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  • 1.
    Akkuratov, Evgeny E.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    The Biophysics of Na+,K+-ATPase in neuronal health and disease2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Na+,K+-ATPase is one of the most important proteins in the mammalian cell. It creates sodium and potassium gradients which are fundamental for the membrane potential and sodium-dependent secondary active transport. It has a second role in the cell as a receptor that by binding chemicals from the cardiotonic steroids family, the most knowledgeable of them is ouabain, triggers various signaling pathways in the cell which regulate gene activation, proliferation, apoptosis, etc. It has been shown that several severe neurological diseases are associated with mutations in the Na+,K+-ATPase encoding genes. Although Na+,K+-ATPase was discovered already in 1957 by the Danish scientist Jens Skou, the knowledge about the function of this enzyme  is still not complete.

     

    In the studies included in the thesis, we have learned more about the function of Na+,K+-ATPase in different aspects of health and disease. In study I we showed a mechanism of ouabain-dependent regulation of the NMDA receptor, one of the most important receptors in the nervous system, via binding with Na+,K+-ATPase. This allows us to look at the Na+,K+-ATPase as regulator via protein-protein interaction. In study II we investigated a different aspect of Na+,K+-ATPase functioning – to look at how binding of ouabain to Na+,K+-ATPase activates a number of signaling cascades by looking at the phosphoproteome status of the cells. This allows us to see the whole picture of ouabain-mediated cascades and further characterize them. In study III we focused on the role of Na+,K+-ATPase in severe epileptic encephalopathy caused by a mutation in the ATP1A1 gene. We performed a molecular and cellular study to describe how mutations affects protein structure and function and found that this mutation converts the ion pump to a nonspecific leak channel. In study IV we performed a translational study of the most common mutation for rapid-onset dystonia-parkinsonism. We studied how this mutation affects the nervous system on the protein-, cellular-, and organism level and found that the complete absence of ultraslow afterhyperpolarization (usAHP) could explain gait disturbances found in patients. In the on-going study we showed that Na+,K+-ATPase can oligomerize and that this effect is triggered by ouabain binding to the Na+,K+-ATPase. In this study, we utilized a novel fluorescence labelling approach and used biophysical techniques with single molecule sensitivity to track Na+,K+-ATPase interactions.

     

    In summary, we applied biophysical and molecular methods to study different aspects of the function of Na+,K+-ATPase, and gained insights that could be helpful not only for answering fundamental questions about Na+,K+-ATPase but also to find a treatment for patients with diseases associated with mutations in this protein.

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  • 2.
    Akkuratov, Evgeny E.
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Sorrell, Frankie
    Souza, Vasco
    Paukar, Martin
    Picton, Laurence
    Jans, Daniel
    Andersson, Magnus
    Fritz, Nicolas
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Zhang, Xiaoqun
    Liebmann, Thomas
    KTH.
    Lindskog, Maria
    KTH.
    Svenningsson, Per
    Miles, Gareth
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Aperia, Anita
    KTH.
    Mechanisms by which the T613M mutation causes mobility and gait disturbances in Rapid-Onset Dystonia-ParkinsonismManuscript (preprint) (Other academic)
  • 3.
    Akkuratov, Evgeny E.
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Westin, Linda
    Vazquez-Juarez, Erika
    de Marothy, Minttu
    Melnikova, Aleksandra K
    Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119234.
    Blom, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lindskog, Maria
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Aperia, Anita
    Ouabain Modulates the Functional Interaction Between Na,K-ATPase and NMDA Receptor.2020In: Molecular Neurobiology, ISSN 0893-7648, E-ISSN 1559-1182, Vol. 57, no 10, p. 4018-4030Article in journal (Refereed)
    Abstract [en]

    The N-methyl-D-aspartate (NMDA) receptor plays an essential role in glutamatergic transmission and synaptic plasticity and researchers are seeking for different modulators of NMDA receptor function. One possible mechanism for its regulation could be through adjacent membrane proteins. NMDA receptors coprecipitate with Na,K-ATPase, indicating a potential interaction of these two proteins. Ouabain, a mammalian cardiotonic steroid that specifically binds to Na,K-ATPase and affects its conformation, can protect from some toxic effects of NMDA receptor activation. Here we have examined whether NMDA receptor activity and downstream effects can be modulated by physiological ouabain concentrations. The spatial colocalization between NMDA receptors and the Na,K-ATPase catalytic subunits on dendrites of cultured rat hippocampal neurons was analyzed with super-resolution dSTORM microscopy. The functional interaction was analyzed with calcium imaging of single hippocampal neurons exposed to 10 μM NMDA in presence and absence of ouabain and by determination of the ouabain effect on NMDA receptor-dependent long-term potentiation. We show that NMDA receptors and the Na,K-ATPase catalytic subunits alpha1 and alpha3 exist in same protein complex and that ouabain in nanomolar concentration consistently reduces the calcium response to NMDA. Downregulation of the NMDA response is not associated with internalization of the receptor or with alterations in its state of Src phosphorylation. Ouabain in nanomolar concentration elicits a long-term potentiation response. Our findings suggest that ouabain binding to a fraction of Na,K-ATPase molecules that cluster with the NMDA receptors will, via a conformational effect on the NMDA receptors, cause moderate but consistent reduction of NMDA receptor response at synaptic activation.

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  • 4. Al-Khalili Szigyarto, Cristina
    et al.
    Sibbons, P.
    Williams, G.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics.
    Metcalfe, S. M.
    The E3 Ligase Axotrophin/MARCH-7: Protein Expression Profiling of Human Tissues Reveals Links to Adult Stem Cells2010In: Journal of Histochemistry and Cytochemistry, ISSN 0022-1554, E-ISSN 1551-5044, Vol. 58, no 4, p. 301-308Article in journal (Refereed)
    Abstract [en]

    Axotrophin/MARCH-7 was first identified in mouse embryonic stem cells as a neural stem cell gene. Using the axotrophin/MARCH-7 null mouse, we discovered profound effects on T lymphocyte responses, including 8-fold hyperproliferation and 5-fold excess release of the stem cell cytokine leukemia inhibitory factor (LIF). Our further discovery that axotrophin/MARCH-7 is required for targeted degradation of the LIF receptor subunit gp190 implies a direct role in the regulation of LIF signaling. Bioinformatics studies revealed a highly conserved RING-CH domain in common with the MARCH family of E3-ubiquitin ligases, and accordingly, axotrophin was renamed "MARCH-7." To probe protein expression of human axotrophin/MARCH-7, we prepared antibodies against different domains of the protein. Each antibody bound its specific target epitope with high affinity, and immunohistochemistry cross-validated target specificity. Forty-eight human tissue types were screened. Epithelial cells stained strongly, with trophoblasts having the greatest staining. In certain tissues, specific cell types were selectively positive, including neurons and neuronal progenitor cells in the hippocampus and cerebellum, endothelial sinusoids of the spleen, megakaryocytes in the bone marrow, crypt stem cells of the small intestine, and alveolar macrophages in the 7 lung. Approximately 20% of central nervous system neuropils were positive. Notably, axotrophin/MARCH-7 has an expression profile that is distinct from that of other MARCH family members. This manuscript contains online supplemental material at http://www.jhc. org. Please visit this article online to view these materials. (J Histochem Cytochem 58:301-308, 2010)

  • 5. Alkharusi, Amira
    et al.
    Yu, Shengze
    KTH, School of Biotechnology (BIO).
    Landazuri, Natalia
    Zadjali, Fahad
    Davodi, Belghis
    Nystrom, Thomas
    Gräslund, Torbjörn
    KTH, School of Biotechnology (BIO), Protein Technology.
    Rahbar, Afsar
    Norstedt, Gunnar
    Stimulation of prolactin receptor induces STAT-5 phosphorylation and cellular invasion in glioblastoma multiforme2016In: Oncotarget, E-ISSN 1949-2553, Vol. 7, no 48, p. 79558-79569Article in journal (Refereed)
    Abstract [en]

    Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumor in humans and is characterized with poor outcome. In this study, we investigated components of prolactin (Prl) system in cell models of GBM and in histological tissue sections obtained from GBM patients. Expression of Prolactin receptor (PrlR) was detected at high levels in U251-MG, at low levels in U87-MG and barely detectable in U373 cell lines and in 66% of brain tumor tissues from 32 GBM patients by immunohistochemical technique. In addition, stimulation of U251-MG and U87-MG cells but not U373 with Prl resulted in increased STAT5 phosphorylation and only in U251-MG cells with increased cellular invasion. Furthermore, STAT5 phosphorylation and cellular invasion induced in Prl stimulated cells were significantly reduced by using a Prl receptor antagonist that consists of Prl with four amino acid replacements. We conclude that Prl receptor is expressed at different levels in the majority of GBM tumors and that blocking of PrlR in U251-MG cells significantly reduce cellular invasion.

  • 6.
    Alm, Tove L.
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Lundberg, Emma
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    The Affinity Binder Knockdown Initiative.2016In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 27Article in journal (Refereed)
  • 7.
    Andersson, Hanna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    The Effect of Chemotherapy Treatment on Bone Marrow Mesenchymal Stromal Cell Adipocyte Differentiation2021Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In an effort to understand the cause of late onset cardiac, metabolic, and musculoskeletal conditions in paediatric acute lymphoblastic leukaemia (ALL) survivors, the adipogenic differentiation of bone marrow (BM) mesenchymal stromal cells (MSCs) has been studied. There is a complex network of factors influencing adipogenesis, which to date is not completely understood. Hence, the overall aim is to better understand the cellular and molecular basis behind the development of these conditions in survivors. To this end, we asked whether treating BM MSCs in vitro with cancer drugs, Doxorubicin and Dexamethasone, will initiate a skewed differentiation towards adipogenesis. BM MSCs were analysed with respect to lipid accumulation, gene expression, and adipokine production. In general, our hypothesis was not confirmed. No lipid accumulations were detected in the cells. In analysis of gene expression of the adipogenic transcription factors PPARγ and C/EBPα, certain changes were seen; however, due to lack of biological replicates, no statistical analyses could be applied to the results. Lastly, the inflammation and adipogenesis associated cytokine IL-6 displayed a slight increase, whereas the cytokines IL-8 and TNF-α were undetectable.

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  • 8.
    Andersson, Hanna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    The Effect of Chemotherapy Treatment on Bone Marrow Mesenchymal Stromal Cell Adipocyte Differentiation2021Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In an effort to understand the cause of late onset cardiac, metabolic, and musculoskeletal conditions in paediatric acute lymphoblastic leukaemia (ALL) survivors, the adipogenic differentiation of bone marrow (BM) mesenchymal stromal cells (MSCs) has been studied. There is a complex network of factors influencing adipogenesis, which to date is not completely understood. Hence, the overall aim is to better understand the cellular and molecular basis behind the development of these conditions in survivors. To this end, we asked whether treating BM MSCs in vitro with cancer drugs, Doxorubicin and Dexamethasone, will initiate a skewed differentiation towards adipogenesis. BM MSCs were analysed with respect to lipid accumulation, gene expression, and adipokine production. In general, our hypothesis was not confirmed. No lipid accumulations were detected in the cells. In analysis of gene expression of the adipogenic transcription factors PPARγ and C/EBPα, certain changes were seen; however, due to lack of biological replicates, no statistical analyses could be applied to the results. Lastly, the inflammation and adipogenesis associated cytokine IL-6 displayed a slight increase, whereas the cytokines IL-8 and TNF-α were undetectable.

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  • 9. Andersson, Sandra
    et al.
    Konrad, Anna
    KTH, School of Biotechnology (BIO), Protein Technology.
    Ashok, Nikhil
    Pontén, Fredrik
    Hober, Sophia
    KTH, School of Biotechnology (BIO), Protein Technology.
    Asplund, Anna
    Antibodies Biotinylated Using a Synthetic Z-domain from Protein A Provide Stringent In Situ Protein Detection2013In: Journal of Histochemistry and Cytochemistry, ISSN 0022-1554, E-ISSN 1551-5044, Vol. 61, no 11, p. 773-784Article in journal (Refereed)
    Abstract [en]

    Antibody-based protein profiling on a global scale using immunohistochemistry constitutes an emerging strategy for mapping of the human proteome, which is crucial for an increased understanding of biological processes in the cell. Immunohistochemistry is often performed indirectly using secondary antibodies for detection, with the benefit of signal amplification. Direct immunohistochemistry instead brings the advantage of multiplexing; however, it requires labeling of the primary antibody. Many antibody-labeling kits do not specifically target IgG and may therefore cause labeling of stabilizing proteins present in the antibody solution. A new conjugation method has been developed that utilizes a modified Z-domain of protein A (ZBPA) to specifically target the Fc part of antibodies. The aim of the present study was to compare the ZBPA conjugation method and a commercially available labeling kit, Lightning-Link, for in situ protein detection. Fourteen antibodies were biotinylated with each method and stained using immunohistochemistry. For all antibodies tested, ZBPA biotinylation resulted in distinct immunoreactivity without off-target staining, regardless of the presence of stabilizing proteins in the buffer, whereas the majority of the Lightning-Link biotinylated antibodies displayed a characteristic pattern of nonspecific staining. We conclude that biotinylated ZBPA domain provides a stringent method for antibody biotinylation, advantageous for in situ protein detection in tissues.

  • 10. Andrews, B. J.
    et al.
    Marian Walhout, A. J.
    Iyengar, R.
    Apweiler, R.
    Ardlie, K.
    Azeloglu, E. U.
    Birtwistle, M. R.
    Coon, J. J.
    Dolinski, K.
    Fan, T.
    FitzGerald, G. A.
    Gavin, A. -C
    Gingras, A. -C
    Gough, N. R.
    Hoffmann, A.
    Lee, M. J.
    Loew, L. M.
    CraigMak, H.
    Murphy, R. C.
    Myers, C.
    Snyder, M. P.
    Sorger, P. K.
    Stolovitzky, G.
    Subramaniam, S.
    Taipale, M.
    Travé, G.
    Troyanskaya, O. G.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Vidal, M.
    Quantitative human cell encyclopedia2016In: Science Signaling, ISSN 1945-0877, E-ISSN 1937-9145, Vol. 9, no 443, article id mr1Article in journal (Refereed)
    Abstract [en]

    Scientists gathered to discuss the necessity, feasibility, and challenges of generating a quantitative catalog of the components in human cells that is essential for our understanding of human physiology in health and disease and to support future breakthroughs in treating diseases. This report summarizes the discussion that emerged at the Human Quantitative Dynamics Workshop held in Bethesda, MD, USA, in December 2015.

  • 11. Bartaula-Brevik, Sushma
    et al.
    Pedersen, Torbjorn O.
    Blois, Anna L.
    Papadakou, Panagiota
    Finne-Wistrand, Anna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Xue, Ying
    Bolstad, Anne Isine
    Mustafa, Kamal
    Leukocyte transmigration into tissue-engineered constructs is influenced by endothelial cells through Toll-like receptor signaling2014In: Stem Cell Research & Therapy, E-ISSN 1757-6512, Vol. 5, p. 143-Article in journal (Refereed)
    Abstract [en]

    Introduction: Inflammation plays a crucial role in tissue regeneration, wound healing, and the success of tissue-engineered constructs. The aim of this study was to investigate the influence of human umbilical vein endothelial cells (ECs) on leukocyte transmigration when co-cultured with primary human bone marrow-derived multipotent stromal cells (MSCs). Methods: MSCs with and without ECs were cultured in poly (L-lactide-co-1, 5-dioxepan-2-one) (poly (LLA-co-DXO)) scaffolds for 1 week in vitro in a bioreactor system, after which they were implanted subcutaneously in non-obese diabetic/severe combined immunodeficient mice. After 1 and 3 weeks, scaffolds were retrieved, and the mRNA expression of interleukin 1-beta (IL-1 beta), IL-6, IL-10, hypoxia-inducible factor 1-alpha (HIF-1 alpha), HIF-1 beta, and mammalian target of rapamycin was examined by real-time reverse transcription-polymerase chain reaction. Furthermore, immunofluorescent staining was performed for IL-1 beta, IL-6, neutrophils, and CD11b. In addition, Western blotting was done for IL-1 beta and IL-6. Leukocyte transmigration genes and genes in Toll-like receptor pathways, expressed by MSCs cultured in vitro with or without ECs, were further investigated with a microarray dataset. Results: In vitro, genes involved in leukocyte transmigration and Toll-like receptor pathways were clearly influenced by the addition of ECs. Platelet/endothelial cell adhesion molecule-1 (PECAM-1) and cadherin-5 (CDH5), both genes involved in leukocyte transmigration, were expressed significantly higher in the MSC/EC group. In vivo, the MSC/EC group showed higher mRNA expression of hypoxia-inducible factors HIF-1 alpha and HIF-1 beta. The mRNA expression of anti-inflammatory cytokine IL-10 showed no significant difference, whereas the mRNA and protein expression of pro-inflammatory cytokines IL-1 beta and IL-6 were lower in the MSC/EC group. The quantitative analysis of immunofluorescent staining revealed a significant difference in the number of neutrophils migrating into constructs, with the highest density found in the MSC/EC group. The number of macrophages positive for IL-6 and CD11b was significantly reduced in the MSC/EC group. Conclusions: The recruitment of leukocytes into tissue-engineered constructs with MSCs is strongly influenced by the addition of ECs via activation of leukocyte transmigration and Toll-like receptor pathways.

  • 12. Bartaula-Brevik, Sushma
    et al.
    Pedersen, Torbjorn O.
    Finne-Wistrand, Anna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Bolstad, Anne Isine
    Mustafa, Kamal
    Angiogenic and Immunomodulatory Properties of Endothelial and Mesenchymal Stem Cells2016In: Tissue Engineering. Part A, ISSN 1937-3341, E-ISSN 1937-335X, Vol. 22, no 3-4, p. 244-252Article in journal (Refereed)
    Abstract [en]

    It has been suggested that the effect of implanted cells on the local environment is important when selecting the appropriate cell type for tissue regeneration. Our aim was to compare the local tissue response to implanted human mesenchymal stem cells (MSC) and human umbilical vein endothelial cells (EC). MSC and EC were cultured in poly(l-lactide-co-1,5-dioxepan-2-one) scaffolds for 1 week in a bioreactor system, after which they were implanted subcutaneously in NOD/SCID mice. After 3 weeks, scaffolds were retrieved, and the mRNA expression of selected genes involved in hypoxia and inflammation was examined by real-time reverse transcription polymerase chain reaction and correlated with immunofluorescent staining for corresponding proteins. The Toll-like receptor signaling pathway was examined by superarray hybridization. The expression of 53 angiogenesis-related proteins was investigated by a proteome profiler angiogenesis antibody array kit. Vascularization was quantified using immunohistochemistry for CD31. The expression of hypoxia-inducible factors and biomarkers for angiogenesis was more strongly upregulated in response to implanted EC than to MSC, suggesting a higher sensitivity to low oxygen tension among EC. Hypoxic signaling was increased after implantation of EC compared with MSC, leading to a prolonged acute inflammatory phase that promoted ingrowth of vascular cells and establishment of the circulation. Inflammatory cytokines were also differently expressed at the gene and protein levels in the two experimental groups, resulting in altered recruitment of acute and chronic inflammatory cells. The end result of these differences was increased vessel formation within the constructs in the EC group.

  • 13.
    Bergstrand, Jan
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Xu, Lei
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics. Royal Inst Technol KTH, Dept Appl Phys, Albanova Univ Ctr, Expt Biomol Phys, SE-10691 Stockholm, Sweden..
    Miao, Xinyan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics. Royal Inst Technol KTH, Dept Appl Phys, Albanova Univ Ctr, Expt Biomol Phys, SE-10691 Stockholm, Sweden..
    Li, Nailin
    Karolinska Inst, Dept Med Solna, Karolinska Univ Hosp Solna, Clin Pharmacol, L7 03, SE-17176 Stockholm, Sweden..
    Öktem, Ozan
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Mathematics (Div.).
    Franzen, Bo
    Karolinska Inst, Dept Oncol Pathol, Karolinska Univ Hosp, K7,Z1 00, S-17176 Stockholm, Sweden..
    Auer, Gert
    Karolinska Inst, Dept Oncol Pathol, Karolinska Univ Hosp, K7,Z1 00, S-17176 Stockholm, Sweden..
    Lomnytska, Marta
    Karolinska Inst, Dept Oncol Pathol, Karolinska Univ Hosp, K7,Z1 00, S-17176 Stockholm, Sweden.;Acad Univ Hosp, Dept Obstet & Gynaecol, SE-75185 Uppsala, Sweden.;Uppsala Univ, Inst Women & Child Hlth, SE-75185 Uppsala, Sweden..
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Super-resolution microscopy can identify specific protein distribution patterns in platelets incubated with cancer cells2019In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 11, no 20, p. 10023-10033Article in journal (Refereed)
    Abstract [en]

    Protein contents in platelets are frequently changed upon tumor development and metastasis. However, how cancer cells can influence protein-selective redistribution and release within platelets, thereby promoting tumor development, remains largely elusive. With fluorescence-based super-resolution stimulated emission depletion (STED) imaging we reveal how specific proteins, implicated in tumor progression and metastasis, re-distribute within platelets, when subject to soluble activators (thrombin, adenosine diphosphate and thromboxane A2), and when incubated with cancer (MCF-7, MDA-MB-231, EFO21) or non-cancer cells (184A1, MCF10A). Upon cancer cell incubation, the cell-adhesion protein P-selectin was found to re-distribute into circular nano-structures, consistent with accumulation into the membrane of protein-storing alpha-granules within the platelets. These changes were to a significantly lesser extent, if at all, found in platelets incubated with normal cells, or in platelets subject to soluble platelet activators. From these patterns, we developed a classification procedure, whereby platelets exposed to cancer cells, to non-cancer cells, soluble activators, as well as non-activated platelets all could be identified in an automatic, objective manner. We demonstrate that STED imaging, in contrast to electron and confocal microscopy, has the necessary spatial resolution and labelling efficiency to identify protein distribution patterns in platelets and can resolve how they specifically change upon different activations. Combined with image analyses of specific protein distribution patterns within the platelets, STED imaging can thus have a role in future platelet-based cancer diagnostics and therapeutic monitoring. The presented approach can also bring further clarity into fundamental mechanisms for cancer cell-platelet interactions, and into non-contact cell-to-cell interactions in general.

  • 14.
    Binder, Zev A.
    et al.
    Univ Penn, Perelman Sch Med, Dept Neurosurg, Philadelphia, PA 19104 USA.;Univ Penn, Perelman Sch Med, Ctr Biomed Image Comp & Analyt, Philadelphia, PA 19104 USA..
    Thorne, Amy Haseley
    Ludwig Inst Canc Res, San Diego, CA 92093 USA..
    Bakas, Spyridon
    Univ Penn, Perelman Sch Med, Ctr Biomed Image Comp & Analyt, Philadelphia, PA 19104 USA.;Univ Penn, Perelman Sch Med, Dept Radiol, Philadelphia, PA 19104 USA..
    Wileyto, E. Paul
    Univ Penn, Perelman Sch Med, Dept Biostat Epidemiol & Informat, Philadelphia, PA 19104 USA..
    Bilello, Michel
    Univ Penn, Perelman Sch Med, Ctr Biomed Image Comp & Analyt, Philadelphia, PA 19104 USA.;Univ Penn, Perelman Sch Med, Dept Radiol, Philadelphia, PA 19104 USA..
    Akbari, Hamed
    Univ Penn, Perelman Sch Med, Ctr Biomed Image Comp & Analyt, Philadelphia, PA 19104 USA.;Univ Penn, Perelman Sch Med, Dept Radiol, Philadelphia, PA 19104 USA..
    Rathore, Saima
    Univ Penn, Perelman Sch Med, Ctr Biomed Image Comp & Analyt, Philadelphia, PA 19104 USA.;Univ Penn, Perelman Sch Med, Dept Radiol, Philadelphia, PA 19104 USA..
    Ha, Sung Min
    Univ Penn, Perelman Sch Med, Ctr Biomed Image Comp & Analyt, Philadelphia, PA 19104 USA.;Univ Penn, Perelman Sch Med, Dept Radiol, Philadelphia, PA 19104 USA..
    Zhang, Logan
    Univ Penn, Perelman Sch Med, Dept Neurosurg, Philadelphia, PA 19104 USA..
    Ferguson, Cole J.
    Washington Univ, Div Neuropathol, Dept Pathol & Immunol, Sch Med, St Louis, MO 63108 USA..
    Dahiya, Sonika
    Washington Univ, Div Neuropathol, Dept Pathol & Immunol, Sch Med, St Louis, MO 63108 USA..
    Bi, Wenya Linda
    Brigham & Womans Hosp, Harvard Med Ctr, Dept Neurosurg, Ctr Skull Base & Pituitary Surg, Boston, MA 02115 USA..
    Reardon, David A.
    Dana Farber Canc Inst, Ctr Neurooncol, Boston, MA 02215 USA..
    Idbaih, Ahmed
    Sorbonne Univ, Hop Univ Pitie Salpetriere Charles Foix, AP HP, Serv Neurol Mazarin 2, Inserm,CNRS,UMR S 1127, F-75013 Paris, France..
    Felsberg, Joerg
    Heinrich Heine Univ, Inst Neuropathol, Med Fac, Moorenstr 5, D-40225 Dusseldorf, Germany..
    Hentschel, Bettina
    Univ Leipzig, Med Fac, Inst Med Informat Stat & Epidemiol, Hartelstr 16, D-04107 Leipzig, Germany..
    Weller, Michael
    Univ Hosp, Dept Neurol, CH-8091 Zurich, Switzerland.;Univ Zurich, CH-8091 Zurich, Switzerland..
    Bagley, Stephen J.
    Univ Penn, Abramson Canc Ctr, Philadelphia, PA 19104 USA..
    Morrissette, Jennifer J. D.
    Univ Penn, Dept Pathol & Lab Med, Perelman Sch Med, Philadelphia, PA 19104 USA..
    Nasrallah, MacLean P.
    Univ Penn, Perelman Sch Med, Dept Pathol & Lab Med, Div Neuropathol, Philadelphia, PA 19104 USA..
    Ma, Jianhui
    Zanca, Ciro
    Scott, Andrew M.
    La Trobe Univ, Olivia Newton John Canc Res Inst, Melbourne, Vic, Australia..
    Orellana, Laura
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
    Davatzikos, Christos
    Furnari, Frank B.
    Ludwig Inst Canc Res, San Diego, CA 92093 USA..
    O'Rourke, Donald M.
    Univ Penn, Perelman Sch Med, Dept Neurosurg, Philadelphia, PA 19104 USA.;Univ Penn, Perelman Sch Med, Ctr Biomed Image Comp & Analyt, Philadelphia, PA 19104 USA.;Univ Penn, Abramson Canc Ctr, Philadelphia, PA 19104 USA..
    Epidermal Growth Factor Receptor Extracellular Domain Mutations in Glioblastoma Present Opportunities for Clinical Imaging and Therapeutic Development2018In: Cancer Cell, ISSN 1535-6108, E-ISSN 1878-3686, Vol. 34, no 1, p. 163--177.e7Article in journal (Refereed)
    Abstract [en]

    We explored the clinical and pathological impact of epidermal growth factor receptor (EGFR) extracellular domain missense mutations. Retrospective assessment of 260 de novo glioblastoma patients revealed a significant reduction in overall survival of patients having tumors with EGFR mutations at alanine 289 (EGFR(A289D/T/V)). Quantitative multi-parametric magnetic resonance imaging analyses indicated increased tumor invasion for EGFR(A289D/T/V) mutants, corroborated in mice bearing intracranial tumors expressing EGFR(A289V) and dependent on ERK-mediated expression of matrix metalloproteinase-1. EGFR(A289V) tumor growth was attenuated with an antibody against a cryptic epitope, based on in silico simulation. The findings of this study indicate a highly invasive phenotype associated with the EGFR(A289V) mutation in glioblastoma, postulating EGFR(A289V) as a molecular marker for responsiveness to therapy with EGFR-targeting antibodies.

  • 15. Bjork, L.
    et al.
    Ait Blal, C.
    Alm, Tove L.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Bäckström, Anna
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Gnann, C.
    Hjelmare, Martin
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schutten, Rutger
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Skogs, Marie
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Stadler, Charlotte
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Lundberg, Emma
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Application specific antibody validation. The Human Protein Atlas validation scheme and how to confirm subcellular protein localization.2016In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 27Article in journal (Refereed)
  • 16. Bjornson, Elias
    et al.
    Mukhopadhyay, Bani
    Asplund, Anna
    Pristovsek, Nusa
    Cinar, Resat
    Romeo, Stefano
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kunos, George
    Nielsen, Jens
    Mardinoglu, Adil
    Stratification of Hepatocellular Carcinoma Patients Based on Acetate Utilization2015In: Cell Reports, E-ISSN 2211-1247, Vol. 13, no 9, p. 2014-2026Article in journal (Refereed)
    Abstract [en]

    Hepatocellular carcinoma (HCC) is a deadly form of liver cancer that is increasingly prevalent. We analyzed global gene expression profiling of 361 HCC tumors and 49 adjacent noncancerous liver samples by means of combinatorial network-based analysis. We investigated the correlation between transcriptome and proteome of HCC and reconstructed a functional genome-scale metabolic model (GEM) for HCC. We identified fundamental metabolic processes required for cell proliferation using the network centric view provided by the GEM. Our analysis revealed tight regulation of fatty acid biosynthesis (FAB) and highly significant deregulation of fatty acid oxidation in HCC. We predicted mitochondrial acetate as an emerging substrate for FAB through upregulation of mitochondrial acetyl-CoA synthetase (ACSS1) in HCC. We analyzed heterogeneous expression of ACSS1 and ACSS2 between HCC patients stratified by high and low ACSS1 and ACSS2 expression and revealed that ACSS1 is associated with tumor growth and malignancy under hypoxic conditions in human HCC.

  • 17. Blau, Helen M.
    et al.
    Gilbert, Penney M.
    Havenstrite, Karen
    Lutolf, Matthias P.
    Magnusson, Klas E. G.
    KTH, School of Electrical Engineering (EES), Signal Processing.
    Ramunas, John
    Elastic substrates and methods of use in cell manipulation and culture2010Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    Methods are provided for the ex vivo manipulation of cells, stem cells and other reproductive cells, by manipulating the cells in a container or device comprising an elastic substrate, wherein the substrate has an elasticity that mimics the elasticity of a native microenvironment of the cell.

  • 18. Blom, M.
    et al.
    Reis, K.
    Nehru, V.
    Blom, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gad, A. K. B.
    Aspenström, P.
    RhoD is a Golgi component with a role in anterograde protein transport from the ER to the plasma membrane2015In: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 333, no 2, p. 208-219Article in journal (Refereed)
    Abstract [en]

    RhoD is a member of the Rho GTPase family and it coordinates actin dynamics and membrane trafficking. Activation of RhoD results in formation of filopodia, dissolution of stress fibers, and the subsequent formation of short actin bundles. In addition, RhoD localizes to early endosomes and recycling endosomes, and has a regulatory role in endosome trafficking. In this study, we report on a function of RhoD in the regulation of Golgi homeostasis. We show that manipulation of protein and activation levels of RhoD, as well as of its binding partner WHAMM, result in derailed localization of Golgi stacks. Moreover, vesicle trafficking from the endoplasmic reticulum to the plasma membrane via the Golgi apparatus measured by the VSV-G protein is severely hampered by manipulation of RhoD or WHAMM. In summary, our studies demonstrate a novel role for this member of the Rho GTPases in the regulation of Golgi function.

  • 19.
    Bo, Stefano
    et al.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm University, Sweden.
    Celani, A.
    Detecting Concentration Changes with Cooperative Receptors2015In: Journal of statistical physics, ISSN 0022-4715, E-ISSN 1572-9613, Vol. 162, no 5, p. 1365-1382Article in journal (Refereed)
    Abstract [en]

    Cells constantly need to monitor the state of the environment to detect changes and timely respond. The detection of concentration changes of a ligand by a set of receptors can be cast as a problem of hypothesis testing, and the cell viewed as a Neyman–Pearson detector. Within this framework, we investigate the role of receptor cooperativity in improving the cell’s ability to detect changes. We find that cooperativity decreases the probability of missing an occurred change. This becomes especially beneficial when difficult detections have to be made. Concerning the influence of cooperativity on how fast a desired detection power is achieved, we find in general that there is an optimal value at finite levels of cooperation, even though easy discrimination tasks can be performed more rapidly by noncooperative receptors.

  • 20.
    Boräng, Stina
    et al.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Andersson, Tove
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Thelin, A.
    Odeberg, Jacob
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Lundeberg, Joakim
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Vascular gene expression in atherosclerotic plaque-prone regions analyzed by representational difference analysis2004In: Pathobiology (Basel), ISSN 1015-2008, E-ISSN 1423-0291, Vol. 71, no 2, p. 107-114Article in journal (Refereed)
    Abstract [en]

    Objectives: Atherosclerotic plaques are known to develop and progress where the endothelium is subjected to turbulent blood flow. We have applied cDNA representational difference analysis (RDA) to study vascular gene expression in mouse aorta in a model for atherosclerosis. Methods: Gene expression profiles were investigated in plaque-prone and plaque-resistant localizations in the ascending aorta and arch in 8-week-oldApoE-/- and LDLR-/- mice. Total RNA was extracted and two rounds of subtraction were performed; the difference products were characterized in detail by shotgun cloning and analysis of more than 2,700 gene sequences. Results: The identified differentially expressed gene sequences include both genes with known involvement in vascular gene expression and genes previously not implicated in vascular processes. For example, CD36 and caveolin, previously reported for their participation in the progression of atherosclerosis, were found to have an increased expression in vessel localizations thought to be especially susceptible to plaque formation. Conclusions: This report provides new in vivo information of expressed genes that can be useful for further investigations of the molecular mechanisms in focal localization of atherosclerosis.

  • 21.
    Brismar, Hjalmar
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Astrid Lindgren Childrens Hosp, Dept Woman & Child Hlth, Sweden.
    Aperia, A
    Westin, L
    Moy, J
    Wang, M
    Guillermier, C
    Poczatek, C
    Lechene, C
    Study of protein and RNA in dendritic spines using multi-isotope imaging mass spectrometry (MIMS).2014In: Surface and Interface Analysis, ISSN 0142-2421, E-ISSN 1096-9918, Vol. 46, no Suppl 1Article in journal (Refereed)
    Abstract [en]

    The classical view of neuronal protein synthesis is that proteins are made in the cell body and then transported to their functional sites in the dendrites and the dendritic spines. Indirect evidence, however, suggests that protein synthesis can directly occur in the distal dendrites, far from the cell body. We are developing protocols for dual labeling of RNA and proteins using (15)N-uridine and (18)O- or (13)C-leucine pulse chase in cultured neurons to identify and localize both protein synthesis and fate of newly synthesized proteins. Pilot experiments show discrete localization of both RNA and newly synthesized proteins in dendrites, close to dendritic spines. We have for the first time directly imaged and measured the production of proteins at the subcellular level in the neuronal dendrites, close to the functional sites, the dendritic spines. This will open a powerful way to study neural growth and synapse plasticity in health and disease.

  • 22.
    Buchmann, Sebastian
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at KI and KTH/ 3 Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Organic Electronics and Microphysiological Systems to Interface, Monitor, and Model Biology2024Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biological processes in the human body are regulated through complex and precise arrangements of cell structures and their interactions. In vivo models serve as the most accurate choice for biological studies to understand these processes. However, they are costly, time-consuming, and raise ethical issues. Microphysiological systems have been developed to create advanced in vitro models that mimic in vivo-like microenvironments. They are often combined with integrated sensing technologies to perform real-time measurements to gain additional information. However, conventional sensing electrodes, made of inorganic materials such as gold or platinum, differ fundamentally from biological materials. Organic bioelectronic devices made from conjugated polymers are promising alternatives for biological sensing applications and aim to improve the interconnection between abiotic electronics and biotic materials. The widespread use of these devices is partly hindered by the limited availability of materials and low-cost fabrication methods. In this thesis, we provide new tools and materials that facilitate the use of organic bioelectronic devices for in vitro sensing applications. We developed a method to pattern the conducting polymer poly(3,4‑ethylenedioxythiophene) polystyrene sulfonate and to fabricate organic microelectronic devices using wax printing, filtering, and tape transfer. The method is low-cost, time-effective, and compatible with in vitro cell culture models. To achieve higher resolution, we further developed a patterning method using femtosecond laser ablation to fabricate organic electronic devices such as complementary inverters or biosensors. The method is maskless and independent of the type of conjugated polymer. Besides fabrication processes, we introduced a newly synthesized material, the semiconducting conjugated polymer p(g42T‑T)‑8%OH. This polymer contains hydroxylated side chains that enable surface modifications, allowing control of cell adhesion. Using the new femtosecond laser-based patterning method, we could fabricate p(g42T‑T)‑8%OH‑based organic electrochemical transistors to monitor cell barrier formations in vitro. Microphysological systems are further dependent on precise compartmentalization to study cellular interaction. We used femtosecond laser 3D printing to develop a co-culture neurite guidance platform to control placement and interactions between different types of brain cells. In summary, the thesis provides new tools to facilitate the fabrication of organic electronic devices and microphysiological systems. This increases their accessibility and widespread use to interface, monitor, and model biological systems. 

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  • 23.
    Buchmann, Sebastian
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Enrico, Alessandro
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Holzreuter, Muriel Alexandra
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Reid, Michael S.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Zeglio, Erica
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Niklaus, Frank
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Stemme, Göran
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Herland, Anna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Probabilistic cell seeding and non-autofluorescent 3D-printed structures as scalable approach for multi-level co-culture modeling2023In: Materials Today Bio, ISSN 2590-0064, Vol. 21, p. 100706-100706, article id 100706Article in journal (Refereed)
    Abstract [en]

    To model complex biological tissue in vitro, a specific layout for the position and numbers of each cell type isnecessary. Establishing such a layout requires manual cell placement in three dimensions (3D) with micrometricprecision, which is complicated and time-consuming. Moreover, 3D printed materials used in compartmentalizedmicrofluidic models are opaque or autofluorescent, hindering parallel optical readout and forcing serial charac-terization methods, such as patch-clamp probing. To address these limitations, we introduce a multi-level co-culture model realized using a parallel cell seeding strategy of human neurons and astrocytes on 3D structuresprinted with a commercially available non-autofluorescent resin at micrometer resolution. Using a two-stepstrategy based on probabilistic cell seeding, we demonstrate a human neuronal monoculture that forms net-works on the 3D printed structure and can establish cell-projection contacts with an astrocytic-neuronal co-cultureseeded on the glass substrate. The transparent and non-autofluorescent printed platform allows fluorescence-based immunocytochemistry and calcium imaging. This approach provides facile multi-level compartmentaliza-tion of different cell types and routes for pre-designed cell projection contacts, instrumental in studying complextissue, such as the human brain.

  • 24.
    Buchmann, Sebastian
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Stoop, Pepijn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Roekevisch, Kim
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Jain, Saumey
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Kroon, Renee
    Department of Science and Technology, Laboratory of Organic Electronics, Linköping University, Norrköping, Sweden.
    Müller, Christian
    Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden.
    Hamedi, Mahiar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Zeglio, Erica
    AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden/ Wallenberg Initiative Materials Science for Sustainability, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
    Herland, Anna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden/ Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    In situ functionalization of polar polythiophene based organic electrochemical transistor to interface in vitro modelsManuscript (preprint) (Other academic)
  • 25.
    Bäckström, Anna
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Kugel, Laura
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Gnann, Christian
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics.
    Xu, Hao
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics.
    Aslan, Joseph E.
    Oregon Hlth & Sci Univ, Knight Cardiovasc Inst, Portland, OR 97201 USA..
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Stadler, Charlotte
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface2020In: Journal of Histochemistry and Cytochemistry, ISSN 0022-1554, E-ISSN 1551-5044, Vol. 68, no 7, p. 473-489, article id 0022155420935403Article in journal (Refereed)
    Abstract [en]

    Imaging is a powerful approach for studying protein expression and has the advantage over other methodologies in providing spatial informationin situat single cell level. Using immunofluorescence and confocal microscopy, detailed information of subcellular distribution of proteins can be obtained. While adherent cells of different tissue origin are relatively easy to prepare for imaging applications, non-adherent cells from hematopoietic origin, present a challenge due to their poor attachment to surfaces and subsequent loss of a substantial fraction of the cells. Still, these cell types represent an important part of the human proteome and express genes that are not expressed in adherent cell types. In the era of cell mapping efforts, overcoming the challenge with suspension cells for imaging applications would enable systematic profiling of hematopoietic cells. In this work, we successfully established an immunofluorescence protocol for preparation of suspension cell lines, peripheral blood mononucleated cells (PBMC) and human platelets on an adherent surface. The protocol is based on a multi-well plate format with automated sample preparation, allowing for robust high throughput imaging applications. In combination with confocal microscopy, the protocol enables systematic exploration of protein localization to all major subcellular structures.

  • 26. Caceres, R.
    et al.
    Bojanala, N.
    Kelley, L. C.
    Dreier, Jes
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Manzi, J.
    Di Federico, F.
    Chi, Q.
    Risler, T.
    Testa, Ilaria
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Sherwood, D. R.
    Plastino, J.
    WASP and WAVE activate the Arp2/3 complex for actin-based force production during basement membrane invasion.2017In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 28Article in journal (Other academic)
  • 27.
    Campinoti, Sara
    et al.
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England.;Kings Coll London, Fac Life Sci & Med, London, England..
    Almeida, Bruna
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England..
    Bencina, Stefan
    Karolinska Inst, Dept Lab Med, Div Pathol, Stockholm, Sweden..
    Goudarzi, Negin
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England.;Kings Coll London, Fac Life Sci & Med, London, England..
    Cox, Jane
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England.;Kings Coll London, Fac Life Sci & Med, London, England..
    Khati, Vamakshi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology.
    Gaudenzi, Giulia
    Karolinska Inst, Dept Global Publ Hlth, Stockholm, Sweden..
    Urbani, Luca
    Fdn Liver Res, Roger Williams Inst Hepatol, London, England.;Kings Coll London, Fac Life Sci & Med, London, England..
    Gramignoli, Roberto
    Karolinska Inst, Dept Lab Med, Div Pathol, Stockholm, Sweden..
    Perfusion bioreactor and decellularized liver matrix in support of human amnion epithelial cell maturation into functional hepatocyte-like cells2023In: Transplantation, ISSN 0041-1337, E-ISSN 1534-6080, Vol. 107, no 10, p. 133-133Article in journal (Other academic)
  • 28.
    Campinoti, Sara
    et al.
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Almeida, Bruna
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Goudarzi, Negin
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Bencina, Stefan
    Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Solna, Sweden.
    Grundland Freile, Fabio
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Bioscience, Faculty of Life Science and Medicine, King’s College London, London, UK.
    McQuitty, Claire
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Natarajan, Dipa
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Cox, I. Jane
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Le Guennec, Adrien
    Centre for Biomolecular Spectroscopy, Randall Centre for Cell and Molecular Biophysics, Kings College London, London, UK.
    Khati, Vamakshi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gaudenzi, Giulia
    Department of Global Public Health, Karolinska Institutet, Solna, Sweden.
    Gramignoli, Roberto
    Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Solna, Sweden; Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Huddinge, Sweden.
    Urbani, Luca
    The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK; Faculty of Life Sciences and Medicine, King’s College London, London, UK.
    Rat liver extracellular matrix and perfusion bioreactor culture promote human amnion epithelial cell differentiation towards hepatocyte-like cells2023In: Journal of Tissue Engineering, ISSN 2041-7314, Vol. 14Article in journal (Refereed)
    Abstract [en]

    Congenital and chronic liver diseases have a substantial health burden worldwide. The most effective treatment available for these patients is whole organ transplantation; however, due to the severely limited supply of donor livers and the side effects associated with the immunosuppressive regimen required to accept allograft, the mortality rate in patients with end-stage liver disease is annually rising. Stem cell-based therapy aims to provide alternative treatments by either cell transplantation or bioengineered construct transplantation. Human amnion epithelial cells (AEC) are a widely available, ethically neutral source of cells with the plasticity and potential of multipotent stem cells and immunomodulatory properties of perinatal cells. AEC have been proven to be able to achieve functional improvement towards hepatocyte-like cells, capable of rescuing animals with metabolic disorders; however, they showed limited metabolic activities in vitro. Decellularised extracellular matrix (ECM) scaffolds have gained recognition as adjunct biological support. Decellularised scaffolds maintain native ECM components and the 3D architecture instrumental of the organ, necessary to support cells’ maturation and function. We combined ECM-scaffold technology with primary human AEC, which we demonstrated being equipped with essential ECM-adhesion proteins, and evaluated the effects on AEC differentiation into functional hepatocyte-like cells (HLC). This novel approach included the use of a custom 4D bioreactor to provide constant oxygenation and media perfusion to cells in 3D cultures over time. We successfully generated HLC positive for hepatic markers such as ALB, CYP3A4 and CK18. AEC-derived HLC displayed early signs of hepatocyte phenotype, secreted albumin and urea, and expressed Phase-1 and -2 enzymes. The combination of liver-specific ECM and bioreactor provides a system able to aid differentiation into HLC, indicating that the innovative perfusion ECM-scaffold technology may support the functional improvement of multipotent and pluripotent stem cells, with important repercussions in the bioengineering of constructs for transplantation.

  • 29.
    Casanova, Alain
    et al.
    Univ Basel, Biozentrum, Basel, Switzerland.;Novartis Pharma Schweiz AG, Rotkreuz, Switzerland..
    Low, Shyan Huey
    Univ Basel, Biozentrum, Basel, Switzerland.;Nanyang Technol Univ, Lee Kong China Sch Med, Singapore, Singapore..
    Quebatte, Maxime
    Univ Basel, Biozentrum, Basel, Switzerland..
    Sedzicki, Jaroslaw
    Univ Basel, Biozentrum, Basel, Switzerland..
    Tschon, Therese
    Univ Basel, Biozentrum, Basel, Switzerland..
    Ketterer, Maren
    Univ Basel, Biozentrum, Basel, Switzerland..
    Smith, Kevin
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Computer Science and Communication (CSC). Univ Basel, Biozentrum, Basel, Switzerland.
    Emmenlauer, Mario
    Univ Basel, Biozentrum, Basel, Switzerland.;BioDataAnalysis GmbH, Munich, Germany..
    Ben-Tekaya, Houchaima
    Univ Basel, Biozentrum, Basel, Switzerland.;Univ Hosp Basel, Basel, Switzerland..
    Dehio, Christoph
    Univ Basel, Biozentrum, Basel, Switzerland..
    A Role for the VPS Retromer in Brucella Intracellular Replication Revealed by Genomewide siRNA Screening2019In: mSphere, E-ISSN 2379-5042, Vol. 4, no 3, article id e00380-19Article in journal (Refereed)
    Abstract [en]

    Brucella, the agent causing brucellosis, is a major zoonotic pathogen with worldwide distribution. Brucella resides and replicates inside infected host cells in membrane-bound compartments called Brucella-containing vacuoles (BCVs). Following uptake, Brucella resides in endosomal BCVs (eBCVs) that gradually mature from early to late endosomal features. Through a poorly understood process that is key to the intracellular lifestyle of Brucella, the eBCV escapes fusion with lysosomes by transitioning to the replicative BCV (rBCV), a replicative niche directly connected to the endoplasmic reticulum (ER). Despite the notion that this complex intracellular lifestyle must depend on a multitude of host factors, a holistic view on which of these components control Brucella cell entry, trafficking, and replication is still missing. Here we used a systematic cell-based small interfering RNA (siRNA) knockdown screen in HeLa cells infected with Brucella abortus and identified 425 components of the human infectome for Brucella infection. These include multiple components of pathways involved in central processes such as the cell cycle, actin cytoskeleton dynamics, or vesicular trafficking. Using assays for pathogen entry, knockdown complementation, and colocalization at single-cell resolution, we identified the requirement of the VPS retromer for Brucella to escape the lysosomal degradative pathway and to establish its intracellular replicative niche. We thus validated the VPS retromer as a novel host factor critical for Brucella intracellular trafficking. Further, our genomewide data shed light on the interplay between central host processes and the biogenesis of the Brucella replicative niche. IMPORTANCE With >300,000 new cases of human brucellosis annually, Brucella is regarded as one of the most important zoonotic bacterial pathogens worldwide. The agent causing brucellosis resides inside host cells within vacuoles termed Brucella-containing vacuoles (BCVs). Although a few host components required to escape the degradative lysosomal pathway and to establish the ER-derived replicative BCV (rBCV) have already been identified, the global understanding of this highly coordinated process is still partial, and many factors remain unknown. To gain deeper insight into these fundamental questions, we performed a genomewide RNA interference (RNAi) screen aiming at discovering novel host factors involved in the Brucella intracellular cycle. We identified 425 host proteins that contribute to Brucella cellular entry, intracellular trafficking, and replication. Together, this study sheds light on previously unknown host pathways required for the Brucella infection cycle and highlights the VPS retromer components as critical factors for the establishment of the Brucella intracellular replicative niche.

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  • 30. Chen, D.
    et al.
    Liu, J.
    Rui, B.
    Gao, M.
    Zhao, Ningwei
    KTH, School of Biotechnology (BIO).
    Sun, S.
    Bi, A.
    Yang, T.
    Guo, Y.
    Yin, Z.
    Luo, L.
    GSTpi protects against angiotensin II-induced proliferation and migration of vascular smooth muscle cells by preventing signal transducer and activator of transcription 3 activation2014In: Biochimica et Biophysica Acta. Molecular Cell Research, ISSN 0167-4889, E-ISSN 1879-2596, Vol. 1843, no 2, p. 454-463Article in journal (Refereed)
    Abstract [en]

    Angiotensin II (Ang II)-elicited excessive proliferation, hypertrophy and migration of vascular smooth muscle cells (VSMCs) are vital to the pathogenesis of atheroclerosis. Glutathione S-transferase pi (GSTpi) exists extensively in various kinds of cells and protects cells against different stresses. However, knowledge remains limited about what GSTpi acts in VSMCs. We investigated the effect of GSTpi on Ang II-induced VSMC proliferation, hypertrophy and migration and its latent mechanism. Overexpression and RNAi experiments demonstrated that GSTpi inhibited Ang II-induced proliferation, hypertrophy and migration of VSMCs and arrested progression of cell cycle from G0/G1 to S phase. Immunoprecipitation, mass spectrometry and confocal microscopy analyses showed that GSTpi directly associated with signal transducer and activator of transcription 3 (STAT3) to prevent Ang II-triggered binding of Src to STAT3 and thus suppressed Ang II-stimulated phosphorylation and nuclear translocation of STAT3, as well as cyclin D1 expression. In contrast, GSTpi didn't affect Ang II-activated extracellular signal-regulated kinase (ERK1/2). GSTpi acts as a negative regulator to prevent Ang II-triggered proliferative signaling in VSMCs, suggesting that it may protect vessels against the stresses associated with atherosclerosis formation.

  • 31. Chen, H.
    et al.
    Xu, J.
    Wang, Y.
    Wang, D.
    Ferrer-Espada, R.
    Zhou, Jingjian
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Pedrazo-Tardajos, A.
    Yang, M.
    Tan, J. -H
    Yang, X.
    Zhang, L.
    Sychugov, Ilya
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Chen, S.
    Bals, S.
    Paulsson, J.
    Yang, Z.
    Color-Switchable Nanosilicon Fluorescent Probes2022In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 16, no 9, p. 15450-15459Article in journal (Refereed)
    Abstract [en]

    Fluorescent probes are vital to cell imaging by allowing specific parts of cells to be visualized and quantified. Color-switchable probes (CSPs), with tunable emission wavelength upon contact with specific targets, are particularly powerful because they not only eliminate the need to wash away all unbound probe but also allow for internal controls of probe concentrations, thereby facilitating quantification. Several such CSPs exist and have proven very useful, but not for all key cellular targets. Here we report a pioneering CSP for in situ cell imaging using aldehyde-functionalized silicon nanocrystals (SiNCs) that switch their intrinsic photoluminescence from red to blue quickly when interacting with amino acids in live cells. Though conventional probes often work better in cell-free extracts than in live cells, the SiNCs display the opposite behavior and function well and fast in universal cell lines at 37 °C while requiring much higher temperature in extracts. Furthermore, the SiNCs only disperse in cytoplasm not nucleus, and their fluorescence intensity correlated linearly with the concentration of fed amino acids. We believe these nanosilicon probes will be promising tools to visualize distribution of amino acids and potentially quantify amino acid related processes in live cells. 

  • 32.
    Cho, Nathan H.
    et al.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Cheveralls, Keith C.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Brunner, Andreas-David
    Max Planck Inst Biochem, Prote & Signal Transduct, Martinsried, Germany..
    Kim, Kibeom
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Michaelis, Andre C.
    Max Planck Inst Biochem, Prote & Signal Transduct, Martinsried, Germany..
    Raghavan, Preethi
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Kobayashi, Hirofumi
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Savy, Laura
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Li, Jason Y.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Canaj, Hera
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Kim, James Y. S.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Stewart, Edna M.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Gnann, Christian
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    McCarthy, Frank
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Cabrera, Joana P.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Brunetti, Rachel M.
    Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA USA..
    Chhun, Bryant B.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Dingle, Greg
    Chan Zuckerberg Initiat, Redwood City, CA USA..
    Hein, Marco Y.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Huang, Bo
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA.;Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA USA.;Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA USA..
    Mehta, Shalin B.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Weissman, Jonathan S.
    Howard Hughes Med Inst, Whitehead Inst, Koch Inst, Cambridge, MA USA.;MIT, Dept Biol, Cambridge, MA USA.;Univ Calif San Francisco, Dept Cellular & Mol Pharmacol, San Francisco, CA USA..
    Gomez-Sjoberg, Rafael
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Itzhak, Daniel N.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Royer, Loic A.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    Mann, Matthias
    Max Planck Inst Biochem, Prote & Signal Transduct, Martinsried, Germany.;Univ Copenhagen, Fac Hlth & Med Sci, NNF Ctr Prot Res, Copenhagen, Denmark..
    Leonetti, Manuel D.
    Chan Zuckerberg Biohub, San Francisco, CA 94158 USA..
    OpenCell: Endogenous tagging for the cartography of human cellular organization2022In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 375, no 6585, p. 1143-+, article id eabi6983Article in journal (Refereed)
    Abstract [en]

    Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era. We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data science to systematically map the localization and interactions of human proteins. Our approach provides a data-driven description of the molecular and spatial networks that organize the proteome. Unsupervised clustering of these networks delineates functional communities that facilitate biological discovery. We found that remarkably precise functional information can be derived from protein localization patterns, which often contain enough information to identify molecular interactions, and that RNA binding proteins form a specific subgroup defined by unique interaction and localization properties. Paired with a fully interactive website (opencell.czbiohub.org), our work constitutes a resource for the quantitative cartography of human cellular organization.

  • 33. Christensen, B M
    et al.
    Zelenina, M
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Aperia, A
    Nielsen, S
    Localization and regulation of PKA-phosphorylated AQP2 in response to V(2)-receptor agonist/antagonist treatment.2000In: American journal of physiology. Renal physiology, ISSN 1931-857X, Vol. 278, no 1, p. F29-42Article in journal (Refereed)
    Abstract [en]

    Phosphorylation of Ser(256), in a PKA consensus site, in AQP2 (p-AQP2) appears to be critically involved in the vasopressin-induced trafficking of AQP2. In the present study, affinity-purified antibodies that selectively recognize AQP2 phosphorylated at Ser(256) were developed. These antibodies were used to determine 1) the subcellular localization of p-AQP2 in rat kidney and 2) changes in distribution and/or levels of p-AQP2 in response to [desamino-Cys(1),D-Arg(8)]vasopressin (DDAVP) treatment or V(2)-receptor blockade. Immunoelectron microscopy revealed that p-AQP2 was localized in both the apical plasma membrane and in intracellular vesicles of collecting duct principal cells. Treatment of rats with V(2)-receptor antagonist for 30 min resulted in almost complete disappearance of p-AQP2 labeling of the apical plasma membrane with only marginal labeling of intracellular vesicles remaining. Immunoblotting confirmed a marked decrease in p-AQP2 levels. In control Brattleboro rats (BB), lacking vasopressin secretion, p-AQP2 labeling was almost exclusively present in intracellular vesicles. Treatment of BB rats with DDAVP for 2 h induced a 10-fold increase in p-AQP2 labeling of the apical plasma membrane. The overall abundance of p-AQP2, however, was not increased, as determined both by immunoelectron microscopy and immunoblotting. Consistent with this, 2 h of DDAVP treatment of normal rats also resulted in unchanged p-AQP2 levels. Thus the results demonstrate that AQP2 phosphorylated in Ser(256) is present in the apical plasma membrane and in intracellular vesicles and that both the intracellular distribution/trafficking, as well as the abundance of p-AQP2, are regulated via V(2) receptors by altering phosphorylation and/or dephosphorylation of Ser(256) in AQP2.

  • 34.
    Colombo, Gloria
    et al.
    Inst Sci & Technol Austria ISTA, Klosterneuburg, Austria..
    Cubero, Ryan John A.
    Inst Sci & Technol Austria ISTA, Klosterneuburg, Austria..
    Kanari, Lida
    Ecole Polytech Fed Lausanne EPFL, Blue Brain Project, Geneva, Switzerland..
    Venturino, Alessandro
    Inst Sci & Technol Austria ISTA, Klosterneuburg, Austria..
    Schulz, Rouven
    Inst Sci & Technol Austria ISTA, Klosterneuburg, Austria..
    Scolamiero, Martina
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Mathematics (Div.).
    Agerberg, Jens
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.).
    Mathys, Hansruedi
    MIT, Picower Inst Learning & Memory, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;MIT, Dept Brain & Cognit Sci, E25-618, Cambridge, MA 02139 USA.;Broad Inst Harvard & MIT, Cambridge, MA USA.;Univ Pittsburgh, Brain Inst, Pittsburgh, PA USA.;Univ Pittsburgh, Sch Med, Dept Neurobiol, Pittsburgh, PA USA..
    Tsai, Li-Huei
    MIT, Picower Inst Learning & Memory, 77 Massachusetts Ave, Cambridge, MA 02139 USA.;MIT, Dept Brain & Cognit Sci, E25-618, Cambridge, MA 02139 USA.;Broad Inst Harvard & MIT, Cambridge, MA USA..
    Chachólski, Wojciech
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Mathematics (Div.).
    Hess, Kathryn
    Ecole Polytech Fed Lausanne EPFL, Lab Topol & Neurosci, Brain Mind Inst, Lausanne, Switzerland..
    Siegert, Sandra
    Inst Sci & Technol Austria ISTA, Klosterneuburg, Austria..
    A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes2022In: Nature Neuroscience, ISSN 1097-6256, E-ISSN 1546-1726, Vol. 25, no 10, p. 1379-+Article in journal (Refereed)
    Abstract [en]

    Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology.

  • 35.
    Danielsson, Frida
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Akesson, L.
    Skogs, Marie
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Lundberg, Emma
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Profiling changes in response to hypoxia in a four-step cell line model for malignant transformation.2016In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 27Article in journal (Refereed)
  • 36.
    Danielsson, Frida
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlen, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gad, A. K.
    Profiling the Molecular changes during malignant transformation and response to different oxygen levels, using a combined transcriptomics and proteomics approach2014In: Molecular Biology of the Cell, ISSN 1059-1524, E-ISSN 1939-4586, Vol. 25, article id P1845Article in journal (Other academic)
  • 37. Dijksterhuis, Jacomijn P.
    et al.
    Arthofer, Elisa
    Marinescu, Voichita D.
    Nelander, Sven
    Uhlen, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Ponten, Frederik
    Mulder, Jan
    Schulte, Gunnar
    High levels of WNT-5A in human glioma correlate with increased presence of tumor-associated microglia/monocytes2015In: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 339, no 2, p. 280-288Article in journal (Refereed)
    Abstract [en]

    Malignant gliomas are among the most severe types of cancer, and the most common primary brain tumors. Treatment options are limited and the prognosis is poor. WNT-5A, a member of the WNT family of lipoglycoproteins, plays a role in oncogenesis and tumor progression in various cancers, whereas the role of WNT-5A in glioma remains obscure. Based on the role of WNT-5A as an oncogene, its potential to regulate microglia cells and the glioma-promoting capacities of microglia cells, we hypothesize that WNT-5A has a role in regulation of immune functions in glioma. We investigated WNT-5A expression by in silico analysis of the cancer genome atlas (TCGA) transcript profiling of human glioblastoma samples and immunohistochemistry experiments of human glioma tissue microarrays (TMA). Our results reveal higher WNT-5A protein levels and mRNA expression in a subgroup of gliomas (WNT-5A(high)) compared to non-malignant control brain tissue. Furthermore, we show a significant correlation between WNT-5A in the tumor and presence of major histocompatibility complex Class II-positive microglia/monocytes. Our data pinpoint a positive correlation between WNT-5A and a proinflammatory signature in glioma. We identify increased presence of microglia/monocytes as an important aspect in the inflammatory transformation suggesting a novel role for WNT-5A in human glioma.

  • 38.
    Dånmark, Staffan
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Finne-Wistrand, Anna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Albertsson, Ann-Christine
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Patarroyo, Manuel
    Institutionen for Odontologi, Karolinska Institute.
    Mustafa, Kamal
    Insititutt for klinisk Odontologi, Medicinska och Odontologiska Fakulteten, Universitetet i Bergen, Norge.
    Integrin-mediated adhesion of human mesenchymal stem cells to extracellular matrix proteins adsorbed to polymer surfaces2012In: Biomedical Materials, ISSN 1748-6041, E-ISSN 1748-605X, Vol. 7, no 3, p. 035011-Article in journal (Refereed)
    Abstract [en]

    In vitro, degradable aliphatic polyesters are widely used as cell carriers for bone tissue engineering, despite their lack of biological cues. Their biological active surface is rather determined by an adsorbed layer of proteins from the surrounding media. Initial cell fate, including adhesion and proliferation, which are key properties for efficient cell carriers, is determined by the adsorbed layer of proteins. Herein we have investigated the ability of human bone marrow derived stem cells (hBMSC) to adhere to extracellular matrix (ECM) proteins, including fibronectin and vitronectin which are present in plasma and serum. hBMSC expressed integrins for collagens, laminins, fibronectin and vitronectin. Accordingly, hBMSC strongly adhered to these purified ECM proteins by using the corresponding integrins. Although purified fibronectin and vitronectin adsorbed to aliphatic polyesters to a lower extent than to cell culture polystyrene, these low levels were sufficient to mediate adhesion of hBMSC. It was found that plasma- and serum-coated polystyrene adsorbed significant levels of both fibronectin and vitronectin, and fibronectin was identified as the major adhesive component of plasma for hBMSC; however, aliphatic polyesters adsorbed minimal levels of fibronectin under similar conditions resulting in impaired cell adhesion. Altogether, the results suggest that the efficiency of aliphatic polyesters cell carriers could be improved by increasing their ability to adsorb fibronectin.

  • 39.
    Dånmark, Staffan
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Finne-Wistrand, Anna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Edlund, Ulrica
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Albertsson, Ann-Christine
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Mustafa, Kamal
    Insititutt for klinisk Odontologi, Medicinska och Odontologiska Fakulteten, Universitetet i Bergen, Norge.
    Enhanced Osteoconductivity of Degradable co-Polyester Scaffolds through Covalent Immobilization of BMP-2Manuscript (preprint) (Other academic)
  • 40.
    Dånmark, Staffan
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Gladnikoff, Micha
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Frisk, Thomas
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Zelenina, Marina
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Mustafa, Kamal
    Insititutt for klinisk Odontologi, Medicinska och Odontologiska Fakulteten, Universitetet i Bergen, Norge.
    Russom, Aman
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Finne-Wistrand, Anna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymer Technology.
    Development of Novel Microfluidic Device for Long-Term in situ Monitoring of Live Cells in 3-dimensional MatricesManuscript (preprint) (Other academic)
  • 41. Edqvist, Per-Henrik D.
    et al.
    Fagerberg, Linn
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hallström, Bjorn M.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Danielsson, Angelika
    Edlund, Karolina
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Pontén, Fredrik
    Expression of Human Skin-Specific Genes Defined by Transcriptomics and Antibody-Based Profiling2015In: Journal of Histochemistry and Cytochemistry, ISSN 0022-1554, E-ISSN 1551-5044, Vol. 63, no 2, p. 129-141Article in journal (Refereed)
    Abstract [en]

    To increase our understanding of skin, it is important to define the molecular constituents of the cell types and epidermal layers that signify normal skin. We have combined a genome-wide transcriptomics analysis, using deep sequencing of mRNA from skin biopsies, with immunohistochemistry-based protein profiling to characterize the landscape of gene and protein expression in normal human skin. The transcriptomics and protein expression data of skin were compared to 26 (RNA) and 44 (protein) other normal tissue types. All 20,050 putative protein-coding genes were classified into categories based on patterns of expression. We found that 417 genes showed elevated expression in skin, with 106 genes expressed at least five-fold higher than that in other tissues. The 106 genes categorized as skin enriched encoded for well-known proteins involved in epidermal differentiation and proteins with unknown functions and expression patterns in skin, including the C1orf68 protein, which showed the highest relative enrichment in skin. In conclusion, we have applied a genome-wide analysis to identify the human skin-specific proteome and map the precise localization of the corresponding proteins in different compartments of the skin, to facilitate further functional studies to explore the molecular repertoire of normal skin and to identify biomarkers related to various skin diseases.

  • 42.
    Edwards, Steven
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nordahl, Linnea
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Bauer, Sebastian
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Graef, Philipp
    Meineke, Birthe
    Blom, Hans
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Elsässer, Simon
    Brismar, Hjalmar
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Dual-colour super resolution expansion microscopy of membrane proteins using bioorthogonal labellingManuscript (preprint) (Other academic)
  • 43. Eklund, D. Magnus
    et al.
    Staldal, Veronika
    Valsecchi, Isabel
    Cierlik, Izabela
    Eriksson, Caitriona
    Hiratsu, Keiichiro
    Ohme-Takagi, Masaru
    Sundstrom, Jens F.
    Thelander, Mattias
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Glycoscience.
    Sundberg, Eva
    The Arabidopsis thaliana STYLISH1 Protein Acts as a Transcriptional Activator Regulating Auxin Biosynthesis2010In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 22, no 2, p. 349-363Article in journal (Refereed)
    Abstract [en]

    The establishment and maintenance of auxin maxima in vascular plants is regulated by auxin biosynthesis and polar intercellular auxin flow. The disruption of normal auxin biosynthesis in mouse-ear cress ( Arabidopsis thaliana) leads to severe abnormalities, suggesting that spatiotemporal regulation of auxin biosynthesis is fundamental for normal growth and development. We have shown previously that the induction of the SHORT-INTERNODES/STYLISH (SHI/STY) family member STY1 results in increased transcript levels of the YUCCA (YUC) family member YUC4 and also higher auxin levels and auxin biosynthesis rates in Arabidopsis seedlings. We have also shown previously that SHI/STY family members redundantly affect development of flowers and leaves. Here, we further examine the function of STY1 by analyzing its DNA and protein binding properties. Our results suggest that STY1, and most likely other SHI/STY members, are DNA binding transcriptional activators that target genes encoding proteins mediating auxin biosynthesis. This suggests that the SHI/STY family members are essential regulators of auxin-mediated leaf and flower development. Furthermore, the lack of a shoot apical meristem in seedlings carrying a fusion construct between STY1 and a repressor domain, SRDX, suggests that STY1, and other SHI/STY members, has a role in the formation and/or maintenance of the shoot apical meristem, possibly by regulating auxin levels in the embryo.

  • 44. Facey, Jody-Ann
    et al.
    Venner, Laura
    Hyde, Michael
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Howard, Rebecca
    Polar substitutions in the ion-conducting pore of GLIC alter gating and alcohol modulation2014In: The FASEB Journal, ISSN 0892-6638, E-ISSN 1530-6860, Vol. 28, no 1, p. 1061.9-Article in journal (Other academic)
  • 45. Fenton, Robert A.
    et al.
    Moeller, Hanne B.
    Zelenina, Marina
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Snaebjornsson, Marteinn T.
    Holen, Torgeir
    MacAulay, Nanna
    Differential water permeability and regulation of three aquaporin 4 isoforms2010In: Cellular and Molecular Life Sciences (CMLS), ISSN 1420-682X, E-ISSN 1420-9071, Vol. 67, no 5, p. 829-840Article in journal (Refereed)
    Abstract [en]

    Aquaporin 4 (AQP4) is expressed in the perivascular glial endfeet and is an important pathway for water during formation and resolution of brain edema. In this study, we examined the functional properties and relative unit water permeability of three functional isoforms of AQP4 expressed in the brain (M1, M23, Mz). The M23 isoform gave rise to square arrays when expressed in Xenopus laevis oocytes. The relative unit water permeability differed significantly between the isoforms in the order of M1 > Mz > M23. None of the three isoforms were permeable to small osmolytes nor were they affected by changes in external K+ concentration. Upon protein kinase C (PKC) activation, oocytes expressing the three isoforms demonstrated rapid reduction of water permeability, which correlated with AQP4 internalization. The M23 isoform was more sensitive to PKC regulation than the longer isoforms and was internalized significantly faster. Our results suggest a specific role for square array formation.

  • 46.
    Fontana, Jacopo
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fritz, Nicolas
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Aperia, Anita
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Apoptosis caused by excessive mitochondrial albumin uptake in renal cells is initiated by increased mitochondrial calcium concentration2015In: The FASEB Journal, ISSN 0892-6638, E-ISSN 1530-6860, Vol. 29Article in journal (Other academic)
  • 47.
    Fontana, Jacopo Maria
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cellular Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Yin, Huijuan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cellular Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Chen, Yun
    Florez, Ricardo
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cellular Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cellular Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fu, Ying
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cellular Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Transport and release of colloidal 3-mercaptopropionic acid-coated CdSe-CdS/ZnS core-multishell quantum dots in human umbilical vein endothelial cells2017In: International Journal of Nanomedicine, ISSN 1176-9114, E-ISSN 1178-2013, Vol. 12, p. 8615-8629Article in journal (Refereed)
    Abstract [en]

    Colloidal semiconductor quantum dots (QDs) have been extensively researched and developed for biomedical applications, including drug delivery and biosensing assays. Hence, it is pivotal to understand their behavior in terms of intracellular transport and toxicological effects. In this study, we focused on 3-mercaptopropionic acid-coated CdSe-CdS/ZnS core-multishell quantum dots (3MPA-QDs) converted from the as-grown octadecylamine-coated quantum dots (ODA-QDs) and their direct and dynamic interactions with human umbilical vein endothelial cells (HUVECs). Live cell imaging using confocal fluorescence microscopy showed that 3MPAQDs first attached to and subsequently aggregated on HUVEC plasma membrane similar to 25 min after QD deposition. The aggregated QDs started being internalized at similar to 2 h and reached their highest internalization degree at similar to 24 h. They were released from HUVECs after similar to 48 h. During the 48 h period, the HUVECs responded normally to external stimulations, grew, proliferated and wound healed without any perceptible apoptosis. Furthermore, 1) 3MPA-QDs were internalized in newly formed LysoTracker-stained early endosomes; 2) adenosine 5'-triphosphateinduced [Ca2+](i) modulation caused a transient decrease in the fluorescence of 3MPA-QDs that were attached to the plasma membrane but a transient increase in the internalized 3MPA-QDs; and 3) fluorescence signal modulations of co-stained LysoTracker and QDs induced by the lysosomotropic agent Gly-Phe-beta-naphthylamide were spatially co-localized and temporally synchronized. Our findings suggest that 3MPA-QDs converted from ODA-QDs are a potential nontoxic fluorescent probe for future use in clinical applications. Moreover, the photophysical strategy and techniques reported in this work are easily applicable to study of direct interactions between other nanoparticles and live cells; contributing to awareness and implementation of the safe applications of nanoparticles.

  • 48.
    Fourati, Zaineb
    et al.
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Heusser, Stephanie A.
    Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Hu, Haidai
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France.;UPMC Univ Paris 6, Sorbonne Univ, F-75005 Paris, France..
    Ruza, Reinis R.
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Sauguet, Ludovic
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.
    Delarue, Marc
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels2018In: Cell Reports, E-ISSN 2211-1247, Vol. 23, no 4, p. 993-1004Article in journal (Refereed)
    Abstract [en]

    Ion channel modulation by general anesthetics is a vital pharmacological process with implications for receptor biophysics and drug development. Functional studies have implicated conserved sites of both potentiation and inhibition in pentameric ligand-gated ion channels, but a detailed structural mechanism for these bimodal effects is lacking. The prokaryotic model protein GLIC recapitulates anesthetic modulation of human ion channels, and it is accessible to structure determination in both apparent open and closed states. Here, we report ten X-ray structures and electrophysiological characterization of GLIC variants in the presence and absence of general anesthetics, including the surgical agent propofol. We show that general anesthetics can allosterically favor closed channels by binding in the pore or favor open channels via various subsites in the transmembrane domain. Our results support an integrated, multi-site mechanism for allosteric modulation, and they provide atomic details of both potentiation and inhibition by one of the most common general anesthetics.

  • 49. Fridberg, M.
    et al.
    Nodin, B.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jirström, K.
    Dachshund homologue 2 is a marker of good prognosis in breast cancer2012In: Histopathology, ISSN 0309-0167, E-ISSN 1365-2559, Vol. 61, p. 19-19Article in journal (Other academic)
  • 50.
    Frisk, Thomas
    et al.
    KTH, School of Electrical Engineering (EES), Microsystem Technology.
    Rydholm, Susanna
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Andersson Svahn, Helene
    KTH, School of Biotechnology (BIO), Nano Biotechnology.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Stemme, Göran
    KTH, School of Electrical Engineering (EES), Microsystem Technology.
    Three dimensional asymmetric microenvironment for cell biologigal studies2005In: Proceedings Micro Total Analysis Systems (muTAS) 2005, 2005Conference paper (Refereed)
1234 1 - 50 of 199
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