title: Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling.
abstract: High-density protein microarrays of recombinant human protein fragments, representing 12,412 unique Ensembl Gene IDs, have here been produced and explored. These protein microarrays were used to analyse antibody off-target interactions, as well as for profiling the human autoantibody repertoire in plasma against the antigens represented by the protein fragments. Affinity-purified polyclonal antibodies produced within the Human Protein Atlas (HPA) were analysed on microarrays of three different sizes, ranging from 384 antigens to 21,120 antigens, for evaluation of the antibody validation criteria in the HPA. Plasma samples from secondary progressive multiple sclerosis patients were also screened in order to explore the feasibility of these arrays for broad-scale profiling of autoantibody reactivity. Furthermore, analysis on these near proteome-wide microarrays was complemented with analysis on HuProt™ Human Proteome protein microarrays. The HPA recombinant protein microarray with 21,120 antigens and the HuProt™ Human Proteome protein microarray are currently the largest protein microarray platforms available to date. The results on these arrays show that the Human Protein Atlas antibodies have few off-target interactions if the antibody validation criteria are kept stringent and demonstrate that the HPA-produced high-density recombinant protein fragment microarrays allow for a high-throughput analysis of plasma for identification of possible autoantibody targets in the context of various autoimmune conditions.
authors.affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Ronald
authors.initials: R
authors.lastname: Sjöberg
authors.affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Mattsson
authors.affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Eni
authors.initials: E
authors.lastname: Andersson
authors.affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Hellström
authors.affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlen
authors.affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Jochen M
authors.initials: JM
authors.lastname: Schwenk
authors.affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Burcu
authors.initials: B
authors.lastname: Ayoglu
authors.affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden. Electronic address: peter.nilsson@scilifelab.se.
authors.forename: Peter
authors.initials: P
authors.lastname: Nilsson
mesh_terms: D000595:Amino Acid Sequence; D001323:Autoantibodies / Q000097:blood*; D001324:Autoantigens / Q000235:genetics / Q000276:immunology; D015551:Autoimmunity; D001709:Biotechnology; D057166:High-Throughput Screening Assays; D006801:Humans; D020528:Multiple Sclerosis, Chronic Progressive / Q000276:immunology; D010446:Peptide Fragments / Q000235:genetics / Q000276:immunology; D019151:Peptide Library; D040081:Protein Array Analysis / Q000379:methods*; D011994:Recombinant Proteins / Q000235:genetics / Q000276:immunology
chemical_list: D001323:Autoantibodies; D001324:Autoantigens; D010446:Peptide Fragments; D019151:Peptide Library; D011994:Recombinant Proteins