| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Amundadottir, Laufey, et al.
(författare)
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Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer.
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 41, s. 986-990
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Tidskriftsartikel (refereegranskat)abstract
- We conducted a two-stage genome-wide association study of pancreatic cancer, a cancer with one of the lowest survival rates worldwide. We genotyped 558,542 SNPs in 1,896 individuals with pancreatic cancer and 1,939 controls drawn from 12 prospective cohorts plus one hospital-based case-control study. We conducted a combined analysis of these groups plus an additional 2,457 affected individuals and 2,654 controls from eight case-control studies, adjusting for study, sex, ancestry and five principal components. We identified an association between a locus on 9q34 and pancreatic cancer marked by the SNP rs505922 (combined P = 5.37 x 10(-8); multiplicative per-allele odds ratio 1.20; 95% confidence interval 1.12-1.28). This SNP maps to the first intron of the ABO blood group gene. Our results are consistent with earlier epidemiologic evidence suggesting that people with blood group O may have a lower risk of pancreatic cancer than those with groups A or B.
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| 3. |
- Azevedo, M, et al.
(författare)
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Infection by Helicobacter pylori expressing the BabA adhesin is influenced by the secretor phenotype
- 2008
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Ingår i: Journal of Pathology. - : Wiley. - 0022-3417 .- 1096-9896. ; 215:3, s. 308-316
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Tidskriftsartikel (refereegranskat)abstract
- Helicobacter pylori (Hp) infects half the world's population and causes diverse gastric lesions, from gastritis to gastric cancer. Our aim was to evaluate the significance of secretor and Lewis status in infection and in vitro adherence by Hp expressing BabA adhesin. We enrolled 304 Hp-infected individuals from Northern Portugal. Gastric biopsies, blood and saliva were collected. Polymerase chain reaction (PCR) and immunofluorescence were used to detect BabA+ Hp in gastric biopsies. In vitro adherence by a BabA expressing Hp strain to gastric biopsies was performed. Secretor status was identified by Ulex, a lectin that recognizes secretor-dependent glycan structures in saliva and in gastric mucosa, and by Lewis(a/b) antibodies, and indirectly by identification of an inactivating mutation in the FUT2 gene (G428A). BabA status of infecting Hp was associated with CagA and VacAs1 (p < 0.05), intercellular localization of Hp (p < 0.01) and the presence of intestinal metaplasia (p < 0.05) and degenerative alterations (p < 0.005) in the biopsies. BabA was associated (p < 0.05) with Ulex staining of gastric biopsies and, although not significantly, to absence of homozygosity for FUT2 G428A inactivating polymorphism. In vitro Hp adherence was higher in cases wild-type or heterozygous for FUT2 G428A mutation (p < 0.0001), cases staining for Ulex (p < 0.0001) and a(-)b+ and a(-)b(-) secretor phenotypes (p < 0.001). In conclusion, BabA+ Hp infection/adhesion is secretor-dependent and associated with the severity of gastric lesions.
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| 4. |
- Roos, Sara, 1979, et al.
(författare)
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Expression of placental mammalian target of rapamycin (mTOR) is altered in relation to fetal growth and mTOR regulates leucine transport
- 2005
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Ingår i: Placenta. - 0143-4004. ; 26:8-9
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Konferensbidrag (refereegranskat)abstract
- Placental transport functions are altered in pregnancies complicated by restricted (IUGR) or accelerated fetal growth (LGA; large-for-gestational-age). We have suggested that the placenta may function as a nutrient sensor, regulating its nutrient transport in response to changes in substrate supply, and consequently altering fetal growth. mTOR is a protein kinase involved in regulating protein translation in response to nutrient stimuli. mTOR mRNA has been shown to be expressed in the placenta, its functional role however is unknown. To test the hypothesis that mTOR is involved in placental nutrient sensing we investigated mTOR protein expression in the human placenta in relation to fetal growth and we assessed the effect of the mTOR inhibitor rapamycin on amino acid transporter activity. Methods: mTOR expression was studied by immunohistochemistry and Western blotting and amino acid transporter activity was measured in term villous fragments. Results: mTOR protein was expressed in the cytoplasm of the syncytiotrophoblast. mTOR protein expression was up-regulated by 51% (p < 0.05) in homogenates of IUGR placentas (n = 9, controls n = 12) and down-regulated by 42% (p < 0.05) in placentas of LGA infants (n = 6, controls n = 15). Rapamycin (100 nM) decreased system L activity by 35% (n = 7, p < 0.05) but did not affect the activity of system A or taurine transporters. Conclusion: Placental mTOR protein expression is inversely related to fetal growth. Inhibition of placental mTOR decreases placental leucine transport, representing a novel regulatory mechanism for the L amino acid transporter. These findings are compatible with the hypothesis that the mTOR signaling system may play a role in placental nutrient sensing.
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| 5. |
- Roos, Sara, 1979, et al.
(författare)
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Mammalian target of rapamycin in the human placenta regulates leucine transport and is down-regulated in restricted fetal growth.
- 2007
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Ingår i: The Journal of physiology. - : Wiley. - 0022-3751. ; 582:Pt 1, s. 449-59
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Tidskriftsartikel (refereegranskat)abstract
- Pathological fetal growth is associated with perinatal morbidity and the development of diabetes and cardiovascular disease later in life. Placental nutrient transport is a primary determinant of fetal growth. In human intrauterine growth restriction (IUGR) the activity of key placental amino acid transporters, such as systems A and L, is decreased. However the mechanisms regulating placental nutrient transporters are poorly understood. We tested the hypothesis that the mammalian target of rapamycin (mTOR) signalling pathway regulates amino acid transport in the human placenta and that the activity of the placental mTOR pathway is reduced in IUGR. Using immunohistochemistry and culture of trophoblast cells, we show for the first time that the mTOR protein is expressed in the transporting epithelium of the human placenta. We further demonstrate that placental mTOR regulates activity of the l-amino acid transporter, but not system A or taurine transporters, by determining the mediated uptake of isotope-labelled leucine, methylaminoisobutyric acid and taurine in primary villous fragments after inhibition of mTOR using rapamycin. The protein expression of placental phospho-S6K1 (Thr-389), a measure of the activity of the mTOR signalling pathway, was markedly reduced in placentas obtained from pregnancies complicated by IUGR. These data identify mTOR as an important regulator of placental amino acid transport, and provide a mechanism for the changes in placental leucine transport in IUGR previously demonstrated in humans. We propose that mTOR functions as a placental nutrient sensor, matching fetal growth with maternal nutrient availability by regulating placental nutrient transport.
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| 6. |
- Roos, Sara, 1979, et al.
(författare)
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Placental mTOR links maternal nutrient availability to fetal growth.
- 2009
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Ingår i: Biochemical Society transactions. - 1470-8752. ; 37:Pt 1, s. 295-8
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Tidskriftsartikel (refereegranskat)abstract
- The mTOR (mammalian target of rapamycin) signalling pathway functions as a nutrient sensor, both in individual cells and, more globally, in organs such as the fat body in Drosophila and the hypothalamus in the rat. The activity of placental amino acid transporters is decreased in IUGR (intrauterine growth restriction), and recent experimental evidence suggests that these changes contribute directly to the restricted fetal growth. We have shown that mTOR regulates the activity of the placental L-type amino acid transporter system and that placental mTOR activity is decreased in IUGR. The present review summarizes the emerging evidence implicating placental mTOR signalling as a key mechanism linking maternal nutrient and growth factor concentrations to amino acid transport in the human placenta. Since fetal growth is critically dependent on placental nutrient transport, placental mTOR signalling plays an important role in the regulation of fetal growth.
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| 7. |
- Roos, Sara, 1979, et al.
(författare)
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Regulation of amino acid transporters by glucose and growth factors in cultured primary trophoblast cells is mediated by mTOR signaling
- 2009
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Ingår i: American Journal of Physiology - Cell Physiology. - : American Physiological Society. - 0363-6143 .- 1522-1563. ; 298, s. C723-C731
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Tidskriftsartikel (refereegranskat)abstract
- Inhibition of mammalian target of rapamycin (mTOR) signaling in cultured human primary trophoblast cells reduces the activity of key placental amino acid transporters. However, the upstream regulators of placental mTOR are unknown. We hypothesized that glucose, insulin, and IGF-I regulate placental amino acid transporters by inducing changes in mTOR signaling. Primary human trophoblast cells were cultured for 24 h with media containing various glucose concentrations, insulin, or IGF-I, with or without the mTOR inhibitor rapamycin, and, subsequently, the activity of system A, system L, and taurine (TAUT) transporters was measured. Glucose deprivation (0.5 mM glucose) did not significantly affect Thr172-AMP-activated protein kinase phosphorylation or REDD1 expression but decreased S6 kinase 1 phosphorylation at Thr389. The activity of system L decreased in a dose-dependent manner in response to decreasing glucose concentrations. This effect was abolished in the presence of rapamycin. Glucose deprivation had two opposing effects on system A activity: 1) an “adaptive” upregulation mediated by an mTOR-independent mechanism and 2) downregulation by an mTOR-dependent mechanism. TAUT activity was increased after incubating cells with glucose-deprived media, and this effect was largely independent of mTOR signaling. Insulin and IGF-I increased system A activity and insulin stimulated system L activity, effects that were abolished by rapamycin. We conclude that the mTOR pathway represents an important intracellular regulatory link between nutrient and growth factor concentrations and amino acid transport in the human placenta.intrauterine growth restriction (IUGR) and accelerated fetal growth represent two important clinical conditions that occur in 15% of all pregnancies (1, 2). Aberrant fetal growth is associated with an increased risk of perinatal morbidity (7) as well as metabolic abnormalities in adult life, such as obesity, type 2 diabetes, and cardiovascular disease (6, 12, 46). The most important determinant of fetal growth is nutrient availability, which is highly dependent on placental transport capacity. The mechanisms underlying altered fetal growth remain to be established, but accumulating evidence implicates changes in the activity of specific placental amino acid transporters as a critical factor contributing to abnormal fetal growth (27, 54). Experimental evidence supports the hypothesis that changes in placental nutrient transporter activity are a cause of rather than a response to altered fetal growth. For example, in pregnant rats subjected to protein malnutrition, it is likely that downregulation of the placental system A amino acid transporter directly contributes to the development of IUGR (26).In IUGR, fetuses may be hypoglycemic (15) and have reduced circulating levels of insulin (43) and IGF-I (4, 34). The maternal levels of glucose (15) and IGF-I (40, 41) may also be reduced in this condition. The placenta of the IUGR fetus could therefore be exposed to decreased levels of glucose, hormones, and growth factors. Both insulin and IGF-I stimulate placental system A activity (24, 30, 31). These results suggest that extracellular cues regulate placental nutrient transporters and, as a consequence, fetal nutrient supply, but the cellular mechanisms remain to be fully established.The mammalian target of rapamycin (mTOR) is a serine/threonine kinase that is regulated by a multitude of intracellular and extracellular signals. For example, mTOR is activated by growth factors and nutrient levels, such as amino acids (59), and inhibited by numerous stress conditions, such as cellular energy depletion (13, 17). Glucose may also regulate mTOR signaling through energy production in the form of ATP (13, 17). The AMP-activated protein kinase (AMPK) is regulated by the AMP-to-ATP ratio, which rises under nutrient deprivation and activates AMPK (10). Activated AMPK can in turn phosphorylate tuberous sclerosis complex 2 (TSC2), leading to mTOR inactivation (23). AMPK is phosphorylated and activated by LKB1 (52), and it has been shown that phosphorylation of LKB1 at Ser428 is essential for AMPK activation by metformin, and the authors speculate that LKB1-Ser428 phosphorylation may be a common pathway required for AMPK activation (60). There might also be additional, AMPK-independent, pathways involved in energy depletion. A recent report has shown that REDD1 (regulated in development and DNA damage responses 1) in mouse embryonic fibroblasts is induced by chronic energy depletion, and this in turn leads to inactivation of mTOR complex 1 (mTORC1) measured as phosphorylation of S6 kinase 1 (S6K1) at Thr389, independent of AMPK (55).Insulin and IGF-I activate the tyrosine kinase activity of its receptors to phosphorylate the insulin receptor substrate 1, which in turn activates phosphatidylinositol 3-kinase (PI3K) to generate PI(3,4,5)P3. Phosphatidylinositol 3,4,5-trisphosphate (PIP3) binding to Akt leads to the translocation of Akt to the plasma membrane, where it is phosphorylated and activated. The activation of Akt positively modulates mTORC1 function, by phosphorylating, and inhibiting, TSC2 (reviewed in Ref. 59).We have previously shown that inhibition of mTOR reduces the activity of placental system L, system A, and the taurine transporter (TAUT) (50). Since the activity of these amino acid transporter systems is downregulated in the placenta in association to IUGR (14, 19, 28, 37, 45) and placental mTOR activity has been reported to be decreased in IUGR (49, 62), it is possible that mTOR signaling plays an important role in regulating placental amino acid transporters in vivo. However, the upstream regulators of placental mTOR are unknown. We hypothesized that glucose, insulin, and IGF-I regulate placental amino acid transporter activity by inducing changes in mTOR signaling. To test this hypothesis, human primary trophoblast cells were incubated with media containing various concentrations of glucose, insulin, or IGF-I in the presence or absence of the specific mTOR inhibitor rapamycin. Subsequently, the activity of system L, system A, and the taurine transporter was measured. To investigate whether the AMPK pathway and/or REDD1 is activated in glucose-deprived primary trophoblasts, the protein expression of phosphorylated (P)-Thr172-AMPKα, total AMPK, P-Ser428-LKB1, and REDD1 in control and glucose-deprived cells was also studied.
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| 8. |
- Roos, Sara, 1979, et al.
(författare)
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Regulation of placental amino acid transporter activity by mammalian target of rapamycin.
- 2009
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Ingår i: American journal of physiology. Cell physiology. - : American Physiological Society. - 0363-6143 .- 1522-1563. ; 296:1
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Tidskriftsartikel (refereegranskat)abstract
- The activity of placental amino acid transporters is decreased in intrauterine growth restriction (IUGR), but the underlying regulatory mechanisms have not been established. Inhibition of the mammalian target of rapamycin (mTOR) signaling pathway has been shown to decrease the activity of the system L amino acid transporter in human placental villous fragments, and placental mTOR activity is decreased in IUGR. In the present study, we used cultured primary trophoblast cells to study mTOR regulation of placental amino acid transporters in more detail and to test the hypothesis that mTOR alters amino acid transport activity by changes in transporter expression. Inhibition of mTOR by rapamycin significantly reduced the activity of system A (-17%), system L (-28%), and taurine (-40%) amino acid transporters. mRNA expression of isoforms of the three amino acid transporter systems in response to mTOR inhibition was measured using quantitative real-time PCR. mRNA expression of l-type amino acid transporter 1 (LAT1; a system L isoform) and taurine transporter was reduced by 13% and 50%, respectively; however, mTOR inhibition did not alter the mRNA expression of system A isoforms (sodium-coupled neutral amino acid transporter-1, -2, and -4), LAT2, or 4F2hc. Rapamycin treatment did not significantly affect the protein expression of any of the transporter isoforms. We conclude that mTOR signaling regulates the activity of key placental amino acid transporters and that this effect is not due to a decrease in total protein expression. These data suggest that mTOR regulates placental amino acid transporters by posttranslational modifications or by affecting transporter translocation to the plasma membrane.
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