Uppsala Biomedical Center

Uppsala, Sweden

Uppsala Biomedical Center

Uppsala, Sweden

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Snir O.,Karolinska University Hospital | Widhe M.,Karolinska University Hospital | Hermansson M.,Karolinska University Hospital | Von Spee C.,Karolinska University Hospital | And 10 more authors.
Arthritis and Rheumatism | Year: 2010

Objective. High titers of specific anti-citrullinated protein antibodies (ACPAs) are frequently present in the serum of rheumatoid arthritis (RA) patients, but their presence in synovial fluid is less well characterized. The purpose of this study was to compare the levels of antibody to 4 well-defined citrullinated candidate RA autoantigens in serum and synovial fluid and to determine whether antibodies to one citrullinated antigen are dominant over another. Furthermore, we studied their relationships with mutated citrullinated vimentin (MCV), a newly identified RA-specific serum assay, and the classic cyclic citrullinated peptide (CCP) in the synovial fluid of well-defined HLA-DR groups. Methods. Paired serum and synovial fluid samples from 290 RA patients and serum samples from 100 age- and sex-matched healthy controls were analyzed for the presence of anti-MCV and anti-CCP antibodies and for reactivity to citrullinated fibrinogen, α-enolase, type II collagen, and vimentin. A total of 219 of the 290 patients were genotyped for the HLA-DR shared epitope alleles. Results. Significantly higher proportions of antibodies against all RA-associated citrullinated antigens were found in synovial fluid as compared with serum. This was also true for the MCV and CCP responses but not for non-RA-associated anti-tetanus toxoid antibodies. As expected, we found a high correlation between citrullinated vimentin and MCV responses. All synovial fluid ACPAs were predominantly associated with HLA-DRB1*04 alleles and were confined to the CCP+/ MCV+ subset of patients. Conclusion. MCV and CCP positivity represent a similar subset of RA patients, whereas ACPAs with different fine specificities fall into subgroups of anti-CCP+/anti-MCV+ patients. The levels of all specific ACPAs were elevated in synovial fluid, suggesting that there is local antibody production and/or retention of ACPAs at the site of inflammation governed by RA-predisposing genes. © 2010, American College of Rheumatology.


Martinez E.,Uppsala Biomedical Center | Martinez E.,University of Barcelona | Hamberg M.,Karolinska Institutet | Busquets M.,University of Barcelona | And 3 more authors.
Journal of Biological Chemistry | Year: 2010

We have studied oxygenation of fatty acids by cell extract of Pseudomonas aeruginosa 42A2. Oleic acid ((9Z)-18:1) was transformed to (10S)-hydroperoxy- (8E)-octadecenoic acid ((10S)-HPOME) and to (7S,10S)-dihydroxy-(8E)-octadecenoic acid (7,10-DiHOME). Experiments under oxygen-18 showed that 7,10-DiHOME contained oxygen from air and was formed sequentially from (10S)-HPOME by isomerization. (10R)-HPOME was not isomerized. The (10S)-dioxygenase and hydroperoxide isomerase activities co-eluted on ion exchange chromatography and on gel filtration with an apparent molecular size of ∼50 kDa. 16:1n-7, 18:2n-6, and 20:1n-11 were also oxygenated to 7,10-dihydroxy fatty acids, and (8Z)-18:1 was oxygenated to 6,9-dihydroxy-(7E)-octadecenoic acid.Aseries of fatty acids with the double bond positioned closer to ((6Z)-18:1, (5Z,9Z)-18:2) or more distant from the carboxyl group ((11Z)-, (13Z)-, and (15Z)-18:1) were poor substrates. The oxygenation mechanism was studied with [7S- 2H]18:1n-9, [7R-2H]18:2n-6, and [8R-2H]18:2n-6 as substrates. The pro-R hydrogen at C-8 was lost in the biosynthesis of (10S)-HPODE, whereas the pro-S hydrogen was lost and the pro-R hydrogen was retained at C-7 during biosynthesis of the 7,10-dihydroxy metabolites. Analysis of the fatty acid composition of P. aeruginosa revealed relatively large amounts of (9E/Z)-16:1 and (11E/Z)-18:1 and only traces of 18:1n-9. We found that (11Z)-18:1 (vaccenic acid) was transformed to (11S,14S)-dihydroxy-(12E)- octadecenoic acid and to a mixture of 11- and 12-HPOME, possibly due to reverse orientation of (11Z)-18:1 at the active site compared with oleic acid. The reaction mechanism of the hydroperoxide isomerase suggests catalytic similarities to cytochrome P450. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.


Jerneren F.,Uppsala Biomedical Center | Garscha U.,Uppsala Biomedical Center | Hoffmann I.,Uppsala Biomedical Center | Hamberg M.,Karolinska Institutet | Oliw E.H.,Uppsala Biomedical Center
Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids | Year: 2010

Aspergilli express fusion proteins of an animal haem peroxidase domain with fatty acid dioxygenase (DOX) activity (∼ 600 amino acids) and a functional or non-functional hydroperoxide isomerase/cytochrome P450 domain (∼ 500 amino acids with EXXR and GPHXCLG motifs). 5,8-Linoleate diol synthases (LDS; ppoA) and 10R-DOX (ppoC) of Aspergillus nidulans and A. fumigatus belong to this group. Our objective was to determine the oxylipins formed from linoleic acid by A. clavatus and their mechanism of biosynthesis. A. clavatus oxidized linoleic acid to (8R)-hydroperoxylinoleic acid (8R-HPODE), (10R)-hydroperoxy-8(E),12(Z)-octadecadienoic acid (10R-HPODE), and to (5S,8R)-dihydroxy- and (8R,11S)-dihydroxylinoleic acids (DiHODE) as major products. This occurred by abstraction of the pro-S hydrogen at C-8 and antarafacial dioxygenation at C-8 or at C-10 with double bond migration. 8R-HPODE was then isomerized to 5S,8R-DiHODE and to 8R,11S-DiHODE by abstraction of the pro-S hydrogens at C-5 and C-11 of 8R-HPODE, respectively, followed by suprafacial oxygenation. The genome of A. clavatus codes for two enzymes, which can be aligned with > 65% amino acid identity to 10R-DOX and 5,8-LDS, respectively. The 5,8-LDS homologue likely forms and isomerizes 8R-HPODE to 5S,8R-DiHODE. A third gene (ppoB) codes for a protein which carries a serine residue at the cysteine position of the P450 motif. This Cys to Ser replacement is known to abolish P450 2B4 catalysis and the hydroperoxide isomerase activity of 5,8-LDS, suggesting that ppoB of A. clavatus may not be involved in the biosynthesis of 8R,11S-DiHODE. © 2009 Elsevier B.V. All rights reserved.


Oliw E.H.,Uppsala Biomedical Center | Wennman A.,Uppsala Biomedical Center | Hoffmann I.,Uppsala Biomedical Center | Garscha U.,Uppsala Biomedical Center | And 2 more authors.
Journal of Lipid Research | Year: 2011

Seven Z-octadecenoic acids having the double bond located in positions 6Z to 13Z were photooxidized. The resulting hydroperoxy-E-octadecenoic acids [HpOME(E)] were resolved by chiral phase-HPLC-MS, and the absolute configurations of the enantiomers were determined by gas chromatographic analysis of diastereoisomeric derivatives. The MS/MS/MS spectra showed characteristic fragments, which were influenced by the distance between the hydroperoxide and carboxyl groups. These fatty acids were then investigated as substrates of cyclooxygenase-1 (COX-1), manganese lipoxygenase (MnLOX), and the (8R)-dioxygenase (8R-DOX) activities of two linoleate diol synthases (LDS) and 10R-DOX. COX-1 and MnLOX abstracted hydrogen at C-11 of (12Z)-18:1 and C-12 of (13Z)-18:1. (11Z)-18:1 was subject to hydrogen abstraction at C-10 by MnLOX and at both allylic positions by COX-1. Both allylic hydrogens of (8Z)-18:1 were also abstracted by 8R-DOX activities of LDS and 10R-DOX, but only the allylic hydrogens close to the carboxyl groups of (11Z)-18:1 and (12Z)-18:1. 8R-DOX also oxidized monoenoic C 14-C 20 fatty acids with double bonds at the (9Z) position, suggesting that the length of the omega end has little influence on positioning for oxygenation. We conclude that COX-1 and MnLOX can readily abstract allylic hydrogens of octadecenoic fatty acids from C-10 to C-12 and 8R-DOX from C-7 and C-12. Copyright © 2011 by the American Society for Biochemistry and Molecular Biology, Inc.


Xu N.,Uppsala Biomedical Center | Akusjarvi G.,Uppsala Biomedical Center
Methods in Molecular Biology | Year: 2011

RNA interference (RNAi) plays novel roles in both host antiviral defense and viral replication. It has been shown that some viruses can exploit the RNAi machinery for their own benefit by encoding for their own viral small RNAs. Here we present a collection of methods to study adenoviral small RNAs, specifically a method for immunopurification of RNA-induced silencing complex (RISC) and a biochemical assay for the activity of purified RISC associated with adenoviral small RNAs. © Springer Science+Business Media, LLC 2011.


Rask-Andersen M.,Uppsala University | Almen M.S.,Uppsala University | Schioth H.B.,Uppsala University | Schioth H.B.,Uppsala Biomedical Center
Nature Reviews Drug Discovery | Year: 2011

The discovery and exploitation of new drug targets is a key focus for both the pharmaceutical industry and academic biomedical research. To provide an insight into trends in the exploitation of new drug targets, we have analysed the drugs that were approved by the US Food and Drug Administration during the past three decades and examined the interactions of these drugs with therapeutic targets that are encoded by the human genome, using the DrugBank database and extensive manual curation. We have identified 435 effect-mediating drug targets in the human genome, which are modulated by 989 unique drugs, through 2,242 drug-target interactions. We also analyse trends in the introduction of drugs that modulate previously unexploited targets, and discuss the network pharmacology of the drugs in our data set. © 2011 Macmillan Publishers Limited. All rights reserved.


Backstrom E.,Uppsala Biomedical Center | Kaufmann K.B.,Uppsala Biomedical Center | Lan X.,Uppsala Biomedical Center | Akusjarvi G.,Uppsala Biomedical Center
Virus Research | Year: 2010

The adenovirus major late promoter (MLP) generates a primary transcript that undergoes a complex pattern of regulated alternative RNA splicing and polyadenylation events. The late-specific activation of the MLP requires binding of two infected-cell specific transcription factor complexes, DEF-A and DEF-B, to the so-called DE sequence located downstream of the MLP start site. Previous studies have shown that DEF-B is a homodimer of the viral IVa2 protein and suggested that DEF-A is a heterodimer of IVa2 and an unknown protein. Two proteins from the adenoviral L4 unit have been suggested as DEF-A candidates. Here we have examined L4-22K and L4-33K for possible DEF-A activity. We show that L4-22K stimulates transcription from the MLP in a DE sequence dependent manner both in vivo and in vitro, and that L4-22K binds to the DE sequence in vitro. Further, the position of the L4-22K DNA binding site in a promoter does not appear to be critical for function. Thus, tethering L4-22K either to a position upstream or downstream of the MLP start site, or upstream of a minimal E1B promoter, resulted in an activation of transcription. We also show that the viral pIX promoter is a natural target, activated by L4-22K. Collectively, our results are compatible with the hypothesis that L4-22K may be the elusive component of DEF-A that partakes in activation of the MLP. © 2010 Elsevier B.V.


Lindh J.,Uppsala Biomedical Center | Fardost A.,Uppsala Biomedical Center | Almeida M.,Dirigentvagen 160 | Nilsson P.,Uppsala Biomedical Center
Tetrahedron Letters | Year: 2010

Palladium catalysis was used in Stille-type carbonylative cross-couplings employing Mo(CO)6 as the carbon monoxide source. Robust and convenient transformations were carried out in closed vessels at 100 °C, providing a set of diaryl ketones in good yields. Aryl triflates and bromides were used as coupling partners with aryl stannanes. Inclusion of the Mo(CO)6 destabilizing agent DBU made this protocol operationally simple and suppressed side-product formation. © 2010 Elsevier Ltd. All rights reserved.


Nilsson T.,Uppsala Biomedical Center | Martinez E.,University of Barcelona | Manresa A.,University of Barcelona | Oliw E.H.,Uppsala Biomedical Center
Rapid Communications in Mass Spectrometry | Year: 2010

Pseudomonas aeruginosa is an opportunistic pathogen, which oxidizes oleic acid to 7(S),10(S)-dihydroxy-8(E)-octadecenoic acid (7,10-(OH)2-18:1) of biological and industrial interest. Electrospray tandem mass spectrometric (MS/MS) analysis of hydroxylated fatty acids usually generates characteristic fragments containing the carboxylate anion and formed by a-cleavage at the oxidized carbon. These fragments indicate the positions of the hydroxyl group. In contrast, liquid chromatography (LC)/MS/MS analysis of 7,10-(OH)2-18:1 yielded a series of other ions with structural information. To study the fragmentation mechanism, we prepared 2H-and 18O-labeled isotopomers. We also performed MS3 analysis of the major ions, and for comparison we generated the corresponding 7,10-dihydroxy metabolites of 16:1n-7, 18:2n-6, and 20:1n-11 with a protein extract of P. aeruginosa. The MS/MS spectra of 7,10-(OH)2-18:1 and its isotopomers, 7,10-(OH)2-16:1, and 7,10-(OH)2-20:1, contained a series of prominent fragments that all hold the omega end. The 8,9-double bond was not essential for this fragmentation, as 7,10-(OH)2-18:0, and its isotopomers, formed essentially the same fragments in the lower mass range. In contrast, 7,10-dihydroxy-8(E),12(Z)-octadecadienoic acid (7,10-(OH)2-18:2) fragmented by a-cleavage at the oxidized carbons with formation of carboxylate anions. Our results demonstrate that C16-C20 fatty acids with a 7,10-dihydroxy-8(E) functionality undergo charge-driven fragmentation after charge migration to the v-end, whereas the main ions of 7,10-(HO)2-18:2 retain charge at the carboxyl group. © 2010 John Wiley & Sons, Ltd.


Jerneren F.,Uppsala Biomedical Center | Hoffmann I.,Uppsala Biomedical Center | Oliw E.H.,Uppsala Biomedical Center
Archives of Biochemistry and Biophysics | Year: 2010

Oxygenation of linoleic acid by Aspergillus terreus was studied with LC-MS/MS. 9(R)-Hydroperoxy-10(E),12(Z)-octadecadienoic acid (9R-HpODE) was identified along with 10(R)-hydroxy-8(E),12(Z)-octadecadienoic acid and variable amounts of 8(R)-hydroxy-9(Z),12(Z)-octadecadienoic acid. 9R-HpODE was formed from [11S-2H]18:2n-6 with loss of the deuterium label, suggesting antarafacial hydrogen abstraction and oxygenation. Two polar metabolites were identified as 9-hydroxy-10-oxo-12(Z)-octadecenoic acid (α-ketol) and 13-hydroxy-10-oxo-11(E)-octadecenoic acid (γ-ketol), likely formed by spontaneous hydrolysis of an unstable allene oxide, 9(R),10-epoxy-10,12(Z)-octadecadienoic acid α-Linolenic acid and 20:2n-6 were oxidized to hydroperoxy fatty acids at C-9 and C-11, respectively, but α- and γ-ketols of these fatty acids could not be detected. The genome of A. terreus lacks lipoxygenases, but contains genes homologous to 5,8-linoleate diol synthases and linoleate 10R-dioxygenases of aspergilli. Our results demonstrate that linoleate 9R-dioxygenase linked to allene oxide synthase activities can be expressed in fungi. © 2009 Elsevier Inc.

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