 as a central transcriptional component of fat cell differentiation.

DOI:http://dx.doi.org/10.7554/eLife.03346.001

The growing rates of obesity and related metabolic diseases are a major public health concern worldwide. People who are overweight or obese are at increased risk for a range of diseases including diabetes and heart disease, which may reduce their quality of life and shorten their lifespans. Obese people have more, larger fat cells than individuals of healthy weight, and so understanding how the body creates fat cells may provide new insights into ways to prevent or treat obesity.

Fat cells arise from a population of stem cells that can also give rise to bone cells and cartilage. Some of the proteins—called transcription factors—that work together to turn on the expression of genes needed for a stem cell to become a fat cell have been identified. However, the exact regulatory processes that cause an unspecialized cell to develop into a fat cell remain unclear.

Gubelmann et al. set out to identify more of the transcription factors that cause stem cells to become fat cells. A high-throughput, automated process was used to test the effect of over-expressing each of 734 transcription factors in mouse cells that are primed to become fat cells. Twenty-six transcription factors were found to increase the number of these primed cells that became mature fat cells—most of which had not previously been shown to affect how fat cells develop. The most powerful driver of fat cell development was ZEB1: a transcription factor that has previously been implicated in many other biological processes. Most notably, ZEB1 was linked to a transition during development that allows cells to migrate to the correct location in the embryo, but also to a mechanism that allows cancerous cells to spread to new tissues.

Using studies of mouse cells and live mice, computational analyses, and biopsies from obese patients, Gubelmann et al. show that ZEB1 regulates numerous other transcription factors that promote the development of fat cells. These include factors that initially set an unspecialized cell on the path to becoming a fat cell and those that guide the changes that occur as the fat cell matures. Further studies will be required to show whether the ZEB1 protein itself is needed to prime stem cells to start becoming fat cells.

DOI:http://dx.doi.org/10.7554/eLife.03346.002

Small ubiquitin-like modifier (SUMO) protein-specific protease 1 de-SUMOylates Sharp-1 protein and controls adipocyte differentiation

Adipocyte differentiation is regulated by a transcriptional cascade that mainly includes CCAAT/enhancer-binding protein family members and the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ). Here we show the defects in adipocyte differentiation as well as PPARγ expression in Senp1(-/-) mouse embryonic fibroblast cells induced by adipogenic stimuli. We further determine that SENP1 is a specific de-SUMOylation protease for Sharp-1, a repressor for PPARγ transcription and adipogenesis. SENP1 enhances adipogenesis through de-SUMOylation of Sharp-1, which then releases Sharp-1 repression of PPARγ expression and adipocyte differentiation. These results reveal SENP1 as a novel regulator in adipogenesis.

The epigenetic bivalency of core pancreatic β-cell transcription factor genes within mouse pluripotent embryonic stem cells is not affected by knockdown of the polycomb repressive complex 2, SUZ12

This study assesses changes in activator and repressor modifications to histones associated with the core transcription factor genes most highly upregulated or downregulated in pancreatic β-cells relative to expression in an embryonic stem cell line. Epigenetic analysis of the Oct4, Utf1, Nanog and Sox2 (pluripotency) and Pdx1, Nkx6.1, Nkx2.2 and MafA (pancreatic β-cells) transcription factor genes in embryonic stem cells and a β-cell line (MIN6) showed the pluripotency genes were enriched for active (histone 3 trimethylated at lysine 4 and histone 3 acetylated at lysine 9) and depleted of repressor modifications (histone 3 trimethylated at lysine 27 and histone 3 trimethylated at lysine 9) around the transcription start site in mouse embryonic stem cells (D3), and this was reversed in MIN6 cells. The β-cell transcription factors were bivalently enriched for activating (histone 3 trimethylated at lysine 4) and repressor (histone 3 trimethylated at lysine 27) modifications in embryonic stem cells but were monovalent for the activator modification (histone 3 trimethylated at lysine 4) in the β-cells. The polycomb repressor complex 2 acts as a histone 3 lysine 27 methylase and an essential component of this complex, SUZ12, was enriched at the β-cell transcription factors in embryonic stem cells and was reduced MIN6. Knock-down of SUZ12 in embryonic stem cells, however, did not reduce the level of histone 3 trimethylated at lysine 27 at β-cell transcription factor loci or break the transcriptional repression of these genes in embryonic stem cells. This study shows the reduction in the total SUZ12 level was not a sufficient cause of the resolution of the epigenetic bivalency of β-cell transcription factors in embryonic stem cells.

Profiling of embryonic stem cell differentiation

Embryonic stem (ES) cells have been shown to recapitulate normal developmental stages. They are therefore a highly useful tool in the study of developmental biology. Profiling of ES cell-derived cells has yielded important information about the characteristics of differentiated cells, and allowed the identification of novel marker genes and pathways of differentiation. In this review, we focus on recent results from profiling studies of mouse embryos, human islets, and human ES cell-derived differentiated cells from several research groups. Global gene expression data from mouse embryos have been used to identify novel genes or pathways involved in the developmental process, and to search for transcription factors that regulate direct reprogramming. We introduce gene expression databases of human pancreas cells (Beta Cell Gene Atlas, EuroDia database), and summarize profiling studies of islet- or human ES cell-derived pancreatic cells, with a focus on gene expression, microRNAs, epigenetics, and protein expression. Then, we describe our gene expression profile analyses and our search for novel endoderm, or pancreatic, progenitor marker genes. We differentiated mouse ES cells into mesendoderm, definitive endoderm (DE), mesoderm, ectoderm, and Pdx1-expressing pancreatic lineages, and performed DNA microarray analyses. Genes specifically expressed in DE, and/or in Pdx1-expressing cells, were extracted and their expression patterns in normal embryonic development were studied by in situ hybridization. Out of 54 genes examined, 27 were expressed in the DE of E8.5 mouse embryos, and 15 genes were expressed in distinct domains in the pancreatic buds of E14.5 mouse embryos. Akr1c19, Aebp2, Pbxip1, and Creb3l1 were all novel, and none has been described as being expressed, either in the DE, or in the pancreas. By introducing the profiling results of ES cell-derived cells, the benefits of using ES cells to study early embryonic development will be discussed.

Adipogenic transcriptome profiling using high throughput technologies

The recent technological innovations in the area of functional genomics, gene expression/transcriptomic profiling can provide new insights to understand the molecular basis of adipogenesis. The focus of this review is to highlight the recent advances in our understanding of the complex interplay of gene expression events and the regulatory mechanisms of adipogenesis in mouse cell lines, humans and farm animals. All these studies have employed the availability of constantly evolving high throughput 'omics' technologies including microarrays, RNA-Seq, chromatin immunoprecipitation, next generation sequencing, RNAi, miRNA profiling and quantitative PCR arrays.

Differential effects of retinoids and inhibitors of ERK and p38 signaling on adipogenic and myogenic differentiation of P19 stem cells

All-trans-retinoic acid (atRA) is an essential signaling molecule in embryonic development. It regulates cell differentiation by activating nuclear retinoic acid receptors (RAR) and retinoid-X receptors (RXR), which both control gene expression. In addition, atRA could act in the cytoplasm by modulating the activity of mitogen-activated protein kinases (MAPK) ERK and p38, which also have a role in cell differentiation. AtRA can induce the differentiation of P19 embryonic carcinoma stem cells into adipocytes, cardiomyocytes, and skeletal muscle cells, concurrently, in the same culture. We postulated that combinations of atRA, atRA analogs exhibiting selectivity for RAR or RXR, and inhibitors of ERK and p38 signaling (ERKi and p38i) could be used to favor one mesodermal fate over the others in the P19 model. In a first series of experiments, we replaced atRA by an agonist of RXR (LG100268) or RAR (TTNPB) to preferentially stimulate one group of receptors over the other. LG100268 was as adipogenic and myogenic as atRA, whereas TTNPB strongly induced adipogenesis, but not myogenesis. ERKi enhanced the myogenic action of atRA, and p38i increased both adipogenesis and myogenesis. In a second series of experiments, we combined atRA with an RAR or RXR antagonist (RARatg or RXRatg) to preferentially deactivate each receptor group in turn. The combinations atRA+RXRatg and atRA+RARatg, including or not ERKi, had similar mesodermal actions as atRA. In contrast, there was no myogenesis with atRA+RXRatg+p38i treatment, and there were no myogenesis and no adipogenesis with the atRA+RARatg+p38i combination. Overall, the results indicate that p38 has a role in mesodermal differentiation that depends on the retinoid context. Indeed, p38 in conjunction with RXR is important in myogenesis, and p38 and RAR in adipogenesis. Under the conditions tested, it was possible to stimulate adipogenesis with a block on myogenesis, whereas increased myogenesis was accompanied by adipogenesis.

Novel pancreatic endocrine maturation pathways identified by genomic profiling and causal reasoning

We have used a previously unavailable model of pancreatic development, derived in vitro from human embryonic stem cells, to capture a time-course of gene, miRNA and histone modification levels in pancreatic endocrine cells. We investigated whether it is possible to better understand, and hence control, the biological pathways leading to pancreatic endocrine formation by analysing this information and combining it with the available scientific literature to generate models using a casual reasoning approach. We show that the embryonic stem cell differentiation protocol is highly reproducible in producing endocrine precursor cells and generates cells that recapitulate many aspects of human embryonic pancreas development, including maturation into functional endocrine cells when transplanted into recipient animals. The availability of whole genome gene and miRNA expression data from the early stages of human pancreatic development will be of great benefit to those in the fields of developmental biology and diabetes research. Our causal reasoning algorithm suggested the involvement of novel gene networks, such as NEUROG3/E2F1/KDM5B and SOCS3/STAT3/IL-6, in endocrine cell development We experimentally investigated the role of the top-ranked prediction by showing that addition of exogenous IL-6 could affect the expression of the endocrine progenitor genes NEUROG3 and NKX2.2.

Developmental origins of the adipocyte lineage: new insights from genetics and genomics studies

The current epidemic of obesity and overweight has caused a surge of interest in the study of adipose tissue formation. Much progress has been made in defining the transcriptional networks controlling the terminal differentiation of adipocyte progenitors into mature adipocytes. However, the early steps of adipocyte development and the embryonic origin of this lineage have been largely disregarded until recently. In mammals, two functionally different types of adipose tissues coexist, which are both involved in energy balance but assume opposite functions. White adipose tissue (WAT) stores energy, while brown adipose tissue (BAT) is specialized in energy expenditure. WAT and BAT can be found as several depots located in various sites of the body. Individual fat depots exhibit different timing of appearance during development, as well as distinct functional properties, suggesting possible differences in their developmental origin. This hypothesis has recently been revisited through large-scale genomics studies and in vivo lineage tracing approaches, which are reviewed in this report. These studies have provided novel fundamental insights into adipocyte biology, pointing out distinct developmental origins for WAT and BAT, as well as for individual WAT depots. They suggest that the adipose tissue is composed of distinct mini-organs, exhibiting developmental and functional differences, as well as variable contribution to obesity-related metabolic diseases.

PBX1: a novel stage-specific regulator of adipocyte development

Although adipocyte terminal differentiation has been extensively studied, the early steps of adipocyte development and the embryonic origin of this lineage remain largely unknown. Here we describe a novel role for the pre-B-cell leukemia transcription factor one (PBX1) in adipocyte development using both mouse embryonic stem cells (mESCs) and human multipotent adipose-derived stem (hMADS) cells. We show that Pbx1(-/-) mESCs are unable to generate adipocytes, despite normal expression of neuroectoderm and neural crest (NC) markers. Early adipocyte lineage markers are not induced in Pbx1(-/-) mESCs, suggesting that Pbx1 controls the generation and/or the maintenance of adipocyte progenitors (APs) from the NC. We further characterize the function of PBX1 in postnatal adipogenesis and show that silencing of PBX1 expression in hMADS cells reduces their proliferation by preventing their entry in the S phase of the cell cycle. Furthermore, it promotes differentiation of hMADS cells into adipocytes and partially substitutes for glucocorticoids and rosiglitazone, two key proadipogenic agents. These effects involve direct modulation of PPARγ activity, most likely through regulation of the biosynthesis of PPARγ natural endogenous ligand(s). Together, our data suggest that PBX1 regulates adipocyte development at multiple levels, promoting the generation of NC-derived APs during embryogenesis, while favoring APs proliferation and preventing their commitment to the adipocyte lineage in postnatal life.

g:Profiler--a web server for functional interpretation of gene lists (2011 update)

Functional interpretation of candidate gene lists is an essential task in modern biomedical research. Here, we present the 2011 update of g:Profiler (http://biit.cs.ut.ee/gprofiler/), a popular collection of web tools for functional analysis. g:GOSt and g:Cocoa combine comprehensive methods for interpreting gene lists, ordered lists and list collections in the context of biomedical ontologies, pathways, transcription factor and microRNA regulatory motifs and protein–protein interactions. Additional tools, namely the biomolecule ID mapping service (g:Convert), gene expression similarity searcher (g:Sorter) and gene homology searcher (g:Orth) provide numerous ways for further analysis and interpretation. In this update, we have implemented several features of interest to the community: (i) functional analysis of single nucleotide polymorphisms and other DNA polymorphisms is supported by chromosomal queries; (ii) network analysis identifies enriched protein–protein interaction modules in gene lists; (iii) functional analysis covers human disease genes; and (iv) improved statistics and filtering provide more concise results. g:Profiler is a regularly updated resource that is available for a wide range of species, including mammals, plants, fungi and insects.