Ola Söderberg
Professor vid Institutionen för farmaceutisk biovetenskap; Forskning; Farmaceutisk cellbiologi
- Telefon:
- 018-471 45 29
- Mobiltelefon:
- 072-999 93 34
- E-post:
- ola.soderberg@uu.se
- Besöksadress:
- BMC, Husargtan 3
75124 uppsala - Postadress:
- Box 591
75124 Uppsala
- Akademiska meriter:
- docent
- ORCID:
- 0000-0003-2883-1925
Forskning
My on-going research and future plans include both method development to provide better tools for investigating cell biology and application of these new methods in basic research and for improved diagnostics of e.g. cancer and infectious diseases. Since the development of the in situ proximity ligation assay (in situ PLA) (Söderberg et al., Nat Methods, 2006), most of our efforts have been related to the use of in situ PLA and to further improve the method, e.g. for multiplex analysis, simultaneous measurement of proteins and mRNA and for detection of protein-DNA interactions. In situ PLA combines multiple recognition of affinity reagents with potent signal amplification, utilizing methods for DNA analysis to generate a signal that will be a surrogate marker of the targeted protein, protein-protein interaction or post-translational modifications of proteins. The method is based on pairs of proximity-probes (i.e. antibodies conjugated to strands of DNA) to detect the proteins of interest. Only upon proximal binding of these probes can an amplifiable DNA molecule be generated by ligation, which enhance the selectivity of the method even further. We have also been working on developing novel methods, such as proximity-dependent initiation of hybridization chain reaction (proxHCR) (Koos et al., Nat Commun, 2015). ProxHCR retains the dual binding requirement of in situ PLA while not needing any enzymatic steps. Our ongoing work is focused on developing methods that will provide a deeper understanding on the biochemistry of the cell, and for analyses of DNA and RNA.

Publikationer
Urval av publikationer
Next-Generation Pathology: Surveillance of Tumor Microecology
Ingår i Journal of Molecular Biology, s. 2013-2022, 2015
Ingår i Scientific Reports, 2015
Proximity-dependent initiation of hybridization chain reaction
Ingår i Nature Communications, 2015
- DOI för Proximity-dependent initiation of hybridization chain reaction
- Ladda ner fulltext (pdf) av Proximity-dependent initiation of hybridization chain reaction
Ingår i Nature Protocols, s. 355-372, 2013
Parallel Visualization of Multiple Protein Complexes in Individual Cells in Tumor Tissue
Ingår i Molecular & Cellular Proteomics, s. 1563-1571, 2013
Increasing the dynamic range of in situ PLA
Ingår i Nature Methods, s. 892-893, 2011
In situ detection and genotyping of individual mRNA molecules
Ingår i Nature Methods, s. 395-397, 2010
Ingår i Molecular & Cellular Proteomics, s. 1500-1509, 2007
Direct observation of individual endogenous protein complexes in situ by proximity ligation
Ingår i Nature Methods, s. 995-1000, 2006
Senaste publikationer
The method developer's guide to oligonucleotide design
Ingår i Expert Review of Proteomics, s. 65-80, 2024
- DOI för The method developer's guide to oligonucleotide design
- Ladda ner fulltext (pdf) av The method developer's guide to oligonucleotide design
Ingår i Journal of Steroid Biochemistry and Molecular Biology, 2024
- DOI för Cellular responses to silencing of PDIA3 (protein disulphide-isomerase A3): Effects on proliferation, migration, and genes in control of active vitamin D
- Ladda ner fulltext (pdf) av Cellular responses to silencing of PDIA3 (protein disulphide-isomerase A3): Effects on proliferation, migration, and genes in control of active vitamin D
Ingår i Biochemical and Biophysical Research Communications - BBRC, 2024
- DOI för Crosstalk between 1,25(OH)2-Vitamin D3 and the growth factors EGF and PDGF-BB: Impact on CYP24A1 expression and cell proliferation
- Ladda ner fulltext (pdf) av Crosstalk between 1,25(OH)2-Vitamin D3 and the growth factors EGF and PDGF-BB: Impact on CYP24A1 expression and cell proliferation
PDGF-induced internalisation promotes proteolytic cleavage of PDGFRβ in mesenchymal cells
Ingår i Growth Factors, s. 147-160, 2024
- DOI för PDGF-induced internalisation promotes proteolytic cleavage of PDGFRβ in mesenchymal cells
- Ladda ner fulltext (pdf) av PDGF-induced internalisation promotes proteolytic cleavage of PDGFRβ in mesenchymal cells
Ingår i Nucleic Acids Research, 2024
- DOI för Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling
- Ladda ner fulltext (pdf) av Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling
Alla publikationer
Artiklar i tidskrift
Ingår i Journal of Steroid Biochemistry and Molecular Biology, 2024
- DOI för Cellular responses to silencing of PDIA3 (protein disulphide-isomerase A3): Effects on proliferation, migration, and genes in control of active vitamin D
- Ladda ner fulltext (pdf) av Cellular responses to silencing of PDIA3 (protein disulphide-isomerase A3): Effects on proliferation, migration, and genes in control of active vitamin D
Ingår i Biochemical and Biophysical Research Communications - BBRC, 2024
- DOI för Crosstalk between 1,25(OH)2-Vitamin D3 and the growth factors EGF and PDGF-BB: Impact on CYP24A1 expression and cell proliferation
- Ladda ner fulltext (pdf) av Crosstalk between 1,25(OH)2-Vitamin D3 and the growth factors EGF and PDGF-BB: Impact on CYP24A1 expression and cell proliferation
PDGF-induced internalisation promotes proteolytic cleavage of PDGFRβ in mesenchymal cells
Ingår i Growth Factors, s. 147-160, 2024
- DOI för PDGF-induced internalisation promotes proteolytic cleavage of PDGFRβ in mesenchymal cells
- Ladda ner fulltext (pdf) av PDGF-induced internalisation promotes proteolytic cleavage of PDGFRβ in mesenchymal cells
Ingår i Nucleic Acids Research, 2024
- DOI för Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling
- Ladda ner fulltext (pdf) av Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling
Purification of DNA oligonucleotides to improve hybridization chain reaction performance
Ingår i New Biotechnology, s. 33-40, 2023
- DOI för Purification of DNA oligonucleotides to improve hybridization chain reaction performance
- Ladda ner fulltext (pdf) av Purification of DNA oligonucleotides to improve hybridization chain reaction performance
Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Ingår i Nature Communications, 2023
- DOI för Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
- Ladda ner fulltext (pdf) av Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Ingår i Biochemical and Biophysical Research Communications - BBRC, s. 195-201, 2023
- DOI för Activated EGFR and PDGFR internalize in separate vesicles and downstream AKT and ERK1/2 signaling are differentially impacted by cholesterol depletion
- Ladda ner fulltext (pdf) av Activated EGFR and PDGFR internalize in separate vesicles and downstream AKT and ERK1/2 signaling are differentially impacted by cholesterol depletion
A method for Boolean analysis of protein interactions at a molecular level
Ingår i Nature Communications, 2022
- DOI för A method for Boolean analysis of protein interactions at a molecular level
- Ladda ner fulltext (pdf) av A method for Boolean analysis of protein interactions at a molecular level
Ingår i Cellular Signalling, 2022
- DOI för Differential impact of lipid raft depletion on platelet-derived growth factor (PDGF)-induced ERK1/2 MAP-kinase, SRC and AKT signaling
- Ladda ner fulltext (pdf) av Differential impact of lipid raft depletion on platelet-derived growth factor (PDGF)-induced ERK1/2 MAP-kinase, SRC and AKT signaling
Ingår i Analytical Chemistry, s. 1842-1850, 2021
Ingår i Mutation research. Genetic toxicology and environmental mutagenesis, 2020
Ingår i Molecular Systems Design & Engineering, s. 1058-1065, 2019
- DOI för Optimization of proximity-dependent initiation of hybridization chain reaction for improved performance
- Ladda ner fulltext (pdf) av Optimization of proximity-dependent initiation of hybridization chain reaction for improved performance
Ingår i Journal of Experimental Biology, 2019
Dynamin inhibitors impair platelet-derived growth factor beta-receptor dimerization and signaling
Ingår i Experimental Cell Research, s. 69-79, 2019
- DOI för Dynamin inhibitors impair platelet-derived growth factor beta-receptor dimerization and signaling
- Ladda ner fulltext (pdf) av Dynamin inhibitors impair platelet-derived growth factor beta-receptor dimerization and signaling
Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes
Ingår i Scientific Reports, 2018
- DOI för Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes
- Ladda ner fulltext (pdf) av Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes
Insufficient antibody validation challenges oestrogen receptor beta research
Ingår i Nature Communications, 2017
- DOI för Insufficient antibody validation challenges oestrogen receptor beta research
- Ladda ner fulltext (pdf) av Insufficient antibody validation challenges oestrogen receptor beta research
Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia
Ingår i Scientific Reports, s. 1-9, 2017
- DOI för Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia
- Ladda ner fulltext (pdf) av Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia
The protein kinase LKB1 negatively regulates bone morphogenetic protein receptor signaling
Ingår i Oncotarget, s. 1120-1143, 2016
- DOI för The protein kinase LKB1 negatively regulates bone morphogenetic protein receptor signaling
- Ladda ner fulltext (pdf) av The protein kinase LKB1 negatively regulates bone morphogenetic protein receptor signaling
Ingår i Scientific Reports, 2016
- DOI för Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout
- Ladda ner fulltext (pdf) av Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout
Ingår i Molecular & Cellular Proteomics, s. 1848-1856, 2016
Ingår i Haematologica, s. 668-669, 2016
Antagonists of IGF: Vitronectin Interactions Inhibit IGF-I-Induced Breast Cancer Cell Functions
Ingår i Molecular Cancer Therapeutics, s. 1602-1613, 2016
Ingår i British journal of virology, s. 11-23, 2016
Crosstalk between Hippo and TGF beta: Subcellular Localization of YAP/TAZ/Smad Complexes
Ingår i Journal of Molecular Biology, s. 3407-3415, 2015
Ingår i Scientific Reports, 2015
Closing in on life - proximity dependent methods for life sciences
Ingår i Oncotarget, s. 17867-17868, 2015
Proximity-dependent initiation of hybridization chain reaction
Ingår i Nature Communications, 2015
- DOI för Proximity-dependent initiation of hybridization chain reaction
- Ladda ner fulltext (pdf) av Proximity-dependent initiation of hybridization chain reaction
Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia
Ingår i Journal of Experimental Medicine, s. 833-843, 2015
- DOI för Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia
- Ladda ner fulltext (pdf) av Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia
E-cadherin can limit the transforming properties of activating beta-catenin mutations
Ingår i EMBO Journal, s. 2321-2333, 2015
Ingår i Molecular Oncology, s. 503-512, 2015
Ingår i PLOS ONE, 2014
- DOI för Fine-Tuning of Smad Protein Function by Poly(ADP-Ribose) Polymerases and Poly(ADP-Ribose) Glycohydrolase during Transforming Growth Factor β Signaling
- Ladda ner fulltext (pdf) av Fine-Tuning of Smad Protein Function by Poly(ADP-Ribose) Polymerases and Poly(ADP-Ribose) Glycohydrolase during Transforming Growth Factor β Signaling
Ingår i Blood, 2014
Ingår i Nature Protocols, s. 355-372, 2013
Parallel Visualization of Multiple Protein Complexes in Individual Cells in Tumor Tissue
Ingår i Molecular & Cellular Proteomics, s. 1563-1571, 2013
Ingår i PLOS ONE, 2013
- DOI för Association of the Protein-Tyrosine Phosphatase DEP-1 with Its Substrate FLT3 Visualized by In Situ Proximity Ligation Assay
- Ladda ner fulltext (pdf) av Association of the Protein-Tyrosine Phosphatase DEP-1 with Its Substrate FLT3 Visualized by In Situ Proximity Ligation Assay
Ingår i Oncogene, s. 3606-3615, 2013
Ingår i New Biotechnology, s. 144-152, 2013
Ingår i European Journal of Human Genetics, s. 301-309, 2013
Ingår i Journal of Pathology, s. 705-718, 2013
Ingår i Journal of Cellular and Molecular Medicine, s. 1474-1484, 2012
Ingår i Journal of Pathology, s. 378-390, 2012
Visualising individual sequence-specific protein-DNA interactions in situ
Ingår i New Biotechnology, s. 589-598, 2012
Ingår i Arteriosclerosis, Thrombosis and Vascular Biology, s. 1255-1263, 2012
Ingår i Molecular & Cellular Proteomics, 2012
Ingår i PLOS ONE, 2011
Ingår i Cytometry Part A, s. 518-527, 2011
Ingår i International Journal of Cancer, s. 1981-1988, 2011
Increasing the dynamic range of in situ PLA
Ingår i Nature Methods, s. 892-893, 2011
In situ proximity ligation assay for microscopy and flow cytometry
Ingår i Current Protocols in Cytometry, 2011
ADP-Ribosylation Factor 6 Mediates E-Cadherin Recovery by Chemical Chaperones
Ingår i PLOS ONE, 2011
Western Blotting via Proximity Ligation for High Performance Protein Analysis
Ingår i Molecular & Cellular Proteomics, 2011
VEGF receptor 2/-3 heterodimers detected in situ by proximity ligation on angiogenic sprouts
Ingår i EMBO Journal, s. 1377-1388, 2010
Ingår i Molecular & Cellular Proteomics, s. 178-183, 2010
Ingår i PLoS biology, 2010
Ingår i Glycobiology, s. 199-206, 2010
Single-cell analyses of protein activity by in situ proximity ligation
Ingår i Journal of Biotechnology, 2010
In situ detection and genotyping of individual mRNA molecules
Ingår i Nature Methods, s. 395-397, 2010
A follicular dendritic cell line promotes somatic hypermutations in Ramos cells in vitro
Ingår i Scandinavian Journal of Immunology, s. 70-71, 2009
Ingår i Cytometry: Part A, s. 833-839, 2009
Platelet-derived growth factor receptor expression and activation in choroid plexus tumors
Ingår i American Journal of Pathology, s. 1631-1637, 2009
Ingår i Human Molecular Genetics, s. 2802-2812, 2009
Ingår i Methods, s. 227-32, 2008
Ingår i Blood, s. 3838-3848, 2008
Novel and highly recurrent chromosomal alterations in Sézary syndrome
Ingår i Cancer Research, s. 2689-2698, 2008
Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 2427-2432, 2008
Ingår i European Journal of Haematology, s. 218-225, 2008
Ligation-based molecular tools for lab-on-a-chip devices
Ingår i New Biotechnology, s. 42-8, 2008
Establishment of a cell line from a chemotherapy resistant diffuse large B-cell lymphoma
Ingår i Leukemia and Lymphoma, s. 1038-1041, 2007
Ingår i Molecular & Cellular Proteomics, s. 1500-1509, 2007
Ingår i Leukemia and Lymphoma, s. 2221-2232, 2007
Direct observation of individual endogenous protein complexes in situ by proximity ligation
Ingår i Nature Methods, s. 995-1000, 2006
Thermoplastic microfluidic platform for single-molecule detection, cell culture and actuation
Ingår i Analytical Chemistry, s. 7122-30, 2005
c-Myc associates with ribosomal DNA and activates RNA polymerase I transcription.
Ingår i Nat Cell Biol, s. 303-10, 2005
Ingår i Haematologica, s. 465-9, 2005
Ingår i Journal of Molecular Recognition, s. 194-7, 2004
Ingår i Blood, s. 2879-85, 2004
Ingår i Leukemia Res, s. 1043-1051, 2004
Differentiation-associated redox-regulation in human B cell lines from stemcell/pro-B to plasma cell
Ingår i Immunology Letters, s. 83-89, 2004
Padlock and proximity probes for in situ and array-based analyses: tools for the post genomic era
Ingår i Comparative and functional genomics, s. 525-30, 2003
Mutated VH genes and preferential VH3-21 use define new subsets of mantle cell lymphoma.
Ingår i Blood, s. 4047-54, 2003
Ingår i Blood, s. 4952-7, 2003
Ingår i Blood, s. 1098-1099, 2002
Polymorphism in the P2X7 receptor gene and survival in chronic lymphocytic leukaemia
Ingår i The Lancet, s. 1935-1939, 2002
Somatically mutated Ig V(H)3-21 genes characterize a new subset of chronic lymphocytic leukemia
Ingår i Blood, s. 2262-2264, 2002
Thioredoxin prolongs survival of B-type chronic lymphocytic leukemia cells
Ingår i Blood, s. 1420-1426, 2000
Ingår i Scand J Immunol, s. 363-70, 1999
Ingår i Scand J Immunol, s. 706-14, 1997
Ingår i Br J Haematol, s. 126-33, 1997
Ingår i Leukemia, s. 1298-304, 1997
Ingår i Br J Haematol, s. 126, 1997
Artiklar, forskningsöversikt
The method developer's guide to oligonucleotide design
Ingår i Expert Review of Proteomics, s. 65-80, 2024
- DOI för The method developer's guide to oligonucleotide design
- Ladda ner fulltext (pdf) av The method developer's guide to oligonucleotide design
Ingår i Current Protocol in Cytometry, 2017
Ingår i Proteomes, 2016
Next-Generation Pathology: Surveillance of Tumor Microecology
Ingår i Journal of Molecular Biology, s. 2013-2022, 2015
Ingår i The EPMA journal, 2012
Molecular tools for companion diagnostics
Ingår i New Biotechnology, s. 634-640, 2012
Proximity ligation assays: a recent addition to the proteomics toolbox
Ingår i Expert Reviews of Proteomics, s. 401-409, 2010
Analysis of Genes, Transcripts, and Proteins via DNA Ligation
Ingår i Annual review of analytical chemistry, s. 215-239, 2009
Proximity ligation assays for sensitive and specific protein analyses.
Ingår i Anal Biochem, s. 2-9, 2005
Ingår i Leuk Lymphoma, s. 221-8, 2004
Kapitel i böcker, delar av antologi
Ingår i Molecular Diagnostics (Third Edition), s. 219-231, Academia Press, 2017
Analysis of protein interactions in situ by proximity ligation assays
Ingår i High-Dimensional Single Cell Analysis, s. 111-26, Springer, 2014
Ingår i Molecular Diagnostics, s. 299-306, Elsevier/Academic Press, 2010
Proximity ligation: a specific and versatile tool for the proteomic era.
Ingår i Genet Eng (N Y)., s. 190, Springer, 2007
Konferensbidrag
Ingår i Oral at microTAS-2004 conference, Lund, Sweden, 2004