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Comparative protein profiling of serum and plasma using an antibody suspension bead array approach
KTH, School of Biotechnology (BIO), Proteomics.ORCID iD: 0000-0001-8141-8449
KTH, School of Biotechnology (BIO), Proteomics.
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2010 (English)In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 10, no 3, 532-540 p.Article in journal (Refereed) Published
Abstract [en]

In the pursuit towards a systematic analysis of human diseases, array-based approaches within antibody proteomics offer high-throughput strategies to discover protein biomarkers in serum and plasma. To investigate the influence of sample preparation on such discovery attempts, we report on a systematic effort to compare serum and plasma protein profiles determined with an antibody suspension bead array. The intensity levels were used to define protein profiles and no significant differences between serum and plasma were observed for 79% of the 174 antibodies (targeting 156 proteins). By excluding 36 antibodies giving rise to differential intensity levels, cluster analysis revealed donor-specific rather than preparation-dependent grouping. With a cohort from a clinically relevant medical condition, the metabolic syndrome, the influence of the sample type on a multiplexed biomarker discovery approach was further investigated. Independent comparisons of protein profiles in serum and plasma revealed an antibody targeting ADAMTSL-4, a protein that would qualify to be studied further in association with the condition. In general, the preparation type had an impact on the results of the applied antibody suspension bead array, and while the technical variability was equal, plasma offered a greater biological variability and allowed to give rise to more discoveries than serum.

Place, publisher, year, edition, pages
2010. Vol. 10, no 3, 532-540 p.
Keyword [en]
Metabolic syndrome, Plasma, Protein arrays, Protein profiling, Serum, Suspension bead array, mass-spectrometry, extracellular-matrix, proteomics, identification, generation, affinity, disease, tissues, atlas
National Category
Biological Sciences
URN: urn:nbn:se:kth:diva-19229DOI: 10.1002/pmic.200900657ISI: 000274707400015ScopusID: 2-s2.0-76649124562OAI: diva2:337276
Knut and Alice Wallenberg Foundation
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2013-08-21Bibliographically approved
In thesis
1. Antibody based plasma protein profiling
Open this publication in new window or tab >>Antibody based plasma protein profiling
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is about protein profiling in serum and plasma using antibody suspension bead arrays for the analysis of biobanked samples and in the context of prostate cancer biomarker discovery. The influence of sample preparation methods on antibody based protein profiles were investigated (Papers I-III) and a prostate cancer candidate biomarker identified and verified (Papers III-V). Furthermore, a perspective on the research area affinity proteomics and its’ employment in biomarker discovery, for improved understanding and potentially improved disease diagnosis, is provided.

Paper I presents the results of a comparative plasma and serum protein profiling study, with a targeted biomarker discovery approach in the context of metabolic syndrome. The study yielded a higher number of significant findings and a low experimental variability in blood samples prepared as plasma. Paper II investigated the effects from post-centrifugation delays at different temperatures prior sample storage of serum and plasma samples. Minor effects were found on the detected levels of more than 300 predicted or known plasma proteins. In Paper III, the detectability of proteins in plasma was explored by exposing samples to different pre-analytical heat treatments, prior target capture. Heat induced epitope retrieval was observed for approximately half of the targeted proteins, and resulted in the discovery of different candidate markers for prostate cancer. Several antibodies towards the prostate cancer candidate biomarker CNDP1 were generated, epitope mapped and evaluated in a bead based sandwich immunoassay, as presented in Papers IV and V. Furthermore, the developed sandwich immunoassay targeting multiple distinct CNDP1 epitopes in more than 1000 samples, confirmed the association of CNDP1 levels to aggres- sive prostate cancer and more specifically to prostate cancer patients with regional lymph node metastasis (Paper V).

As an outcome of the present investigations and in parallel to studies within the Biobank profiling research group, valuable lessons from study design and multiplex antibody analysis of plasma within biomarker discovery to experimental, technical and biological verifications have been collected.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2013. viii, 68 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2013:12
protein profiling, plasma, antibody, affinity proteomics, biomark- ers, multiplex, assay development
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
urn:nbn:se:kth:diva-126270 (URN)978-91-7501-829-4 (ISBN)
Public defence
2013-09-06, Gamma house lecture hall, SciLifeLab, Tomtebodavägen 23a, Solna, 10:00 (English)

QC 20130821

Available from: 2013-08-21 Created: 2013-08-20 Last updated: 2013-08-21Bibliographically approved

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