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      Disruption of STAT5b-Regulated Sexual Dimorphism of the Liver Transcriptome by Diverse Factors Is a Common Event

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          Abstract

          Signal transducer and activator of transcription 5b (STAT5b) is a growth hormone (GH)-activated transcription factor and a master regulator of sexually dimorphic gene expression in the liver. Disruption of the GH hypothalamo-pituitary-liver axis controlling STAT5b activation can lead to metabolic dysregulation, steatosis, and liver cancer. Computational approaches were developed to identify factors that disrupt STAT5b function in a mouse liver gene expression compendium. A biomarker comprised of 144 STAT5b-dependent genes was derived using comparisons between wild-type male and wild-type female mice and between STAT5b-null and wild-type mice. Correlations between the STAT5b biomarker gene set and a test set comprised of expression datasets (biosets) with known effects on STAT5b function were evaluated using a rank-based test (the Running Fisher algorithm). Using a similarity p-value ≤ 10 −4, the test achieved a balanced accuracy of 99% and 97% for detection of STAT5b activation or STAT5b suppression, respectively. The STAT5b biomarker gene set was then used to identify factors that activate (masculinize) or suppress (feminize) STAT5b function in an annotated mouse liver and primary hepatocyte gene expression compendium of ~1,850 datasets. Disruption of GH-regulated STAT5b is a common phenomenon in liver in vivo, with 5% and 29% of the male datasets, and 11% and 13% of the female datasets, associated with masculinization or feminization, respectively. As expected, liver STAT5b activation/masculinization occurred at puberty and suppression/feminization occurred during aging and in mutant mice with defects in GH signaling. A total of 70 genes were identified that have effects on STAT5b activation in genetic models in which the gene was inactivated or overexpressed. Other factors that affected liver STAT5b function were shown to include fasting, caloric restriction and infections. Together, these findings identify diverse factors that perturb the hypothalamo-pituitary-liver GH axis and disrupt GH-dependent STAT5b activation in mouse liver.

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          Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

          Recent advances in cDNA and oligonucleotide DNA arrays have made it possible to measure the abundance of mRNA transcripts for many genes simultaneously. The analysis of such experiments is nontrivial because of large data size and many levels of variation introduced at different stages of the experiments. The analysis is further complicated by the large differences that may exist among different probes used to interrogate the same gene. However, an attractive feature of high-density oligonucleotide arrays such as those produced by photolithography and inkjet technology is the standardization of chip manufacturing and hybridization process. As a result, probe-specific biases, although significant, are highly reproducible and predictable, and their adverse effect can be reduced by proper modeling and analysis methods. Here, we propose a statistical model for the probe-level data, and develop model-based estimates for gene expression indexes. We also present model-based methods for identifying and handling cross-hybridizing probes and contaminating array regions. Applications of these results will be presented elsewhere.
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            Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis.

            Quality Control is a fundamental aspect of successful microarray data analysis. Simpleaffy is a BioConductor package that provides access to a variety of QC metrics for assessing the quality of RNA samples and of the intermediate stages of sample preparation and hybridization. Simpleaffy also offers fast implementations of popular algorithms for generating expression summaries and detection calls. Simpleaffy can be downloaded from http://www.bioconductor.org. Additional information can be found on the supplementary website located at http://bioinformatics.picr.man.ac.uk.
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              The starvation hormone, fibroblast growth factor-21, extends lifespan in mice

              Introduction Caloric restriction without malnutrition is a proven means of inhibiting aging in species ranging from worms to nonhuman primates (Masoro, 2005; Bishop and Guarente, 2007; Kenyon, 2010). The effect of caloric restriction on longevity appears to be mediated by multiple nutrient-sensing pathways including those involving insulin and insulin-like growth factor (IGF-1), target of rapamycin (TOR), AMP kinase and sirtuins. Pharmacologic and/or genetic manipulation of these pathways increases longevity to varying degrees, suggesting the feasibility of drugs that increase lifespan in the absence of caloric restriction (Bishop and Guarente, 2007; Kenyon, 2010; Barzilai et al., 2012). Fibroblast growth factor-21 (FGF21) is an atypical FGF that functions as an endocrine hormone (Potthoff et al., 2012). In mice, FGF21 is strongly induced in liver in response to prolonged fasts through a peroxisome proliferator-activated receptor α-dependent mechanism. FGF21 in turn elicits diverse aspects of the adaptive starvation response. Among these, FGF21 increases insulin sensitivity and causes a corresponding decrease in basal insulin concentrations; FGF21 increases hepatic fatty acid oxidation, ketogenesis and gluconeogenesis; and, FGF21 sensitizes mice to torpor, a hibernation-like state of reduced body temperature and physical activity (Potthoff et al., 2012). FGF21 also blocks somatic growth by causing GH resistance, a phenomenon associated with starvation. Transgenic (Tg) mice overexpressing FGF21 are markedly smaller than wild-type mice and have a corresponding decrease in circulating IGF-1 concentrations despite having elevated growth hormone (GH) levels (Inagaki et al., 2008). Conversely, FGF21-knockout mice grow more than wild-type mice under conditions of nutrient deprivation (Kubicky et al., 2012). In liver, FGF21 inhibits the GH signaling pathway by blocking JAK2-mediated phosphorylation and nuclear translocation of the transcription factor, STAT5. This suppresses the transcription of Igf1 and other GH/STAT5-regulated genes (Inagaki, et al., 2008). Thus, FGF21-mediated repression of the GH/IGF-1 axis provides a mechanism for blocking growth and conserving energy under starvation conditions. Dwarf mice, including the pituitary loss-of-function Ames and Snell strains and GH receptor/GH binding protein-knockout mice, are the longest living mouse mutants discovered to date, living up to ∼70% longer than their wild-type counterparts (Liang et al., 2003; Bartke and Brown-Borg, 2004; Brown-Borg and Bartke, 2012). Interestingly, FGF21-Tg mice share a number of phenotypes with these long-lived mice including small size, enhanced insulin sensitivity and a blunted GH/IGF-1 signaling axis. In this report, using FGF21-Tg mice, we examine the consequences of chronic FGF21 exposure on lifespan. Results We previously described FGF21-Tg mice in which the FGF21 transgene is selectively expressed in hepatocytes under the control of the apoE promoter (Inagaki et al., 2007, 2008). Circulating concentrations of FGF21 are ∼5–10-fold higher in the FGF21-Tg mice than under fasted conditions. Younger FGF21-Tg mice ( 30% of the age-matched female FGF21-Tg mice were still alive at 44 months of age. 10.7554/eLife.00065.006 Figure 3. FGF21 extends lifespan. (A–C) Kaplan–Meyer survival curves for wild-type (WT) and FGF21-transgenic (Tg) mice are shown. (A) Combined male and female data; (B) male data; (C) female data. (D) Median survival time (at 50th percentile) and maximum lifespan (at 95th percentile) for each cohort. Hazard ratios (HR) and 95% confidence intervals are shown for Tg vs WT mice. DOI: http://dx.doi.org/10.7554/eLife.00065.006 Since FGF21 is induced by fasting and elicits diverse aspects of the adaptive starvation response, we examined whether chronic FGF21 exposure mimics nutrient deprivation with respect to changes in gene expression. Comprehensive transcriptome analysis was performed by microarray using RNA from liver, gastrocnemius muscle and epididymal white adipose tissue of wild-type and FGF21-Tg mice and mice subjected to either caloric restriction or a 24 hr fast. Using a false discovery rate 2 as criteria, we found that expression of 33, 8 and 22 genes was changed in liver, muscle and adipose of FGF21-Tg mice, respectively (Figure 4A). Many more genes were regulated by caloric restriction or fasting than by the FGF21 transgene in all three tissues. As expected, Fgf21 was strongly induced in liver by fasting. Surprisingly, however, Fgf21 was not induced by the caloric restriction regimen (Figure 4B). Likewise, there was no increase in plasma FGF21 concentrations in response to caloric restriction (data not shown). While the molecular basis for this differential regulation of Fgf21 by fasting and caloric restriction is not yet known, these data indicate that FGF21 is not an endogenous mediator of the caloric restriction response. Notably, 30 of the 33 genes with changed expression in liver of FGF21-Tg mice were also regulated by caloric restriction, while 20 of these genes were regulated by fasting (Figure 4B). Eight of the genes with altered expression in liver of FGF21-Tg mice (highlighted in red in Figure 4B; see Discussion) are similarly regulated in long-lived dwarf mice (Swindell, 2007). In contrast, there was little overlap in genes regulated by FGF21 and either caloric restriction or fasting in muscle or adipose. These data suggest that FGF21 may extend lifespan by regulating a small subset of genes also regulated by caloric restriction in liver. 10.7554/eLife.00065.007 Figure 4. Genes regulated by FGF21 and caloric restriction overlap in liver. (A) Venn diagrams showing overlap of genes significantly regulated in liver, muscle and adipose tissue of FGF21-transgenic (Tg) vs wild-type (WT) mice (FDR twofold regulation) compared to the same gene expression analysis in calorically restricted (CR) vs ad libitum (AL) or fasted vs AL mice. (B) Heat map of genes significantly regulated in liver of FGF21-Tg vs WT (FDR twofold regulation) compared to expression of the same liver gene set regulated by fasting or CR. Microarray analysis was performed using liver, epididymal white adipose tissue and gastrocnemius muscle from wild-type and FGF21-Tg male mice and male C57BL/6J mice subjected to 60% caloric restriction for 2 weeks or a 24 hr fast. All mice used in these studies were 3 months old at the end of the study. DOI: http://dx.doi.org/10.7554/eLife.00065.007 Increases in AMP kinase and sirtuin activity and decreases in mTOR activity are associated with increased longevity (Bishop and Guarente, 2007; Kenyon, 2010). To begin to assess whether these pathways are affected by FGF21, we measured phosphorylated and total levels of AMP kinase and the mTOR targets S6 and 4E-BP1in liver, muscle and adipose tissue of male and female wild-type and FGF21-Tg mice. We also determined mitochondrial DNA content in liver as a downstream measure of AMP kinase activity. Phospho-AMP kinase levels were not increased in tissues from FGF21-Tg mice (Figure 5A–C). Consistent with these data, mitochondrial DNA content was unchanged in liver (Figure 5D). While Phospho-S6 and phospho-4E-BP1 levels were decreased in muscle of male FGF21-Tg mice (Figure 5B), they were unchanged in muscle of longer-lived FGF21-Tg females or in liver or adipose from either sex (Figure 5A–C). We also did not observe increases in NAD+ concentrations (Figure 5E) or the mRNA levels of Sirtuins 1–7 (data not shown) in liver of FGF21-Tg mice, suggesting that sirtuin activity is unlikely to be increased. Taken together, these data suggest that FGF21 may increase longevity through a mechanism independent of the AMP kinase, mTOR and sirtuin pathways. 10.7554/eLife.00065.008 Figure 5. Evaluation of markers of AMP kinase, mTOR and sirtuin pathway activity in FGF21-Tg mice. Phosphorylated levels of AMP kinase, S6, and 4E-BP1 in (A) liver, (B) gastrocnemius muscle, and (C) epididymal white adipose tissue; (D) mitochondrial DNA content and (E) NAD+ concentrations in liver of 26_28-month-old male and female wild-type (WT) and FGF21-transgenic (Tg) mice (n=4/group except for female adipose tissue, where n=2/group; all data are presented as the mean ± SEM; *p 2 as criteria. Statistical analyses Results were analyzed by a Student’s unpaired t-test using GraphPad Prism (GraphPad Software, Inc.). All data are presented as the mean ± SEM. Accession numbers The microarray data have been deposited in the NCBI Gene Expression Omnibus with accession number GSE39313.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                9 March 2016
                2016
                : 11
                : 3
                : e0148308
                Affiliations
                [1 ]Integrated Systems Toxicology Division, NHEERL/ORD, US-EPA, Research Triangle Park, NC 27711, United States of America
                [2 ]Division of Cell and Molecular Biology, Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215, United States of America
                University of Nebraska Medical Center, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: JCC KO. Performed the experiments: JCC KO NV. Analyzed the data: JCC KO NV. Wrote the paper: JCC KO NV DW.

                [¤]

                Current address: Toray Industries, Inc., Kanagawa, Japan

                Article
                PONE-D-15-27914
                10.1371/journal.pone.0148308
                4784905
                26959975
                2ca946b5-af94-4082-ac2f-69a880823b6a

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 25 June 2015
                : 15 January 2016
                Page count
                Figures: 7, Tables: 0, Pages: 27
                Funding
                The information in this document has been funded in part by the U.S. Environmental Protection Agency, and by NIH grant DK33765 (to DJW). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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                All raw microarray files are available from the Gene Expression Omnibus database (accession numbers are listed in the manuscript).

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