Affinity-based proteomics utilizes affinity binders to detect target proteins in a large-scale manner. This thesis describes a high-throughput method, which enables the search for biomarker candidates in human plasma and serum. A highly multiplexed antibody-based suspension bead array is created by coupling antibodies generated in the Human Protein Atlas project to color-coded beads. The beads are combined for parallel analysis of up to 384 analytes in patient and control samples. This provides data to compare protein levels from the different groups. In paper I osteoporosis patients are compared to healthy individuals to find disease-linked proteins. An untargeted discovery screening was conducted using 4608 antibodies in 16 cases and 6 controls. This revealed 72 unique proteins, which appeared differentially abundant. A validation screening of 91 cases and 89 controls confirmed that the protein autocrine motility factor receptor (AMFR) is decreased in the osteoporosis patients. Paper II investigates the risk proteome of inflammatory bowel disease (IBD). Antibodies targeting 209 proteins corresponding to 163 IBD genetic risk loci were selected. To find proteins related to IBD or its subgroups, sera from 49 patients with Crohn’s disease, 51 with ulcerative colitis and 50 matched controls were analyzed. From these targeted assays, the known inflammation-related marker serum amyloid protein A (SAA) was shown to be elevated in the IBD cases. In addition, the protein laccase (multi-copper oxidoreductase) domain containing 1 (LACC1) was found to be decreased in the IBD subjects. In conclusion, assays using affinity-based bead arrays were developed and applied to screen human plasma and serum samples in two disease contexts. Untargeted and targeted screening strategies were applied to discover disease-associated proteins. Upon further validation, these potential biomarker candidates could be valuable in future disease studies. / <p>QC 20180412</p>

Für die Therapie chronisch entzündlicher Darmerkrankungen (CED) ist die Diagnostik befallener Darmabschnitte und enteraler Komplikationen ebenso von Bedeutung, wie die Einschätzung der klinischen und endoskopischen Entzündungsaktivität. In einer Studie soll die Wertigkeit der Magnetresonanztomographie (MRT) untersucht werden, die Entzündungsaktivität CED anhand visueller Befunde und Komplikationen einzuschätzen. Außerdem soll überprüft werden, ob auf eine Kontrastierung des Darmes zugunsten eines höheren Patientenkomforts und einer schnelleren Untersuchung verzichtet werden kann. 64 Patienten mit bekannter oder vermuteter CED wurden vor und nach intravenöser Gd-DTPA-Injektion mit dem MR-Tomographen untersucht. Während 35 Patienten eine orale und rektale Kontrastierung mit Endoskopielösung erhielten, wurden 31 nicht enteral kontrastiert. 53 der untersuchten Patienten wurden zeitnah koloskopiert. Ein neu entwickelter MR-Aktivitätsindex (MRAI), die Kontrastmittelanreicherung in der Darmwand sowie die gemessenen Darmwanddicken wurden mit klinischen Indizes (CAI, CDAI) und dem Endoskopie-Aktivitätsindex (EAI) korreliert. Weiterhin wurden koronare Bilder aller Patienten bezüglich der Distension des Darmes und der Abgrenzbarkeit der Darmwand begutachtet. Im Vergleich mit dem EAI konnten signifikante Unterschiede für die Verteilung des Darmwand-Enhancements und der gemessenen Darmdicken nachgewiesen werden. Der MRAI zeigte eine Korrelation von Eta = 0,43 mit der klinischen Aktivität. Für Colitis ulcerosa-Patienten konnte ein Eta = 0,64 erstellt werden. Untersuchte, die eine Kontrastierung des Darmes erhielten, wiesen eine exzellente Korrelation (Eta = 0,76) zwischen MRAI und CAI / CDAI auf, während dieser Zusammenhang für Patienten ohne enterale Auffüllung fehlte. Weiterhin konnten signifikante Zusammenhänge zwischen enteraler Kontrastierung und der Distension des Darmes sowie der Abgrenzbarkeit der Darmwand gezeigt werden. Die Arbeit macht deutlich, daß es möglich ist, CED mittels MRT zuverlässig zu diagnostizieren und mit Hilfe des MRAI in ihrer klinischen und endoskopischen Entzündungsaktivität einzuschätzen. Dabei sollte auf die Anwendung eines enteralen Kontrastmittels nicht verzichtet werden. Ein Einsatz der MRT ist somit nicht nur bei der Diagnostik sondern auch zur Verlaufskontrolle der CED sinnvoll. / For the therapy of Inflammatory Bowel Diseases (IBD), not only the diagnosis of affected bowel segments and enteral complications but also the assessment of the clinical and endoscopic activity is important. The value of Magnetic Resonance Imaging (MRI) to asses the activity of IBD by visual findings and complications shall be determined by a clinical study. Furthermore shall be tested how the application of enteral contrast media affects patient comfort and examination time. 64 patients with known or supposed IBD were examined by MRI before and after intravenous injection of Gd-DTPA. 35 patients received oral and rectal contrast medium (2,5% mannitol solution) while 31 patients remaining without enteral replenishment. 53 patients underwent colonoscopy.A newly developed MR Activity Index (MRAI), based on visual findings, contrast-enhancement of the bowel wall and measured wall thickness were correlated with clinical (Crohn�s Disease Activity Index, CDAI; Colitis Activity Index, CAI) and endoscopic (Endoscopy Activity Index, EAI) activity. Coronal images of all patients were evaluated referring to bowel distension and demarcation of the bowel wall. The comparision with EAI shows significant differences in the distribution for wall contrast-enhancement and wall thickness. A good correlation is determined between the MRAI and the clinical activity (Eta = 0,43). Considering only patients with Ulcerative Colitis the correlation between MRAI and CAI shows Eta = 0,64. An excellent correlation of Eta = 0,76 between MRAI and CDAI / CAI for all patients with oral and enteral replenishment was found, while there was no correlation in the group, which did not receive mannitol solution. Significant correlations were also seen between the enteral mannitol solution replenishment and bowel distension and demarcation of the bowel wall. MRI shows good accuracy in detecting the changes the of IBD. The new developed MRAI allows an assessment of the activity of IBD. The results demonstrate that oral and enteral contrast media should be applied for MR examination of the abdomen. The utilization of MRI is furthermore useful in the follow up of IBD.

Ankylosing spondylitis (AS) is a common inflammatory arthritis of the spine and other affected joints, which is highly heritable, being strongly influenced by the HLA-B27 status, as well as hundreds of mostly unknown genetic variants of smaller effect. The aim of my research was to confirm some of the previously observed genetic associations and to identify new associations, many of which are in biological pathways relevant to AS pathogenesis, most notably the IL-23/T_H17 axis (IL23R) and antigen presentation (ERAP1 and ERAP2). Studies presented in this thesis include replication and refinement of several potential associations initially identified by earlier GWAS (WTCCC-TASC, 2007 and TASC, 2010). I conducted an extended study of IL23R association with AS and undertook a meta-analysis, confirming the association between AS and IL23R (non-synonymous SNP rs11209026, p=1.5 x 10-9, OR=0.61). An extensive re-sequencing and fine mapping project, including a meta-analysis, to replicate and refine the association of TNFRSF1A with AS was also undertaken; a novel variant in intron 6 was identified and a weak association with a low frequency variant, rs4149584 (p=0.01, OR=1.58), was detected. Somewhat stronger associations were seen with rs4149577 (p=0.002, OR=0.91) and rs4149578 (p=0.015, OR=1.14) in the meta-analysis. Associations at several additional loci had been identified by a more recent GWAS (WTCCC2-TASC, 2011). I used in silico techniques, including imputation using a denser panel of variants from the 1000 Genomes Project, conditional analysis and rare/low frequency variant analysis, to refine these associations. Imputation analysis (1782 cases/5167 controls) revealed novel associations with ERAP2 (rs4869313, p=7.3 x 10-8, OR=0.79) and several additional candidate loci including IL6R, UBE2L3 and 2p16.3. Ten SNPs were then directly typed in an independent sample (1804 cases/1848 controls) to replicate selected associations and to determine the imputation accuracy. I established that imputation using the 1000 Genomes Project pilot data was largely reliable, specifically for common variants (genotype concordence~97%). However, more accurate imputation of low frequency variants may require larger reference populations, like the most recent 1000 Genomes reference panels. The results of my research provide a better understanding of the complex genetics of AS, and help identify future targets for genetic and functional studies.