| 1. |
- Kanellis, Dimitris C., et al.
(författare)
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The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output
- 2021
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:32
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Tidskriftsartikel (refereegranskat)abstract
- Eukaryotic initiation factor 4A-III (eIF4A3), a core helicase component of the exon junction complex, is essential for splicing, mRNA trafficking, and nonsense-mediated decay processes emerging as targets in cancer therapy. Here, we unravel eIF4A3's tumor-promoting function by demonstrating its role in ribosome biogenesis (RiBi) and p53 (de)regulation. Mechanistically, eIF4A3 resides in nucleoli within the small subunit processome and regulates rRNA processing via R-loop clearance. EIF4A3 depletion induces cell cycle arrest through impaired RiBi checkpoint-mediated p53 induction and reprogrammed translation of cell cycle regulators. Multilevel omics analysis following eIF4A3 depletion pinpoints pathways of cell death regulation and translation of alternative mouse double minute homolog 2 (MDM2) transcript isoforms that control p53. EIF4A3 expression and subnuclear localization among clinical cancer specimens correlate with the RiBi status rendering eIF4A3 an exploitable vulnerability in high-RiBi tumors. We propose a concept of eIF4A3's unexpected role in RiBi, with implications for cancer pathogenesis and treatment.
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| 2. |
- Altun, Mikael
(författare)
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Old-age muscle atrophy : cellular mechanisms and behavioral consequenses
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- With advancing age, humans and rodents alike lose about one third of the skeletal muscle mass. A process referred to as old-age muscle atrophy or sarcopenia. Atrophy is a major contributor to disability and morbidity among elderly adults hence the aim of this thesis is to shed light on the molecular mechanisms underlying old-age associated muscle atrophy and behavioral changes related to age in a rat model. In Paper I, we characterized the growth patterns, survival and behavioral alterations linked to advancing age in the rat. The median survival age was, on average, between 29 30 months for both female and male Sprague Dawley (SD) rats. There was a gradual decline in locomotor activity and explorative behavior associated with age, while disturbances in both coordination and balance did not become evident until later times points. In old age, weight carrying capacity, limb movement and temperature threshold were also impaired. While body weight continues to increase over the better part of the life span of rats, the behavioral changes in old age associated with a decrease in both total body weight and, in particular, muscle mass. Dietary restriction (DR) was found to increase median life span expectancy and impede the development of sarcopenia, and to retard the pace of behavioral aging. In Paper II, we used two-dimensional gel electrophoresis and mass spectrometry techniques to determine changes in protein expression as well as cDNA profiling to assess transcriptional regulations in skeletal muscle of adult and aged male SD rats. Among the highly expressed proteins, thirty-five were differentially expressed in aged muscle. Proteins and mRNA transcripts involved in redox homeostasis and iron load were increased, representing novel components previously not associated with sarcopenia. Iron levels in tissue were elevated in senescence, paralleling an increase in transferrin. Proteins involved in redox homeostasis were found to display a complex pattern of changes involving increases in SOD1 and decreases in SOD2. Together these results suggest that an elevated iron load is a significant component of sarcopenia with a potential to be exploited clinically and that the mitochondria of aged striated muscle may be more vulnerable to radicals produced during cell respiration. Muscle atrophy, in many conditions, shares a common mechanism for up-regulation of the muscle-specific ubiquitin E3-ligases Atrogin-1 and MuRF1. E3-ligases are part of the ubiquitin proteasome system (UPS) utilized for protein degradation during muscle atrophy. In Paper III, we show that Atrogin-1 and MuRF1 are down-regulated in old age-associated muscle atrophy. Our results suggest that this is mediated by AKT-induced inactivation of FOXO4. DR impeded sarcopenia as well as both FOXO4 inactivation and up-regulation of Atrogin-1 and MuRF1 transcripts. Our findings allow us to conclude that sarcopenia is mechanistically different from acute atrophies induced by disuse, disease, and denervation. The 26S proteasome is responsible for most cytosolic proteolysis. Molecules that inhibit or specially tag proteasomes are helpful tools for analysis of the UPS. In Paper IV, we present a new class of proteasome inhibitors, considerably extended in comparison to the commonly used fluorescent substrates and peptide-based inhibitors. Modification of the most active compound, Ada-Ahx3L3VS, capable of proteasome inhibition in living cells, afforded a new set of radio- and affinity labels. N-terminal extension of peptide vinyl sulfones was found to have a profound influence on both their efficacy and selectivity as proteasome inhibitors. Results demonstrated that such extensions greatly enhanced inhibition and largely obliterated their selectivity towards individual catalytic activities. The role of the UPS in aging-related muscle atrophy is highly controversial. In Paper V, we showed an accumulation of assembled proteasome particles with a corresponding increase in both proteasomal activity and protein degradation in old age muscle atrophy. This was accompanied by a wide range of UPS enzyme-regulation, including an increase in the activity of deubiquitylating enzymes. The accumulation of proteasomes was found to correlate well with muscle wasting. Both the accumulation of proteasome particles as well as the progression of muscle atrophy, were impeded when the normal pattern of aging was challenged by DR. In contrast to many conditions with UPS-associated muscle catabolism, the accumulation of proteasomes during senile muscle atrophy is not caused by transcriptional induction, but rather by decreases in their degradation. The lysosomal pathway is a candidate for degrading proteasomes. In Paper V, we demonstrated that impaired lysosomal function, achieved through chloroquine treatment, induced accumulation of proteasomes in adult rats. This emphasizes the existence of a functional link between the lysosomal pathway and the UPS suggesting that a decline in lysosomal function may contribute to increased proteasomal proteolysis in old-age skeletal muscle atrophy.
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| 3. |
- Azimi, Alireza, et al.
(författare)
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Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors
- 2018
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Ingår i: Molecular Systems Biology. - : EMBO. - 1744-4292. ; 14:3
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Tidskriftsartikel (refereegranskat)abstract
- Novel therapies are undergoing clinical trials, for example, the Hsp90 inhibitor, XL888, in combination with BRAF inhibitors for the treatment of therapy-resistant melanomas. Unfortunately, our data show that this combination elicits a heterogeneous response in a panel of melanoma cell lines including PDX-derived models. We sought to understand the mechanisms underlying the differential responses and suggest a patient stratification strategy. Thermal proteome profiling (TPP) identified the protein targets of XL888 in a pair of sensitive and unresponsive cell lines. Unbiased proteomics and phosphoproteomics analyses identified CDK2 as a driver of resistance to both BRAF and Hsp90 inhibitors and its expression is regulated by the transcription factor MITF upon XL888 treatment. The CDK2 inhibitor, dinaciclib, attenuated resistance to both classes of inhibitors and combinations thereof. Notably, we found that MITF expression correlates with CDK2 upregulation in patients; thus, dinaciclib would warrant consideration for treatment of patients unresponsive to BRAF-MEK and/or Hsp90 inhibitors and/or harboring MITF amplification/overexpression.
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| 4. |
- Boström, Johan, et al.
(författare)
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Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 12:12
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Tidskriftsartikel (refereegranskat)abstract
- The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchro-nized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development.
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| 5. |
- Gad, Helge, et al.
(författare)
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MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool
- 2014
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 508:7495, s. 215-221
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Tidskriftsartikel (refereegranskat)abstract
- Cancers have dysfunctional redox regulation resulting in reactive oxygen species production, damaging both DNA and free dNTPs. The MTH1 protein sanitizes oxidized dNTP pools to prevent incorporation of damaged bases during DNA replication. Although MTH1 is non-essential in normal cells, we show that cancer cells require MTH1 activity to avoid incorporation of oxidized dNTPs, resulting in DNA damage and cell death. We validate MTH1 as an anticancer target in vivo and describe small molecules TH287 and TH588 as first-in-class nudix hydrolase family inhibitors that potently and selectively engage and inhibit the MTH1 protein in cells. Protein co-crystal structures demonstrate that the inhibitors bindin the active site of MTH1. The inhibitors cause incorporation of oxidized dNTPs in cancer cells, leading to DNA damage, cytotoxicity and therapeutic responses in patient-derived mouse xenografts. This study exemplifies the non-oncogene addiction concept for anticancer treatment and validates MTH1 as being cancer phenotypic lethal.
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| 6. |
- Grönholdt-Klein, Max, et al.
(författare)
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Muscle atrophy and regeneration associated with behavioural loss and recovery of function after sciatic nerve crush
- 2019
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Ingår i: Acta Physiologica. - : John Wiley & Sons. - 1748-1708 .- 1748-1716. ; 227:3
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Tidskriftsartikel (refereegranskat)abstract
- Aim To resolve timing and coordination of denervation atrophy and the re-innervation recovery process to discern correlations indicative of common programs governing these processes. Methods Female Sprague-Dawley (SD) rats had a unilateral sciatic nerve crush. Based on longitudinal behavioural observations, the triceps surae muscle was analysed at different time points post-lesion. Results Crush results in a loss of muscle function and mass (-30%) followed by a recovery to almost pre-lesion status at 30 days post-crush (dpc). There was no loss of fibres nor any significant change in the number of nuclei per fibre but a shift in fibres expressing myosins I and II that reverted back to control levels at 30 dpc. A residual was the persistence of hybrid fibres. Early on a CHNR -epsilon to -gamma switch and a re-expression of embryonic MyHC showed as signs of denervation. Foxo1, Smad3, Fbxo32 and Trim63 transcripts were upregulated but not Myostatin, InhibinA and ActivinR2B. Combined this suggests that the mechanism instigating atrophy provides a selectivity of pathway(s) activated. The myogenic differentiation factors (MDFs: Myog, Myod1 and Myf6) were upregulated early on suggesting a role also in the initial atrophy. The regulation of these transcripts returned towards baseline at 30 dpc. The examined genes showed a strong baseline covariance in transcript levels which dissolved in the response to crush driven mainly by the MDFs. At 30 dpc the naive expression pattern was re-established. Conclusion Peripheral nerve crush offers an excellent model to assess and interfere with muscle adaptions to denervation and re-innervation.
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| 7. |
- Herr, Patrick, et al.
(författare)
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Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics
- 2020
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Ingår i: Molecular & Cellular Proteomics. - : Elsevier BV. - 1535-9476 .- 1535-9484. ; 19:4, s. 608-623
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Tidskriftsartikel (refereegranskat)abstract
- The cell cycle is a highly conserved process involving the coordinated separation of a single cell into two daughter cells. To relate transcriptional regulation across the cell cycle with oscillatory changes in protein abundance and activity, we carried out a proteome- and phospho-proteome-wide mass spectrometry profiling. We compared protein dynamics with gene transcription, revealing many transcriptionally regulated G2 mRNAs that only produce a protein shift after mitosis. Integration of CRISPR/Cas9 survivability studies further highlighted proteins essential for cell viability. Analyzing the dynamics of phosphorylation events and protein solubility dynamics over the cell cycle, we characterize predicted phospho-peptide motif distributions and predict cell cycle-dependent translocating proteins, as exemplified by the S-adenosylmethionine synthase MAT2A. Our study implicates this enzyme in translocating to the nucleus after the G1/S-checkpoint, which enables epigenetic histone methylation maintenance during DNA replication. Taken together, this data set provides a unique integrated resource with novel insights on cell cycle dynamics.
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| 8. |
- Orban, Istvan, 1980-, et al.
(författare)
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Experimental dielectronic recombination rate coefficientsfor Na-like S VI and Na-like Ar VIII
- 2009
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 498, s. 909-914
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Tidskriftsartikel (refereegranskat)abstract
- Aims. Absolute recombination rate coefficients for two astrophysically relevant Na-like ions are presented.Methods. Recombination rate coefficients of S vi and Ar viii are determined from merged-beam type experiments at the CRYRINGelectron cooler. Calculated rate coefficients are used to account for recombination into states that are field-ionized and therefore notdetected in the experiment.Results. Dielectronic recombination rate coefficients were obtained over an energy range covering Δ n = 0 core excitations. ForNa-like Ar a measurement was also performed over the Δn = 1 type of resonances. In the low-energy part of the Ar viii spectrum,enhancements of more than one order of magnitude are observed as compared to the calculated radiative recombination. The plasmarecombination rate coefficients of the two Na-like ions are compared with calculated results from the literature. In the 103−104 Krange, large discrepancies are observed between calculated plasma rate coefficients and our data. At higher temperatures, above105 K, in the case of both ions our data is 30% higher than two calculated plasma rate coefficients, other data from the literaturehaving even lower values.Conclusions. Discrepancies below 104 K show that at such temperatures even state-of-the-art calculations yield plasma rate coefficientsthat have large uncertainties. The main reason for these uncertainties are the contributions from low-energy resonances, whichare difficult to calculate accurately.
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| 9. |
- Visnes, Torkild, et al.
(författare)
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Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation
- 2018
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 362:6416, s. 834-
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Tidskriftsartikel (refereegranskat)abstract
- The onset of inflammation is associated with reactive oxygen species and oxidative damage to macromolecules like 7,8-dihydro-8-oxoguanine (8-oxoG) in DNA. Because 8-oxoguanine DNA glycosylase 1 (OGG1) binds 8-oxoG and because Ogg1-deficient mice are resistant to acute and systemic inflammation, we hypothesized that OGG1 inhibition may represent a strategy for the prevention and treatment of inflammation. We developed TH5487, a selective active-site inhibitor of OGG1, which hampers OGG1 binding to and repair of 8-oxoG and which is well tolerated by mice. TH5487 prevents tumor necrosis factor-alpha-induced OGG1-DNA interactions at guanine-rich promoters of proinflammatory genes. This, in turn, decreases DNA occupancy of nuclear factor kappa B and proinflammatory gene expression, resulting in decreased immune cell recruitment to mouse lungs. Thus, we present a proof of concept that targeting oxidative DNA repair can alleviate inflammatory conditions in vivo.
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| 10. |
- Visnes, Torkild, et al.
(författare)
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Targeting OGG1 arrests cancer cell proliferation by inducing replication stress
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:21, s. 12234-12251
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Tidskriftsartikel (refereegranskat)abstract
- Altered oncogene expression in cancer cells causes loss of redox homeostasis resulting in oxidative DNA damage, e.g. 8-oxoguanine (8-oxoG), repaired by base excision repair (BER). PARP1 coordinates BER and relies on the upstream 8-oxoguanine-DNA glycosylase (OGG1) to recognise and excise 8-oxoG. Here we hypothesize that OGG1 may represent an attractive target to exploit reactive oxygen species (ROS) elevation in cancer. Although OGG1 depletion is well tolerated in non-transformed cells, we report here that OGG1 depletion obstructs A3 T-cell lymphoblastic acute leukemia growth in vitro and in vivo, validating OGG1 as a potential anti-cancer target. In line with this hypothesis, we show that OGG1 inhibitors (OGG1i) target a wide range of cancer cells, with a favourable therapeutic index compared to non-transformed cells. Mechanistically, OGG1i and shRNA depletion cause S-phase DNA damage, replication stress and proliferation arrest or cell death, representing a novel mechanistic approach to target cancer. This study adds OGG1 to the list of BER factors, e.g. PARP1, as potential targets for cancer treatment.
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