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Drobin, K., Assadi, G., Hong, M.-G., Anggraeni Andersson, M., Fredolini, C., Forsström, B., . . . Halfvarson, J. (2019). Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci. Inflammatory Bowel Diseases, 25(2), 306-316
Open this publication in new window or tab >>Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci
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2019 (English)In: Inflammatory Bowel Diseases, ISSN 1078-0998, E-ISSN 1536-4844, Vol. 25, no 2, p. 306-316Article in journal (Refereed) Published
Abstract [en]

Few studies have investigated the blood proteome of inflammatory bowel disease (IBD). We characterized the serum abundance of proteins encoded at 163 known IBD risk loci and tested these proteins for their biomarker discovery potential. Based on the Human Protein Atlas (HPA) antibody availability, 218 proteins from genes mapping at 163 IBD risk loci were selected. Targeted serum protein profiles from 49 Crohns disease (CD) patients, 51 ulcerative colitis (UC) patients, and 50 sex- and age-matched healthy individuals were obtained using multiplexed antibody suspension bead array assays. Differences in relative serum abundance levels between disease groups and controls were examined. Replication was attempted for CD-UC comparisons (including disease subtypes) by including 64 additional patients (33 CD and 31 UC). Antibodies targeting a potentially novel risk protein were validated by paired antibodies, Western blot, immuno-capture mass spectrometry, and epitope mapping. By univariate analysis, 13 proteins mostly related to neutrophil, T-cell, and B-cell activation and function were differentially expressed in IBD patients vs healthy controls, 3 in CD patients vs healthy controls and 2 in UC patients vs healthy controls (q < 0.01). Multivariate analyses further differentiated disease groups from healthy controls and CD subtypes from UC (P < 0.05). Extended characterization of an antibody targeting a novel, discriminative serum marker, the laccase (multicopper oxidoreductase) domain containing 1 (LACC1) protein, provided evidence for antibody on-target specificity. Using affinity proteomics, we identified a set of IBD-associated serum proteins encoded at IBD risk loci. These candidate proteins hold the potential to be exploited as diagnostic biomarkers of IBD.

Place, publisher, year, edition, pages
Oxford University Press, 2019
Keywords
inflammatory bowel disease, affinity proteomics, LACC1
National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:kth:diva-249898 (URN)10.1093/ibd/izy326 (DOI)000462580900020 ()30358838 (PubMedID)2-s2.0-85059799081 (Scopus ID)
Note

QC 20190423

Available from: 2019-04-23 Created: 2019-04-23 Last updated: 2019-04-23Bibliographically approved
Byström, S., Eklund, M., Hong, M.-G., Fredolini, C., Eriksson, M., Czene, K., . . . Gabrielson, M. (2018). Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density. Breast Cancer Research, 20, Article ID 14.
Open this publication in new window or tab >>Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density
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2018 (English)In: Breast Cancer Research, ISSN 1465-5411, E-ISSN 1465-542X, Vol. 20, article id 14Article in journal (Refereed) Published
Abstract [en]

Background: Mammographic breast density is one of the strongest risk factors for breast cancer, but molecular understanding of how breast density relates to cancer risk is less complete. Studies of proteins in blood plasma, possibly associated with mammographic density, are well-suited as these allow large-scale analyses and might shed light on the association between breast cancer and breast density. Methods: Plasma samples from 1329 women in the Swedish KARMA project, without prior history of breast cancer, were profiled with antibody suspension bead array (SBA) assays. Two sample sets comprising 729 and 600 women were screened by two different SBAs targeting a total number of 357 proteins. Protein targets were selected through searching the literature, for either being related to breast cancer or for being linked to the extracellular matrix. Association between proteins and absolute area-based breast density (AD) was assessed by quantile regression, adjusting for age and body mass index (BMI). Results: Plasma profiling revealed linear association between 20 proteins and AD, concordant in the two sets of samples (p < 0.05). Plasma levels of seven proteins were positively associated and 13 proteins negatively associated with AD. For eleven of these proteins evidence for gene expression in breast tissue existed. Among these, ABCC11, TNFRSF10D, F11R and ERRF were positively associated with AD, and SHC1, CFLAR, ACOX2, ITGB6, RASSF1, FANCD2 and IRX5 were negatively associated with AD. Conclusions: Screening proteins in plasma indicates associations between breast density and processes of tissue homeostasis, DNA repair, cancer development and/or progression in breast cancer. Further validation and follow-up studies of the shortlisted protein candidates in independent cohorts will be needed to infer their role in breast density and its progression in premenopausal and postmenopausal women.

Place, publisher, year, edition, pages
BIOMED CENTRAL LTD, 2018
Keywords
Mammographic breast density, Plasma, Protein profiling, Suspension bead array, Affinity proteomics, KARMA cohort
National Category
Clinical Medicine
Identifiers
urn:nbn:se:kth:diva-223790 (URN)10.1186/s13058-018-0940-z (DOI)000425114200001 ()29444691 (PubMedID)2-s2.0-85042063089 (Scopus ID)
Funder
Swedish Research CouncilThe Kamprad Family FoundationKnut and Alice Wallenberg FoundationSwedish Cancer SocietyScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20180307

Available from: 2018-03-07 Created: 2018-03-07 Last updated: 2018-03-07Bibliographically approved
Chen, Z., Dodig-Crnkovic, T., Schwenk, J. M. & Tao, S.-c. (2018). Current applications of antibody microarrays. Clinical Proteomics, 15, Article ID 7.
Open this publication in new window or tab >>Current applications of antibody microarrays
2018 (English)In: Clinical Proteomics, ISSN 1542-6416, E-ISSN 1559-0275, Vol. 15, article id 7Article, review/survey (Refereed) Published
Abstract [en]

The concept of antibody microarrays is one of the most versatile approaches within multiplexed immunoassay technologies. These types of arrays have increasingly become an attractive tool for the exploratory detection and study of protein abundance, function, pathways, and potential drug targets. Due to the properties of the antibody microarrays and their potential use in basic research and clinical analytics, various types of antibody microarrays have already been developed. In spite of the growing number of studies utilizing this technique, few reviews about antibody microarray technology have been presented to reflect the quality and future uses of the generated data. In this review, we provide a summary of the recent applications of antibody microarray techniques in basic biology and clinical studies, providing insights into the current trends and future of protein analysis.

Place, publisher, year, edition, pages
BioMed Central, 2018
Keywords
Antibody microarray, Signalling, Drug mechanism, Clinical application, Systems biology, Technology advances
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-224692 (URN)10.1186/s12014-018-9184-2 (DOI)000426761800001 ()29507545 (PubMedID)2-s2.0-85042706257 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceKnut and Alice Wallenberg Foundation
Note

QC 20180322

Available from: 2018-03-22 Created: 2018-03-22 Last updated: 2018-03-22Bibliographically approved
Djureinovic, D., Dodig-Crnkovic, T., Hellström, C., Holgersson, G., Bergqvist, M., Mattsson, J. S., . . . Micke, P. (2018). Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer. Lung Cancer, 125, 157-163
Open this publication in new window or tab >>Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer
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2018 (English)In: Lung Cancer, ISSN 0169-5002, E-ISSN 1872-8332, Vol. 125, p. 157-163Article in journal (Refereed) Published
Abstract [en]

Objectives: Cancer-testis antigens (CTAs) are defined as proteins that are specifically expressed in testis or placenta and their expression is frequently activated in cancer. Due to their ability to induce an immune response, CTAs may serve as suitable targets for immunotherapy. The aim of this study was to evaluate if there is reactivity against CTAs in the plasma of non-small cell lung cancer (NSCLC) patients through the detection of circulating antibodies. Materials and methods: To comprehensively analyze autoantibodies against CTAs the multiplexing capacities of suspension bead array technology was used. Bead arrays were created with 120 protein fragments, representing 112 CTAs. Reactivity profiles were measured in plasma samples from 133 NSCLC patients and 57 cases with benign lung diseases. Results: Altogether reactivity against 69 antigens, representing 81 CTAs, was demonstrated in at least one of the analyzed samples. Twenty-nine of the antigens (45 CTAs) demonstrated exclusive reactivity in NSCLC samples. Reactivity against cancer-testis antigen family 47; member A (CT47A) genes, P antigen family member 3 (PAGE3), variable charge X-linked (VCX), melanoma antigen family B1 (MAGEB1), lin-28 homolog B (LIN28B) and chromosome 12 open reading frame 54 (C12orf54) were only found in NSCLC patients at a frequency of 1%–4%. The presence of autoantibodies towards these six antigens was confirmed in an independent group of 34 NSCLC patients. Conclusion: We identified autoantibodies against CTAs in the plasma of lung cancer patients. The reactivity pattern of autoantibodies was higher in cancer patients compared to the benign group, stable over time, but low in frequency of occurrence. The findings suggest that some CTAs are immunogenic and that these properties can be utilized as immune targets. 

Place, publisher, year, edition, pages
Elsevier Ireland Ltd, 2018
Keywords
Adenocarcinoma, Cancer immunity, Lung cancer, MAGE, Squamous cell cancer, Tumor markers
National Category
Clinical Medicine
Identifiers
urn:nbn:se:kth:diva-236616 (URN)10.1016/j.lungcan.2018.09.012 (DOI)000450378500023 ()2-s2.0-85054035205 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceKnut and Alice Wallenberg FoundationSwedish Cancer Society, 2012/738
Note

Export Date: 22 October 2018; Article; CODEN: LUCAE; Correspondence Address: Djureinovic, D.; Department of Immunology, Genetics and Pathology, Uppsala UniversitySweden; email: dijana.djureinovic@igp.uu.se; Funding details: SciLifeLab, Science for Life Laboratory; Funding details: Knut och Alice Wallenbergs Stiftelse; Funding details: 2012/738, Cancerfonden; Funding text: This study was supported by the Swedish Cancer Society Cancerfonden (2012/738), Lions Cancer Foundation Uppsala, Sweden, Erik, Karin and Gösta Selanders Foundation, Sweden as well as grants for SciLifeLab and the Human Protein Atlas funded by the Knut and Alice Wallenberg foundation.; Funding text: We thank the Human Protein Atlas team, the Uppsala Biobank and everyone in the Division of Affinity Proteomics and the Autoimmunity Profiling facility at SciLifeLab for their support. Appendix A. QC 20181119

Available from: 2018-11-19 Created: 2018-11-19 Last updated: 2018-12-10Bibliographically approved
Sjöberg, R., Andersson, E., Hellström, C., Mattsson, C., Schwenk, J. M., Nilsson, P. & Ayoglu, B. (2018). High-density antigen microarrays for the assessment of antibody selectivity and off-target binding. In: Epitope Mapping Protocols: (pp. 231-238). Humana Press Inc.
Open this publication in new window or tab >>High-density antigen microarrays for the assessment of antibody selectivity and off-target binding
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2018 (English)In: Epitope Mapping Protocols, Humana Press Inc. , 2018, p. 231-238Chapter in book (Refereed)
Abstract [en]

With the increasing availability of collections of antibodies, their evaluation in terms of binding selectivity becomes an important but challenging task. Planar antigen microarrays are very suitable tools to address this task and provide a powerful proteomics platform for the characterization of the binding selectivity of antibodies toward thousands of antigens in parallel. In this chapter, we describe our in-house developed procedures for the generation of high-density planar antigen microarrays with over 21,000 features. We also provide the details of the assay protocol, which we routinely use for the assessment of binding selectivity of the polyclonal antibodies generated within the Human Protein Atlas. © Springer Science+Business Media, LLC, part of Springer Nature 2018.

Place, publisher, year, edition, pages
Humana Press Inc., 2018
Series
Methods in Molecular Biology, ISSN 1064-3745 ; 1785
Keywords
Affinity proteomics, Antibody selectivity, Antigen microarrays, Protein microarrays
National Category
Other Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-238338 (URN)10.1007/978-1-4939-7841-0_15 (DOI)2-s2.0-85046366884 (Scopus ID)978-1-4939-7839-7 (ISBN)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20181115

Available from: 2018-11-15 Created: 2018-11-15 Last updated: 2018-11-15Bibliographically approved
Ayoglu, B., Nilsson, P. & Schwenk, J. M. (2018). Multiplexed antigen bead arrays for the assessment of antibody selectivity and epitope mapping. In: Epitope Mapping Protocols: (pp. 239-248). Humana Press Inc.
Open this publication in new window or tab >>Multiplexed antigen bead arrays for the assessment of antibody selectivity and epitope mapping
2018 (English)In: Epitope Mapping Protocols, Humana Press Inc. , 2018, p. 239-248Chapter in book (Refereed)
Abstract [en]

With the increasing number of binding reagents for affinity-based investigations of the human proteome, high-throughput tools for the characterization of the used reagents become essential. For the analysis of binding selectivity, bead-based antigen arrays offer a miniaturized and parallelized assay platform to meet such needs, as they enable two-dimensional multiplexing to analyze up to 384 samples against up to 500 analytes in a single round of analysis. In this chapter, we describe our protocols for the generation of multiplex bead arrays built on immobilized protein fragments, as well as biotinylated peptides. Combined together, these two versions of antigen arrays offer a versatile approach for multiplexed characterization of antibody binding selectivity, off-target interactions, as well as mapping for the amino acids of epitopes involved in antibody binding.

Place, publisher, year, edition, pages
Humana Press Inc., 2018
Series
Methods in Molecular Biology, ISSN 1064-3745 ; 1785
Keywords
Affinity proteomics, Antibody selectivity, Antigen arrays, Epitope mapping, Peptide arrays, Protein arrays, Suspension bead arrays
National Category
Other Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-238377 (URN)10.1007/978-1-4939-7841-0_16 (DOI)2-s2.0-85046341154 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20181121

Available from: 2018-11-21 Created: 2018-11-21 Last updated: 2018-11-21Bibliographically approved
Matic, L. P., Iglesias, M. J., Vesterlund, M., Lengquist, M., Hong, M.-G., Saieed, S., . . . Hedin, U. (2018). Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage. JACC: Basic to Translational Science, 3(4), 464-480
Open this publication in new window or tab >>Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage
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2018 (English)In: JACC: Basic to Translational Science, ISSN 2452-302X, Vol. 3, no 4, p. 464-480Article in journal (Refereed) Published
Abstract [en]

Clinical tools to identify individuals with unstable atherosclerotic lesions are required to improve prevention of myocardial infarction and ischemic stroke. Here, a systems-based analysis of atherosclerotic plaques and plasma from patients undergoing carotid endarterectomy for stroke prevention was used to identify molecular signatures with a causal relationship to disease. Local plasma collected in the lesion proximity following clamping prior to arteriotomy was profiled together with matched peripheral plasma. This translational workflow identified biliverdin reductase B as a novel marker of intraplaque hemorrhage and unstable carotid atherosclerosis, which should be investigated as a potential predictive biomarker for cardiovascular events in larger cohorts.

Keywords
atherosclerosis, biomarkers, intraplaque hemorrhage, omics analyses, translational studies
National Category
Basic Medicine
Identifiers
urn:nbn:se:kth:diva-238051 (URN)10.1016/j.jacbts.2018.04.001 (DOI)2-s2.0-85053830575 (Scopus ID)
Note

Export Date: 30 October 2018; Article; Correspondence Address: Hedin, U.; Department of Molecular Medicine and Surgery, L8:03, Karolinska Institute, Sweden; email: Ulf.Hedin@ki.se

QC 20190115

Available from: 2019-01-15 Created: 2019-01-15 Last updated: 2019-01-21Bibliographically approved
Omenn, G. S., Lane, L., Overall, C. M., Corrales, F. J., Schwenk, J. M., Paik, Y.-K., . . . Deutsch, E. W. (2018). Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. Journal of Proteome Research, 17(12), 4031-4041
Open this publication in new window or tab >>Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project
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2018 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 17, no 12, p. 4031-4041Article in journal (Refereed) Published
Abstract [en]

The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PEI proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2018
Keywords
metrics, missing proteins, HPP Guidelines, neXtProt, PeptideAtlas, Human Proteome Project (HPP), Chromosome-centric HPP (C-HPP), Biology and Disease-driven HPP (B/D-HPP), Human Proteome Organization (HUPO)
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-240748 (URN)10.1021/acs.jproteome.8b00441 (DOI)000452930000002 ()30099871 (PubMedID)2-s2.0-85052309961 (Scopus ID)
Funder
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20190108

Available from: 2019-01-08 Created: 2019-01-08 Last updated: 2019-01-08Bibliographically approved
Persson, M., Zandian, A., Wingard, L., Nilsson, H., Sjostedt, E., Johansson, D., . . . Nilsson, P. (2018). Searching for Novel Autoantibodies with Clinical Relevance in Psychiatric Disorders. Paper presented at 6th Biennial Conference of the Schizophrenia-International-Research-Society (SIRS), APR 04-08, 2018, Florence, Italy. Schizophrenia Bulletin, 44, S120-S121
Open this publication in new window or tab >>Searching for Novel Autoantibodies with Clinical Relevance in Psychiatric Disorders
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2018 (English)In: Schizophrenia Bulletin, ISSN 0586-7614, E-ISSN 1745-1701, Vol. 44, p. S120-S121Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
Oxford University Press, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-226780 (URN)000429541800296 ()
Conference
6th Biennial Conference of the Schizophrenia-International-Research-Society (SIRS), APR 04-08, 2018, Florence, Italy
Funder
EU, European Research Council, 670821
Note

QC 20180522

Available from: 2018-05-22 Created: 2018-05-22 Last updated: 2018-05-22Bibliographically approved
Glimelius, B., Melin, B., Enblad, G., Alafuzoff, I., Beskow, A., Ahlström, H., . . . Sjöblom, T. (2018). U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden. Acta Oncologica, 57(2), 187-194
Open this publication in new window or tab >>U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden
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2018 (English)In: Acta Oncologica, ISSN 0284-186X, E-ISSN 1651-226X, Vol. 57, no 2, p. 187-194Article in journal (Refereed) Published
Abstract [en]

Background: Progress in cancer biomarker discovery is dependent on access to high-quality biological materials and high-resolution clinical data from the same cases. To overcome current limitations, a systematic prospective longitudinal sampling of multidisciplinary clinical data, blood and tissue from cancer patients was therefore initiated in 2010 by Uppsala and Umea Universities and involving their corresponding University Hospitals, which are referral centers for one third of the Swedish population. Material and Methods: Patients with cancer of selected types who are treated at one of the participating hospitals are eligible for inclusion. The healthcare-integrated sampling scheme encompasses clinical data, questionnaires, blood, fresh frozen and formalin-fixed paraffin-embedded tissue specimens, diagnostic slides and radiology bioimaging data. Results: In this ongoing effort, 12,265 patients with brain tumors, breast cancers, colorectal cancers, gynecological cancers, hematological malignancies, lung cancers, neuroendocrine tumors or prostate cancers have been included until the end of 2016. From the 6914 patients included during the first five years, 98% were sampled for blood at diagnosis, 83% had paraffin-embedded and 58% had fresh frozen tissues collected. For Uppsala County, 55% of all cancer patients were included in the cohort. Conclusions: Close collaboration between participating hospitals and universities enabled prospective, longitudinal biobanking of blood and tissues and collection of multidisciplinary clinical data from cancer patients in the U-CAN cohort. Here, we summarize the first five years of operations, present U-CAN as a highly valuable cohort that will contribute to enhanced cancer research and describe the procedures to access samples and data.

Place, publisher, year, edition, pages
Taylor & Francis Group, 2018
National Category
Cancer and Oncology
Identifiers
urn:nbn:se:kth:diva-222452 (URN)10.1080/0284186X.2017.1337926 (DOI)000423473200003 ()28631533 (PubMedID)2-s2.0-85021081885 (Scopus ID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20180209

Available from: 2018-02-09 Created: 2018-02-09 Last updated: 2018-02-09Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-8141-8449

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