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Kampf, Caroline
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Publications (10 of 41) Show all publications
Mikus, M., Drobin, K., Gry, M., Bachmann, J., Lindberg, J., Yimer, G., . . . Schuppe-Koistinen, I. (2017). Elevated levels of circulating CDH5 and FABP1 in association with human drug-induced liver injury. Liver international (Print), 37(1), 132-140
Open this publication in new window or tab >>Elevated levels of circulating CDH5 and FABP1 in association with human drug-induced liver injury
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2017 (English)In: Liver international (Print), ISSN 1478-3223, E-ISSN 1478-3231, Vol. 37, no 1, p. 132-140Article in journal (Refereed) Published
Abstract [en]

Background & Aims: The occurrence of drug-induced liver injury (DILI) is a major issue in all phases of drug development. To identify novel biomarker candidates associated with DILI, we utilised an affinity proteomics strategy, where antibody suspension bead arrays were applied to profile plasma and serum samples from human DILI cases and controls. Methods: An initial screening was performed using 4594 randomly selected antibodies, representing 3450 human proteins. Resulting candidate proteins together with proposed DILI biomarker candidates generated a DILI array of 251 proteins for subsequent target analysis and verifications. In total, 1196 samples from 241 individuals across four independent cohorts were profiled: healthy volunteers receiving acetaminophen, patients with human immunodeficiency virus and/or tuberculosis receiving treatment, DILI cases originating from a wide spectrum of drugs, and healthy volunteers receiving heparins. Results: We observed elevated levels of cadherin 5, type 2 (CDH5) and fatty acid-binding protein 1 (FABP1) in DILI cases. In the two longitudinal cohorts, CDH5 was elevated already at baseline. FABP1 was elevated after treatment initiation and seemed to respond more rapidly than alanine aminotransferase (ALT). The elevations were verified in the DILI cases treated with various drugs. In the heparin cohort, CDH5 was stable over time whereas FABP1 was elevated. Conclusions: These results suggest that CDH5 may have value as a susceptibility marker for DILI. FABP1 was identified as a biomarker candidate with superior characteristics regarding tissue distribution and kinetics compared to ALT but likely with limited predictive value for the development of severe DILI. Further studies are needed to determine the clinical utility of the proposed markers.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2017
Keywords
drug-induced liver injury, biomarker discovery, affinity proteomics, plasma profiling, suspension bead arrays
National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:uu:diva-319330 (URN)10.1111/liv.13174 (DOI)000393769900014 ()27224670 (PubMedID)
Available from: 2017-04-03 Created: 2017-04-03 Last updated: 2017-11-29Bibliographically approved
Ghaffari, P., Mardinoglu, A., Asplund, A., Shoaie, S., Kampf, C., Uhlen, M. & Nielsen, J. (2015). Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling. Scientific Reports, 5, 8183
Open this publication in new window or tab >>Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling
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2015 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, p. 8183-Article in journal (Refereed) Published
Abstract [en]

Human cancer cell lines are used as important model systems to study molecular mechanisms associated with tumor growth, hereunder how genomic and biological heterogeneity found in primary tumors affect cellular phenotypes. We reconstructed Genome scale metabolic models (GEMs) for eleven cell lines based on RNA-Seq data and validated the functionality of these models with data from metabolite profiling. We used cell line-specific GEMs to analyze the differences in the metabolism of cancer cell lines, and to explore the heterogeneous expression of the metabolic subsystems. Furthermore, we predicted 85 antimetabolites that can inhibit growth of, or even kill, any of the cell lines, while at the same time not being toxic for 83 different healthy human cell types. 60 of these antimetabolites were found to inhibit growth in all cell lines. Finally, we experimentally validated one of the predicted antimetabolites using two cell lines with different phenotypic origins, and found that it is effective in inhibiting the growth of these cell lines. Using immunohistochemistry, we also showed high or moderate expression levels of proteins targeted by the validated antimetabolite. Identified anti-growth factors for inhibition of cell growth may provide leads for the development of efficient cancer treatment strategies.

National Category
Basic Medicine
Identifiers
urn:nbn:se:uu:diva-245341 (URN)10.1038/srep08183 (DOI)000348671000003 ()25640694 (PubMedID)
Available from: 2015-03-03 Created: 2015-02-26 Last updated: 2018-01-11Bibliographically approved
Lindskog, C., Linné, J., Fagerberg, L., Hallstrom, B. M., Sundberg, C. J., Lindholm, M., . . . Uhlen, M. (2015). The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling. BMC Genomics, 16, Article ID 475.
Open this publication in new window or tab >>The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling
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2015 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 16, article id 475Article in journal (Refereed) Published
Abstract [en]

Background: To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents and also to identify similarities and differences in the gene expression in these two different striated muscle tissues. Here, we have investigated the genes and proteins with elevated expression in cardiac and skeletal muscle in relation to all other major human tissues and organs using a global transcriptomics analysis complemented with antibody-based profiling to localize the corresponding proteins on a single cell level. Results: Our study identified a comprehensive list of genes expressed in cardiac and skeletal muscle. The genes with elevated expression were further stratified according to their global expression pattern across the human body as well as their precise localization in the muscle tissues. The functions of the proteins encoded by the elevated genes are well in line with the physiological functions of cardiac and skeletal muscle, such as contraction, ion transport, regulation of membrane potential and actomyosin structure organization. A large fraction of the transcripts in both cardiac and skeletal muscle correspond to mitochondrial proteins involved in energy metabolism, which demonstrates the extreme specialization of these muscle tissues to provide energy for contraction. Conclusions: Our results provide a comprehensive list of genes and proteins elevated in striated muscles. A number of proteins not previously characterized in cardiac and skeletal muscle were identified and localized to specific cellular subcompartments. These proteins represent an interesting starting point for further functional analysis of their role in muscle biology and disease.

Keywords
Transcriptome, Proteome, Cardiac and skeletal muscle
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-258326 (URN)10.1186/s12864-015-1686-y (DOI)000356761400001 ()26109061 (PubMedID)
Available from: 2015-07-15 Created: 2015-07-13 Last updated: 2017-12-04Bibliographically approved
Uhlen, M., Fagerberg, L., Hallstroem, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., . . . Pontén, F. (2015). Tissue-based map of the human proteome. Science, 347(6220), 394-+
Open this publication in new window or tab >>Tissue-based map of the human proteome
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2015 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 347, no 6220, p. 394-+Article in journal (Refereed) Published
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.

National Category
Biological Sciences Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-247157 (URN)10.1126/science.1260419 (DOI)000348225800036 ()
Available from: 2015-03-16 Created: 2015-03-13 Last updated: 2017-12-04Bibliographically approved
Landegren, N., Sharon, D., Shum, A. K., Khan, I. S., Fasano, K. J., Hallgren, Å., . . . Kämpe, O. (2015). Transglutaminase 4 as a prostate autoantigen in male subfertility. Science Translational Medicine, 7(292), Article ID 292ra101.
Open this publication in new window or tab >>Transglutaminase 4 as a prostate autoantigen in male subfertility
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2015 (English)In: Science Translational Medicine, ISSN 1946-6234, E-ISSN 1946-6242, Vol. 7, no 292, article id 292ra101Article in journal (Refereed) Published
Abstract [en]

Autoimmune polyendocrine syndrome type 1 (APS1), a monogenic disorder caused by AIRE gene mutations, features multiple autoimmune disease components. Infertility is common in both males and females with APS1. Although female infertility can be explained by autoimmune ovarian failure, the mechanisms underlying male infertility have remained poorly understood. We performed a proteome-wide autoantibody screen in APS1 patient sera to assess the autoimmune response against the male reproductive organs. By screening human protein arrays with male and female patient sera and by selecting for gender-imbalanced autoantibody signals, we identified transglutaminase 4 (TGM4) as a male-specific autoantigen. Notably, TGM4 is a prostatic secretory molecule with critical role in male reproduction. TGM4 autoantibodies were detected in most of the adult male APS1 patients but were absent in all the young males. Consecutive serum samples further revealed that TGM4 autoantibodies first presented during pubertal age and subsequent to prostate maturation. We assessed the animal model for APS1, the Aire-deficient mouse, and found spontaneous development of TGM4 autoantibodies specifically in males. Aire-deficient mice failed to present TGM4 in the thymus, consistent with a defect in central tolerance for TGM4. In the mouse, we further link TGM4 immunity with a destructive prostatitis and compromised secretion of TGM4. Collectively, our findings in APS1 patients and Aire-deficient mice reveal prostate autoimmunity as a major manifestation of APS1 with potential role in male subfertility.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-258338 (URN)10.1126/scitranslmed.aaa9186 (DOI)000356390500008 ()26084804 (PubMedID)
Funder
Swedish Research CouncilSwedish Research Council Formas
Available from: 2015-07-14 Created: 2015-07-13 Last updated: 2017-12-04Bibliographically approved
Bachmann, J., Burte, F., Pramana, S., Conte, I., Brown, B. J., Orimadegun, A. E., . . . Nilsson, P. (2014). Affinity Proteomics Reveals Elevated Muscle Proteins in Plasma of Children with Cerebral Malaria. PLoS Pathogens, 10(4), e1004038
Open this publication in new window or tab >>Affinity Proteomics Reveals Elevated Muscle Proteins in Plasma of Children with Cerebral Malaria
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2014 (English)In: PLoS Pathogens, ISSN 1553-7366, E-ISSN 1553-7374, Vol. 10, no 4, p. e1004038-Article in journal (Refereed) Published
Abstract [en]

Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria.

National Category
Basic Medicine
Identifiers
urn:nbn:se:uu:diva-235651 (URN)10.1371/journal.ppat.1004038 (DOI)000342033600017 ()
Available from: 2014-11-07 Created: 2014-11-06 Last updated: 2018-01-11Bibliographically approved
Fagerberg, L., Hallström, B. M., Oksvold, P., Kampf, C., Djureinovic, D., Odeberg, J., . . . Uhlén, M. (2014). Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Molecular & Cellular Proteomics, 13(2), 397-406
Open this publication in new window or tab >>Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
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2014 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 13, no 2, p. 397-406Article in journal (Refereed) Published
Abstract [en]

Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to ∼80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-221324 (URN)10.1074/mcp.M113.035600 (DOI)000331369000002 ()24309898 (PubMedID)
Available from: 2014-03-28 Created: 2014-03-28 Last updated: 2017-12-05Bibliographically approved
Algenas, C., Agaton, C., Fagerberg, L., Asplund, A., Bjorling, L., Bjorling, E., . . . Hober, S. (2014). Antibody performance in western blot applications is context-dependent. Biotechnology Journal, 9(3), 435-445
Open this publication in new window or tab >>Antibody performance in western blot applications is context-dependent
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2014 (English)In: Biotechnology Journal, ISSN 1860-6768, E-ISSN 1860-7314, Vol. 9, no 3, p. 435-445Article in journal (Refereed) Published
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.

Keywords
Immunohistochemistry, Monoclonal antibodies, Polyclonal antibodies, Validation, Western blot
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-222744 (URN)10.1002/biot.201300341 (DOI)000332339100014 ()
Available from: 2014-04-14 Created: 2014-04-14 Last updated: 2017-12-05Bibliographically approved
Howat, W. J., Lewis, A., Jones, P., Kampf, C., Pontén, F., van der Loos, C. M., . . . Warford, A. (2014). Antibody validation of immunohistochemistry for biomarker discovery: Recommendations of a consortium of academic and pharmaceutical based histopathology researchers. Methods, 70(1), 34-38
Open this publication in new window or tab >>Antibody validation of immunohistochemistry for biomarker discovery: Recommendations of a consortium of academic and pharmaceutical based histopathology researchers
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2014 (English)In: Methods, ISSN 1046-2023, E-ISSN 1095-9130, Vol. 70, no 1, p. 34-38Article in journal (Refereed) Published
Abstract [en]

As biomarker discovery takes centre-stage, the role of immunohistochemistry within that process is increasing. At the same time, the number of antibodies being produced for "research use" continues to rise and it is important that antibodies to be used as biomarkers are validated for specificity and sensitivity before use. This guideline seeks to provide a stepwise approach for the validation of an antibody for immunohistochemical assays, reflecting the views of a consortium of academic and pharmaceutical based histopathology researchers. We propose that antibodies are placed into a tier system, level 1-3, based on evidence of their usage in immunohistochemistry, and that the degree of validation required is proportionate to their place on that tier.

National Category
Basic Medicine
Identifiers
urn:nbn:se:uu:diva-239502 (URN)10.1016/j.ymeth.2014.01.018 (DOI)000345199200006 ()24525140 (PubMedID)
Available from: 2014-12-29 Created: 2014-12-29 Last updated: 2018-01-11Bibliographically approved
Gardberg, M., Heuser, V. D., Iljin, K., Kampf, C., Uhlen, M. & Carpen, O. (2014). Characterization of Leukocyte Formin FMNL1 Expression in Human Tissues. Journal of Histochemistry and Cytochemistry, 62(6), 460-470
Open this publication in new window or tab >>Characterization of Leukocyte Formin FMNL1 Expression in Human Tissues
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2014 (English)In: Journal of Histochemistry and Cytochemistry, ISSN 0022-1554, E-ISSN 1551-5044, Vol. 62, no 6, p. 460-470Article in journal (Refereed) Published
Abstract [en]

Formins are cytoskeleton regulating proteins characterized by a common FH2 structural domain. As key players in the assembly of actin filaments, formins direct dynamic cytoskeletal processes that influence cell shape, movement and adhesion. The large number of formin genes, fifteen in the human, suggests distinct tasks and expression patterns for individual family members, in addition to overlapping functions. Several formins have been associated with invasive cell properties in experimental models, linking them to cancer biology. One example is FMNL1, which is considered to be a leukocyte formin and is known to be overexpressed in lymphomas. Studies on FMNL1 and many other formins have been hampered by a lack of research tools, especially antibodies suitable for staining paraffin-embedded formalin-fixed tissues. Here we characterize, using bioinformatics tools and a validated antibody, the expression pattern of FMNL1 in human tissues and study its subcellular distribution. Our results indicate that FMNL1 expression is not restricted to hematopoietic tissues and that neoexpression of FMNL1 can be seen in epithelial cancer.

Keywords
FMNL1, FRL1, formin, actin cytoskeleton, immunohistochemistry
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-228546 (URN)10.1369/0022155414532293 (DOI)000337598700006 ()
Available from: 2014-07-17 Created: 2014-07-16 Last updated: 2017-12-05Bibliographically approved
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