| 1. |
- Atteia, A., et al.
(författare)
-
Structure, organization and expression of the genes encoding mitochondrial cytochrome c1 and the Rieske iron-sulfur protein in Chlamydomonas reinhardtii
- 2003
-
Ingår i: Molecular Genetics and Genomics. - : Springer Verlag. - 1617-4615 .- 1617-4623. ; 268:5, s. 637-644
-
Tidskriftsartikel (refereegranskat)abstract
- The sequence and organization of the Chlamydomonas reinhardtii genes encoding cytochrome c 1 ( Cyc1) and the Rieske-type iron-sulfur protein ( Isp), two key nucleus-encoded subunits of the mitochondrial cytochrome bc 1 complex, are presented. Southern hybridization analysis indicates that both Cyc1 and Isp are present as single-copy genes in C. reinhardtii. The Cyc1 gene spans 6404 bp and contains six introns, ranging from 178 to 1134 bp in size. The Isp gene spans 1238 bp and contains four smaller introns, ranging in length from 83 to 167 bp. In both genes, the intron/exon junctions follow the GT/AG rule. Internal conserved sequences were identified in only some of the introns in the Cyc1 gene. The levels of expression of Isp and Cyc1 genes are comparable in wild-type C. reinhardtii cells and in a mutant strain carrying a deletion in the mitochondrial gene for cytochrome b (dum-1). Nevertheless, no accumulation of the nucleus-encoded cytochrome c 1 or of core proteins I and II was observed in the membranes of the respiratory mutant. These data show that, in the green alga C. reinhardtii, the subunits of the cytochrome bc1 complex fail to assemble properly in the absence of cytochrome b.
|
|
| 2. |
- Kleftogiannis, Dimitrios, et al.
(författare)
-
Identification of single nucleotide variants using position-specific error estimation in deep sequencing data.
- 2019
-
Ingår i: BMC medical genomics. - : Springer Science and Business Media LLC. - 1755-8794. ; 12:1
-
Tidskriftsartikel (refereegranskat)abstract
- Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling. However, identification of SNVs using deep sequencing data is a challenging computational problem as different sequencing artifacts limit the analytical sensitivity of SNV detection, especially at low variant allele frequencies (VAFs).To address the problem of relatively high noise levels in amplicon-based deep sequencing data (e.g. with the Ion AmpliSeq technology) in the context of SNV calling, we have developed a new bioinformatics tool called AmpliSolve. AmpliSolve uses a set of normal samples to model position-specific, strand-specific and nucleotide-specific background artifacts (noise), and deploys a Poisson model-based statistical framework for SNV detection.Our tests on both synthetic and real data indicate that AmpliSolve achieves a good trade-off between precision and sensitivity, even at VAF below 5% and as low as 1%. We further validate AmpliSolve by applying it to the detection of SNVs in 96 circulating tumor DNA samples at three clinically relevant genomic positions and compare the results to digital droplet PCR experiments.AmpliSolve is a new tool for in-silico estimation of background noise and for detection of low frequency SNVs in targeted deep sequencing data. Although AmpliSolve has been specifically designed for and tested on amplicon-based libraries sequenced with the Ion Torrent platform it can, in principle, be applied to other sequencing platforms as well. AmpliSolve is freely available at https://github.com/dkleftogi/AmpliSolve .
|
|
| 3. |
- Nissen, Lars Johan, et al.
(författare)
-
Angiogenic factors FGF2 and PDGF-BB synergistically promote murine tumor neovascularization and metastasis.
- 2007
-
Ingår i: The Journal of clinical investigation. - 0021-9738. ; 117:10, s. 2766-77
-
Tidskriftsartikel (refereegranskat)abstract
- Tumors produce multiple growth factors, but little is known about the interplay between various angiogenic factors in promoting tumor angiogenesis, growth, and metastasis. Here we show that 2 angiogenic factors frequently upregulated in tumors, PDGF-BB and FGF2, synergistically promote tumor angiogenesis and pulmonary metastasis. Simultaneous overexpression of PDGF-BB and FGF2 in murine fibrosarcomas led to the formation of high-density primitive vascular plexuses, which were poorly coated with pericytes and VSMCs. Surprisingly, overexpression of PDGF-BB alone in tumor cells resulted in dissociation of VSMCs from tumor vessels and decreased recruitment of pericytes. In the absence of FGF2, capillary ECs lacked response to PDGF-BB. However, FGF2 triggers PDGFR-alpha and -beta expression at the transcriptional level in ECs, which acquire hyperresponsiveness to PDGF-BB. Similarly, PDGF-BB-treated VSMCs become responsive to FGF2 stimulation via upregulation of FGF receptor 1 (FGFR1) promoter activity. These findings demonstrate that PDGF-BB and FGF2 reciprocally increase their EC and mural cell responses, leading to disorganized neovascularization and metastasis. Our data suggest that intervention of this non-VEGF reciprocal interaction loop for the tumor vasculature could be an important therapeutic target for the treatment of cancer and metastasis.
|
|
| 4. |
- Uramoto, Hidetaka, et al.
(författare)
-
p73 competes with co-activators and recruits histone deacetylase to NF-Y in the repression of PDGF beta-receptor.
- 2004
-
Ingår i: Journal of cell science. - : The Company of Biologists. - 0021-9533 .- 1477-9137. ; 117:Pt 22, s. 5323-31
-
Tidskriftsartikel (refereegranskat)abstract
- We investigated mechanisms of the p73alpha-mediated repression of the platelet-derived growth factor beta-receptor (PDGFRB) promoter caused by its interaction with NF-Y. Treatment of cells with the histone deacetylase (HDAC) inhibitor, Trichostatin A, increases PDGFRB promoter activity through the CCAAT motif and counteracts the repression caused by p73alpha. Activation of the PDGFRB promoter by the co-activator p300 also occurs through the CCAAT motif. Expression of p73alpha counteracts both p300- and P/CAF-mediated activation of the PDGFRB promoter, and expression of p300 or P/CAF attenuates the p73alpha-mediated repression of the promoter activity. In concordance, p73alpha decreases the p300-mediated acetylation of NF-YC, p300 competes with p73alpha for binding NF-YB, and P/CAF competes with p73alpha for binding NF-YB and NF-YC. Furthermore, p73alpha, but not the oncogenic DeltaNp73alpha, binds directly to HDAC1. We performed chromatin immunoprecipitation with antibodies against p73, DeltaNp73, NFYB, p300 and HDAC1 at different periods after serum stimulation in serum-starved NIH3T3 cells. A marked decrease of DeltaNp73, NF-YB and p300 was detected 6 hours after serum stimulation when the expression of PDGFRB decreased. Conversely, HDAC1 was found bound at its maximum and the anti-p73 detecting both TAp73 and DeltaNp73 was found at all time points, indicating that p73, but not DeltaNp73, remains bound at this time. Double immunofluorescence staining of TAp73 and HDAC1 revealed that both of these molecules exist in the nucleus at this time point, supporting the presence of endogenous interaction. These results suggest that p73 and DeltaNp73 behave as physiological regulators for the transcription of the PDGFRB promoter.
|
|
| 5. |
- Uramoto, Hidetaka, et al.
(författare)
-
pRb, Myc and p53 are critically involved in SV40 large T antigen repression of PDGF beta-receptor transcription.
- 2004
-
Ingår i: Journal of cell science. - : The Company of Biologists. - 0021-9533 .- 1477-9137. ; 117:Pt 17, s. 3855-65
-
Tidskriftsartikel (refereegranskat)abstract
- The expression of the PDGF beta-receptor is tightly regulated during a normal cell cycle. c-Myc and p73alpha repress transcription of the receptor through interaction with NF-Y. In ST15A cells which stably express the temperature-sensitive SV40 large T antigen (LT) the receptor expression and ligand binding decreased under the permissive condition. Transient expression of the LT, but not small t, decreased the endogenous receptor expression at mRNA and protein levels in NIH3T3 cells but not in the myc-null HO15.19 cells. The wild-type LT, but not the various pRb or p53 binding defective LT mutants, represses the PDGF beta-receptor promoter activity. Moreover, the inability of the LT-mediated repression in the myc-null cells, the Rb-null 3T3 cells, and the Saos-2 cells lacking pRb and p53, indicates that Myc, pRb and p53 are all necessary elements. PDGF beta-receptor promoter-luciferase assays revealed that the CCAAT motif is important for the repression. Furthermore, p53 was found to increase the promoter activity mainly via the upstream Sp1 binding sites together with the CCAAT motif in the NIH 3T3 cells. This was confirmed by Schneider's Drosophila line (SL2) cells deficient in both endogenous NF-Y and Sp1. Chromatin immunoprecipitation using ST15A cells revealed that both LT and p53 bound the PDGF beta-receptor promoter and the binding of p53 diminished when LT was expressed in the permissive condition. However, LT binds the promoter in the absence of pRb and p53 in Saos-2 cells stably expressing LT. These results suggest that LT binds the promoter and interferes with NF-Y and Sp1 to repress it in the presence of Myc, pRb and p53.
|
|
| 6. |
- Wetterskog, Daniel, 1978, et al.
(författare)
-
Dysregulation of platelet-derived growth factor beta-receptor expression by DeltaNp73 in neuroblastoma
- 2009
-
Ingår i: Molecular Cancer Research. - 1541-7786. ; 7:12, s. 2031-2039
-
Tidskriftsartikel (refereegranskat)abstract
- We have previously characterized how p53 family proteins control the transcriptional regulation of the platelet-derived growth factor beta-receptor (PDGFRB) and found that DeltaNp73alpha, acting dominant-negatively to p53 and p73, can upregulate PDGFRB promoter activity. Here, we report that PDGFRB regulation differs between two neuroblastoma cell lines, correlating with the actions of DeltaNp73. We found that PDGFRB was highly expressed in IMR-32 cells, and serum stimulation of IMR-32 cells did not downregulate PDGFRB expression, as seen in SH-SY5Y cells. In IMR-32, DeltaNp73 was found constitutively bound to the PDGFRB promoter, and silencing of DeltaNp73 resulted in repression of PDGFRB promoter activity as well as decreased PDGFRB protein expression. However, the anticancer drug cisplatin, known to stabilize and activate p53 and p73, downregulated PDGFRB expression not only in SH-SY5Y but also in IMR-32. Chromatin immunoprecipitation showed that cisplatin removed DeltaNp73 from the PDGFRB promoter and recruited p53 and p73, leading to binding of histone deacetylase 4. These results suggest a direct role of DeltaNp73 in the constantly enhanced PDGFRB expression seen in tumors.
|
|
| 7. |
- Wetterskog, Daniel, 1978, et al.
(författare)
-
Loss of redness (a*) as a method to measure hemoglobin-mediated lipid oxidation in washed cod mince
- 2004
-
Ingår i: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 52:24, s. 7214-7221
-
Tidskriftsartikel (refereegranskat)abstract
- Instrumental measurement of redness loss (decrease in a* value) was evaluated as a tool to follow hemoglobin (Hb)-mediated lipid oxidation in fish muscle. Two washed cod mince model systems were used (prepared at pH 6.5 and 5.5), both fortified with 15 μmol/kg of trout Hb and adjusted to pH 6.5 and 81% moisture. The rate of oxidation was varied through pH alterations (pH 6.1 and 6.9) and addition of an antioxidative cod muscle press juice. During ice storage, TBARS, painty odor, and a* values were followed. In all “oxidizing” samples, a* values correlated well with TBARS and painty odor development; r = −0.95 and −0.77, respectively. In press juice containing samples, the correlation was lower (0.55 for a* vs TBARS) because there was a slight a* value decrease even in the absence of measurable lipid oxidation. a* values distinguished between “oxidizing” and stable samples within 1 day, before any lipid oxidation products could be chemically detected. It was confirmed in an aqueous phosphate buffer model system that the redness loss corresponded to a buildup of brownish met-Hb at the expense of oxy- and deoxy-Hb. The a* value data were best used as a lipid oxidation index by calculating the rate of decrease (k value) in the “initial phase” of the redness loss (before accumulation of lipid oxidation products) or in the “differentiation phase” (during the exponential raise in TBARS/painty odor). Calibration to lipid oxidation products must, however, be made for each specific sample type. Washing method, pH, Hb-type, etc., all affected both k values and absolute a* readings. Small yellowness (b*) increases also occurred along with a* value losses, possibly the result of polymerized Schiff bases.
|
|
| 8. |
- Wetterskog, Daniel, 1978, et al.
(författare)
-
Mutation profiling of adenoid cystic carcinomas from multiple anatomical sites identifies mutations in the RAS pathway, but no KIT mutations
- 2013
-
Ingår i: Histopathology. - : Wiley. - 0309-0167. ; 62:4, s. 543-550
-
Tidskriftsartikel (refereegranskat)abstract
- Aims The majority of adenoid cystic carcinomas (AdCCs), regardless of anatomical site, harbour the MYB–NFIB fusion gene. The aim of this study was to characterize the repertoire of somatic genetic events affecting known cancer genes in AdCCs. Methods and results DNA was extracted from 13 microdissected breast AdCCs, and subjected to a mutation survey using the Sequenom OncoCarta Panel v1.0. Genes found to be mutated in any of the breast AdCCs and genes related to the same canonical molecular pathways, as well as KIT, a proto-oncogene whose protein product is expressed in AdCCs, were sequenced in an additional 68 AdCCs from various anatomical sites by Sanger sequencing. Using the Sequenom MassARRAY platform and Sanger sequencing, mutations in BRAF and HRAS were identified in three and one cases, respectively (breast, and head and neck). KIT, which has previously been reported to be mutated in AdCCs, was also investigated, but no mutations were identified. Conclusions Our results demonstrate that mutations in genes pertaining to the canonical RAS pathway are found in a minority of AdCCs, and that activating KIT mutations are either absent or remarkably rare in these cancers, and unlikely to constitute a driver and therapeutic target for patients with AdCC.
|
|
| 9. |
- Wetterskog, Daniel, 1978
(författare)
-
Transcriptional Regulation of the Platelet-Derived Growth Factor B-receptor by p53 Family Members
- 2008
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Aims: The platelet-derived growth factor ?-receptor (PDGFRB) is critically involved in embryonic development and has a role in many diseases. In cells, signaling through PDGFRB affects growth, migration and death. The role of PDGFRB in these crucial processes necessitates strict regulation and therefore it is regulated in many ways, including transcription, dephosphorylation, internalization, and degradation. Of these, transcriptional regulation is the least studied. Previously, PDGFRB transcription has been shown to be under the control of the transcription factors nuclear factor y (NF-Y), specificity protein 1 (Sp1) and the p53 family member p73. In the present thesis we investigated the role of p53 family members and their mechanisms for transcriptional regulation of PDGFRB. Results: In search for the mechanism behind p73?-mediated repression of the PDGFRB, we found that p73? competed with histone acetyltransferases for binding to NF-Y. The recruitment of p73? and ?Np73 to the PDGFRB promoter corresponded with PDGFRB expres¬sion. In repression of the PDGFRB promoter, p73 was recruited with the co-repressor HDAC1. Binding of ?Np73 and the co-activator p300, on the other hand, corresponded to PDGFRB promoter induction. Overexpression of the p53 interacting viral large T antigen (LT) in NIH3T3 fibroblasts resulted in repressed PDGFRB promoter activity and decreased expression of PDGFRB protein and mRNA. The same type of overexpression in c-Myc?/? HO15.19 fibroblasts, Rb?/?NIH3T3, and pRb- and p53-lacking osteosarcoma, Saos2 did not repress PDGFRB promoter activity, showing the importance of these molecules for LT-mediated repression of PDGFRB. In order to identify the role of p53, we overexpressed p53 in mouse embryonic fibroblasts (MEF), p53?/? MEF, and Saos2, which induced repression of PDGFRB promoter activity and decreased mRNA and pro¬tein expression. Endogenous p53 activated by mitomycin treatment also downregulated PDGFRB expres¬sion. Experiments showed that p53 could bind the PDGFRB promoter region surrounding the CCAAT-motif. Upon p53 induction, when PDGFRB expression was repressed, p53 and HDAC1 bound the PDGFRB promoter and the co-activator p300 was dismissed. The role of ?Np73 in PDGFRB expression was investigated using the neuroblastoma cell line IMR-32 which had dysregulated PDGFRB expression and SH-SY5Y which had regulated expression. Silencing of ?Np73 repressed PDGFRB promoter activity and protein expression in IMR-32 but not in SH-SY5Y and ?Np73 was constitutively bound to the PDGFRB promoter only in IMR-32. Treatment with the anticancer drug cisplatin decreased PDGFRB protein, mRNA and promoter activity in both cell lines. In IMR-32, cisplatin was found to dismiss ?Np73 and p300 from the PDGFRB promoter and recruit HDAC4. Conclusions: Results presented in this thesis suggest a role for p53 family members in downregulation of PDGFRB expression upon growth stimulation or in response to DNA damage. In addition, we demonstrated that ?Np73 have a role in dysregulated PDGFRB expression. Also, we propose a potential for tyrosine kinase inhibitors in the treatment of neuroblastoma with high ?Np73 and PDGFR expression.
|
|
| 10. |
- Yang, Weiwen, 1967, et al.
(författare)
-
Kinetics of repression by modified p53 on the PDGF beta-receptor promoter.
- 2008
-
Ingår i: International journal of cancer. Journal international du cancer. - : Wiley. - 1097-0215. ; 123:9, s. 2020-30
-
Tidskriftsartikel (refereegranskat)abstract
- Herein, we show that both exogenously transfected and endogenously activated p53 repress promoter activity and expression of PDGFRB. p53 binds the proximal promoter containing the CCAAT motif as examined by EMSA and chromatin immunoprecipitation. However, gradual induction of p53 in tet-onSAOS2 cells resulted in a transient increase of the PDGFRB-promoter activity and its expression. As binding of p53 to the promoter increased, previously bound p73, DeltaNp73, c-Myc, HDAC1 and HDAC4 were dismissed from the repressed promoter, and p300 was recruited. The transient increase of the promoter activity was therefore induced by the release of the p73, Myc and HDACs, previously shown to act as repressors to this promoter. Along with further increase of p53, p300 was replaced by HDAC1 and HDAC4, resulting in decreased PDGFRB expression. For the repression, acetylation of the C-terminal lysines of p53 is important, and both acetyl-K373p53 and methyl-K370p53 became bound to the promoter. The acetyl-K373p53 was accumulated in the nucleus and colocalized with promyelocytic leukemia protein. Mitomycin treatment of MEF induced similar epigenetic modification of p53 and its binding to the promoter chromatin. Addition of a PDGFR tyrosine-kinase inhibitor to p53-inducing tet-onSAOS2 increased the number of apoptotic cells. These results suggest that p53 represses the PDGFRB promoter, facilitating the p53-induced apoptosis, whereas tumor cells with p53 mutation or a high level of DeltaNp73 or Myc could become refractory to the regulation.
|
|
