| 1. |
- Al-Amin, Rasel A., Researcher, 1983-, et al.
(författare)
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Monitoring drug–target interactions through target engagement-mediated amplification on arrays and in situ
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 50:22, s. e129-e129
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Tidskriftsartikel (refereegranskat)abstract
- Drugs are designed to bind their target proteins in physiologically relevant tissues and organs to modulate biological functions and elicit desirable clinical outcomes. Information about target engagement at cellular and subcellular resolution is therefore critical for guiding compound optimization in drug discovery, and for probing resistance mechanisms to targeted therapies in clinical samples. We describe a target engagement-mediated amplification (TEMA) technology, where oligonucleotide-conjugated drugs are used to visualize and measure target engagement in situ, amplified via rolling-circle replication of circularized oligonucleotide probes. We illustrate the TEMA technique using dasatinib and gefitinib, two kinase inhibitors with distinct selectivity profiles. In vitro binding by the dasatinib probe to arrays of displayed proteins accurately reproduced known selectivity profiles, while their differential binding to fixed adherent cells agreed with expectations from expression profiles of the cells. We also introduce a proximity ligation variant of TEMA to selectively investigate binding to specific target proteins of interest. This form of the assay serves to improve resolution of binding to on- and off-target proteins. In conclusion, TEMA has the potential to aid in drug development and clinical routine by conferring valuable insights in drug–target interactions at spatial resolution in protein arrays, cells and in tissues.
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| 2. |
- Al-Amin, Rasel A., 1983-, et al.
(författare)
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Target Engagement-Mediated Amplification for Monitoring Drug-Target Interactions in Situ
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- It is important to determine the localization of drugs or drug candidates at cellular and subcellular resolution in relevant clinical specimens. This is necessary to evaluate drug candidates from early stages of drug development to clinical evaluation of mutations potentially causing resistance to targeted therapy. We describe a technology where oligonucleotide-conjugated drug molecules are used to visualize and measure target engagement in situ via rolling-circle amplification (RCA) of circularized oligonucleotide probes (padlock probes). We established this target engagement-mediated amplification (TEMA) technique using kinase inhibitor precursor compounds, and we applied the assay to investigate target interactions by microscopy in pathology tissue sections and using flow cytometry for blood samples from patients, as well as in commercial arrays including almost half of all human proteins. In the variant proxTEMAtechnique, in situ proximity ligation assays were performed by combining drug-DNA conjugates with antibody-DNA conjugates to specifically reveal drug binding to particular on- or off-targets in pathological tissues sections. In conclusion, the TEMA methods successfully visualize drug-target interaction by experimental and clinically approved kinase inhibitors in situ and with kinases among a large collection of arrayed proteins.
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| 3. |
- Allard, Christina, et al.
(författare)
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Rasbiologiskt språkbruk i statens rättsprocess mot sameby : DN Debatt 2015-06-11
- 2015
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Annan publikation (populärvet., debatt m.m.)abstract
- Statens hantering av forskningsresultat i rättsprocessen med Girjas sameby utgör ett hot mot Sverige som rättsstat och kunskapsnation. Åratal av svensk och internationell forskning underkänns och man använder ett språkbruk som skulle kunna vara hämtat från rasbiologins tid. Nu måste staten ta sitt ansvar och börja agera som en demokratisk rättsstat, skriver 59 forskare.
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| 4. |
- Arvidsson, Daniel, et al.
(författare)
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Neighborhood Walkability, Income, and Hour-by-Hour Physical Activity Patterns.
- 2013
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Ingår i: Medicine & Science in Sports & Exercise. - 1530-0315. ; 45:4, s. 698-705
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: To investigate both the mean daily physical activity and the hour by hour physical activity pattern across the day using accelerometry, and how they are associated with neighborhood walkability and individual income. METHODS: Moderate physical activity (MPA) was assessed by accelerometry in 2,252 adults in the City of Stockholm, Sweden. Neighborhood walkability (residential density, street connectivity, land use mix) was objectively assessed within 1,000m network buffers around the participants´ residence and individual income was self-reported. RESULTS: Living in a high walkability neighborhood was associated with more mean daily MPA compared with living in a low walkability neighborhood on weekdays and weekend days. Hour by hour analyses showed that this association appeared mainly in the afternoon/early evening during weekdays, while it appeared across the middle of the day during weekend days. Individual income was associated with mean daily MPA on weekend days. On weekdays, the hour by hour analyses showed that high income was associated with more MPA around noon and in late afternoon/early evening, while low income was associated with more MPA at the hours before noon and in the early afternoon. During the weekend, high income was more consistently associated with higher MPA. CONCLUSIONS: Hour by hour accelerometry physical activity patterns provides a more comprehensive picture of the associations between neighborhood walkability and individual income and physical activity and the variability of these associations across the day.
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| 5. |
- Björkesten, Johan, et al.
(författare)
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A multiplex platform for digital measurement of circular DNA reaction products
- 2020
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Ingår i: Nucleic Acids Research. - : OXFORD UNIV PRESS. - 0305-1048 .- 1362-4962. ; 48:13
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Tidskriftsartikel (refereegranskat)abstract
- Digital PCR provides high sensitivity and unprecedented accuracy in DNA quantification, but current approaches require dedicated instrumentation and have limited opportunities for multiplexing. Here, we present an isothermal platform for digital enumeration of DNA reaction products in multiplex via standard fluorescence microscopy. Circular DNA strands, which may result from a wide range of molecular detection reactions, are captured on streptavidin-coated surfaces via hybridized biotinylated primers, followed by rolling circle amplification (RCA). The addition of 15% polyethylene glycol 4000 during RCA resulted in uniform, easily recorded reaction products. Immobilized DNA circles were visualized as RCA products with 100% efficiency, as determined by droplet digital PCR. We confirmed previous reports about the influence on RCA by sequence composition and size of RCA templates, and we developed an efficient one-step restaining procedure for sequential multiplexing using toehold-triggered DNA strand displacement. Finally, we exemplify applications of this digital readout platform by demonstrating more than three orders of magnitude improved sensitivity by digital measurement of prostate specific antigen (PSA) (detection threshold similar to 100 pg/l), compared to a commercial enzyme-linked immunosorbent assay (ELISA) with analogue readout (detection threshold similar to 500 ng/l), using the same antibody pair.
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| 6. |
- Björkesten, Johan, et al.
(författare)
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Multiplex digital enumeration of circular DNA molecules on solid supports
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Digital PCR is a detection method with unprecedented accuracy for DNA quantification, but with some limitations in the form of complexity of instrumentation and limited multiplexing. Here we present an isothermal platform for digital enumeration of DNA reaction products in multiplex via standard fluorescence microscopy, to overcome limitations of digital PCR. In this method, sets of small DNA circles, resulting from detection reactions, are captured on a streptavidin-coated surface and subjected to rolling circle amplification (RCA). We found that the addition of 15% polyethylene glycol 4000 to RCA on planar surfaces ensured uniform, easily counted signals, each of which represents an individual reaction product. The DNA circles were immobilized and detected with efficiencies of 50 and 100%, respectively, as determined by droplet digital PCR. We confirmed previous reports about the effect on RCA efficiency by sequence composition and size of the RCA templates at the level of individual amplified molecules, and we developed an efficient one-step de- and re-staining procedure for sequential multiplexing via toehold-triggered DNA strand displacement.
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| 7. |
- Grandin, Ulf, et al.
(författare)
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Allozyme variation at a PGI locus in differently aged populations of Moehringia trinervia (Caryophyllaceae) in a successional area
- 2002
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Ingår i: Nordic Journal of Botany. - : Wiley. - 0107-055X .- 1756-1051. ; 22:3, s. 303-311
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Tidskriftsartikel (refereegranskat)abstract
- We studied genetic effects of the colonisation process during primary succession by analysing allozyme variation at a PGI locus in differently aged populations of Moehringia trinervia, which is a selfing annual with low dispersal ability. The populations studied come from islands and shores created in the 1880s by a drop in the water table of a Swedish lake and from old parts of a large island and of the mainland. The population age is known from five vegetation analyses over a century. We have also analysed the genetic composition of M. trinervia derived from seeds in the soil. Mainland populations had a higher genetic diversity than island populations that were little differentiated and differed genetically from the mainland populations. There was no temporal trend in the distribution of genetic variation on the new islands. The presence of alleles in the extant populations was associated with the proportion of that allele in the seed bank, indicating a main recruitment from the seed bank and not by repeated immigrations. We suggest that some of the new islands were colonised by a few early founders from the mainland. Later colonisation has occurred between adjacent islands, which preserves the founder effect and could explain the uniform, low genetic variation in the island populations
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| 8. |
- Granfeldt, Hans, et al.
(författare)
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The Linkoping-Lund surgical experience with the HeartMate left ventricular assist system
- 1995
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Ingår i: Annals of Thoracic Surgery. - 1552-6259. ; 59:Suppl. 1, s. 52-55
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Tidskriftsartikel (refereegranskat)abstract
- Four transplant candidates fulfilling the Food and Drug Administration criteria for a permanent left ventricular assist device received a pneumatic HeartMate system as a bridge to heart transplantation. All patients survived and were fully rehabilitated at the time of transplantation, which was carried out 2 to 6 months after the initial operation. There were no major complications associated with the procedures. We are impressed by the effectiveness and safety of the device.
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| 9. |
- Hellebö Johanson, Else, 1969, et al.
(författare)
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Early alterations in the postprandial VLDL1 apoB-100 and apoB-48 metabolism in men with strong heredity for type 2 diabetes
- 2004
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Ingår i: J Intern Med. - 0954-6820. ; 255:2, s. 273-9
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: To study the postprandial triglyceride-rich lipoprotein (TRL) metabolism, specifically the concentrations of very low-density lipoproteins (VLDL); from intestine (apoB-48) and liver (apoB-100), in men with normal fasting triglycerides but at increased risk of developing type 2 diabetes. DESIGN: Cross-sectional study. SUBJECTS AND SETTINGS: Sixteen healthy men with at least two first-degree relatives with type 2 diabetes were individually matched with 16 control subjects without known diabetes heredity for: age, body mass index, and fasting triglyceride level. They underwent an 8-h meal tolerance test (919 kcal, 51 g fat) during which lipoproteins were separated by density gradient ultracentrifugation. They were characterized by euglycaemic hyperinsulinaemic clamp, peak VO2, 7-day diet registration and computed tomography. RESULTS: The relatives were, as expected, more insulin resistant than the controls and had increased concentration of postprandial VLDL1 particles (49% higher for VLDL1 apoB-48, P = 0.04 and 21% higher for VLDL1 apoB-100, P = 0.048). The elevation was related to insulin sensitivity, but not to lifestyle and body composition. Moreover, the concentration of postprandial triglycerides in VLDL1 fraction was inversely related to low-density lipoprotein (LDL) size in both relatives (rs = -0.60, P = 0.03) and controls (rs = -0.72, P = 0.004). There were no differences in the concentration of triglycerides or apoB-48 and apoB-100 particles in the other fractions (plasma, chylomicron or VLDL2). CONCLUSION: Increased postprandial concentration of TRLs in the VLDL1 fraction seems to be present at an early stage in the development of diabetes and probably contributes to the excess risk of future coronary events in insulin-resistant men.
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| 10. |
- Johanson, Else H, et al.
(författare)
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Fat distribution, lipid accumulation in the liver, and exercise capacity do not explain the insulin resistance in healthy males with a family history for type 2 diabetes.
- 2003
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Ingår i: The Journal of clinical endocrinology and metabolism. - 0021-972X. ; 88:9, s. 4232-8
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Tidskriftsartikel (refereegranskat)abstract
- To explore the mechanisms for the insulin resistance associated with a family history of type 2 diabetes, we studied 16 healthy men with at least two first-degree relatives with type 2 diabetes and 16 control subjects without known heredity. They were pair-wise matched for age, body mass index, and fasting triglycerides and underwent an oral glucose tolerance test, iv glucose infusion to measure the early insulin secretion, euglycemic hyperinsulinemic clamp, computed tomography scan, 7-d food record, and a cardiopulmonary exercise test to measure peak oxygen uptake. Insulin sensitivity index was 30% lower (P = 0.02) in relatives, compared with controls, but fasting and 2-h blood glucose and first-phase insulin secretion were similar. There were no differences in mean fasting free fatty acid levels, amount of sc or visceral adipose tissue, or fat accumulation in the liver. Dietary intake and peak oxygen uptake were also similar. However, multiple regression analysis of both groups showed that fat in the liver and physical capacity were, like known heredity for type 2 diabetes, independent predictors of insulin sensitivity. Thus, lipid accumulation in the liver and physical capacity are related to insulin sensitivity, but neither of these factors nor the amount and distribution of the body fat can explain the insulin resistance associated with a family history for type 2 diabetes.
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| 11. |
- Lönn, Peter, et al.
(författare)
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Close Encounters : Probing Proximal Proteins in Live or Fixed Cells
- 2017
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Ingår i: TIBS -Trends in Biochemical Sciences. Regular ed.. - : Elsevier BV. - 0968-0004 .- 1362-4326. ; 42:7, s. 504-515
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Forskningsöversikt (refereegranskat)abstract
- The well-oiled machinery of the cellular proteome operates via variable expression, modifications, and interactions of proteins, relaying genomic and transcriptomic information to coordinate cellular functions. In recent years, a number of techniques have emerged that serve to identify sets of proteins acting in close proximity in the course of orchestrating cellular activities. These proximi dependent assays, including BiFC, BioID, APEX, FRET, and isPLA, have opened up new avenues to examine protein interactions in live or fixed cells. We review herein the current status of proximity-dependentin situ techniques. We compare the advantages and limitations of the methods, underlining recent progress and the growing importance of these techniques in basic research, and we discuss their potential as tools for drug development and diagnostics.
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| 12. |
- Lönn, Peter, et al.
(författare)
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High-throughput in situ mapping of phosphorylated protein complexes across the cell cycle and in response to drugs
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Interactions and posttranslational modifications (PTMs) of proteins orchestrate cellular responses to cytokines, drugs or other agents, but it has been difficult to monitor and characterize these dynamic events at high-throughput. Here, we have established a semi-automated system for large-scale in situ proximity ligation assays (isPLA). The protocol combines isPLA in microtiter wells with automated microscopy and computer-based image analysis whereby specific protein phosphorylations and interactions are digitally recorded in cells, along with measurements of morphological features. We demonstrate how this platform can improve analysis of cellular signaling by investigating TGF-b responsive Smad2 linker phosphorylations and complex formations over time and across millions of individual cells. We depict single cell responses in relation to e.g. local cell crowding and cell cycle progression via measurements of DNA content and nuclear size. Finally, we illustrate the application of the protocol for demonstrating drug effects by screening a library of phosphatase inhibitors. In summary, our approach expands the scope for image-based single cell analyses by combining observations of protein interactions and modifications with morphological details of individual cells at high throughput.
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| 13. |
- Lönn, Peter, et al.
(författare)
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Image-based high-throughput mapping of TGF-beta-induced phosphocomplexes at a single-cell level
- 2021
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- To improve our ability to monitor cellular responses to e.g. cytokines or drugs, Lonn et al have developed a semi-automated system for large-scale in situ proximity ligation assays (isPLA) in HaCAT keratinocyte cells. Their approach expands the scope for image-based single cell analyses by combining observations of protein interactions and modifications with morphological details of individual cells at high throughput. Protein interactions and posttranslational modifications orchestrate cellular responses to e.g. cytokines and drugs, but it has been difficult to monitor these dynamic events in high-throughput. Here, we describe a semi-automated system for large-scale in situ proximity ligation assays (isPLA), combining isPLA in microtiter wells with automated microscopy and computer-based image analysis. Phosphorylations and interactions are digitally recorded along with subcellular morphological features. We investigated TGF-beta-responsive Smad2 linker phosphorylations and complex formations over time and across millions of individual cells, and we relate these events to cell cycle progression and local cell crowding via measurements of DNA content and nuclear size of individual cells, and of their relative positions. We illustrate the suitability of this protocol to screen for drug effects using phosphatase inhibitors. Our approach expands the scope for image-based single cell analyses by combining observations of protein interactions and modifications with morphological details of individual cells at high throughput.
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| 14. |
- Lönn, Peter, et al.
(författare)
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PARP-1 attenuates Smad-mediated transcription
- 2010
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Ingår i: Molecular Cell. - : Elsevier BV. - 1097-2765 .- 1097-4164. ; 40:4, s. 521-532
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Tidskriftsartikel (refereegranskat)abstract
- The versatile cytokine transforming growth factor β (TGF-β) regulates cellular growth, differentiation, and migration during embryonic development and adult tissue homeostasis. Activation of TGF-β receptors leads to phosphorylation of Smad2 and Smad3, which oligomerize with Smad4 and accumulate in the nucleus where they recognize gene regulatory regions and orchestrate transcription. Termination of Smad-activated transcription involves Smad dephosphorylation, nuclear export, or ubiquitin-mediated degradation. In an unbiased proteomic screen, we identified poly(ADP-ribose) polymerase-1 (PARP-1) as a Smad-interacting partner. PARP-1 dissociates Smad complexes from DNA by ADP-ribosylating Smad3 and Smad4, which attenuates Smad-specific gene responses and TGF-β-induced epithelial-mesenchymal transition. Thus, our results identify ADP-ribosylation of Smad proteins by PARP-1 as a key step in controlling the strength and duration of Smad-mediated transcription.
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| 15. |
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| 16. |
- Olofsson, Roger, 1978, et al.
(författare)
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Isolated hepatic perfusion as a treatment for uveal melanoma liver metastases (the SCANDIUM trial) : study protocol for a randomized controlled trial
- 2014
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Ingår i: Trials. - : Springer Science and Business Media LLC. - 1745-6215. ; 15, s. 317-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Uveal melanoma is the most common primary intraocular malignancy in adults. Despite successful control of the primary tumor, metastatic disease will ultimately develop in approximately 50% of patients, with the liver being the most common site for metastases. The median survival for patients with liver metastases is between 6 and 12 months, and no treatment has in randomized trials ever been shown to prolong survival. A previous phase II trial using isolated hepatic perfusion (IHP) has suggested a 14-month increase in overall survival compared with a historic control group consisting of the longest surviving patients in Sweden during the same time period (26 versus 12 months). Methods/Design: This is the protocol for a multicenter phase III trial randomizing patients with isolated liver metastases of uveal melanoma to IHP or best alternative care (BAC). Inclusion criteria include liver metastases (verified by biopsy) and no evidence of extra-hepatic tumor manifestations by positron emission tomography-computed tomography (PET-CT). The primary endpoint is overall survival at 24 months, with secondary endpoints including response rate, progression-free survival, and quality of life. The planned sample size is 78 patients throughout five years. Discussion: Patients with isolated liver metastases of uveal melanoma origin have a short expected survival and no standard treatment option exists. This is the first randomized clinical trial to evaluate IHP as a treatment option with overall survival being the primary endpoint.
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| 17. |
- Palming, Jenny, 1975, et al.
(författare)
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Plasma cells and Fc receptors in human adipose tissue--lipogenic and anti-inflammatory effects of immunoglobulins on adipocytes
- 2006
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Ingår i: Biochem Biophys Res Commun. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 343:1, s. 43-8
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Tidskriftsartikel (refereegranskat)abstract
- We have previously reported high immunoglobulin expression in human omental adipose tissue. The aim of this work was to investigate plasma cell density and Fc receptor (FcR) expression in human adipose tissue depots and in vitro effects of immunoglobulins on adipocyte function. Plasma cell density was higher in the visceral compared to the subcutaneous depot (10.0+/-1.56% and 5.2+/-0.98%, respectively, n=20, p<0.05). Microarray analysis revealed expression of four FcR genes in adipose tissue; FCGR2A, FCGR2B, FCER1G, and FCGRT. FCGR2A was highly expressed in adipocytes in both depots and this was verified by immunohistochemistry. Expression of IL-1beta and IL-6 was markedly reduced in adipocytes after incubation with the Fc moiety of immunoglobulin G (Fc) (p<0.01). Furthermore, Fc stimulated adipocyte lipogenesis as potently as insulin (p<0.05), but did not influence lipolysis. In conclusion, immunoglobulins produced by plasma cells in human adipose tissue could influence adipocyte metabolism and cytokine production.
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| 18. |
- Peterzén, Bengt, et al.
(författare)
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Management of patients with end-stage heart disease treated with an implantable left ventricular assist device in a nontransplanting center
- 2000
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Ingår i: Journal of cardiothoracic and vascular anesthesia. - : Elsevier BV. - 1053-0770. ; 14:4, s. 438-443
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To describe the setup of a left ventricular assist device (LVAD) program in a nontransplanting center. Design: A prospective study from February 1993 to June 1999. Setting: A university hospital. Participants: Ten patients, 6 men, with a mean age of 44 years (range 16 to 63 years) and with end-stage heart failure resulting from dilated cardiomyopathy (n = 7) or ischemic heart disease (n = 3). Interventions: The patients received the TCI (Thermo Cardiosystems Inc, Woburn, MA) Heart Mate implantable assist device. Five patients had a pneumatic device, and 5 had an electric device. All except 1 patient with an electric device had the pump for an extended period. Measurements and Main Results: Median time on the ventilator was 6.2 days, and median time in the ICU was 14 days. Significant hemodynamic improvement was observed by echocardiography and invasive monitoring. Milrinone and epinephrine supplemented by prostaglandin E1 were the most commonly used drugs to avoid right-sided heart failure. Nine patients were transplanted after pump therapy of 241 days (median) (range, 56 to 873 days). One patient died because of endovascular infection and septicemia. Infectious complications were frequent, especially when the pump time was extended. Conclusions: The introduction of an LVAD program in a nontransplanting center can be achieved with good results. Intense collaboration with a transplant center is mandatory. The complication rate increased when treatment times were extended.
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| 19. |
- Vandenput, Liesbeth, 1974, et al.
(författare)
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Androgens and Glucuronidated Androgen Metabolites are Associated with Metabolic Risk Factors in Men.
- 2007
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Ingår i: Journal of clinical endocrinology and metabolism. - : The Endocrine Society. - 0021-972X .- 1945-7197. ; 92:11, s. 4130-7
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Tidskriftsartikel (refereegranskat)abstract
- Context: Androgens are associated with metabolic risk factors in men. However, the independent impact of androgens and androgen metabolites on metabolic risk factors in men is unclear. Objective: Our objective was to determine the predictive value of serum levels of androgens and glucuronidated androgen metabolites for metabolic risk factors. Design and Study Subjects: We conducted a population-based study of two Swedish cohorts (1068 young adult and 1001 elderly men). Main Outcome Measures: We measured correlation of serum dihydrotestosterone (DHT), testosterone (T) and glucuronidated androgen metabolites with fat mass, fat distribution, serum lipids and insulin resistance. Results: Both DHT and T were negatively associated with different measures of fat mass in both cohorts (P<0.001). Further statistical analysis indicated that DHT, but not T, was independently negatively associated with different measures of fat mass and insulin resistance (P<0.001). The glucuronidated androgen metabolite androstane-3alpha,17beta-diol-17glucuronide (17G) was independently positively associated with fat mass (P<0.001). Most importantly, the 17G/DHT ratio was strongly correlated, not only with fat mass, but also with central fat distribution, intra-hepatic fat, disturbed lipid profile, insulin resistance and diabetes, explaining a substantial part of the total variance in total body fat (12% in young adult men, 15% in elderly men), the HOMA index (10%) and HDL cholesterol (7%). Conclusion: Our findings demonstrate that 17-glucuronidation of the DHT metabolite androstane-3alpha,17beta-diol is strongly associated with several metabolic risk factors in men. Future longitudinal studies are required to determine the possible impact of the 17G/DHT ratio as a metabolic risk factor in men.
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