Autoimmunity ProfilingNational facility
The Autoimmunity profiling facility provides infrastructure and technologies for analysis of the autoantibody repertoire in body fluids and antibody validation using custom designed protein and peptide arrays.
Supported by the resource of more than 42 000 unique human protein fragments generated within the Human Protein Atlas, representing more than 18 000 human protein coding genes, we offer proteome wide screening for autoantibody reactivity on large microarrays in individual or pooled samples, as well as downstream solutions for investigation of autoantibody repertoires in hundreds of patient samples in parallel. Instrumentation and know-how is available for generating customized spotted protein microarrays as well as measurement and analysis of commercially available protein microarrays.
- A new microarrayer, Arrayjet Super Marathon with JetMosphere Max™, was installed in July 2019 to allow more efficient and accurate printing under highly controlled environmental conditions.
- The procurement process for the purchase of a new microarray scanner has been initiated.
- Autoantibody profiling
- Epitope mapping
- Antibody validation
- Infrastructure for commercial protein arrays
Proposed projects are assessed and prioritized according to the following model.
1) Initial assessment by facility:
- Technical feasibility and suitability
- Required capacity and resources for the project
2) Project prioritization by committee:
- Scientific potential
- Supporting preliminary data
- Significance of facility specific technique for project
- Supports facility development (competence and techniques)
- Profiling the autoantibody repertoire in plasma, serum or CSF by screening on microarrays of randomly selected antigens. Usually done in the range of the lower hundreds of samples and lower thousands of antigens.
- Verification of autoantibody profiles on suspension bead arrays with selected antigens. Usually in the range of lower hundreds of antigens and higher hundreds of samples.
- Epitope mapping and off-target analysis of affinity reagents as well as identified autoantibodies on antigen or peptide microarrays.
- Infrastructure and know-how to analyze commercial protein arrays such as ProtoArray (ThermoFisher), HuProt (Cambridge Protein Arrays), Immunome (Sengenics), and peptide arrays from Nimblegen Roche, Pepperprint and JPT.
- Access to affinity reagents and high density arrays.
- 42 100 mass spectrometry validated antigens (protein fragments) from the Human Protein Atlas project.
- High density antigen array containing 42 100 protein fragments from the Human Protein Atlas
- Ultra-high-density peptide microarrays from Roche NimbleGen, specifically designed and containing 2.9M peptides in one array or 173 000 peptides in 12 replicate subarrays.
- Liquid-handling: Tecan FLUENT, 2x Tecan EVO150, CyBio® SELMA.
- Microarray printer: Arrayjet Super Marathon with JetMosphere Max™ controlled environment.
- Microarray scanners: CapitalBio LuxScan HT24 and Roche NimbleGen Inc. MS200.
- Bead array instruments: 2x FLEXMAP 3D and 1x MAGPIX, all from Luminex®.
- Plate washer: Biotek EL406.
- The facility printed the world's largest protein array, which is available for autoantibody screenings.
- Autoantibody screening using planar protein arrays based on Human Protein Atlas protein fragments, with subsequent verification using suspension bead arrays in a larger patient sample material.
- Epitope mapping of a selection of antibodies using peptide arrays containing 175 000 peptides covering hundreds of proteins.
- Using assay infrastructure for autoantibody profiling with commercially available protein arrays
- Verification of monoclonal antibody target interaction using protein arrays containing Human Protein Atlas protein fragments
Publications associated to the facility:
Mining the Proteome Associated with Rheumatic and Autoimmune Diseases. C. Ruiz-Romero et al., J. Proteome Res. 2019.
The autoantibody response to cyclic citrullinated collagen type II peptides in rheumatoid arthritis. B. Liang et al., Rheumatology (Oxford) 2019.
Array-Based Profiling of Proteins and Autoantibody Repertoires in CSF. E. Pin et al., Methods Mol. Biol. 2019.
Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk. K. Tengvall et al., Proc. Natl. Acad. Sci. U.S.A. 2019.
Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles. C. Fredolini et al., Sci Rep 2019.
Individual and stable autoantibody repertoires in healthy individuals. M. Neiman et al., Autoimmunity 2019.
The antimicrobial protein S100A12 identified as a potential autoantigen in a subgroup of atopic dermatitis patients. M. Mikus et al., Clinical and Translational Allergy 2019.
Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer. D. Djureinovic et al., Lung Cancer 2018.
Autoantibody profiling reveals four protein candidate autoantigens associated with systemic lupus erythematosus. J. Frostegård et al., Lupus 2018.
Structural basis of cross-reactivity of anti-citrullinated protein antibodies. C. Ge et al., Arthritis Rheumatol 2018.
Human plasma cell derived monoclonal antibodies to post-translationally modified proteins recognize amino acid motifs rather than specific proteins. J. Steen et al., Arthritis & rheumatology (Hoboken, N.J.) 2018.
SURGE complex of Plasmodium falciparum in the rhoptry-neck (SURFIN4.2-RON4-GLURP) contributes to merozoite invasion. MDP. Quintana et al., PLoS ONE 2018.
Autoantibody profiling in intraocular fluid of patients with uveitis. JC. Ten Berge et al., Exp. Eye Res. 2018.
Multiplexed Antigen Bead Arrays for the Assessment of Antibody Selectivity and Epitope Mapping. B. Ayoglu et al., Methods Mol. Biol. 2018.
High-Density Antigen Microarrays for the Assessment of Antibody Selectivity and Off-Target Binding. R. Sjöberg et al., Methods Mol. Biol. 2018.
ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease. HD. Bremer et al., Sci Rep 2018.
Antibodies in children with malaria to PfEMP1, RIFIN and SURFIN expressed at the Plasmodium falciparum parasitized red blood cell surface. MDP. Quintana et al., Sci Rep 2018.
Thiol-ene-epoxy thermoset for low-temperature bonding to biofunctionalized microarray surfaces. XC. Zhou et al., Lab Chip 2017.
Clonal Evolution of Autoreactive Germinal Centers. SE. Degn et al., Cell 2017.
Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis. A. Zandian et al., Transl Psychiatry 2017.
Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage. C. Ge et al., JCI Insight 2017.
High-Density Serum/Plasma Reverse Phase Protein Arrays. C. Hellström et al., Methods Mol. Biol. 2017.
Neuroproteomic Profiling of Cerebrospinal Fluid (CSF) by Multiplexed Affinity Arrays. A. Häggmark-Månberg et al., Methods Mol. Biol. 2017.
Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies. Á. Sierra-Sánchez et al., J. Proteome Res. 2017.
A Preliminary Report: Radical Surgery and Stem Cell Transplantation for the Treatment of Patients With Pancreatic Cancer. B. Omazic et al., J. Immunother. 2017.
Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy. A. Zandian et al., J. Proteome Res. 2017.
Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing. JH. Ch'ng et al., Sci Rep 2017.
Towards encoded particles for highly multiplexed colorimetric point of care autoantibody detection. G. Svedberg et al., Lab Chip 2017.
Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer. E. Pin et al., J. Proteome Res. 2017.
Serum Autoantibody Profiling of Patients with Paraneoplastic and Non-Paraneoplastic Autoimmune Retinopathy. JC. Ten Berge et al., PLoS ONE 2016.
Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling. R. Sjöberg et al., N Biotechnol 2016.
Autoantibody targets in vaccine-associated narcolepsy. A. Häggmark-Månberg et al., Autoimmunity 2016.
Antigen arrays for profiling autoantibody repertoires. B. Ayoglu et al., Bioanalysis 2016.
Neuroproteomic profiling of human body fluids. A. Häggmark et al., Proteomics Clin Appl 2016.
Anoctamin 2 identified as an autoimmune target in multiple sclerosis. B. Ayoglu et al., Proc. Natl. Acad. Sci. U.S.A. 2016.
Transglutaminase 4 as a prostate autoantigen in male subfertility. N. Landegren et al., Sci Transl Med 2015.
Proteomic profiling reveals autoimmune targets in sarcoidosis. A. Häggmark et al., Am. J. Respir. Crit. Care Med. 2015.