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Autoantibody profiling in multiple sclerosis using arrays of human protein fragments
KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-7843-2960
KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-0056-1313
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2013 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 12, no 9, 2657-2672 p.Article in journal (Refereed) Published
Abstract [en]

Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing ̃38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then reevaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.

Place, publisher, year, edition, pages
2013. Vol. 12, no 9, 2657-2672 p.
Keyword [en]
autoantibody, immunoglobulin G, adult, aged, article, controlled study, female, human, major clinical study, male, multiple sclerosis, priority journal, protein microarray, transcription regulation
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-133813DOI: 10.1074/mcp.M112.026757ISI: 000330536400021Scopus ID: 2-s2.0-84884389479OAI: oai:DiVA.org:kth-133813DiVA: diva2:675752
Funder
VinnovaKnut and Alice Wallenberg FoundationAFA InsuranceSwedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20131204

Available from: 2013-12-04 Created: 2013-11-11 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Affinity Arrays for Profiling Proteins and Autoantibody Repertoires
Open this publication in new window or tab >>Affinity Arrays for Profiling Proteins and Autoantibody Repertoires
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2014. xi, 159 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2014:12
National Category
Biomedical Laboratory Science/Technology
Identifiers
urn:nbn:se:kth:diva-150398 (URN)978-91-7595-209-3 (ISBN)
Public defence
2014-09-05, Inghesalen, Karolinska Institute, Tomtebodavägen 18 A, Solna, 10:00 (English)
Opponent
Supervisors
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20140902

Available from: 2014-09-02 Created: 2014-09-02 Last updated: 2014-09-02Bibliographically approved
2. Neuroproteomic profiling of human body fluids
Open this publication in new window or tab >>Neuroproteomic profiling of human body fluids
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis provides results from affinity based studies where human body fluids were profiled to find markers for neurological diseases. Both proteins and autoantibodies were analysed using microarray technologies that can profile hundreds of analytes and hundreds of samples in parallel using small sample volumes. A central element in this work was to develop and apply new methods to study cerebrospinal fluid (CSF), which is the fluid in direct contact with the brain. CSF contains proteins reflecting the physiological state of the central nervous system and therefore offers a unique insight into proteins associated to neurological disorders. As a complement to CSF, bloodderived samples such as serum and plasma, were also investigated as these represent potential sources of disease related proteins. The work presented here summarises the development of assay protocols to study protein and autoantibodies in CSF and blood using planar and bead-based microarrays.

In Paper I, an antibody-based protocol was developed to enable multiplexed protein profiling in CSF. The protocol was then applied for a first analysis within multiple sclerosis (MS) patients. In Paper II, the results were further evaluated in additional CSF as well as plasma samples. Based on the CSF analysis we found two proteins associated to MS; GAP43, a protein related to disease progression and SERPINA3, a protein involved in inflammation. In addition, four other proteins; IRF8, METTL14, IL7 and SLC30A7, were found to have altered plasma levels between the patient groups. The expression of these proteins were further investigated by immunofluorescent staining of human brain tissue, revealing differential localisation of proteins in diseased and healthy brain. In Paper III, a study on extensive protein profiling of plasma in the context of another neurodegenerative disorder, amyotrophic lateral sclerosis (ALS), is described. The levels of three proteins, namely NEFM, RGS18 and SCL25A20, were found to be elevated in ALS patients compared to controls. Among these, NEFM also indicated association to disease subtype as the levels were elevated in patients with definite compared to suspected diagnosis.

In addition to antibodies, we also utilised antigens on microarrays to screen for the presence of autoantibodies in body fluids. In Paper IV, a strategy for this analysis was developed using protein fragments and two types of microarrays. This strategy was then applied for profiling of the autoantibody repertoire of MS patients, revealing 51 protein fragments with potential disease relevance. Interestingly, comparison of plasma and CSF samples obtained from the same patients indicated high concordance of antibodies between the two body fluids. In Paper V, a similar strategy was applied to narcolepsy, another neurological disorder. Our investigation of antibodies in serum revealed higher reactivity towards METTL22, NT5C1A and TMEM134 compared to controls in two independent sample materials.

In conclusion, the presented work constitutes a framework of proteomic assays for enhanced exploration of proteins and autoantibodies in neuroscience. Moreover, we have reported identification of several potential disease markers to be further investigated within neurological disorders.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2015. viii, 67 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2015:2
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-158944 (URN)978-91-7595-402-8 (ISBN)
Public defence
2015-02-06, Rockefellersalen, KI, Solna, 09:00 (English)
Opponent
Supervisors
Note

QC 20150116

Available from: 2015-01-16 Created: 2015-01-15 Last updated: 2015-01-16Bibliographically approved

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Ayoglu, BurcuHäggmark, AnnaUhlén, MathiasSchwenk, Jochen M.

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