Ola Söderberg

Summary

Affiliation: Uppsala University
Country: Sweden

Publications

  1. doi Characterizing proteins and their interactions in cells and tissues using the in situ proximity ligation assay
    Ola Söderberg
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Methods 45:227-32. 2008
  2. ncbi Chronic lymphocytic leukemias utilizing the VH3-21 gene display highly restricted Vlambda2-14 gene use and homologous CDR3s: implicating recognition of a common antigen epitope
    Gerard Tobin
    Department of Genetics and Pathology, Uppsala University, Sweden
    Blood 101:4952-7. 2003
  3. ncbi Proximity ligation assays for sensitive and specific protein analyses
    Sigrun M Gustafsdottir
    Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE 75185 Uppsala, Sweden
    Anal Biochem 345:2-9. 2005
  4. ncbi Prospects for in situ analyses of individual and complexes of DNA, RNA, and protein molecules with padlock and proximity probes
    Ulf Landegren
    Department of Genetics and Pathology, University of Uppsala, S 751 85 Uppsala, Sweden
    Methods Cell Biol 75:787-97. 2004
  5. pmc Parallel visualization of multiple protein complexes in individual cells in tumor tissue
    Karl Johan Leuchowius
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, University of Uppsala, Uppsala, Sweden
    Mol Cell Proteomics 12:1563-71. 2013
  6. ncbi Somatically mutated Ig V(H)3-21 genes characterize a new subset of chronic lymphocytic leukemia
    Gerard Tobin
    Department of Genetics and Pathology, Uppsala University, SE 751 85 Uppsala, Sweden
    Blood 99:2262-4. 2002
  7. pmc High content screening for inhibitors of protein interactions and post-translational modifications in primary cells by proximity ligation
    Karl Johan Leuchowius
    Molecular Medicine, Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds väg 20, S 751 85 Uppsala, Sweden
    Mol Cell Proteomics 9:178-83. 2010
  8. ncbi Patients with chronic lymphocytic leukemia with mutated VH genes presenting with Binet stage B or C form a subgroup with a poor outcome
    Gerard Tobin
    Dept of Genetics and Pathology, Uppsala University, Uppsala, Sweden
    Haematologica 90:465-9. 2005
  9. ncbi Direct observation of individual endogenous protein complexes in situ by proximity ligation
    Ola Söderberg
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, SE 75185 Uppsala, Sweden
    Nat Methods 3:995-1000. 2006
  10. doi Visualising individual sequence-specific protein-DNA interactions in situ
    Irene Weibrecht
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    N Biotechnol 29:589-98. 2012

Collaborators

Detail Information

Publications36

  1. doi Characterizing proteins and their interactions in cells and tissues using the in situ proximity ligation assay
    Ola Söderberg
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Methods 45:227-32. 2008
    ....
  2. ncbi Chronic lymphocytic leukemias utilizing the VH3-21 gene display highly restricted Vlambda2-14 gene use and homologous CDR3s: implicating recognition of a common antigen epitope
    Gerard Tobin
    Department of Genetics and Pathology, Uppsala University, Sweden
    Blood 101:4952-7. 2003
    ....
  3. ncbi Proximity ligation assays for sensitive and specific protein analyses
    Sigrun M Gustafsdottir
    Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE 75185 Uppsala, Sweden
    Anal Biochem 345:2-9. 2005
  4. ncbi Prospects for in situ analyses of individual and complexes of DNA, RNA, and protein molecules with padlock and proximity probes
    Ulf Landegren
    Department of Genetics and Pathology, University of Uppsala, S 751 85 Uppsala, Sweden
    Methods Cell Biol 75:787-97. 2004
  5. pmc Parallel visualization of multiple protein complexes in individual cells in tumor tissue
    Karl Johan Leuchowius
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, University of Uppsala, Uppsala, Sweden
    Mol Cell Proteomics 12:1563-71. 2013
    ....
  6. ncbi Somatically mutated Ig V(H)3-21 genes characterize a new subset of chronic lymphocytic leukemia
    Gerard Tobin
    Department of Genetics and Pathology, Uppsala University, SE 751 85 Uppsala, Sweden
    Blood 99:2262-4. 2002
    ..We therefore suggest that B-CLL cases with mutated V(H)3-21 genes may constitute an additional entity of B-CLL...
  7. pmc High content screening for inhibitors of protein interactions and post-translational modifications in primary cells by proximity ligation
    Karl Johan Leuchowius
    Molecular Medicine, Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds väg 20, S 751 85 Uppsala, Sweden
    Mol Cell Proteomics 9:178-83. 2010
    ..In addition, inhibitor-induced perturbation of protein-protein interactions of the PDGF signaling pathway could be quantified, further demonstrating the usefulness of the assay in drug discovery...
  8. ncbi Patients with chronic lymphocytic leukemia with mutated VH genes presenting with Binet stage B or C form a subgroup with a poor outcome
    Gerard Tobin
    Dept of Genetics and Pathology, Uppsala University, Uppsala, Sweden
    Haematologica 90:465-9. 2005
    ..We investigated whether an alternative cut-off should be applied and the relation of mutational status to another prognostic marker, Binet staging...
  9. ncbi Direct observation of individual endogenous protein complexes in situ by proximity ligation
    Ola Söderberg
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, SE 75185 Uppsala, Sweden
    Nat Methods 3:995-1000. 2006
    ..We used this method to show specific regulation of protein-protein interactions between endogenous Myc and Max oncogenic transcription factors in response to interferon-gamma (IFN-gamma) signaling and low-molecular-weight inhibitors...
  10. doi Visualising individual sequence-specific protein-DNA interactions in situ
    Irene Weibrecht
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    N Biotechnol 29:589-98. 2012
    ..Although efficiency of detection currently is limiting, we conclude that in situ PLA can be used to achieve a highly selective analysis of PDIs in single cells...
  11. doi In situ proximity ligation assay for microscopy and flow cytometry
    Karl Johan Leuchowius
    Department of Immunology, Uppsala University, Uppsala, Sweden
    Curr Protoc Cytom . 2011
    ..It also includes information on expected results and information on how to troubleshoot the assay...
  12. doi Flow cytometric in situ proximity ligation analyses of protein interactions and post-translational modification of the epidermal growth factor receptor family
    Karl Johan Leuchowius
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, Uppsala SE 75185, Sweden
    Cytometry A 75:833-9. 2009
    ..The combination of in situ PLA and flow cytometry provided a statistically powerful way of analyzing protein-protein interactions and post-translational modifications on a single-cell basis...
  13. ncbi Mutated VH genes and preferential VH3-21 use define new subsets of mantle cell lymphoma
    Sarah H Walsh
    Department of Genetics and Pathology, Uppsala University, Sweden
    Blood 101:4047-54. 2003
    ..03), but they tended to be younger at diagnosis. The combined use of V(H)3-21/V(lambda)3-19 suggests a possible role for antigen(s) in the pathogenesis of these tumors and indicates that V(H)3-21(+) patients constitute a new MCL entity...
  14. pmc Western blotting via proximity ligation for high performance protein analysis
    Yanling Liu
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
    Mol Cell Proteomics 10:O111.011031. 2011
    ....
  15. ncbi Proximity ligation assays: a recent addition to the proteomics toolbox
    Irene Weibrecht
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, Uppsala, Sweden
    Expert Rev Proteomics 7:401-9. 2010
    ..Lastly, we apply the approach of recombining subcomponents to develop a few novel hypothetical methods hoping this might stimulate the readers to utilize this approach themselves...
  16. ncbi Proximity ligation: a specific and versatile tool for the proteomic era
    Ola Söderberg
    University of Uppsala, Department of Genetics and Pathology, Rudbeck Laboratory, SE 751 85 Uppsala, Sweden
    Genet Eng (N Y) 28:85-93. 2007
    ..In this review we discuss commonly used detection methods and compare these to the recently-developed proximity ligation technique...
  17. doi Analysis of genes, transcripts, and proteins via DNA ligation
    Tim Conze
    Department of Genetics and Pathology, The Rudbeck Lab, Uppsala University, Uppsala, Sweden
    Annu Rev Anal Chem (Palo Alto Calif) 2:215-39. 2009
    ....
  18. doi In situ detection and genotyping of individual mRNA molecules
    Chatarina Larsson
    Department of Genetics and Pathology, Uppsala University, Sweden
    Nat Methods 7:395-7. 2010
    ..We detect a somatic point mutation, differentiate between members of a gene family and perform multiplex detection of transcripts in human and mouse cells and tissue...
  19. doi Ligation-based molecular tools for lab-on-a-chip devices
    Jonas Melin
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, SE 75185 Uppsala, Sweden
    N Biotechnol 25:42-8. 2008
    ..We discuss these problems and describe a series of molecular tools that may present new opportunities for lab-on-a-chip devices at the point-of-care...
  20. ncbi In situ detection of phosphorylated platelet-derived growth factor receptor beta using a generalized proximity ligation method
    Malin Jarvius
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, SE 75185, Uppsala, Sweden
    Mol Cell Proteomics 6:1500-9. 2007
    ..The method should be of great value to study signal transduction, screen for effects of pharmacological agents, and enhance the diagnostic potential in histopathology...
  21. doi Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation
    Gucci Jijuan Gu
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    N Biotechnol 30:144-52. 2013
    ....
  22. doi In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay
    Irene Weibrecht
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
    Nat Protoc 8:355-72. 2013
    ..Both padlock probes and in situ PLA provide the ability to directly visualize single molecules by standard microscopy in fixed cells or tissue sections, and these methods may thus be valuable for both research and diagnostic purposes...
  23. ncbi Thermoplastic microfluidic platform for single-molecule detection, cell culture, and actuation
    Jonas Melin
    Beijer Laboratory, Department of Genetics and Pathology, Rudbeck Laboratory, Angstrom Laboratory, University of Uppsala, Sweden
    Anal Chem 77:7122-30. 2005
    ..Biocompatibility of the platform was illustrated by culturing Chinese hamster ovary cells for 7 days in the microfluidic channels...
  24. pmc Methods for analysis of the cancer microenvironment and their potential for disease prediction, monitoring and personalized treatments
    Carl Magnus Clausson
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, University of Uppsala, S 751 85, Uppsala, Sweden
    EPMA J 3:7. 2012
    ..Herein we describe how padlock probes and in situ PLA can be used for visualization of nucleic acids and protein activity, respectively, directly in tissue sections, and their potential future role in personalized medicine...
  25. pmc Simultaneous visualization of both signaling cascade activity and end-point gene expression in single cells
    Irene Weibrecht
    Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    PLoS ONE 6:e20148. 2011
    ..g. pinpoint effector sites of drugs in a signaling pathway...
  26. doi Automated classification of multicolored rolling circle products in dual-channel wide-field fluorescence microscopy
    Milan Gavrilović
    Department of Information Technology, Centre for Image Analysis, Uppsala University, Uppsala, Sweden
    Cytometry A 79:518-27. 2011
    ..We also demonstrate how the methods can be used as tools to evaluate biochemical protocols by measuring detection probe quality and accuracy. Finally, the method is used to evaluate single-molecule detection events in situ...
  27. doi Analysis of Protein Interactions in situ by Proximity Ligation Assays
    Björn Koos
    Department of Immunology, Genetics and Pathology Science for Life Laboratory, BMC, Uppsala University, SE 751 85, Uppsala, Sweden
    Curr Top Microbiol Immunol 377:111-26. 2014
    ..Furthermore, examples of how in situ PLA can be combined with other methods for a comprehensive view of the cellular activity status are discussed. ..
  28. pmc VEGF receptor 2/-3 heterodimers detected in situ by proximity ligation on angiogenic sprouts
    Ingrid Nilsson
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    EMBO J 29:1377-88. 2010
    ..We conclude that VEGFR2/-3 heterodimers on angiogenic sprouts induced by VEGFA or VEGFC may serve to positively regulate angiogenic sprouting...
  29. doi Molecular tools for companion diagnostics
    Agata Zieba
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    N Biotechnol 29:634-40. 2012
    ....
  30. pmc Functional overlap between chondroitin and heparan sulfate proteoglycans during VEGF-induced sprouting angiogenesis
    Sebastien Le Jan
    Rudbeck Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    Arterioscler Thromb Vasc Biol 32:1255-63. 2012
    ..The present study was undertaken to investigate if there is a functional overlap between heparan sulfate proteoglycans and chondroitin sulfate proteoglycans during sprouting angiogenesis...
  31. ncbi Molecular tools for a molecular medicine: analyzing genes, transcripts and proteins using padlock and proximity probes
    Ulf Landegren
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
    J Mol Recognit 17:194-7. 2004
    ..The procedures permit highly specific solution-phase or localized analyses of large sets of target molecules as required in future molecular analyses...
  32. ncbi V(H)3-21 gene usage in chronic lymphocytic leukemia--characterization of a new subgroup with distinct molecular features and poor survival
    Gerard Tobin
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    Leuk Lymphoma 45:221-8. 2004
    ..All in all, it appears that V(H)3-21 gene usage define a new entity of CLL. The remaining question now to be clarified is if antigen(s) actually are involved in the pathogenesis of V(H)3-21+ CLL...
  33. doi U-2973, a novel B-cell line established from a patient with a mature B-cell leukemia displaying concurrent t(14;18) and MYC translocation to a non-IG gene partner
    Hans Bostrom
    Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
    Eur J Haematol 81:218-25. 2008
    ..1...
  34. ncbi Subsets with restricted immunoglobulin gene rearrangement features indicate a role for antigen selection in the development of chronic lymphocytic leukemia
    Gerard Tobin
    Dept of Genetics and Pathology, Uppsala University, SE 751 85 Uppsala, Sweden
    Blood 104:2879-85. 2004
    ....
  35. doi Transcriptional profiling of human glioblastoma vessels indicates a key role of VEGF-A and TGFβ2 in vascular abnormalization
    Lothar C Dieterich
    Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
    J Pathol 228:378-90. 2012
    ..This indicates a key role of TGFβ signalling in regulating vascular phenotype and suggests that, in addition to VEGF-A, TGFβ2 may represent a new target for vascular normalization therapy...
  36. doi MUC2 mucin is a major carrier of the cancer-associated sialyl-Tn antigen in intestinal metaplasia and gastric carcinomas
    Tim Conze
    Department of Genetics and Pathology, University of Uppsala, Uppsala, Sweden
    Glycobiology 20:199-206. 2010
    ..Identification of the mucin which is the carrier of a carbohydrate structure offers unique advantages for future development of more accurate diagnostic and prognostic markers...