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<p>Žučne kiseline deluju kao signalni molekuli u organizmu i uključene su u regulaciju brojnih metaboličkih, inflamatornih i imunomodulatornih procesa. Ova endogena jedinjenja ostvaruju svoje efekte najvećim delom putem nuklearnih receptora. Farnezoid X receptor (FXR) je glavni regulator homeostaze žučnih kiselina, a pokazano je da je značajno uključen i u procese inflamacije i kancerogeneze, prevashodno u jetri i intestinalnom traktu. Aktivacija FXR receptora predstavlja značajnu farmakolo&scaron;ku strategiju za terapiju holestatskih bolesti jetre, inflamatorne bolesti creva i karcinoma kolona. Definisana je uloga žučnih kiselina u signalnim putevima koji reguli&scaron;u ćelijski ciklus i doprinose razvoju ili regresiji maligniteta, ali je malo poznat uticaj ovih jedinjenja na epigenetske mehanizme regulacije ključnih ćelijskih procesa. Imajući u vidu da su efekti žučnih kiselina determinisani njihovom polarno&scaron;ću, cilj istraživanja je bio da se ispita uticaj sintetski dobijenog keto derivata holne kiseline, 12-monoketoholne kiseline (MKH), u komparaciji sa prirodnim žučnim kiselinama, hidrofobnom henodeoksiholnom kiselinom (HDH) i hidrofilnom ursodeoksiholnom kiselinom (UDH), na ćelijske procese apoptoze, oksidativnog stresa i inflamacije, koji su od značaja za hemoprevenciju i terapiju karcinoma kolona, u in vitro i in vivo sistemima. Cilj istraživanja je takođe obuhvatao i ispitivanje uloge odabranih žučnih kiselina u epigenetskoj regulaciji ovih procesa u ćelijama karcinoma kolona. Na in vivo modelu intrahepatične holestaze kod eksperimentalnih životinja, pokazano je da UDH i MKH ispoljavaju antiapoptotski, antioksidativni i antiinflamatorni efekat u jetri i intestinumu. Utvrđeno je da UDH i MKH sprečavaju mitohondrijalni put aktivacije apoptoze u jetri, dok UDH ispoljava antiapoptotski efekat i u intestinumu eksperimentalnih životinja sa holestazom. Ove dve žučne kiseline su u značajnoj meri modulirale ekspresiju gena uključenih u antioksidativnu za&scaron;titu, kao i aktivnost antioksidativnih enzima, u jetri i intestinumu eksperimentalnih životinja sa holestazom, ka nivoima ekspresije i aktivnosti kod zdravih, netretiranih životinja. Dok su UDH i MKH u dozi od 4 mg/kg ispoljile antiinflamatorno dejstvo u jetri i intestinumu smanjenjem ekspresije gena za proinflamatorni transkripcioni faktor NF-&kappa;B, primena HDH i MKH u dozi od 20 mg/kg je imala suprotan efekat. Na modelu HT-29 ćelijske linije adenokarcinoma kolona, utvrđeno je da polusintetska žučna kiselina MKH ispoljava značajno manju citotoksičnost u odnosu na HDH i ne&scaron;to veću citotoksičnost u odnosu na UDH. Epigenetski lek vorinostat je ispoljio sinergističko citotoksično dejstvo sa sve tri ispitivane žučne kiseline. Vorinostat je ostvario proapoptotski i antiproliferativni efekat u HT-29 ćelijama, koji je bio najizraženiji u kombinaciji sa MKH, s obzirom da je do&scaron;lo do značajnog povećanja odnosa ekspresije BAX i BCL2 gena i smanjenja ekspresije gena za marker proliferacije ciklin D1. Vorinostat je, takođe, značajno smanjio antioksidativni kapacitet HT-29 ćelija smanjenjem ekspresije NRF2 gena i sledstvenim smanjenjem ekspresije gena za antioksidativne enzime. HDH je dodatno smanjila, a MKH pobolj&scaron;ala antioksidativni kapacitet HT-29 ćelija modulacijom ekspresije NRF2 gena. U in vitro i in vivo sistemu u okviru ove doktorske disertacije je pokazano da, pored HDH kao poznatog endogenog agoniste FXR receptora, MKH takođe povećava ekspresiju gena za FXR i njegovog ciljnog gena za transkripcioni korepresor SHP, &scaron;to ukazuje da ova polusintetska žučna kiselina može da aktivira FXR. Osim toga, utvrđeno je da žučne kiseline ispoljavaju različite efekte prema ekspresiji gena za histon deacetilaze HDAC1 i HDAC2 u jetri i intestinumu eksperimentalnih životinja, kao i u HT-29 ćelijama karcinoma kolona, a jedino je UDH značajno smanjila ekspresiju gena za oba ispitivana enzima uključena u epigenetsku regulaciju ćelijskih procesa, i u isptivanim tkivima i HT-29 ćelijama. Rezultati na&scaron;eg rada ukazuju da bi se UDH i MKH mogle koristiti u hemoprevenciji karcinoma kolona u niskim dozama, s obzirom na utvrđene efekte u modulaciji ekspresije gena uključenih u procese apoptoze, oksidativnog stresa i inflamacije. Takođe, s obzirom na ostvaren sinergistički efekat žučnih kiselina sa epigenetskim antitumorskim agensom vorinostatom, otvara se mogućnost kombinovane farmakolo&scaron;ke strategije u terapiji solidnih tumora, koji u najvećem procentu pokazuju rezistenciju prema samom vorinostatu.</p> / <p>Bile acids act as signaling molecules in the organism and they are involved in the regulation of numerous metabolic, inflammatory and immunomodulatory processes. These endogenous compounds exert their effects mostly by binding and activation of nuclear receptors. Farnesoid X receptor (FXR) is the main regulator of bile acid homeostasis, and has been shown to be significantly involved in processes of inflammation and carcinogenesis, primarily in the liver and intestinal tract. Activation of FXR receptor represents a significant pharmacological strategy for the treatment of cholestatic liver disease, inflammatory bowel disease, and colon carcinoma. The role of bile acids in signaling pathways regulating the cell cycle and contributing to the development or regression of malignancies is well determined, but the effects of these compounds on epigenetic mechanisms of key cellular processes regulation is yet to be elucidated. Given that the effects of bile acids are mostly determined by their polarity, the aim of our study was to investigate in vitro and in vivo effects of semi-synthetic keto derivative of cholic acid, 12-monoketocholic acid (MKC), in comparison to natural bile acids, hydrophobic chenodeoxycholic acid (CDC) and hydrophilic ursodeoxycholic acid (UDC), on processes of apoptosis, oxidative stress and inflammation, which are significant for both&nbsp; chemoprevention and therapy of colon cancer. Besides, the aim of our study was to examine the role of selected bile acids in the epigenetic regulation of these processes in colon cancer cells. In in vivo model of intrahepatic cholestasis in experimental animals, it has been demonstrated that UDC and MKC exhibit antiapoptotic, antioxidant, and antiinflammatory effects in the liver and intestine. It was shown that UDC and MKC prevent the mitochondrial pathway of apoptosis activation in the liver, while UDC exhibits an antiapoptotic effect in the intestine of experimental animals with cholestasis as well. These two bile acids significantly modulated the expression of genes involved in antioxidant protection, as well as the activity of antioxidant enzymes, in the liver and intestine of experimental animals with cholestasis, towards levels of expression and activity in healthy, untreated animals. While UDC and MKC at a low dose of 4 mg/kg exhibited an antiinflammatory effect in the liver and intestine by reducing the expression of the gene encoding the proinflammatory transcription factor NF-&kappa;B, the application of CDC and MKC at a high dose of 20 mg/kg exerted the opposite effect. In HT-29 human adenocarcinoma cell line, it has been demonstrated that semi-synthetic bile acid MKC exhibits significantly lower cytotoxicity than CDC and slightly higher cytotoxicity than UDC. The epigenetic drug vorinostat has exhibited a synergistic cytotoxic effect with all three investigated bile acids. Vorinostat exerted proapoptotic and antiproliferative effects in HT-29 cells, which were most pronounced in combination with MKC, as there was a significant increase in the ratio of BAX and BCL2 genes expression and a decrease of the proliferation marker cyclin D1 gene expression. Vorinostat also significantly reduced the antioxidant capacity of HT-29 cells by reducing the expression of NRF2 gene and consequently decreasing the expression of genes encoding antioxidant enzymes. CDC further reduced, while MKC improved the antioxidant capacity of HT-29 cells by modulating the expression of NRF2 gene. In both in vitro and in vivo systems, it was demonstrated that, in addition to CDC as a known endogenous FXR agonist, MKC also increased the expression of the gene encoding FXR, and FXR target gene encoding transcriptional co-repressor SHP as well, indicating that this semi-synthetic bile acid can also activate FXR. Besides, bile acids have been shown to exert distinct effects on the expression of the histone deacetylases HDAC1 and HDAC2 gene in the liver and intestine of experimental animals, and in HT-29 colon cancer cells. Only UDC significantly reduced the expression of the genes for both studied enzymes involved in the epigenetic regulation of cell processes, in both tissues and HT-29 cells. The results of our work indicate that UDC and MKC could be used in chemoprevention of colon cancer at low doses, considering determined effects in the modulation of expression of the genes involved in processes of apoptosis, oxidative stress and inflammation. Furthermore, synergistic effects of bile acids with the epigenetic antitumor agent vorinostat open up the possibility of a combined pharmacological strategy in the treatment of solid tumors, which are at the high percentage resistant to the effects of vorinostat alone.</p>

This research focused on the study of the amino sugar recycling and sialic acid degradation pathway as a possible entry point for N-acyl glucosamines for the production of sialic acid analogs. Meeting this objective would allow the development of a bacterial strain capable of producing non-natural nonulosonic acids that could be used in the development of medicines, vaccines or useful compounds for the study of interactions between pathogenic organisms and their host. The first step was to understand how N-acetyl-D-glucosamine-6-phosphate deacetylase reacts to different types of substrates in order to determine its tolerance to the size of acyl groups in acyl amino sugars. This was achieved by studying the enzymatic activity in an in vitro system. We determine that the enzyme has a preference for small and slightly bulky acyl groups. Then, an in silico docking modeling and an in vivo system experiment were carried out. These experiments allowed to confirm the previous results. The second project was carried out due to the uncertainty of whether the kinase involved in the catabolic pathway would be able to phosphorylate the substrates. By quantifying residual ATP, the high specificity of N-acetyl-D-glucosamine kinase could be verified. This result led us to think about the design of an organic synthesis strategy that would allow the phosphorylation of glucosamine in carbon 6. A simple synthetic route was designed based on the protection of the two most reactive moieties of the amino sugars and the reactivity of the hydroxy group on carbon 6. However, we had problems with the purification step of the final product due to its high polarity. The next stage of this investigation was to confirm the transformation of GlcNAc into ManNAc. For this, an NMR analysis was designed that would detect the presence of both sugars in the reaction system. The epimerization of ManNAc to GlcNAc was detected successfully. Notwithstanding, the reverse reaction could not be detected. Based on the results obtained in the previous stage, we realized that an error was made in the epimerization reaction since we placed the wrong kinase because we did not take into account its substrate specificity. Finally, we tried to produce sialic acid analogs in a fermentative system using different genetic variants of Escherichia coli. Two of the expected analogs, Neu5Pr and Neu5nBu, were obtained. In addition, NagA activity towards substrates with small acyl groups was confirmed.

<p>In the extracellular space, many specialized proteins are located to support cells and to mediate cell-cell signalling. One class of such molecules is heparan sulfate (HS) proteoglycans, which are proteins with different properties and locations but all of them decorated with long unbranched HS polysaccharide chains. During biosynthesis the HS chains are modified by sulfation and a C5-epimerase converts some glucuronic acid residues to iduronic acid. The patterns of the modifications vary distinctly between tissues and developing stages and give HS chains different affinity for biologically important proteins. Thus, the regulation of HS biosynthesis is likely to influence a wide variety of biological events.</p><p>This thesis focuses on the biosynthesis of HS in animals with targeted disruptions in genes important for HS production. The N-deacetylase N-sulfotransferase (NDST) is a key enzyme in HS biosynthesis, directing other modifications. We show that NDST isoforms have very different roles in HS biosynthesis. Inactivation of NDST1 affects HS biosynthesis in all tissues. In embryonic liver HS from NDST1-/- mice the N-sulfation was decresed with twothirds, while the absence of NDST2 did not affect HS structure. In the absence of NDST1 in the liver, however, NDST2 is active in HS N-sulfation. </p><p>In a study of embryonic stem cells lacking both NDST1 and NDST2, no N-sulfate groups could be detected. 6-O-sulfate groups were, however, still present at half of its normal level. This was an unexpected finding since 6-O-sulfotransferases have been thought to be strictly dependent on N-sulfate groups for substrate recognition.</p><p>By adapting an automated method for HS analysis to mammalian tissues, we could extend our analyses to more tissues and other transgene models. We also developed a protocol to create a sensitive “fingerprint” of HS structure. With these methods we could determine the individual HS structure of different mouse tissues. </p>

<p>Heparan sulfate (HS) is a ubiquitous polysaccharide on the cell surface and in the extracellular matrix. HS is an important actor in the regulation of cell signaling, especially in the developing embryo. In combination with cell culture and biochemical experiments, <i>in vivo</i> studies of genetically modified animals have pointed out the sulfation pattern of HS as highly important for binding of ligands, their receptors and other signaling modulators.</p><p>The sulfation pattern of an HS chain is gained by several modifying steps, performed by multiple enzymes during biosynthesis in the Golgi apparatus. By alterations of sulfation pattern, and the amount of sulfate groups, a cell can regulate the binding properties of its HS to different molecules. The most highly sulfated form of HS is called heparin, and can only be found intracellularly in mast cells.</p><p>This thesis describes the phenotypes and the alterations in HS/heparin biosynthesis of two genetically modified mouse strains deficient in N-deacetylase/N-sulfotransferase-1 (NDST1) and -2 (NDST2) respectively. We have found NDST1 to be important for correct sulfation of HS and that NDST2 is crucial in heparin biosynthesis. NDST2 deficient mice completely lack heparin and therefore have a severe mast cell phenotype. NDST1 deficient mice produce undersulfated HS and show several developmental disturbances. Some NDST1 embryos die in utero while the rest die neonatally due to breathing difficulties. Defect brain, eye and skeletal development has also been observed while some organs, such as the liver, appear to be largely unaffected. Several phenotypes are similar to defects seen in other mouse strains with impaired fibroblast growth factor and bone morphogenetic protein signaling, among others. This suggests the phenotypes of NDST1 deficient embryos to be of a multi factorial origin, in complete accordance to the many signaling pathways HS is suggested to modulate.</p>

<p>Heparan sulfate (HS) proteoglycans consist of sulfated HS chains covalently bound to core proteins. They are ubiquitously expressed, on the cell surface and in the extracellular matrix, throughout the body. During biosynthesis the HS chain is modified to generate a highly variable pattern of sulfated residues, able to interact with a wide variety of ligands, such as growth factors, morphogens and extracellular matrix molecules. The presence of HS proteoglycans is crucial during various developmental processes as they are involved in generation of morphogen gradients and influence the function of several growth factor pathways essential for tissue assembly and differentiation.</p><p>In this thesis the phenotypes of two mouse strains, deficient in different isoforms of the HS biosynthetic enzyme N-deacetylase/N-sulfotransferase (NDST) have been analyzed. In addition, NDST deficient embryonic stem (ES) cells have been analyzed with regard to HS structure and differentiation capacity. Mice deficient in NDST1 die peri-natally. The embryos display an overall low-sulfated HS and several developmental defects, with a lung phenotype as the predominant cause of death. Mice deficient in NDST2 lack sulfated heparin in connective tissue type mast cells while HS structure is unaltered. These results indicate that NDST1 is the isoform mainly responsible for HS biosynthesis during development. However, NDST1/2 deficient embryos do not survive beyond E5.5 and have a greatly disturbed morphology, suggesting that NDST2 has an essential role during early embryonic development. HS synthesized by NDST1/2 deficient ES cells had a total lack of N-sulfate groups while, interestingly, about half of the 6-O-sulfate groups remained. This result was unexpected since 6-O-sulfotransferases have been thought to be strictly dependent on N-sulfate groups for substrate recognition. Further characterization of the NDST1/2 deficient ES cells during in vitro differentiation demonstrated that the expression pattern of markers for all three germ layers was disturbed. In addition, it was demonstrated that NDST1 is not needed for mast cell development, that lack of NDST2 results in abnormal mast cells and that no mast cells is formed from NDST1/2 deficient ES cells.</p>

In the extracellular space, many specialized proteins are located to support cells and to mediate cell-cell signalling. One class of such molecules is heparan sulfate (HS) proteoglycans, which are proteins with different properties and locations but all of them decorated with long unbranched HS polysaccharide chains. During biosynthesis the HS chains are modified by sulfation and a C5-epimerase converts some glucuronic acid residues to iduronic acid. The patterns of the modifications vary distinctly between tissues and developing stages and give HS chains different affinity for biologically important proteins. Thus, the regulation of HS biosynthesis is likely to influence a wide variety of biological events. This thesis focuses on the biosynthesis of HS in animals with targeted disruptions in genes important for HS production. The N-deacetylase N-sulfotransferase (NDST) is a key enzyme in HS biosynthesis, directing other modifications. We show that NDST isoforms have very different roles in HS biosynthesis. Inactivation of NDST1 affects HS biosynthesis in all tissues. In embryonic liver HS from NDST1-/- mice the N-sulfation was decresed with twothirds, while the absence of NDST2 did not affect HS structure. In the absence of NDST1 in the liver, however, NDST2 is active in HS N-sulfation. In a study of embryonic stem cells lacking both NDST1 and NDST2, no N-sulfate groups could be detected. 6-O-sulfate groups were, however, still present at half of its normal level. This was an unexpected finding since 6-O-sulfotransferases have been thought to be strictly dependent on N-sulfate groups for substrate recognition. By adapting an automated method for HS analysis to mammalian tissues, we could extend our analyses to more tissues and other transgene models. We also developed a protocol to create a sensitive “fingerprint” of HS structure. With these methods we could determine the individual HS structure of different mouse tissues.

Heparan sulfate (HS) is a ubiquitous polysaccharide on the cell surface and in the extracellular matrix. HS is an important actor in the regulation of cell signaling, especially in the developing embryo. In combination with cell culture and biochemical experiments, in vivo studies of genetically modified animals have pointed out the sulfation pattern of HS as highly important for binding of ligands, their receptors and other signaling modulators. The sulfation pattern of an HS chain is gained by several modifying steps, performed by multiple enzymes during biosynthesis in the Golgi apparatus. By alterations of sulfation pattern, and the amount of sulfate groups, a cell can regulate the binding properties of its HS to different molecules. The most highly sulfated form of HS is called heparin, and can only be found intracellularly in mast cells. This thesis describes the phenotypes and the alterations in HS/heparin biosynthesis of two genetically modified mouse strains deficient in N-deacetylase/N-sulfotransferase-1 (NDST1) and -2 (NDST2) respectively. We have found NDST1 to be important for correct sulfation of HS and that NDST2 is crucial in heparin biosynthesis. NDST2 deficient mice completely lack heparin and therefore have a severe mast cell phenotype. NDST1 deficient mice produce undersulfated HS and show several developmental disturbances. Some NDST1 embryos die in utero while the rest die neonatally due to breathing difficulties. Defect brain, eye and skeletal development has also been observed while some organs, such as the liver, appear to be largely unaffected. Several phenotypes are similar to defects seen in other mouse strains with impaired fibroblast growth factor and bone morphogenetic protein signaling, among others. This suggests the phenotypes of NDST1 deficient embryos to be of a multi factorial origin, in complete accordance to the many signaling pathways HS is suggested to modulate.

Heparan sulfate (HS) proteoglycans consist of sulfated HS chains covalently bound to core proteins. They are ubiquitously expressed, on the cell surface and in the extracellular matrix, throughout the body. During biosynthesis the HS chain is modified to generate a highly variable pattern of sulfated residues, able to interact with a wide variety of ligands, such as growth factors, morphogens and extracellular matrix molecules. The presence of HS proteoglycans is crucial during various developmental processes as they are involved in generation of morphogen gradients and influence the function of several growth factor pathways essential for tissue assembly and differentiation. In this thesis the phenotypes of two mouse strains, deficient in different isoforms of the HS biosynthetic enzyme N-deacetylase/N-sulfotransferase (NDST) have been analyzed. In addition, NDST deficient embryonic stem (ES) cells have been analyzed with regard to HS structure and differentiation capacity. Mice deficient in NDST1 die peri-natally. The embryos display an overall low-sulfated HS and several developmental defects, with a lung phenotype as the predominant cause of death. Mice deficient in NDST2 lack sulfated heparin in connective tissue type mast cells while HS structure is unaltered. These results indicate that NDST1 is the isoform mainly responsible for HS biosynthesis during development. However, NDST1/2 deficient embryos do not survive beyond E5.5 and have a greatly disturbed morphology, suggesting that NDST2 has an essential role during early embryonic development. HS synthesized by NDST1/2 deficient ES cells had a total lack of N-sulfate groups while, interestingly, about half of the 6-O-sulfate groups remained. This result was unexpected since 6-O-sulfotransferases have been thought to be strictly dependent on N-sulfate groups for substrate recognition. Further characterization of the NDST1/2 deficient ES cells during in vitro differentiation demonstrated that the expression pattern of markers for all three germ layers was disturbed. In addition, it was demonstrated that NDST1 is not needed for mast cell development, that lack of NDST2 results in abnormal mast cells and that no mast cells is formed from NDST1/2 deficient ES cells.

No description available.