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Antibody-based bead arrays for high-throughput protein profiling in human plasma and serum
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
2018 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
KTH Royal Institute of Technology, 2018. , p. 58
Series
TRITA-CBH-FOU ; 2018:9
Keywords [en]
proteomics, affinity proteomics, immunoassay, antibody microarray, suspension bead array, protein profiling, plasma, serum, biomarker discovery, osteoporosis, inflammatory bowel disease, Crohn's disease, ulcerative colitis
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Medical Technology
Identifiers
URN: urn:nbn:se:kth:diva-225980ISBN: 978-91-7729-739-0 (print)OAI: oai:DiVA.org:kth-225980DiVA, id: diva2:1197234
Presentation
2018-05-04, 10:00 (English)
Opponent
Supervisors
Note

QC 20180412

Available from: 2018-04-12 Created: 2018-04-12 Last updated: 2018-04-12Bibliographically approved
List of papers
1. Affinity proteomics discovers decreased levels of AMFR in plasma from Osteoporosis patients
Open this publication in new window or tab >>Affinity proteomics discovers decreased levels of AMFR in plasma from Osteoporosis patients
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2016 (English)In: PROTEOMICS - Clinical Applications, ISSN 1862-8346, E-ISSN 1862-8354, Vol. 10, no 6, p. 681-690Article in journal (Refereed) Published
Abstract [en]

Purpose: Affinity proteomic approaches by antibody bead arrays enable multiplexed analysis of proteins in body fluids. In the presented study, we investigated blood plasma within osteoporosis to discovery differential protein profiles and to propose novel biomarkers candidates for subsequent studies. Experimental design: Starting with 4608 antibodies and plasma samples from 22 women for an untargeted screening, a set of 72 proteins were suggested for further analysis. Complementing these with targets from literature and other studies, a targeted bead array of 180 antibodies was built to profile for 92 proteins in plasma samples of 180 women from two independent population-based studies. Results: Differential profiles between osteoporosis patients and matched controls were discovered for 12 proteins in at least one of the two study sets. Among these targets, the levels of autocrine motility factor receptor (AMFR) were concordantly lower in plasma of female osteoporosis patients. Subsequently, verification of anti-AMFR antibody selectivity was conducted using high-density peptide and protein arrays, and Western blotting. Conclusions and clinical relevance: Further validation in additional study sets will be needed to determine the clinical value of the observed decrease in AMFR plasma levels in osteoporosis patients, but AMFR may aid our understanding of disease mechanisms and could support existing tools for diagnosis and monitoring of patient mobility within osteoporosis.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2016
Keywords
Antibody bead arrays, Biomarker discovery, Osteoporosis, Plasma
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-194026 (URN)10.1002/prca.201400167 (DOI)000383846700007 ()25689831 (PubMedID)2-s2.0-84928139985 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceKnut and Alice Wallenberg Foundation
Note

QC 20161017

Available from: 2016-10-17 Created: 2016-10-14 Last updated: 2018-04-12Bibliographically approved
2. Targeted analysis of serum proteins encoded at known inflammatory bowel disease risk loci
Open this publication in new window or tab >>Targeted analysis of serum proteins encoded at known inflammatory bowel disease risk loci
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(English)Manuscript (preprint) (Other academic)
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:kth:diva-225979 (URN)
Note

QC 20180418

Available from: 2018-04-12 Created: 2018-04-12 Last updated: 2018-04-18Bibliographically approved

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