Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells.

Adipocyte differentiation is driven by waves of transcriptional regulators that reprogram the enhancer landscape and change the wiring of the promoter interactome. Here, we use high-throughput chromosome conformation enhancer capture to interrogate the role of enhancer-to-enhancer interactions during differentiation of human mesenchymal stem cells. We find that enhancers form an elaborate network that is dynamic during differentiation and coupled with changes in enhancer activity. Transcription factors (TFs) at baited enhancers amplify TF binding at target enhancers, a phenomenon we term cross-interaction stabilization of TFs. Moreover, highly interconnected enhancers (HICE) act as integration hubs orchestrating differentiation by the formation of three-dimensional enhancer communities, inside which, HICE, and other enhancers, converge on phenotypically important gene promoters. Collectively, these results indicate that enhancer interactions play a key role in the regulation of enhancer function, and that HICE are important for both signal integration and compartmentalization of the genome.

Representativeness of personality and involvement preferences in a web-based survey on healthcare decision-making.

BACKGROUND: Obtaining a sample that is representative of the group of interest is of utmost importance in questionnaire studies. In a survey using a state authorized web-portal for citizen communication with authorities, we wanted to investigate the view of adult men on patient involvement in health care decision-making regarding Prostate-Specific Antigen test for prostatic cancer. In this paper, we report on sample characteristics and representativeness of our sample in terms of personality and baseline involvement preferences. METHODS: We compared personality profiles (BFI-10) and baseline healthcare decision-making preferences (CPS) in our sample (n = 6756) to internationally available datasets. Pooled data from a) US, UK, Canada, Australia, and New Zealand (n = 1512), b) Germany, Netherlands, Switzerland, and Belgium (n = 1136), and c) Norway, Sweden, Finland, and Denmark (n = 1313) were used for BFI-10 comparisons. Regarding CPS, we compared our sample with three previous datasets relating to decision-making in cancer (n = 425, 387, and 199). RESULTS: Although statistically significant differences particularly appeared in large dataset comparisons, sample BFI-10 and CPS profiles mostly were within the range of those previously reported. Similarity was greatest in BFI-10 comparisons with group a) where no statistically significant difference could be established in factors 'agreeableness' and 'neuroticism' (p = .095 and .578, respectively). CONCLUSION: Despite some variation, our sample displays personality and baseline preference profiles that are generally similar to those described in previous international studies. For example, this was the case with the BFI-10 'agreeableness' measure (incl. trust and fault-finding items), an important factor in healthcare decision-making.

Sociodemographic Representativeness in a Nationwide Web-Based Survey of the View of Men on Involvement in Health Care Decision-Making: Cross-Sectional Questionnaire Study.

BACKGROUND: Being able to generalize research findings to a broader population outside of the study sample is an important goal in surveys on the internet. We conducted a nationwide, cross-sectional, web-based survey with vignettes illustrating different levels of patient involvement to investigate men's preferences regarding participation in health care decision-making. Following randomization into vignette variants, we distributed the survey among men aged 45 to 70 years through the state-authorized digital mailbox provided by the Danish authorities for secure communication with citizens. OBJECTIVE: This study aimed to investigate the sociodemographic representativeness of our sample of men obtained in a nationwide web-based survey using the digital mailbox. METHODS: Response rate estimates were established, and comparisons were made between responders and nonresponders in terms of age profiles (eg, average age) and municipality-level information on sociodemographic characteristics. RESULTS: Among 22,288 men invited during two waves, a total of 6756 (30.31%) participants responded to the survey. In adjusted analyses, responders' characteristics mostly resembled those of nonresponders. Response rates, however, were significantly higher in older men (odds ratio [OR] 2.83 for responses among those aged 65-70 years compared with those aged 45-49 years, 95% CI 2.58-3.11; P<.001) and in rural areas (OR 1.10 compared with urban areas, 95% CI 1.03-1.18; P=.005). Furthermore, response rates appeared lower in areas with a higher tax base (OR 0.89 in the highest tertile, 95% CI 0.81-0.98; P=.02). CONCLUSIONS: Overall, the general population of men aged 45 to 70 years was represented very well by the responders to our web-based survey. However, the imbalances identified highlight the importance of supplementing survey findings with studies of the representativeness of other characteristics of the sample like trait and preference features, so that proper statistical corrections can be made in upcoming analyses of survey responses whenever needed.

Men's view on participation in decisions about prostate-specific antigen (PSA) screening: patient and public involvement in development of a survey.

BACKGROUND: Prostate-Specific Antigen (PSA) screening for early detection of prostate cancer (PCa) may prevent some cancer deaths, but also may miss some cancers or lead to unnecessary and potentially harmful treatment. Therefore, involving patients in decision-making about PSA screening is recommended. However, we know little about the attitude of men regarding participation in decisions about PSA screening and how to assess such attitudes. The purpose of this paper is to describe patient and public participation in the development of a national, web-based case vignette survey for studying men's view on participation in decision-making about PSA screening. METHODS: The project group developed a first draft plan for the survey, its vignettes and choice of measurements. This included multiple vignette variants representing various levels of patient participation in decision-making about PSA screening with different outcomes. Additionally, it included questions on respondents' satisfaction with imagined courses of health care, their propensity to initiate a malpractice complaint, their own health care experiences, socio-demography, personality, and preferences for control regarding health care decision-making. Following feedback from a workshop with academic peers on the draft plan, a group of 30 adult men was engaged to help develop case vignette versions and questionnaire items by providing feedback on structure, comprehension, response patterns, and time required to complete the survey. Furthermore, a panel of three patients with PCa experience was assembled to assist development through a separate review-and-feedback process. RESULTS: Based on reviews of survey drafts, the large group made further suggestions about construction of the survey (e.g. clarification and modification of case vignette versions, deletion of items and adjustment of wording, instructions to guide respondents, replacement of technical terms, and optimization of sequence of survey elements). The patient panel ensured fine-tuning of vignette versions and questionnaire items and helped review the internet version of the survey. CONCLUSIONS: Patient and public involvement during various phases of the survey development helped modify and refine survey structure and content. The survey exemplifies a way to measure health care users' satisfaction with imagined courses of health care and wish to complain, taking into account their characteristics.

Metabolic programming determines the lineage-differentiation fate of murine bone marrow stromal progenitor cells.

Enhanced bone marrow adipogenesis and impaired osteoblastogenesis have been observed in obesity, suggesting that the metabolic microenvironment regulates bone marrow adipocyte and osteoblast progenitor differentiation fate. To determine the molecular mechanisms, we studied two immortalized murine cell lines of adipocyte or osteoblast progenitors (BMSCsadipo and BMSCsosteo, respectively) under basal and adipogenic culture conditions. At baseline, BMSCsadipo, and BMSCsosteo exhibit a distinct metabolic program evidenced by the presence of specific global gene expression, cellular bioenergetics, and metabolomic signatures that are dependent on insulin signaling and glycolysis in BMSCsosteo versus oxidative phosphorylation in BMSCsadipo. To test the flexibility of the metabolic program, we treated BMSCsadipo with parathyroid hormone, S961 (an inhibitor of insulin signaling) and oligomycin (an inhibitor of oxidative phosphorylation). The treatment induced significant changes in cellular bioenergetics that were associated with decreased adipocytic differentiation. Similarly, 12 weeks of a high-fat diet in mice led to the expansion of adipocyte progenitors, enhanced adipocyte differentiation and insulin signaling in cultured BMSCs. Our data demonstrate that BMSC progenitors possess a distinct metabolic program and are poised to respond to exogenous metabolic cues that regulate their differentiation fate.

Obesity-Associated Hypermetabolism and Accelerated Senescence of Bone Marrow Stromal Stem Cells Suggest a Potential Mechanism for Bone Fragility.

Obesity is associated with increased risk for fragility fractures. However, the cellular mechanisms are unknown. Using a translational approach combining RNA sequencing and cellular analyses, we investigated bone marrow stromal stem cells (BM-MSCs) of 54 men divided into lean, overweight, and obese groups on the basis of BMI. Compared with BM-MSCs obtained from lean, obese BM-MSCs exhibited a shift of molecular phenotype toward committed adipocytic progenitors and increased expression of metabolic genes involved in glycolytic and oxidoreductase activity. Interestingly, compared with paired samples of peripheral adipose tissue-derived stromal cells (AT-MSCs), insulin signaling of obese BM-MSCs was enhanced and accompanied by increased abundance of insulin receptor positive (IR+) and leptin receptor positive (LEPR+) cells in BM-MSC cultures. Their hyper-activated metabolic state was accompanied by an accelerated senescence phenotype. Our data provide a plausible explanation for the bone fragility in obesity caused by enhanced insulin signaling leading to accelerated metabolic senescence of BM-MSCs.

Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets.

Introduction: Drug-resistant infections are becoming increasingly frequent worldwide, causing hundreds of thousands of deaths annually. This is partly due to the very limited set of protein drug targets known for human-infecting viral genomes. The eleven influenza virus proteins, for instance, exploit host cell factors for replication and suppression of the antiviral immune responses. A systems medicine approach to identify relevant and druggable host factors would dramatically expand therapeutic options. Therapeutic target identification, however, has hitherto relied on static molecular networks, whereas in reality the interactome, in particular during an infection, is subject to constant change. Methods: We developed time-course network enrichment (TiCoNE), an expert-centered approach for discovering temporal response pathways. In the first stage of TiCoNE, time-series expression data is clustered in a human-augmented manner to identify groups of biological entities with coherent temporal responses. Throughout this process, the expert can add, remove, merge, or split temporal patterns. The resulting groups can then be mapped to an interaction network to identify enriched pathways and to analyze cross-talk enrichments and depletions between groups. Finally, temporal response groups of two experiments can be intersected, to identify condition-variant response patterns that represent promising drug-target candidates. Results: We applied TiCoNE to human gene expression data for influenza A virus infection and rhino virus infection, respectively. We then identified coherent temporal response patterns and employed our cross-talk analysis to establish two potential timelines of systems-level host responses for either infection. Next, we compared the two phenotypes and unraveled condition-variant temporal groups interacting on a networks level. The highest-ranking ones we then validated via literature search and wet-lab experiments. This not only confirmed many of our candidates as previously known, but we also identified phospholipid scramblase 1 (encoded by PLSCR1) as a previously not recognized host factor that is essential for influenza A virus infection. Conclusion: With TiCoNE we developed a novel approach for conjointly analyzing molecular networks with time-series expression data and demonstrated its power by identifying temporal drug-targets. We provide proof-of-concept that not only novel targets can be identified using our approach, but also that anti-infective drug target discovery can be enhanced by investigating temporal molecular networks of the host in response to viral infection.

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Mesenchymal (stromal) stem cells (MSCs) constitute populations of mesodermal multipotent cells involved in tissue regeneration and homeostasis in many different organs. Here we performed comprehensive characterization of the transcriptional and epigenomic changes associated with osteoblast and adipocyte differentiation of human MSCs. We demonstrate that adipogenesis is driven by considerable remodeling of the chromatin landscape and de novo activation of enhancers, whereas osteogenesis involves activation of preestablished enhancers. Using machine learning algorithms for in silico modeling of transcriptional regulation, we identify a large and diverse transcriptional network of pro-osteogenic and antiadipogenic transcription factors. Intriguingly, binding motifs for these factors overlap with SNPs related to bone and fat formation in humans, and knockdown of single members of this network is sufficient to modulate differentiation in both directions, thus indicating that lineage determination is a delicate balance between the activities of many different transcription factors.

Author Correction: Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

In the version of this article initially published, in the graph keys in Fig. 1i, the colors indicating 'Ob' and 'Ad' were red and blue, respectively, but should have been blue and red, respectively; the shapes indicating 'MUS' and 'BM' were a triangle and a square, respectively, but should have been a square and a triangle, respectively. The errors have been corrected in the HTML and PDF versions of the article.

PPARγ and the global map of adipogenesis and beyond.

Peroxisome proliferator-activated receptor γ (PPARγ) is a member of the nuclear receptor (NR) superfamily of ligand-dependent transcription factors (TFs) and function as a master regulator of adipocyte differentiation and metabolism. We review recent breakthroughs in the understanding of PPARγ gene regulation and function in the chromatin context. It is now clear that multiple TFs team up to induce PPARγ during adipogenesis, and that other TFs cooperate with PPARγ to ensure adipocyte-specific genomic binding and function. We discuss how this differs in other PPARγ-expressing cells such as macrophages and how these genome-wide mechanisms are preserved across species despite modest conservation of specific binding sites. These emerging considerations inform our understanding of PPARγ function as well as of adipocyte development and physiology.

Acute genome-wide effects of rosiglitazone on PPARγ transcriptional networks in adipocytes.

Peroxisome proliferator-activated receptor γ (PPARγ) is a master regulator of adipocyte differentiation, and genome-wide studies indicate that it is involved in the induction of most adipocyte genes. Here we report, for the first time, the acute effects of the synthetic PPARγ agonist rosiglitazone on the transcriptional network of PPARγ in adipocytes. Treatment with rosiglitazone for 1 hour leads to acute transcriptional activation as well as repression of a number of genes as determined by genome-wide RNA polymerase II occupancy. Unlike what has been shown for many other nuclear receptors, agonist treatment does not lead to major changes in the occurrence of PPARγ binding sites. However, rosiglitazone promotes PPARγ occupancy at many preexisting sites, and this is paralleled by increased occupancy of the mediator subunit MED1. The increase in PPARγ and MED1 binding is correlated with an increase in transcription of nearby genes, indicating that rosiglitazone, in addition to activating the receptor, also promotes its association with DNA, and that this is causally linked to recruitment of mediator and activation of genes. Notably, both rosiglitazone-activated and -repressed genes are induced during adipogenesis. However, rosiglitazone-activated genes are markedly more associated with PPARγ than repressed genes and are highly dependent on PPARγ for expression in adipocytes. By contrast, repressed genes are associated with the other key adipocyte transcription factor CCAAT-enhancer binding proteinα (C/EBPα), and their expression is more dependent on C/EBPα. This suggests that the relative occupancies of PPARγ and C/EBPα are critical for whether genes will be induced or repressed by PPARγ agonist.

Short-chain fatty acids stimulate angiopoietin-like 4 synthesis in human colon adenocarcinoma cells by activating peroxisome proliferator-activated receptor γ.

Angiopoietin-like protein 4 (ANGPTL4/FIAF) has been proposed as a circulating mediator between the gut microbiota and fat storage. Here, we show that transcription and secretion of ANGPTL4 in human T84 and HT29 colon adenocarcinoma cells is highly induced by physiological concentrations of short-chain fatty acids (SCFA). SCFA induce ANGPTL4 by activating the nuclear receptor peroxisome proliferator activated receptor γ (PPARγ), as demonstrated using PPARγ antagonist, PPARγ knockdown, and transactivation assays, which show activation of PPARγ but not PPARα and PPARδ by SCFA. At concentrations required for PPARγ activation and ANGPTL4 induction in colon adenocarcinoma cells, SCFA do not stimulate PPARγ in mouse 3T3-L1 and human SGBS adipocytes, suggesting that SCFA act as selective PPARγ modulators (SPPARM), which is supported by coactivator peptide recruitment assay and structural modeling. Consistent with the notion that fermentation leads to PPAR activation in vivo, feeding mice a diet rich in inulin induced PPAR target genes and pathways in the colon. We conclude that (i) SCFA potently stimulate ANGPTL4 synthesis in human colon adenocarcinoma cells and (ii) SCFA transactivate and bind to PPARγ. Our data point to activation of PPARs as a novel mechanism of gene regulation by SCFA in the colon, in addition to other mechanisms of action of SCFA.