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  • 201.
    Steen, Johanna
    et al.
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Forsström, Björn
    KTH Royal Inst Technol, Stockholm, Sweden.
    Sahlström, Peter
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden;KTH Royal Inst Technol, Stockholm, Sweden;Charite, Berlin, Germany.
    Odowd, Victoria
    UCB Pharma, Slough, Berks, England.
    Israelsson, Lena
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Krishnamurthy, Akilan
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Badreh, Sara
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Mathsson Alm, Linda
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology. Thermo Fisher Sci, Uppsala, Sweden.
    Compson, Joanne
    UCB Pharma, Slough, Berks, England.
    Ramsköld, Daniel
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Ndlovu, Welcome
    UCB Pharma, Slough, Berks, England.
    Rapecki, Stephen
    UCB Pharma, Slough, Berks, England.
    Hansson, Monika
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Titcombe, Philip J.
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden;Univ Minnesota, Med Sch, Minneapolis, MN 55455 USA.
    Bang, Holger
    Orgentec Diagnost, Mainz, Germany.
    Mueller, Daniel L.
    Univ Minnesota, Med Sch, Minneapolis, MN 55455 USA.
    Catrina, Anca I.
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Grönwall, Caroline
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Skriner, Karl
    Charite, Berlin, Germany.
    Nilsson, Peter
    Lightwood, Daniel
    UCB Pharma, Slough, Berks, England.
    Klareskog, Lars
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Malmström, Vivianne
    Karolinska Inst, Karolinska Univ Hosp, Stockholm, Sweden.
    Recognition of Amino Acid Motifs, Rather Than Specific Proteins, by Human Plasma Cell-Derived Monoclonal Antibodies to Posttranslationally Modified Proteins in Rheumatoid Arthritis2019In: Arthritis & Rheumatology, ISSN 2326-5191, E-ISSN 2326-5205, Vol. 71, no 2, p. 196-209Article in journal (Refereed)
    Abstract [en]

    Objective: Antibodies against posttranslationally modified proteins are a hallmark of rheumatoid arthritis (RA), but the emergence and pathogenicity of these autoantibodies are still incompletely understood. The aim of this study was to analyze the antigen specificities and mutation patterns of monoclonal antibodies (mAb) derived from RA synovial plasma cells and address the question of antigen cross-reactivity.

    Methods: IgG-secreting cells were isolated from RA synovial fluid, and the variable regions of the immunoglobulins were sequenced (n = 182) and expressed in full-length mAb (n = 93) and also as germline-reverted versions. The patterns of reactivity with 53,019 citrullinated peptides and 49,211 carbamylated peptides and the potential of the mAb to promote osteoclastogenesis were investigated.

    Results: Four unrelated anti-citrullinated protein autoantibodies (ACPAs), of which one was clonally expanded, were identified and found to be highly somatically mutated in the synovial fluid of a patient with RA. The ACPAs recognized >3,000 unique peptides modified by either citrullination or carbamylation. This highly multireactive autoantibody feature was replicated for Ig sequences derived from B cells from the peripheral blood of other RA patients. The plasma cell-derived mAb were found to target distinct amino acid motifs and partially overlapping protein targets. They also conveyed different effector functions as revealed in an osteoclast activation assay.

    Conclusion: These findings suggest that the high level of cross-reactivity among RA autoreactive B cells is the result of different antigen encounters, possibly at different sites and at different time points. This is consistent with the notion that RA is initiated in one context, such as in the mucosal organs, and thereafter targets other sites, such as the joints.

  • 202.
    Steen, Johanna
    et al.
    Karolinska Inst, Dept Med, Rheumatol Unit, Stockholm, Sweden..
    Titcombe, Philip J.
    Univ Minnesota, Sch Med, Dept Med, Ctr Immunol, Minneapolis, MN 55455 USA..
    Forsstrom, Bjorn
    Royal Technol Highsch, SciLifeLab, Stockholm, Sweden..
    Gronwall, Caroline
    Karolinska Inst, Dept Med, Rheumatol Unit, Stockholm, Sweden..
    Catrina, Anca I.
    Karolinska Inst, Karolinska Univ Hosp, Rheumatol Unit, Med, Stockholm, Sweden..
    Lightwood, Daniel
    UCB Celltech, Antibody Discovery, Slough, Berks, England..
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Klareskog, Lars
    Karolinska Inst, Dept Med, Rheumatol Unit, Stockholm, Sweden..
    Malmstrom, Vivianne
    Karolinska Inst, Dept Med, Rheumatol Unit, Stockholm, Sweden..
    Monoclonal Anti-Citrullinated Protein Antibodies Generated from RA-Derived B Cells Recognize Amino Acid Motifs Rather Than Specific Proteins2018In: Arthritis & Rheumatology, ISSN 2326-5191, E-ISSN 2326-5205, Vol. 70Article in journal (Other academic)
  • 203.
    Sterky, Fredrik
    et al.
    KTH, Superseded Departments, Biotechnology.
    Bhalerao, Rupali R.
    KTH, Superseded Departments, Biotechnology.
    Unneberg, Per
    KTH, Superseded Departments, Biotechnology.
    Segerman, B.
    Nilsson, Peter
    KTH, Superseded Departments, Biotechnology.
    Brunner, A. M.
    Charbonnel-Campaa, L.
    Lindvall, J. J.
    Tandre, K.
    Strauss, S. H.
    Sundberg, B.
    Gustafsson, P.
    Uhlén, Mathias
    KTH, Superseded Departments, Biotechnology.
    Nilsson, O.
    Sandberg, G.
    Karlsson, J.
    Lundeberg, Joakim
    KTH, Superseded Departments, Biotechnology.
    Jansson, S.
    A Populus EST resource for plant functional genomics2004In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 38, p. 13951-13956Article in journal (Refereed)
    Abstract [en]

    Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

  • 204. Street, Nathaniel Robert
    et al.
    Skogstrom, Oskar
    Sjodin, Andreas
    Tucker, James
    Rodriguez-Acosta, Maricela
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Jansson, Stefan
    Taylor, Gail
    The genetics and genomics of the drought response in Populus2006In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 48, no 3, p. 321-341Article in journal (Refereed)
    Abstract [en]

    The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F-2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that 'genetical genomics' can be used to provide information on adaptation at the species level. The grandparents and F-2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.

  • 205. Stromberg, Sara
    et al.
    Bjorklund, Marcus Gry
    Asplund, Anna
    Rimini, Rebecca
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Ponten, Fredrik
    Olsson, Mats J.
    Transcriptional profiling of melanocytes from patients with vitiligo vulgaris2008In: Pigment Cell & Melanoma Research, ISSN 1755-1471, Vol. 21, no 2, p. 162-171Article in journal (Refereed)
    Abstract [en]

    Vitiligo is a complex, polygenic disorder characterized by patchy loss of skin pigmentation due to abnormal melanocyte function. Both genetic and environmental etiological factors have been proposed for vitiligo and lack of molecular markers renders difficulties to predict development and progression of the disease. Identification of dysregulated genes has the potential to unravel biological pathways involved in vitiligo pathogenesis, facilitating discovery of potential biomarkers and novel therapeutic approaches. In this study, we characterized the transcriptional profile of melanocytes from vitiligo patients. Oligonucleotide microarrays containing similar to 16 000 unique genes were used to analyse mRNA expression in melanocytes from vitiligo patients and age-matched healthy controls. In total, 859 genes were identified as differentially expressed. A substantial number of these genes were involved in (i) melanocyte development, (ii) intracellular processing and trafficking of tyrosinase gene family proteins, (iii) packing and transportation of melanosomes, (iv) cell adhesion and (v) antigen processing and presentation. In conclusion, our results show a significantly different transcription profile in melanocytes from vitiligo patients compared with controls. Several genes of potential importance for the pathogenesis and development of vitiligo were identified. Our data indicate that autoimmunity involving melanocytes may be a secondary event in vitiligo patients caused by abnormal melanocyte function.

  • 206.
    Strömberg, Sara
    et al.
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.
    Gry Björklund, Marcus
    KTH, School of Biotechnology (BIO), Proteomics.
    Asplund, Caroline
    KTH, School of Biotechnology (BIO), Proteomics.
    Sköllermo, Anna
    KTH, School of Biotechnology (BIO), Proteomics.
    Persson, Anja
    KTH, School of Biotechnology (BIO), Proteomics.
    Wester, Kenneth
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.
    Kampf, Caroline
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Andersson, Ann-Catrin
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Kononen, Juha
    Beecher Instruments, Sun Prairie, WI, United States.
    Pontén, Fredrik
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.
    Asplund, Anna
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University.
    A high-throughput strategy for protein profiling in cell microarrays using automated image analysis2007In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 7, no 13, p. 2142-2150Article in journal (Refereed)
    Abstract [en]

    Advances in antibody production render a growing supply of affinity reagents for immunohistochemistry (IHC), and tissue microarray (TMA) technologies facilitate simultaneous analysis of protein expression in a multitude of tissues. However, collecting validated IHC data remains a bottleneck problem, as the standard method is manual microscopical analysis. Here we present a high-throughput strategy combining IHC on a recently developed cell microarray with a novel, automated image-analysis application (TMAx). The software was evaluated on 200 digital images of IHC-stained cell spots, by comparing TMAx annotation with manual annotation performed by seven human experts. A high concordance between automated and manual annotation of staining intensity and fraction of IHC-positive cells was found. in a limited study, we also investigated the possibility to assess the correlation between mRNA and protein levels, by using TMAx output results for relative protein quantification and quantitative real-time PCR for the quantification of corresponding transcript levels. In conclusion, automated analysis of immunohistochemically stained in vitro-cultured cells in a microarray format can be used for high-throughput protein profiling, and extraction of RNA from the same cell lines provides a basis for comparing transcription and protein expression on a global scale.

  • 207.
    Svedberg, Gustav
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Jeong, Yunjin
    Na, Hunjong
    Jang, Jisung
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kwon, Sunghoon
    Gantelius, Jesper
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Svahn Andersson, Helene
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Towards encoded particles for highly multiplexed colorimetric point of care autoantibody detection2017In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 17, no 3, p. 549-556Article in journal (Refereed)
    Abstract [en]

    Highly multiplexed point of care tests could improve diagnostic accuracy and differential diagnostic capacity in for instance emergency medicine and low resource environments. Available technology platforms for POC biomarker detection are typically simplex or low-plexed, whereas common lab-based microarray systems allow for the simultaneous detection of thousands of DNA or protein biomarkers. In this study, we demonstrate a novel suspension particle array platform that utilizes 900 mu m bricks for POC amenable colorimetric biomarker detection with an encoding capacity of over two million. Due to the mm-scale size, both the lithographic codes and colorimetric signals of individual particles can be visualized using a consumer grade office flatbed scanner, with a potential for simultaneous imaging of around 19000 particles per scan. The analytical sensitivity of the assay was determined to be 4 ng ml(-1) using an antibody model system. As a proof of concept, autoantibodies toward anoctamin 2 were detected in order to discriminate between multiple sclerosis plasma samples and healthy controls with p < 0.0001 and an inter-assay % CV of 9.44%.

  • 208. ten Berge, Josianne C.
    et al.
    van Rosmalen, Joost
    Vermeer, Jacolien
    Hellström, Cecilia
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lindskog, Cecilia
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Qundos, Ulrika
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rothova, Aniki
    Schreurs, Marco W. J.
    Serum Autoantibody Profiling of Patients with Paraneoplastic and Non-Paraneoplastic Autoimmune Retinopathy2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 12, article id e0167909Article in journal (Refereed)
    Abstract [en]

    Purpose Although multiple serum antiretinal autoantibodies (ARAs) have been reported in patients with paraneoplastic and non-paraneoplastic autoimmune retinopathy ((n)pAIR), not all retinal antigens involved in (n)pAIR are specified. This study aims to serologically identify patients with presumed (n)pAIR through determination of both known and unknown ARAs by autoantibody profiling. Methods An antigen suspension bead array using 188 different antigens representing 97 ocular proteins was performed to detect ARAs in serum samples of patients with presumed (n)pAIR (n = 24), uveitis (n = 151) and cataract (n = 21). Logistic regressions were used to estimate the associations between ocular antigens and diagnosis. Validation of interphotoreceptor matrix proteoglycan 2 (IMPG2) and recoverin antigens was performed by immunohistochemistry and immunoblot, respectively. Results Samples of patients with presumed (n)pAIR exhibited a broad spectrum of ARAs. We identified retinal antigens that have already been described previously (e.g. recoverin), but also identified novel ARA targets. Most ARAs were not specific for (n)pAIR since their presence was also observed in patients with cataract or uveitis. High titers of autoantibodies directed against photoreceptor-specific nuclear receptor and retinol-binding protein 3 were more common in patients with presumed (n)pAIR compared to uveitis (p = 0.015 and p = 0.018, respectively). The presence of all other ARAs did not significantly differ between groups. In patients with presumed (n)pAIR, anti-recoverin autoantibodies were the most prevalent ARAs. Validation of bead array results by immunohistochemistry (anti-IMPG2) and immunoblot (anti-recoverin) showed concordant results in (n)pAIR patients. Conclusions Patients with (n)pAIR are characterized by the presence of a broad spectrum of ARAs. The diagnosis of (n)pAIR cannot be based on the mere presence of serum ARAs, as these are also commonly present in uveitis as well as in age-related cataract patients.

  • 209.
    Tengvall, Katarina
    et al.
    Karolinska Inst, Karolinska Neuroimmunol & Multiple Sclerosis Ctr, Dept Clin Neurosci, Neuroimmunol Unit, S-17176 Stockholm, Sweden.;Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden..
    Huang, Jesse
    Karolinska Inst, Karolinska Neuroimmunol & Multiple Sclerosis Ctr, Dept Clin Neurosci, Neuroimmunol Unit, S-17176 Stockholm, Sweden.;Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden..
    Hellström, Cecilia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kammer, Patrick
    German Canc Res Ctr, Infect & Canc Epidemiol Infect Inflammat & Canc R, D-69120 Heidelberg, Germany..
    Bistrom, Martin
    Umea Univ, Dept Pharmacol & Clin Neurosci, S-90185 Umea, Sweden..
    Ayoglu, Burcu
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Bomfim, Izaura Lima
    Karolinska Inst, Karolinska Neuroimmunol & Multiple Sclerosis Ctr, Dept Clin Neurosci, Neuroimmunol Unit, S-17176 Stockholm, Sweden.;Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden..
    Stridh, Pernilla
    Karolinska Inst, Karolinska Neuroimmunol & Multiple Sclerosis Ctr, Dept Clin Neurosci, Neuroimmunol Unit, S-17176 Stockholm, Sweden.;Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden..
    Butt, Julia
    German Canc Res Ctr, Infect & Canc Epidemiol Infect Inflammat & Canc R, D-69120 Heidelberg, Germany..
    Brenner, Nicole
    German Canc Res Ctr, Infect & Canc Epidemiol Infect Inflammat & Canc R, D-69120 Heidelberg, Germany..
    Michel, Angelika
    German Canc Res Ctr, Infect & Canc Epidemiol Infect Inflammat & Canc R, D-69120 Heidelberg, Germany..
    Lundberg, Karin
    Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden.;Karolinska Inst, Dept Med Solna, Div Rheumatol, S-17176 Stockholm, Sweden..
    Padyukov, Leonid
    Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden.;Karolinska Inst, Dept Med Solna, Div Rheumatol, S-17176 Stockholm, Sweden..
    Lundberg, Ingrid E.
    Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden.;Karolinska Inst, Dept Med Solna, Div Rheumatol, S-17176 Stockholm, Sweden..
    Svenungsson, Elisabet
    Karolinska Inst, Dept Med Solna, Div Rheumatol, S-17176 Stockholm, Sweden..
    Ernberg, Ingemar
    Karolinska Inst, Dept Microbiol Tumor & Cell Biol, S-17177 Stockholm, Sweden..
    Olafsson, Sigurgeir
    Amgen Inc, deCODE Genet, IS-101 Reykjavik, Iceland..
    Dilthey, Alexander T.
    Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England.;Heinrich Heine Univ Dusseldorf, Inst Med Microbiol & Hosp Hyg, D-40225 Dusseldorf, Germany..
    Hillert, Jan
    Karolinska Inst, Karolinska Neuroimmunol & Multiple Sclerosis Ctr, Dept Clin Neurosci, Neuroimmunol Unit, S-17176 Stockholm, Sweden..
    Alfredsson, Lars
    Karolinska Inst, Inst Environm Med, S-17177 Stockholm, Sweden.;Stockholm Cty Council, Ctr Occupat & Environm Med, S-17177 Stockholm, Sweden..
    Sundstrom, Peter
    Umea Univ, Dept Pharmacol & Clin Neurosci, S-90185 Umea, Sweden..
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Waterboer, Tim
    German Canc Res Ctr, Infect & Canc Epidemiol Infect Inflammat & Canc R, D-69120 Heidelberg, Germany..
    Olsson, Tomas
    Karolinska Inst, Karolinska Neuroimmunol & Multiple Sclerosis Ctr, Dept Clin Neurosci, Neuroimmunol Unit, S-17176 Stockholm, Sweden.;Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden..
    Kockum, Ingrid
    Karolinska Inst, Karolinska Neuroimmunol & Multiple Sclerosis Ctr, Dept Clin Neurosci, Neuroimmunol Unit, S-17176 Stockholm, Sweden.;Karolinska Univ Hosp, Ctr Mol Med, S-17176 Stockholm, Sweden..
    Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 34, p. 16955-16960Article in journal (Refereed)
    Abstract [en]

    Multiple sclerosis (MS) is a chronic inflammatory, likely autoimmune disease of the central nervous system with a combination of genetic and environmental risk factors, among which Epstein-Barr virus (EBV) infection is a strong suspect. We have previously identified increased autoantibody levels toward the chloride-channel protein Anoctamin 2 (ANO2) in MS. Here, IgG antibody reactivity toward ANO2 and EBV nuclear antigen 1 (EBNA1) was measured using bead-based multiplex serology in plasma samples from 8,746 MS cases and 7,228 controls. We detected increased anti-ANO2 antibody levels in MS (P = 3.5 x 10(-36)) with 14.6% of cases and 7.8% of controls being ANO2 seropositive (odds ratio [OR] = 1.6; 95% confidence intervals [95% CI]: 1.5 to 1.8). The MS risk increase in ANO2-seropositive individuals was dramatic when also exposed to 3 known risk factors for MS: HLA-DRB1*15: 01 carriage, absence of HLA-A*02: 01, and high anti-EBNA1 antibody levels (OR = 24.9; 95% CI: 17.9 to 34.8). Reciprocal blocking experiments with ANO2 and EBNA1 peptides demonstrated antibody cross-reactivity, mapping to ANO2 [aa 140 to 149] and EBNA1 [aa 431 to 440]. HLA gene region was associated with anti-ANO2 antibody levels and HLADRB1*04: 01 haplotype was negatively associated with ANO2 seropositivity (OR = 0.6; 95% CI: 0.5 to 0.7). Anti-ANO2 antibody levels were not increased in patients from 3 other inflammatory disease cohorts. The HLA influence and the fact that specific IgG production usually needs T cell help provides indirect evidence for a T cell ANO2 autoreactivity in MS. We propose a hypothesis where immune reactivity toward EBNA1 through molecular mimicry with ANO2 contributes to the etiopathogenesis of MS.

  • 210. Thelin, Eric Peter
    et al.
    Just, David
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Frostell, Arvid
    Häggmark-Månberg, Anna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Risling, Mårten
    Svensson, Mikael
    Nilsson, Peter
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bellander, Bo-Michael
    Protein profiling in serum after traumatic brain injury in rats reveals potential injury markers2018In: Behavioural Brain Research, ISSN 0166-4328, E-ISSN 1872-7549, Vol. 340, p. 71-80Article in journal (Refereed)
    Abstract [en]

    Introduction: The serum proteome following traumatic brain injury (TBI) could provide information for outcome prediction and injury monitoring. The aim with this affinity proteomic study was to identify serum proteins over time and between normoxic and hypoxic conditions in focal TBI. Material and methods: Sprague Dawley rats (n = 73) received a 3 mm deep controlled cortical impact ("severe injury"). Following injury, the rats inhaled either a normoxic (22% O-2) or hypoxic (11% O-2) air mixture for 30 min before resuscitation. The rats were sacrificed at day 1, 3, 7, 14 and 28 after trauma. A total of 204 antibodies targeting 143 unique proteins of interest in TBI research, were selected. The sample proteome was analyzed in a suspension bead array set-up. Comparative statistics and factor analysis were used to detect differences as well as variance in the data. Results: We found that complement factor 9 (C9), complement factor B (CFB) and aldolase c (ALDOC) were detected at higher levels the first days after trauma. In contrast, hypoxia inducing factor (HIF)1 alpha, amyloid precursor protein (APP) and WBSCR17 increased over the subsequent weeks. S100A9 levels were higher in hypoxic-compared to normoxic rats, together with a majority of the analyzed proteins, albeit few reached statistical significance. The principal component analysis revealed a variance in the data, highlighting clusters of proteins. Conclusions: Protein profiling of serum following TBI using an antibody based microarray revealed temporal changes of several proteins over an extended period of up to four weeks. Further studies are warranted to confirm our findings.

  • 211.
    Thul, Peter J.
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Åkesson, Lovisa
    KTH, School of Biotechnology (BIO). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wiking, Mikaela
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mahdessian, Diana
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Geladaki, A.
    Ait Blal, Hammou
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Alm, Tove L.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Asplund, A.
    Björk, Lars
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Breckels, L. M.
    Bäckström, Anna
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Danielsson, Frida
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fagerberg, Linn
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fall, Jenny
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gatto, L.
    Gnann, Christian
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Protein Technology.
    Hjelmare, Martin
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Johansson, Fredric
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lee, Sunjae
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lindskog, C.
    Mulder, J.
    Mulvey, C. M.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Oksvold, Per
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Schutten, Rutger
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sivertsson, Åsa
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sjöstedt, E.
    Skogs, Marie
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Stadler, Charlotte
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sullivan, Devin P.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Tegel, Hanna
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Winsnes, Casper F.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zhang, Cheng
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zwahlen, Martin
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mardinoglu, Adil
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pontén, F.
    von Feilitzen, Kalle
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lilley, K. S.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    A subcellular map of the human proteome2017In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 356, no 6340, article id 820Article in journal (Refereed)
    Abstract [en]

    Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.

  • 212.
    Uhlén, Mathias
    et al.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Björling, Erik
    KTH, School of Biotechnology (BIO).
    Agaton, Charlotta
    KTH, School of Biotechnology (BIO).
    Al-Khalili Szigyarto, Cristina
    KTH, School of Biotechnology (BIO).
    Amini, Bahram
    KTH, School of Biotechnology (BIO).
    Andersen, Elisabet
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Andersson, Ann-Catrin
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Angelidou, Pia
    KTH, School of Biotechnology (BIO).
    Asplund, Anna
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Asplund, Caroline
    KTH, School of Biotechnology (BIO).
    Berglund, Lisa
    KTH, School of Biotechnology (BIO).
    Bergström, Kristina
    KTH, School of Biotechnology (BIO).
    Brumer, Harry
    KTH, School of Biotechnology (BIO).
    Cerjan, Dijana
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Ekström, Marica
    KTH, School of Biotechnology (BIO).
    Elobeid, Adila
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Eriksson, Cecilia
    KTH, School of Biotechnology (BIO).
    Fagerberg, Linn
    KTH, School of Biotechnology (BIO).
    Falk, Ronny
    KTH, School of Biotechnology (BIO).
    Fall, Jenny
    KTH, School of Biotechnology (BIO).
    Forsberg, Mattias
    KTH, School of Biotechnology (BIO).
    Gry Björklund, Marcus
    KTH, School of Biotechnology (BIO).
    Gumbel, Kristoffer
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Halimi, Asif
    KTH, School of Biotechnology (BIO).
    Hallin, Inga
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Hamsten, Carl
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Hansson, Marianne
    KTH, School of Biotechnology (BIO).
    Hedhammar, My
    KTH, School of Biotechnology (BIO).
    Hercules, Görel
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Kampf, Caroline
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Larsson, Karin
    KTH, School of Biotechnology (BIO).
    Lindskog, Mats
    KTH, School of Biotechnology (BIO).
    Lodewyckx, Wald
    KTH, School of Biotechnology (BIO).
    Lund, Jan
    KTH, School of Biotechnology (BIO).
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO).
    Magnusson, Kristina
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Malm, Erik
    KTH, School of Biotechnology (BIO).
    Nilsson, Peter
    KTH, School of Biotechnology (BIO).
    Ödling, Jenny
    KTH, School of Biotechnology (BIO).
    Oksvold, Per
    KTH, School of Biotechnology (BIO).
    Olsson, Ingmarie
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Öster, Emma
    KTH, School of Biotechnology (BIO).
    Ottosson, Jenny
    KTH, School of Biotechnology (BIO).
    Paavilainen, Linda
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Persson, Anja
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Rimini, Rebecca
    KTH, School of Biotechnology (BIO).
    Rockberg, Johan
    KTH, School of Biotechnology (BIO).
    Runeson, Marcus
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Sivertsson, Åsa
    KTH, School of Biotechnology (BIO).
    Sköllermo, Anna
    KTH, School of Biotechnology (BIO).
    Steen, Johanna
    KTH, School of Biotechnology (BIO).
    Stenvall, Maria
    KTH, School of Biotechnology (BIO).
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO).
    Strömberg, Sara
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Sundberg, Mårten
    KTH, School of Biotechnology (BIO).
    Tegel, Hanna
    KTH, School of Biotechnology (BIO).
    Tourle, Samuel
    KTH, School of Biotechnology (BIO).
    Wahlund, Eva
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Waldén, Annelie
    KTH, School of Biotechnology (BIO).
    Wan, Jinghong
    KTH, School of Biotechnology (BIO), Molecular Biotechnology (closed 20130101).
    Wernérus, Henrik
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Westberg, Joakim
    KTH, School of Biotechnology (BIO).
    Wester, Kenneth
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    Wrethagen, Ulla
    KTH, School of Biotechnology (BIO).
    Xu, Lan Lan
    KTH, School of Biotechnology (BIO).
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Pontén, Fredrik
    Uppsala Univ, Rudbeck Lab, Dept Genet & Pathol.
    A human protein atlas for normal and cancer tissues based on antibody proteomics2005In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 4, no 12, p. 1920-1932Article in journal (Refereed)
    Abstract [en]

    Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, similar to 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.

  • 213.
    Uhlén, Mathias
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hallström, Björn M
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Lindskog, Cecilia
    Oksvold, Per
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mardinoglu, Adil
    Sivertsson, Åsa
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kampf, Caroline
    Sjöstedt, Evelina
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Asplund, Anna
    Olsson, IngMarie
    Edlund, Karolina
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Navani, Sanjay
    Szigyarto, Cristina Al-Khalili
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Odeberg, Jacob
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Djureinovic, Dijana
    Takanen, Jenny Ottosson
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Alm, Tove
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Edqvist, Per-Henrik
    Berling, Holger
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Tegel, Hanna
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Mulder, Jan
    Rockberg, Johan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hamsten, Marica
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    von Feilitzen, Kalle
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Forsberg, Mattias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Persson, Lukas
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Johansson, Fredric
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zwahlen, Martin
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    von Heijne, Gunnar
    Nielsen, Jens
    Pontén, Fredrik
    Tissue-based map of the human proteome2015In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 347, no 6220, p. 1260419-Article in journal (Refereed)
    Abstract [en]

    Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.

  • 214.
    Uhlén, Mathias
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. Center for Biosustainability, Danish Technical University, Copenhagen, Denmark..
    Zhang, Cheng
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lee, Sunjae
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sjöstedt, Evelina
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden..
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bidkhori, Gholamreza
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Benfeitas, Rui
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Arif, Muhammad
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Liu, Zhengtao
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Edfors, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sanli, Kemal
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    von Feilitzen, Kalle
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Oksvold, Per
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hober, Sophia
    KTH, School of Biotechnology (BIO).
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mattsson, Johanna
    Schwenk, Jochen M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brunnstrom, Hans
    Glimelius, Bengt
    Sjoblom, Tobias
    Edqvist, Per-Henrik
    Djureinovic, Dijana
    Micke, Patrick
    Lindskog, Cecilia
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Ponten, Fredrik
    A pathology atlas of the human cancer transcriptome2017In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 357, no 6352, p. 660-+Article in journal (Refereed)
    Abstract [en]

    Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.

  • 215. van der Griendt, J. C.
    et al.
    Eefting, M.
    van der Meijden, E. D.
    Ayoglu, Burcu
    KTH, School of Biotechnology (BIO), Proteomics.
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Falkenburg, J. H. F.
    Griffioen, M.
    Antibodies against intracellular antigens develop as a result of tissue damage induced by donor lymphocyte infusion after allogeneic stem cell transplantation2012In: Immunology, ISSN 0019-2805, E-ISSN 1365-2567, Vol. 137, p. 737-737Article in journal (Other academic)
  • 216. van der Griendt, Judith C.
    et al.
    van der Meijden, Edith D.
    Ayoglu, Burcu
    KTH, School of Biotechnology (BIO), Proteomics.
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Falkenburg, J. H. Frederik
    Griffioen, Marieke
    High Throughput Screening for Antibody Responses Against H-Y Antigens and Their X-Variants in Allogeneic Hematopoeietic Stem Cell Transplantation2011In: Blood, ISSN 0006-4971, E-ISSN 1528-0020, Vol. 118, no 21, p. 1749-1750Article in journal (Other academic)
  • 217. Velazquez-Fernandez, David
    et al.
    Laurell, Cecilia
    KTH, School of Biotechnology (BIO), Gene Technology.
    Geli, Janos
    Höög, Anders
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO), Gene Technology.
    Kjellman, Magnus
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology.
    Hamberger, Bertil
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Gene Technology.
    Bäckdahl, Martin
    Expression profiling of adrenocortical neoplasms suggests a molecular signature of malignancy.2005In: Surgery, ISSN 0039-6060, E-ISSN 1532-7361, Surgery, Vol. 138, no 6, p. 1087-1094Article in journal (Refereed)
    Abstract [en]

    Background. Distinguishing between adrenocortical adenomas and carcinomas is often difficult. Our aim was to investigate the differences in transcriptional profiles between benign and malignant adrenocortical neoplasms using complementary DNA microarray techniques.

    Methods. We studied 7 patients with adrenocortical carcinomas and 13 with adenomas. Histopathology was reviewed in all patients, clinical follow-up was at least 1 year. Hybridizations were Performed in duplicate against RNA reference. Expression levels were analyzed in the R environment for statistical computing with the use of aroma, limma, statistics, and class packages.

    Results. Transcriptional profiles were homogeneous among adenomas, while carcinomas were much more heterogeneous. Hierarchical clustering and self-organizing maps could separate clearly carcinomas from adenomas. Among genes that were most significantly upregulated in carcinomas were 2 ubiquilin-related genes (USP4 and UFD1L) and several insulinlike growth factor-related genes (IGF2, IGF2R, IGFBP3 and IGFBP6). Among genes that were most significantly downregulated in carcinomas were a cylokine gene (CXCL10), several genes related to cell metabolism (RARRES2, ALDH1A1, CYBRD1 and GSTA4), and the cadherin 2 gene (CDH2).

    Conclusions. Through the use of cDNA arrays, adrenocortical adenomas and carcinomas appear to be clearly distinguishable on the basis of their specific molecular signature. The biologic importance of the up- and downregulated genes is yet to be determined.

  • 218.
    Waldén, Annelie
    et al.
    KTH, School of Biotechnology (BIO).
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fabrication using contact spotter2009In: Vol. 529, p. 101-113Article in journal (Refereed)
    Abstract [en]

    Many steps of optimization are needed to achieve large-scale fabrication of high-quality DNA microarrays. These steps involve the printing instrument, the probes to be printed, microarray slides, and spotting buffer together with the surrounding environment, such as humidity and temperature. Robust microarray production requires not only appropriate reagents, equipment, and established procedures, but also devoted and experienced personnel. It is a challenging and craftsman like activity, but at the same time highly rewarding in terms of flexibility and cost efficiency. Outlined here is the workflow of a high-throughput microarray production line.

  • 219.
    Wiklundh, E.
    et al.
    Karolinska Inst, Dept Med, Stockholm, Sweden..
    Hellström, Cecilia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Van Moorsel, C. H.
    St Antonius Hosp Pulmonol, Nieuwegein, Netherlands..
    Grutters, J. C.
    St Antonius Hosp, Dept Pulmonol, NL-3435 CM Nieuwegein, Netherlands..
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Crestani, B.
    Hop Bichat Claude Bernard, Serv Pneumol, Paris, France..
    The Autoimmune Repertoire in Idiopathic Pulmonary Fibrosis2018In: American Journal of Respiratory and Critical Care Medicine, ISSN 1073-449X, E-ISSN 1535-4970, Vol. 197Article in journal (Other academic)
  • 220.
    Wirta, Valtteri
    et al.
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Holmberg, Anders
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Lukacs, Morten
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Hilson, Pierre
    Uhlén, Mathias
    Bhalerao, Rishikesh
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Assembly of a gene sequence tag microarray by reversible biotin-streptavidin capture for transcript analysis of Arabidopsis thaliana2005In: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 5, p. 5-Article in journal (Refereed)
    Abstract [en]

    Background: Transcriptional profiling using microarrays has developed into a key molecular tool for the elucidation of gene function and gene regulation. Microarray platforms based on either oligonucleotides or purified amplification products have been utilised in parallel to produce large amounts of data. Irrespective of platform examined, the availability of genome sequence or a large number of representative expressed sequence tags ( ESTs) is, however, a pre-requisite for the design and selection of specific and high-quality microarray probes. This is of great importance for organisms, such as Arabidopsis thaliana, with a high number of duplicated genes, as cross-hybridisation signals between evolutionary related genes cannot be distinguished from true signals unless the probes are carefully designed to be specific.

    Results: We present an alternative solid-phase purification strategy suitable for efficient preparation of short, biotinylated and highly specific probes suitable for large-scale expression profiling. Twenty-one thousand Arabidopsis thaliana gene sequence tags were amplified and subsequently purified using the described technology. The use of the arrays is exemplified by analysis of gene expression changes caused by a four-hour indole-3-acetic ( auxin) treatment. A total of 270 genes were identified as differentially expressed ( 120 up-regulated and 150 down-regulated), including several previously known auxin-affected genes, but also several previously uncharacterised genes.

    Conclusions: The described solid-phase procedure can be used to prepare gene sequence tag microarrays based on short and specific amplified probes, facilitating the analysis of more than 21 000 Arabidopsis transcripts.

  • 221.
    Zandian, Arash
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Forsström, Björn
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Häggmark-Månberg, Anna
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101). KTH, School of Biotechnology (BIO), Nano Biotechnology (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ayoglu, Burcu
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy2017In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 16, no 3, p. 1300-1314Article in journal (Refereed)
    Abstract [en]

    The underlying molecular mechanisms of autoimmune diseases are poorly understood. To unravel the autoimmune processes across diseases, comprehensive and unbiased analyses of proteins targets recognized by the adaptive immune system are needed. Here we present an approach starting from high-density peptide arrays to characterize autoantibody repertoires and to identify new autoantigens. A set of ten plasma and serum samples from subjects with multiple sclerosis, narcolepsy, and without any disease diagnosis were profiled on a peptide array representing the whole proteome, hosting 2.2 million 12-mer peptides with a six amino acid lateral shift. On the basis of the IgG reactivities found on these whole-proteome peptide micro arrays, a set of 23 samples was then studied on a targeted array with 174 000 12-mer peptides of single amino acid lateral shift. Finally, verification of IgG reactivities was conducted with a larger sample set (n = 448) using the bead-based peptide microarrays. The presented workflow employed three different peptide microarray formats to discover and resolve the epitopes of human autoantibodies and revealed two potentially new autoantigens: MAP3K7 in multiple sclerosis and NRXN1 in narcolepsy. The presented strategy provides insights into antibody repertoire reactivity at a peptide level and may accelerate the discovery and validation of autoantigens in human diseases.

  • 222.
    Zandian, Arash
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wingård, L.
    Nilsson, H.
    Sjöstedt, E.
    Johansson, D. X.
    Just, David
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hellström, Cecilia
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schwenk, Jochen M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Häggmark-Månberg, Anna
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Norbeck, O.
    Owe-Larsson, B.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Persson, M. A. A.
    Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis2017In: Translational Psychiatry, ISSN 2158-3188, E-ISSN 2158-3188, Vol. 7, article id e1177Article in journal (Refereed)
    Abstract [en]

    Immunological and inflammatory reactions have been suggested to have a role in the development of schizophrenia, a hypothesis that has recently been supported by genetic data. The aim of our study was to perform an unbiased search for autoantibodies in patients with a first psychotic episode, and to explore the association between any seroreactivity and the development of a Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM-IV) disorder characterized by chronic or relapsing psychotic symptoms. We collected plasma samples from 53 patients when they were treated for their first-episode psychosis, and 41 non-psychotic controls, after which the patients were followed for a mean duration of 7 years. Thirty patients were diagnosed with schizophrenia, delusional disorder, schizoaffective disorder, bipolar disorder or a long-term unspecified nonorganic psychosis during follow-up, whereas 23 patients achieved complete remission. At the end of follow-up, plasma samples were analyzed for IgG reactivity to 2304 fragments of human proteins using a multiplexed affinity proteomic technique. Eight patient samples showed autoreactivity to the N-terminal fragment of the PAGE (P antigen) protein family (PAGE2B/PAGE2/PAGE5), whereas no such autoreactivity was seen among the controls. PAGE autoreactivity was associated with a significantly increased risk of being diagnosed with schizophrenia during follow-up (odds ratio 6.7, relative risk 4.6). An immunohistochemistry analysis using antisera raised against the N-terminal fragment stained an unknown extracellular target in human cortical brain tissue. Our findings suggest that autoreactivity to the N-terminal portion of the PAGE protein family is associated with schizophrenia in a subset of patients with first-episode psychosis.

  • 223.
    Älgenäs, Cajsa
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Agaton, Charlotta
    Fagerberg, Linn
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Asplund, Anna
    Björling, Lisa
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Björling, Erik
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Kampf, Caroline
    Lundberg, Emma
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Persson, Anja
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Wester, Kenneth
    Pontén, Fredrik
    Wernerus, Henrik
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ottosson Takanen, Jenny
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Protein Technology.
    Antibody performance in western blot applications is context- dependent2014In: Biotechnology Journal, ISSN 1860-6768, E-ISSN 1860-7314, Vol. 9, no 3, p. 435-445Article in journal (Refereed)
    Abstract [en]

    An important concern for the use of antibodies in various applications, such as western blot (WB) or immunohistochemistry (IHC), is specificity. This calls for systematic validations using well-designed conditions. Here, we have analyzed 13000 antibodies using western blot with lysates from human cell lines, tissues, and plasma. Standardized stratification showed that 45% of the antibodies yielded supportive staining, and the rest either no staining (12%) or protein bands of wrong size (43%). A comparative study of WB and IHC showed that the performance of antibodies is application-specific, although a correlation between no WB staining and weak IHC staining could be seen. To investigate the influence of protein abundance on the apparent specificity of the antibody, new WB analyses were performed for 1369 genes that gave unsupportive WBs in the initial screening using cell lysates with overexpressed full-length proteins. Then, more than 82% of the antibodies yielded a specific band corresponding to the full-length protein. Hence, the vast majority of the antibodies (90%) used in this study specifically recognize the target protein when present at sufficiently high levels. This demonstrates the context- and application-dependence of antibody validation and emphasizes that caution is needed when annotating binding reagents as specific or cross-reactive. WB is one of the most commonly used methods for validation of antibodies. Our data implicate that solely using one platform for antibody validation might give misleading information and therefore at least one additional method should be used to verify the achieved data.

2345 201 - 223 of 223
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