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3. Targeted proteomics as a tool for porcine acute phase proteins measurements

Author

Marco-Ramell, Anna, Bassols, Anna, Dyrlund, Thomas F., Bislev, Stine L., Sanggaard, Kristian W., Enghild, Jan J., Bendixen, Emøke, Fraile, Lorenzo, de Almeida, André, editor, Eckersall, David, editor, Bencurova, Elena, editor, Dolinska, Saskia, editor, Mlynarcik, Patrik, editor, Vincova, Miroslava, editor, and Bhide, Mangesh, editor

Published
2013
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7. Detection of proteolytic signatures for Parkinson's disease

Author

Jordal, Peter Lüttge, Dyrlund, Thomas F., Winge, Kristian, Larsen, Martin R., Danielsen, Erik H., Wells, James A., Otzen, Daniel E., Enghild, Jan J., Jordal, Peter Lüttge, Dyrlund, Thomas F., Winge, Kristian, Larsen, Martin R., Danielsen, Erik H., Wells, James A., Otzen, Daniel E., and Enghild, Jan J.

Abstract

Aim: To investigate if idiopathic Parkinson's disease (IPD) is associated with distinct proteolytic signatures relative to non-neurodegenerative controls (NND) and patients with multiple system atrophy (MSA). Materials & methods: A subtiligase-based N-terminomics screening method was exploited for semiquantitative comparison of protein N-termini in cerebrospinal fluid for pooled samples of IPD (n = 6) and NND (n = 8) individuals. Subsequently, targeted selected reaction monitoring mass spectrometry measured the relative concentration of the proteolytic signature peptides in individual IPD (n = 22), NND (n = 11) and MSA (n = 18) samples. Results: The discovery screen detected 300 N-termini for 156 proteins. Selected reaction monitoring analysis revealed that two of these peptides differentiate IPD from NND while three peptides differentiate IPD from MSA. Conclusion: IPD is associated with distinct proteolytic signatures.

Published
2016

8. Corrigendum: Spider genomes provide insight into composition and evolution of venom and silk

Author

Sanggaard, Kristian W., Bechsgaard, Jesper S., Fang, Xiaodong, Duan, Jinjie, Dyrlund, Thomas F., Gupta, Vikas, Jiang, Xuanting, Cheng, Ling, Fan, Dingding, Feng, Yue, Han, Lijuan, Huang, Zhiyong, Wu, Zongze, Liao, Li, Settepani, Virginia, Thøgersen, Ida B., Vanthournout, Bram, Wang, Tobias, Zhu, Yabing, Funch, Peter, Enghild, Jan J., Schauser, Leif, Andersen, Stig U., Villesen, Palle, Schierup, Mikkel H., Bilde, Trine, and Wang, Jun

Subjects
Corrigenda
Published
2014

14. Correction: Corrigendum: Spider genomes provide insight into composition and evolution of venom and silk

Author

Sanggaard, Kristian W., primary, Bechsgaard, Jesper S., additional, Fang, Xiaodong, additional, Duan, Jinjie, additional, Dyrlund, Thomas F., additional, Gupta, Vikas, additional, Jiang, Xuanting, additional, Cheng, Ling, additional, Fan, Dingding, additional, Feng, Yue, additional, Han, Lijuan, additional, Huang, Zhiyong, additional, Wu, Zongze, additional, Liao, Li, additional, Settepani, Virginia, additional, Thøgersen, Ida B., additional, Vanthournout, Bram, additional, Wang, Tobias, additional, Zhu, Yabing, additional, Funch, Peter, additional, Enghild, Jan J., additional, Schauser, Leif, additional, Andersen, Stig U., additional, Villesen, Palle, additional, Schierup, Mikkel H., additional, Bilde, Trine, additional, and Wang, Jun, additional

Published
2014
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15. Proteomics of Fuchs’ Endothelial Corneal Dystrophy Support That the Extracellular Matrix of Descemet’s Membrane Is Disordered

Author

Poulsen, Ebbe Toftgaard, primary, Dyrlund, Thomas F., additional, Runager, Kasper, additional, Scavenius, Carsten, additional, Krogager, Toke Peter, additional, Højrup, Peter, additional, Thøgersen, Ida B., additional, Sanggaard, Kristian W., additional, Vorum, Henrik, additional, Hjortdal, Jesper, additional, and Enghild, Jan J., additional

Published
2014
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17. Spider genomes provide insight into composition and evolution of venom and silk

Author

Sanggaard, Kristian W., primary, Bechsgaard, Jesper S., additional, Fang, Xiaodong, additional, Duan, Jinjie, additional, Dyrlund, Thomas F., additional, Gupta, Vikas, additional, Jiang, Xuanting, additional, Cheng, Ling, additional, Fan, Dingding, additional, Feng, Yue, additional, Han, Lijuan, additional, Huang, Zhiyong, additional, Wu, Zongze, additional, Liao, Li, additional, Settepani, Virginia, additional, Thøgersen, Ida B., additional, Vanthournout, Bram, additional, Wang, Tobias, additional, Zhu, Yabing, additional, Funch, Peter, additional, Enghild, Jan J., additional, Schauser, Leif, additional, Andersen, Stig U., additional, Villesen, Palle, additional, Schierup, Mikkel H, additional, Bilde, Trine, additional, and Wang, Jun, additional

Published
2014
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19. Comparison of two phenotypically distinct lattice corneal dystrophies caused by mutations in the transforming growth factor beta induced (TGFBI ) gene

Author

Poulsen, Ebbe Toftgaard, primary, Runager, Kasper, additional, Risør, Michael W., additional, Dyrlund, Thomas F., additional, Scavenius, Carsten, additional, Karring, Henrik, additional, Praetorius, Jeppe, additional, Vorum, Henrik, additional, Otzen, Daniel E., additional, Klintworth, Gordon K., additional, and Enghild, Jan J., additional

Published
2014
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20. Proteome reference maps of the Lotus japonicus nodule and root

Author

Dam, Svend, primary, Dyrlund, Thomas F., additional, Ussatjuk, Anna, additional, Jochimsen, Bjarne, additional, Nielsen, Kasper, additional, Goffard, Nicolas, additional, Ventosa, Miguel, additional, Lorentzen, Andrea, additional, Gupta, Vikas, additional, Andersen, Stig U., additional, Enghild, Jan J., additional, Ronson, Clive W., additional, Roepstorff, Peter, additional, and Stougaard, Jens, additional

Published
2014
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22. Investigations on Collectin Liver 1

Author

Axelgaard, Esben, primary, Jensen, Lisbeth, additional, Dyrlund, Thomas F., additional, Nielsen, Hans J., additional, Enghild, Jan J., additional, Thiel, Steffen, additional, and Jensenius, Jens C., additional

Published
2013
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23. The Protein Composition of the Digestive Fluid from the Venus Flytrap Sheds Light on Prey Digestion Mechanisms

Author

Schulze, Waltraud X., primary, Sanggaard, Kristian W., additional, Kreuzer, Ines, additional, Knudsen, Anders D., additional, Bemm, Felix, additional, Thøgersen, Ida B., additional, Bräutigam, Andrea, additional, Thomsen, Line R., additional, Schliesky, Simon, additional, Dyrlund, Thomas F., additional, Escalante-Perez, Maria, additional, Becker, Dirk, additional, Schultz, Jörg, additional, Karring, Henrik, additional, Weber, Andreas, additional, Højrup, Peter, additional, Hedrich, Rainer, additional, and Enghild, Jan J., additional

Published
2012
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26. Coagulation Factor XIIIa Substrates in Human Plasma.

Author

Lund Nikolajsen, Camilla, Dyrlund, Thomas F., Toftgaard Poulsen, Ebbe, Enghild, Jan J., and Scavenius, Carsten

Subjects
*TRANSGLUTAMINASES, *BLOOD coagulation, *LYSINE, *CROSSLINKING (Polymerization), *PROTEOMICS
Abstract

Coagulation factor XIII (FXIII) is a transglutaminase with a well defined role in the final stages of blood coagulation. Active FXIII (FXIIIa) catalyzes the formation of ∈-(γ-glutamyl)lysine isopeptide bonds between specific Gln and Lys residues. The primary physiological outcome of this catalytic activity is stabilization of the fibrin clot during coagulation. The stabilization is achieved through the introduction of cross-links between fibrin monomers and through cross-linking of proteins with anti-fibrinolytic activity to fibrin. FXIIIa additionally cross-links several proteins with other functionalities to the clot. Cross-linking of proteins to the clot is generally believed to modify clot characteristics such as proteolytic susceptibility and hereby affect the outcome of tissue damage. In the present study, we use a proteomic approach in combination with transglutaminase-specific labeling to identify FXIIIa plasma protein substrates and their reactive residues. The results revealed a total of 147 FXIIIa substrates, of which 132 have not previously been described. We confirm that 48 of the FXIIIa substrates were indeed incorporated into the insoluble fibrin clot during the coagulation of plasma. The identified substrates are involved in, among other activities, complement activation, coagulation, inflammatory and immune responses, and extracellular matrix organization. [ABSTRACT FROM AUTHOR]

Published
2014
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28. Comparison of two phenotypically distinct lattice corneal dystrophies caused by mutations in the transforming growth factor beta induced (TGFBI) gene.

Author

Poulsen ET, Runager K, Risør MW, Dyrlund TF, Scavenius C, Karring H, Praetorius J, Vorum H, Otzen DE, Klintworth GK, and Enghild JJ

Subjects
Amino Acid Substitution genetics, Amyloid metabolism, Chromatography, Liquid, Cornea metabolism, Corneal Dystrophies, Hereditary metabolism, Corneal Dystrophies, Hereditary pathology, Extracellular Matrix Proteins biosynthesis, Extracellular Matrix Proteins chemistry, Humans, Laser Capture Microdissection, Mutation, Proteolysis, Tandem Mass Spectrometry, Transforming Growth Factor beta chemistry, Cornea pathology, Corneal Dystrophies, Hereditary genetics, Extracellular Matrix Proteins genetics, Transforming Growth Factor beta genetics
Abstract

Purpose: In this study, we investigated whether the phenotypic difference observed between two lattice corneal dystrophy type 1 (LCD type 1) cases caused by either a single A546D substitution or an A546D/P551Q double substitution in TGFBIp (transforming growth factor beta induced protein) can be ascribed to (i) a difference in the proteomes of corneal amyloid deposits, (ii) altered proteolysis of TGFBIp, or (iii) structural changes of TGFBIp introduced by the P551Q amino acid substitution., Experimental Design: Amyloid deposits were isolated from the corneas of two siblings with LCD type 1 resulting from A546D/P551Q mutations in the TGFBI gene using laser capture microdissection and subsequently analyzed by LC-MS/MS. Proteolytic processing of TGFBIp was addressed by counting peptide spectra. Lastly, to study the possible effect of the P551Q substitution, recombinant FAS1-4 domain variants were subjected to in vitro stability assays., Results: The amyloid proteomes and TGFBIp processing of the two A546D/P551Q LCD type 1 cases were similar to each other as well as to the A546D amyloid proteome previously reported by us. The stability assays revealed a minor destabilization of the FAS1-4 domain upon the addition of the P551Q mutation, moreover, it resulted in different accessibility to tryptic cleavage sites between the A546D and A546D/P551Q mutant FAS1-4 domain variants., Conclusion and Clinical Relevance: The difference in A546D and A546D/P551Q LCD type 1 phenotypes cannot be ascribed to altered corneal amyloid composition or altered in vivo proteolytic processing of TGFBIp. Instead, a small difference in thermodynamic stability introduced by the P551Q mutation most likely causes structural changes of TGFBIp. The MS proteomics data have been deposited to the ProteomeXchange with identifier PXD000307 (http://proteomecentral.proteomexchange.org/dataset/PXD000307)., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Published
2014
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