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  • DKFZ Publication Database  (2,305)
  • CELL  (2,305)
  • 1
    Keywords: APOPTOSIS ; CANCER ; EXPRESSION ; CELL ; antibody ; IDENTIFICATION ; IMMUNOTHERAPY ; EFFECTOR ; CYTOKINE PRODUCTION ; CCR9
    Abstract: The success of T cell-based cancer immunotherapy is limited by tumor's resistance against killing by cytotoxic T lymphocytes (CTLs). Tumor-immune resistance is mediated by cell surface ligands that engage immune-inhibitory receptors on T cells. These ligands represent potent targets for therapeutic inhibition. So far, only few immune-suppressive ligands have been identified. We here describe a rapid high-throughput siRNA-based screening approach that allows a comprehensive identification of ligands on human cancer cells that inhibit CTL-mediated tumor cell killing. We exemplarily demonstrate that CCR9, which is expressed in many cancers, exerts strong immune-regulatory effects on T cell responses in multiple tumors. Unlike PDL1, which inhibits TCR signaling, CCR9 regulates STAT signaling in T cells, resulting in reduced T-helper-1 cytokine secretion and reduced cytotoxic capacity. Moreover, inhibition of CCR9 expression on tumor cells facilitated immunotherapy of human tumors by tumor-specific T cells in vivo. Taken together, this method allows a rapid and comprehensive determination of immune-modulatory genes in human tumors which, as an entity, represent the immune modulatome' of cancer.
    Type of Publication: Journal article published
    PubMed ID: 25691366
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  • 2
    Keywords: CANCER ; CELL ; CLASSIFICATION ; DIFFERENTIATION ; DEHYDROGENASE ; CEREBRAL BLOOD-VOLUME ; GLIOBLASTOMA ; tumor grade ; GROWTH-FACTOR EXPRESSION ; ONCOMETABOLITE 2-HYDROXYGLUTARATE
    Abstract: The recent identification of IDH mutations in gliomas and several other cancers suggests that this pathway is involved in oncogenesis; however effector functions are complex and yet incompletely understood. To study the regulatory effects of IDH on hypoxia-inducible-factor 1-alpha (HIF1A), a driving force in hypoxia-initiated angiogenesis, we analyzed mRNA expression profiles of 288 glioma patients and show decreased expression of HIF1A targets on a single-gene and pathway level, strong inhibition of upstream regulators such as HIF1A and downstream biological functions such as angio- and vasculogenesis in IDH mutant tumors. Genotype/imaging phenotype correlation analysis with relative cerebral blood volume (rCBV) MRI - a robust and non-invasive estimate of tumor angiogenesis - in 73 treatment-naive patients with low-grade and anaplastic gliomas showed that a one-unit increase in rCBV corresponded to a two-third decrease in the odds for an IDH mutation and correctly predicted IDH mutation status in 88% of patients. Together, these findings (1) show that IDH mutation status is associated with a distinct angiogenesis transcriptome signature which is non-invasively predictable with rCBV imaging and (2) highlight the potential future of radiogenomics (i.e. the correlation between cancer imaging and genomic features) towards a more accurate diagnostic workup of brain tumors.
    Type of Publication: Journal article published
    PubMed ID: 26538165
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  • 3
    Keywords: CELL ; CLINICAL-TRIAL ; RADIATION-THERAPY ; PROGNOSTIC-FACTORS ; OUTCOMES ; reirradiation ; BRONCHOGENIC-CARCINOMA ; PHASE-II TRIAL ; PROTON-BEAM THERAPY ; ACCELERATED RADIOTHERAPY ; SALVAGE ; Post-pneumonectomy ; DATA METAANALYSIS
    Abstract: Background: Treatment options are very limited for patients with lung cancer who experience contralateral central or mediastinal relapse following pneumonectomy. We present results of an accelerated salvage chemoradiotherapy regimen. Methods: Patients with localized contralateral central intrapulmonary or mediastinal relapse after pneumonectomy were offered combined chemoradiotherapy including concurrent weekly cisplatin (25 mg/m2) and accelerated radiotherapy [accelerated fractionated (AF), 60 Gy, 8x2 Gy per week] to reduce time for repopulation. Based on 4D-CT-planning, patients were irradiated using multifield intensity-modulated radiotherapy (IMRT) or helical tomotherapy. Results: Between 10/2011 and 12/2012, seven patients were treated. Initial stages were IIB/IIIA/IIIB: 3/1/3; histopathological subtypes scc/adeno/large cell: 4/1/2. Tumour relapses were located in mediastinal nodal stations in five patients with endobronchial tumour in three patients. The remaining patients had contralateral central tumour relapses. All patients received 60 Gy (AF), six patients received concurrent chemotherapy. Median dose to the remaining contralateral lung, esophagus, and spinal cord was 6.8 (3.3-11.4), 8.0 (5.1-15.5), and 7.6 (2.8-31.2) Gy, respectively. With a median follow-up of 29 [17-32] months, no esophageal or pulmonary toxicity exceeding grade 2 [Common terminology criteria for adverse events (CTC-AE) v. 3] was observed. Median survival was 17.2 months, local in-field control at 12 months 80%. Only two local recurrences were observed, both in combination with out-field metastases. Conclusions: This intensified accelerated chemoradiotherapy schedule was safely applicable and offers a curative chance in these pretreated frail lung cancer patients.
    Type of Publication: Journal article published
    PubMed ID: 25922702
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  • 4
    Keywords: SURVIVAL ; CELL ; polymorphism ; ELEMENTS ; susceptibility loci ; GENOME-WIDE ASSOCIATION ; MODIFIERS ; EXPRESSION SIGNATURE ; CHIP-SEQ ; GENETIC INTERACTION NETWORKS
    Abstract: While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood approach. The association of HMMR rs299290 with breast cancer risk in BRCA1 mutation carriers was confirmed: per-allele hazard ratio (HR) = 1.10, 95% confidence interval (CI) 1.04 - 1.15, p = 1.9 x 10-4 (false discovery rate (FDR)-adjusted p = 0.043). Variation in CSTF1, located next to AURKA, was also found to be associated with breast cancer risk in BRCA2 mutation carriers: rs2426618 per-allele HR = 1.10, 95% CI 1.03 - 1.16, p = 0.005 (FDR-adjusted p = 0.045). Assessment of pairwise interactions provided suggestions (FDR-adjusted pinteraction values 〉 0.05) for deviations from the multiplicative model for rs299290 and CSTF1 rs6064391, and rs299290 and TUBG1 rs11649877 in both BRCA1 and BRCA2 mutation carriers. Following these suggestions, the expression of HMMR and AURKA or TUBG1 in sporadic breast tumors was found to potentially interact, influencing patients' survival. Together, the results of this study support the hypothesis of a causative link between altered function of AURKA-HMMR-TPX2-TUBG1 and breast carcinogenesis in BRCA1/2 mutation carriers.
    Type of Publication: Journal article published
    PubMed ID: 25830658
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  • 5
    Keywords: EXPRESSION ; CELL ; LUNG-CANCER ; TUMORS ; HIGH-FREQUENCY ; UROTHELIAL CARCINOMA ; GENE PROMOTER ; THYROID-CANCER ; WHOLE-GENOME ; DISEASE RECURRENCE
    Abstract: Mutations in the promoter of the telomerase reverse transcriptase (TERT) and fibroblast growth factor receptor 3 (FGFR3) genes constitute the most recurrent somatic alterations in urothelial carcinoma of bladder. In this study, we screened DNA from 327 urothelial bladder carcinomas from well-documented patients, with different stages and grades and known TERT promoter mutational status, for FGFR3 alterations and measured relative telomere length (RTL). Although, the frequency of the TERT promoter mutations was higher than those in FGFR3; however, the alterations at the two loci occurred together more frequently than per chance [Odds ratio (OR) = 4.93, 95% CI = 2.72-8.92, p 〈 0.0001]. While tumors with TERT promoter and FGFR3 mutations had shorter RTL than those without mutations (p 〈 0.0001), the TERT promoter mutations in conjunction with the common allele of the rs2853669 polymorphism defined sub-group of patients with an observed decreased overall survival (OR = 2.15, 95% CI = 1.00-4.61) and increased recurrence in patients with TaG1+TaG2 disease categories (OR = 3.68, 95%CI = 1.12-12.05). The finding of shorter telomeres in tumors with TERT promoter and/or FGFR3 mutations than without mutations implies mechanistic relevance of telomere biology in cancer progression. The observed association with recurrence and survival shows that the TERT promoter mutations can potentially be used as markers to refine selection of patients for different treatments. The overwhelming frequency of the TERT promoter mutations also represents a case for development of an eventual therapeutic target.
    Type of Publication: Journal article published
    PubMed ID: 25809917
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  • 6
    Keywords: brain ; CELL ; DOWN-REGULATION ; REPRESSION ; ASTROCYTIC GLIOMAS
    Abstract: OBJECTIVES: Measuring concentrations of the differentiation-promoting hormone retinoic acid (RA) in glioblastoma tissues would help to understand the reason why RA treatment has been inefficient in clinical trials involving brain tumor patients. Here, we apply a recently established extraction and measurement protocol to screen glioblastoma tissues for the levels of the RA precursor retinol and biologically active RA. Combining this approach with mRNA analyses of 26 tumors and 8 normal brains, we identify a multifaceted disturbance of RA synthesis in glioblastoma, involving multiple aldehyde dehydrogenase 1 family and retinol dehydrogenase enzymes. Through database studies and methylation analyses, we narrow down chromosomal deletions and aberrant promoter hypermethylation as potential mechanisms accounting for these alterations. Employing chromatin immunoprecipitation analyses and cell-culture studies, we further show that chromatin at RA target genes is poised to RA substitution, but most glioblastoma cell cultures are completely resistant to RA treatment. This paradoxical RA response is unrelated to alternative RA signaling through the fatty acid-binding protein 5/peroxisome proliferator-activated receptor delta axis. Our data suggest a multifaceted disturbance of RA synthesis in glioblastoma and contribute to reconsider current RA treatment strategies. GLIA 2015;63:1850-1859.
    Type of Publication: Journal article published
    PubMed ID: 25944104
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  • 7
    Keywords: CELL ; DYNAMICS ; SEQUENCES ; MOVEMENT ; 3D ; SPOTS
    Abstract: Automatic fluorescent particle tracking is an essential task to study the dynamics of a large number of biological structures at a sub-cellular level. We have developed a probabilistic particle tracking approach based on multi-scale detection and two-step multiframe association. The multi-scale detection scheme allows coping with particles in close proximity. For finding associations, we have developed a two-step multi-frame algorithm which is based on a temporally semi-global formulation as well as spatially local and global optimization. In the first step, reliable associations are determined for each particle individually in local neighborhoods. In the second step, the global spatial information over multiple frames is exploited jointly to determine optimal associations. The multi-scale detection scheme and the multi-frame association finding algorithm have been combined with a probabilistic tracking approach based on the Kalman filter. We have successfully applied our probabilistic tracking approach to synthetic as well as real microscopy image sequences of virus particles and quantified the performance. We found that the proposed approach outperforms previous approaches.
    Type of Publication: Journal article published
    PubMed ID: 26208342
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  • 8
    Keywords: EXPRESSION ; CELL ; POPULATION ; TUMORS ; CYCLE ; WOMEN ; NORMAL SERUM CONCENTRATIONS ; INHIBITING SUBSTANCE ; ANTIMULLERIAN HORMONE ; TRIMESTER
    Abstract: PURPOSE: Epithelial ovarian cancers either arise directly from Mullerian-type epithelium or acquire Mullerian characteristics in the course of neoplastic transformation. The anti-Mullerian hormone (AMH) causes regression of Mullerian structures during fetal development in males and has been shown to inhibit the growth of epithelial ovarian cancer. Therefore, we hypothesized that pre-diagnostic serum concentrations of AMH are inversely associated with risk of invasive serous ovarian cancer. METHODS: A case-control study (107 cases, 208 controls) was nested within the population-based Finnish Maternity Cohort (1986-2007). The sample donated during the first trimester of the last pregnancy preceding cancer diagnosis of the case subjects was selected for the study. For each case, two controls, matched on age and date at sampling, as well as parity at sampling and at cancer diagnosis were selected. AMH was measured by a second-generation AMH ELISA. Conditional logistic regression was used to compute odds ratios (OR) and 95 % confidence intervals (CI) for invasive serous ovarian cancer associated with AMH concentrations. RESULTS: Overall AMH concentrations were not associated with risk of invasive serous ovarian cancer (OR 0.93; 95 % CI 0.49-1.77 for top vs. bottom tertile, P trend=0.83). In women older than the median age at sampling (32.7 years), a doubling of AMH was associated with decreased risk (OR 0.69; 95 % CI 0.49-0.96), whereas an increased risk (OR 1.64; 95 % CI 1.06-2.54) was observed in younger women, P homogeneity = 0.002. CONCLUSIONS: In this first prospective investigation, risk of invasive serous ovarian cancer was not associated with pre-diagnostic AMH concentrations overall; however, the association may depend on age at AMH measurement.
    Type of Publication: Journal article published
    PubMed ID: 24562905
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  • 9
    Keywords: CELL ; NETWORKS ; DYNAMICS ; REVEALS ; BEHAVIOR ; ARCHITECTURE ; EPIDERMAL KERATIN FILAMENTS ; MECHANICS ; TRANSMISSION ELECTRON-MICROSCOPY ; TETRAMERIC VIMENTIN
    Abstract: Actin filaments, microtubules, and intermediate filaments (IFs) are central elements of the metazoan cytoskeleton. At the molecular level, the assembly mechanism for actin filaments and microtubules is fundamentally different from that of IFs. The former two types of filaments assemble from globular proteins. By contrast, IFs assemble from tetrameric complexes of extended, half-staggered, and antiparallel oriented coiled-coils. These tetramers laterally associate into unit-length filaments; subsequent longitudinal annealing of unit-length filaments yields mature IFs. In vitro, IFs form open structures without a fixed number of tetramers per cross-section along the filament. Therefore, a central question for the structural biology of IFs is whether individual subunits can dissociate from assembled filaments and rebind at other sites. Using the fluorescently labeled IF-protein vimentin for assembly, we directly observe and quantitatively determine subunit exchange events between filaments as well as with soluble vimentin pools. Thereby we demonstrate that the cross-sectional polymorphism of donor and acceptor filaments plays an important role. We propose that in segments of donor filaments with more than the standard 32 molecules per cross-section, subunits are not as tightly bound and are predisposed to be released from the filament.
    Type of Publication: Journal article published
    PubMed ID: 25517157
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  • 10
    Keywords: ANGIOGENESIS ; EXPRESSION ; CELL ; GENES ; TUMOR PROGRESSION ; PATHOGENESIS ; CHRONIC LYMPHOCYTIC-LEUKEMIA ; MicroRNAs ; MIR-16 FAMILY ; P53 NETWORK
    Abstract: The transcription factor AP4 mediates epithelial-mesenchymal transition (EMT) in colorectal cancer (CRC) but its control in this setting is not fully understood. Here we report the definition of a double-negative feedback loop involving AP4 and miR-15a/16-1 that regulates EMT and metastatic progression. In CRC cells, AP4 was downregulated by DNA damage in a p53-dependent manner. AP4 downregulation by p53 was mediated indirectly by the tumor suppressive microRNAs miR-15a and miR-16-1, which targeted the 3'-UTR of AP4 mRNA, induced mesenchymal-epithelial transition (MET) and promoted CRC cell migration. However, miR-15a/16-1 also acted downstream of p53 to induce MET and limit CRC cell migration. This latter pathway acted as a negative feedback on AP4, the downregulation of which relied upon MET induction by miR-15a/16-1. In tumor xenoplants, ectopic miR-15a/16-1 suppressed formation of lung metastases whereas ectopic AP4 suppressed expression of miR-15a/16-1. In clinical specimens of colorectal cancer, miR-15a levels inversely correlated with AP4 protein levels shown previously to correlate with distant metastasis and poor survival. In summary, our results define a double-negative feedback loop involving miR-15a/16-1 and AP4 that stabilizes epithelial and mesenchymal states, respectively, that may determine metastatic prowess.
    Type of Publication: Journal article published
    PubMed ID: 24285725
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  • 11
    Keywords: EXPRESSION ; CELL ; BREAST-CANCER ; TRANSCRIPTION FACTORS ; PROSTATE-CANCER ; UROTHELIAL CARCINOMA ; PROGNOSTIC-FACTOR ; tissue microarray ; SELF-RENEWAL ; EAU GUIDELINES
    Abstract: About 70% of newly diagnosed cases of bladder cancer are low-stage, low-grade, non muscle-invasive. Standard treatment is transurethral resection. About 60% of the tumors will recur, however, and in part progress to become invasive. Therefore, surveillance cystoscopy is performed after resection. However, in the USA and Europe alone, about 54 000 new patients per year undergo repeated cystoscopies over several years, who do not experience recurrence. Analysing in a pilot study resected tumors from patients with (n = 19) and without local recurrence (n = 6) after a period of 5 years by means of an antibody microarray that targeted 724 cancer-related proteins, we identified 255 proteins with significantly differential abundance. Most are involved in the regulation and execution of apoptosis and cell proliferation. A multivariate classifier was constructed based on 20 proteins. It facilitates the prediction of recurrence with a sensitivity of 80% and a specificity of 100%. As a measure of overall accuracy, the area under the curve value was found to be 91%. After validation in additional sample cohorts with a similarly long follow-up, such a signature could support decision making about the stringency of surveillance or even different treatment options.
    Type of Publication: Journal article published
    PubMed ID: 24610664
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  • 12
    Keywords: EXPRESSION ; CELL ; HEPATOCELLULAR-CARCINOMA ; COMPLEX ; inactivation ; RENAL-CARCINOMA ; GLIOBLASTOMA ; IDH1 ; ONCOMETABOLITE 2-HYDROXYGLUTARATE ; FREQUENT ATRX
    Abstract: Recurrent mutations affecting the histone H3.3 residues Lys27 or indirectly Lys36 are frequent drivers of pediatric high-grade gliomas (over 30 % of HGGs). To identify additional driver mutations in HGGs, we investigated a cohort of 60 pediatric HGGs using whole-exome sequencing (WES) and compared them to 543 exomes from non-cancer control samples. We identified mutations in SETD2, a H3K36 trimethyltransferase, in 15 % of pediatric HGGs, a result that was genome-wide significant (FDR = 0.029). Most SETD2 alterations were truncating mutations. Sequencing the gene in this cohort and another validation cohort (123 gliomas from all ages and grades) showed SETD2 mutations to be specific to high-grade tumors affecting 15 % of pediatric HGGs (11/73) and 8 % of adult HGGs (5/65) while no SETD2 mutations were identified in low-grade diffuse gliomas (0/45). Furthermore, SETD2 mutations were mutually exclusive with H3F3A mutations in HGGs (P = 0.0492) while they partly overlapped with IDH1 mutations (4/14), and SETD2-mutant tumors were found exclusively in the cerebral hemispheres (P = 0.0055). SETD2 is the only H3K36 trimethyltransferase in humans, and SETD2-mutant tumors showed a substantial decrease in H3K36me3 levels (P 〈 0.001), indicating that the mutations are loss-of-function. These data suggest that loss-of-function SETD2 mutations occur in older children and young adults and are specific to HGG of the cerebral cortex, similar to the H3.3 G34R/V and IDH mutations. Taken together, our results suggest that mutations disrupting the histone code at H3K36, including H3.3 G34R/V, IDH1 and/or SETD2 mutations, are central to the genesis of hemispheric HGGs in older children and young adults.
    Type of Publication: Journal article published
    PubMed ID: 23417712
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  • 13
    Keywords: CELL ; MODEL ; GENE-EXPRESSION ; MICE ; NEPHRIN ; kidney development ; AMINONUCLEOSIDE NEPHROSIS ; PROTEIN PODOCALYXIN ; PODOCYTE FUNCTION ; GLOMERULI
    Abstract: Focal segmental glomerulosclerosis (FSGS) is a frequent and severe glomerular disease characterized by destabilization of podocyte foot processes. We report that transgenic expression of the microRNA miR-193a in mice rapidly induces FSGS with extensive podocyte foot process effacement. Mechanistically, miR-193a inhibits the expression of the Wilms' tumor protein (WT1), a transcription factor and master regulator of podocyte differentiation and homeostasis. Decreased expression levels of WT1 lead to downregulation of its target genes PODXL (podocalyxin) and NPHS1 (nephrin), as well as several other genes crucial for the architecture of podocytes, initiating a catastrophic collapse of the entire podocyte-stabilizing system. We found upregulation of miR-193a in isolated glomeruli from individuals with FSGS compared to normal kidneys or individuals with other glomerular diseases. Thus, upregulation of miR-193a provides a new pathogenic mechanism for FSGS and is a potential therapeutic target.
    Type of Publication: Journal article published
    PubMed ID: 23502960
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  • 14
    Keywords: EXPRESSION ; CELL ; SUSCEPTIBILITY ; VIRAL-INFECTION ; ANNOTATION ; METAANALYSIS ; GENOME-WIDE ASSOCIATION ; T-BET ; CHROMATIN STATES ; EOMESODERMIN
    Abstract: In addition to HLA, recent genome-wide association studies (GWASs) of Hodgkin's lymphoma (HL) have identified susceptibility loci for HL at 2p16.1, 8q24.21 and 10p14. In this study, we perform a GWAS meta-analysis with published GWAS (totalling 1,465 cases and 6,417 controls of European background), and follow-up the most significant association signals in 2,024 cases and 1,853 controls. A combined analysis identifies new HL susceptibility loci mapping to 3p24.1 (rs3806624; P = 1.14 x 10(-12), odds ratio (OR) = 1.26) and 6q23.3 (rs7745098; P = 3.42 x 10(-9), OR = 1.21). rs3806624 localizes 5' to the EOMES (eomesodermin) gene within a p53 response element affecting p53 binding. rs7745098 maps intergenic to HBS1L and MYB, a region previously associated with haematopoiesis. These findings provide further insight into the genetic and biological basis of inherited susceptibility to HL.
    Type of Publication: Journal article published
    PubMed ID: 24149102
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  • 15
    Keywords: CELL ; STRESS ; METASTASIS ; MIGRATION ; cytoskeleton ; ORGANIZATION ; ALPHA-B-CRYSTALLIN ; ARCHITECTURE ; F-ACTIN NETWORKS ; KINETICS DETERMINE
    Abstract: The mechanical properties of living cells are essential for many processes. They are defined by the cytoskeleton, a composite network of protein fibers. Thus, the precise control of its architecture is of paramount importance. Our knowledge about the molecular and physical mechanisms defining the network structure remains scarce, especially for the intermediate filament cytoskeleton. Here, we investigate the effect of small heat shock proteins on the keratin 8/18 intermediate filament cytoskeleton using a well-controlled model system of reconstituted keratin networks. We demonstrate that Hsp27 severely alters the structure of such networks by changing their assembly dynamics. Furthermore, the C-terminal tail domain of keratin 8 is shown to be essential for this effect. Combining results from fluorescence and electron microscopy with data from analytical ultracentrifugation reveals the crucial role of kinetic trapping in keratin network formation.
    Type of Publication: Journal article published
    PubMed ID: 24138853
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  • 16
    Keywords: ANGIOGENESIS ; EXPRESSION ; GROWTH ; CELL ; IN-VIVO ; MICE ; molecular imaging ; CARCINOMAS ; MANAGEMENT ; ONCOLOGY ; ANEMIA ; STIMULATING AGENTS ; CT,erythropoietin ; fluorescence molecular tomography
    Abstract: The putative presence of the erythropoietin receptor (EpoR) on human cancer cells has given rise to controversial discussion about the use of recombinant human erythropoietin (rhuEpo) for treatment of patients with chemotherapy-induced anemia. In vivo analysis of the EpoR status in tumors could help in elucidating the role of erythropoietin in cancer. Thus, the aim of this study was to develop a targeted EpoR probe for the investigation of EpoR expression in human lung cancer xenografts by fluorescence-mediated tomography. Methods: Epo-Cy5.5 was generated by coupling Cy5.5 to rhuEpo. In vitro binding assays were performed using the EpoR-positive non-small cell lung cancer (NSCLC) cell lines A549 (lower EpoR expression) and H838 (higher EpoR expression), the EpoR-negative cell line H2030, and EpoR/EGFP-overexpressing HeLa cells. In vivo specificity of Epo-Cy5.5 was confirmed by competition analyses using micro-CT/fluorescence-mediated tomography fusion imaging. Biodistribution was analyzed over 50 h after injection. Binding of Epo-Cy5.5 was validated on tumor cryosections. Results: After intravenous injection, the probe was rapidly cleared from the circulation. An accumulation was observed in liver and kidneys, with a maximum at 7 h after injection followed by a decline, indicating renal excretion. Almost constant accumulation of Epo-Cy5.5 was found in bone marrow and tumors, indicating specific receptor binding. The probe allowed the discrimination between H838 with higher EpoR expression (89.54 +/- 15.91 nM at 25 h) and A549 tumors with lower EpoR expression (60.45 +/- 14.59 nM at 25 h, P 〈 0.05). Tumor accumulation of Epo-Cy5.5 could be significantly reduced by adding unlabeled rhuEpo (P 〈 0.05 at 4, 7, and 24 h). In vitro validation confirmed specific binding of Epo-Cy5.5 to the tumor cells, and this binding correlated with the EpoR expression level. Binding was also observed on endothelial cells. Vessel density and Epo-Cy5.5 binding on endothelial cells were comparable. Conclusion: Epo-Cy5.5 allows the longitudinal analysis of EpoR expression in tumors and thereby can investigate the influence of erythropoietin on EpoR expression, tumor growth, and angiogenesis
    Type of Publication: Journal article published
    PubMed ID: 22228796
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  • 17
    Keywords: GROWTH ; CELL ; PROTEIN ; PROTEINS ; BINDING ; leukemia ; TARGETS ; INHIBITORS ; ubiquitylation ; proteasomal degradation ; PROMYELOCYTIC LEUKEMIA-CELLS ; Siah-1 ; MALIGNANT HEMATOPOIESIS ; PML-RAR alpha ; RING DOMAIN ; SIAH ; TRIAD1 ; UBCH8 ; Ubiquitinylating enzymes
    Abstract: The ubiquitin proteasome system plays an important role in normal and malignant hematopoiesis and relies on the concerted action of three enzyme families. The E2 ubiquitin conjugase UBCH8 (ubiquitin conjugating enzyme [human] 8) cooperates with the E3 ubiquitin ligases SIAH1 and SIAH2 (seven in absentia homolog 1/2) to mediate the proteasomal degradation of oncoproteins. One such protein is the leukemia fusion protein PML-RARalpha (promyelocytic leukemia-retinoic acid receptoralpha) that is associated with acute promyelocytic leukemia. A limited number of UBCH8 interaction partners that participate in the UBCH8-dependent depletion of cancer-relevant proteins are known. We report here that TRIAD1 (two RING fingers and DRIL [double RING finger linked] 1), an E3 ubiquitin ligase relevant for the clonogenic growth of myloid progenitors, binds UBCH8 as well as PML-RARalpha. Moreover, there is concurrent induction of TRIAD1 and UBCH8 upon combinatorial treatment of acute promyelocytic leukemia cells with the pro-apoptotic epigenetic modulator valproic acid and the differentiation inducing agent all-trans retinoic acid. However, in sharp contrast to SIAH1/SIAH2 and UBCH8, TRIAD1 binding to PML-RARalpha has no effect on its turnover. In summary, our data exclude TRIAD1 as crucial regulator of the leukemic determinant PML-RARalpha, but highlight the prominence of the UBCH8/SIAH axis in PML-RARalpha degradation.
    Type of Publication: Journal article published
    PubMed ID: 22037423
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  • 18
    Keywords: ANGIOGENESIS ; ENDOTHELIAL-CELLS ; EXPRESSION ; GROWTH ; tumor ; CELL ; IN-VIVO ; INHIBITION ; PROTEINS ; MICE ; ACTIVATION ; SUPERFAMILY ; innate immunity ; DMBT1 ; HENSIN ; galectin-3 ; MATRIX ; extracellular matrix ; endothelium ; SHEAR-STRESS ; POSTNATAL ARTERIOGENESIS
    Abstract: OBJECTIVE: Deleted in malignant brain tumors 1 (DMBT1) belongs to the scavenger receptor cysteine-rich superfamily of proteins and is implicated in innate immunity, cell polarity, and differentiation. Here we studied the role of DMBT1 in endothelial cells. METHODS AND RESULTS: DMBT1 was secreted into the extracellular matrix (ECM) by endothelial cells in vitro and in situ and the presence of DMBT1 in the ECM increased endothelial cell adherence. Endothelial cell-derived DMBT1 associated with galectin-3 (coprecipitation), and human recombinant DMBT1 bound EGF, vascular endothelial growth factor and Delta-like (Dll) 4 (specific ELISAs). Compared to cells from wild-type mice, endothelial cells from DMBT1(-/-) mice demonstrated reduced migration, proliferation, and tube formation. In vivo recovery from hindlimb ischemia was attenuated in DMBT1(-/-) animals as was vascular endothelial growth factor -induced endothelial sprouting from isolated aortic rings; the latter response could be rescued by the addition of recombinant DMBT1. The Notch pathway is involved in multiple aspects of vascular development, including arterial-venous differentiation and we found that endothelial cells from DMBT1(-/-) mice expressed more EphrinB2 than cells from wild-type mice. Levels of Dll1, Dll4, Hes1, Hey1, and EphB4, on the other hand, were decreased. CONCLUSIONS: Taken together, the results of this study indicate that DMBT1 functions as an important endothelium-derived ECM protein that is able to bind angiogenic factors and promote adhesion, migration, proliferation, and angiogenesis as well as vascular repair. Mechanistically, DMBT1 interacts with galectin-3 and modulates the Notch signaling pathway as well as the differential expression of ephrin-B2 and EphB4.
    Type of Publication: Journal article published
    PubMed ID: 22053071
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  • 19
    Keywords: CELL ; PROTEINS ; EVOLUTION ; WALL ; VENOM ; BIOLOGICAL ROLES ; CNIDARIAN NEMATOCYST ; DISCHARGE ; MINI-COLLAGENS ; MINICOLLAGENS ; RICH PROTEIN
    Abstract: Stinging cells or nematocytes of jellyfish and other cnidarians represent one of the most poisonous and sophisticated cellular inventions in animal evolution. This ancient cell type is unique in containing a giant secretory vesicle derived from the Golgi apparatus. The organelle structure within the vesicle comprises an elastically stretched capsule (nematocyst) to which a long tubule is attached. During exocytosis, the barbed part of the tubule is accelerated with 〉5 million g in 〈700 ns, enabling a harpoon-like discharge (Nuchter, T., Benoit, M., Engel, U., Ozbek, S., and Holstein, T. W. (2006) Curr. Biol. 16, R316-R318). Hitherto, the molecular components responsible for the organelle's biomechanical properties were largely unknown. Here, we describe the proteome of nematocysts from the freshwater polyp Hydra magnipapillata. Our analysis revealed an unexpectedly complex secretome of 410 proteins with venomous and lytic but also adhesive or fibrous properties. In particular, the insoluble fraction of the nematocyst represents a functional extracellular matrix structure of collagenous and elastic nature. This finding suggests an evolutionary scenario in which exocytic vesicles harboring a venomous secretome assembled a sophisticated predatory structure from extracellular matrix motif proteins.
    Type of Publication: Journal article published
    PubMed ID: 22291027
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  • 20
    Keywords: CANCER ; CELL ; IDENTIFICATION ; REGION ; REPLICATION ; MOLECULAR-BASIS ; FRA3B ; FHIT GENE ; CHROMOSOME BREAKAGE ; DNA INSTABILITY
    Abstract: Common fragile sites (cFSs) are non-random chromosomal regions that are prone to breakage under conditions of replication stress. DNA damage and chromosomal alterations at cFSs appear to be critical events in the development of various human diseases, especially carcinogenesis. Despite the growing interest in understanding the nature of cFS instability, only a few cFSs have been molecularly characterised. In this study, we fine-mapped the location of FRA2H using six-colour fluorescence in situ hybridisation and showed that it is one of the most active cFSs in the human genome. FRA2H encompasses approximately 530 kb of a gene-poor region containing a novel large intergenic non-coding RNA gene (AC097500.2). Using custom-designed array comparative genomic hybridisation, we detected gross and submicroscopic chromosomal rearrangements involving FRA2H in a panel of 54 neuroblastoma, colon and breast cancer cell lines. The genomic alterations frequently involved different classes of long terminal repeats and long interspersed nuclear elements. An analysis of breakpoint junction sequence motifs predominantly revealed signatures of microhomology-mediated non-homologous recombination events. Our data provide insight into the molecular structure of cFSs and sequence motifs affected by their activation in cancer. Identifying cFS sequences will accelerate the search for DNA biomarkers and targets for individualised therapies.
    Type of Publication: Journal article published
    PubMed ID: 22476624
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  • 21
  • 22
    Keywords: CANCER ; CELLS ; EXPRESSION ; GROWTH ; CELL ; SYSTEM ; transcription ; MICE ; TRANSDUCTION ; DNA ; MINUTE VIRUS ; REPLICATION ; ADENOVIRUS ; AUTONOMOUS PARVOVIRUSES ; RECOMBINANT PARVOVIRUS ; ADENOASSOCIATED VIRUS VECTORS ; pXX6 ; virus helper ; virus production
    Abstract: Preclinical studies using various cell culture and animal systems highlight the potential of recombinant rodent parvoviruses (recPVs) for cancer therapy. Production of these viruses is, however, not efficient and this hampers the clinical applications of these agents. In this study, we show that the adenovirus genes E2a, E4(orf6) and VA RNA increase the production of recPVs by more than 10-fold and reduce the time of production from 3 to 2 days in HEK293T cells. The helper effects of these genes can be observed with different recPVs, regardless of the nature and size of the inserted transgene. Furthermore, we generated a recombinant Adenovirus 5 carrying the parvovirus VP transcription unit. This helper, named Ad-VP, allows recPVs to be efficiently produced through a protocol based only on cell infection, making possible to use cell lines, such as NB324K, which are good producers of parvoviruses but are hardly transfectable. Hence, we could further improve viral titers and reduce time and costs of production. This Ad-VP helper-based protocol could be scaled up to a bioreactor format for the generation of the large amounts of recPVs needed for future clinical applications.
    Type of Publication: Journal article published
    PubMed ID: 21102423
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  • 23
    Keywords: CANCER ; CANCER CELLS ; CELLS ; EXPRESSION ; CELL ; transcription ; PHOSPHORYLATION ; CELL-DEATH ; p53 ; DAMAGE ; DNA-DAMAGE ; ADHESION ; cytoskeleton ; UBIQUITIN LIGASE ; NUCLEAR-BODIES ; HOMEODOMAIN-INTERACTING PROTEIN-KINASE-2 ; ACTIN ; PROTEIN KINASE-2 ; P53 PHOSPHORYLATION
    Abstract: HIPK2 activates the apoptotic arm of the DNA damage response by phosphorylating tumor suppressor p53 at serine 46. Unstressed cells keep HIPK2 levels low through targeted polyubiquitination and subsequent proteasomal degradation. Here we identify the LIM domain protein Zyxin as a novel regulator of the HIPK2-p53 signaling axis in response to DNA damage. Remarkably, depletion of endogenous Zyxin, which colocalizes with HIPK2 at the cytoskeleton and in the cell nucleus, stimulates proteasome-dependent HIPK2 degradation. In contrast, ectopic expression of Zyxin stabilizes HIPK2, even upon enforced expression of its ubiquitin ligase Siah-1. Consistently, Zyxin physically interacts with Siah-1, and knock-down of Siah-1 rescues HIPK2 expression in Zyxin-depleted cancer cells. Mechanistically, our data suggest that Zyxin regulates Siah-1 activity through interference with Siah-1 dimerization. Furthermore, we show that endogenous Zyxin coaccumulates with HIPK2 in response to DNA damage in cancer cells, and that depletion of endogenous Zyxin results in reduced HIPK2 protein levels and compromises DNA damage-induced p53 Ser46 phosphorylation and caspase activation. These findings suggest an unforeseen role for Zyxin in DNA damage-induced cell fate control through modulating the HIPK2-p53 signaling axis.
    Type of Publication: Journal article published
    PubMed ID: 21248071
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  • 24
    Keywords: APOPTOSIS ; CELL ; DEATH ; SURGERY ; CHROMATIN ; REPAIR ; DAMAGE ; skin tumors ; OXIDATIVE STRESS ; singlet oxygen ; ROS ; DNA STRAND BREAKS ; fluorescent proteins ; FREE-RADICAL THEORY ; KillerRed ; Photo-Dynamic-Therapy (PDT) ; POLY(ADP-RIBOSE) POLYMERASE PARP ; STRUCTURE/FUNCTION RELATIONSHIPS ; subcellular Localization
    Abstract: Fluorescent proteins (FPs) are established tools for new applications, not-restricted to the cell biological research. They could also be ideal in surgery enhancing the precision to differentiate between the target tissue and the surrounding healthy tissue. FPs like the KillerRed (KRED), used here, can be activated by excitation with visible day-light for emitting active electrons which produce reactive oxygen species (ROS) resulting in photokilling processes. It is a given that the extent of the KRED's cell toxicity depends on its subcellular localization. Evidences are documented that the nuclear lamina as well as especially the chromatin are critical targets for KRED-mediated ROS-based DNA damaging. Here we investigated the damaging effects of the KRED protein fused to the nuclear lamina and to the histone H2A DNA-binding protein. We detected a frequency of DNA strand breaks, dependent first on the illumination time, and second on the spatial distance between the localization at the chromatin and the site of ROS production. As a consequence we could identify defined DNA bands with 200, 400 and (600) bps as most prominent degradation products, presumably representing an internucleosomal DNA cleavage induced by KRED. These findings are not restricted to the detection of programmed cell death processes in the therapeutic field like PDT, but they can also contribute to a better understanding of the structure-function relations in the epigenomic world.
    Type of Publication: Journal article published
    PubMed ID: 21278894
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  • 25
    Keywords: CELLS ; CELL ; IN-VIVO ; VIVO ; DISEASE ; RNA ; ACTIVATION ; T-CELLS ; PROMOTER ; acetylation ; PCAF BROMODOMAIN ; METHYLATION ; IMMUNODEFICIENCY-VIRUS TYPE-1 ; INHIBITORS ; LATENT INFECTION ; CHROMATIN-REMODELING COMPLEX ; HISTONE ; LSD1
    Abstract: The essential transactivator function of the HIV Tat protein is regulated by multiple posttranslational modifications. Although individual modifications are well characterized, their crosstalk and dynamics of occurrence during the HIV transcription cycle remain unclear. We examine interactions between two critical modifications within the RNA-binding domain of Tat: monomethylation of lysine 51 (K51) mediated by Set7/9/KMT7, an early event in the Tat transactivation cycle that strengthens the interaction of Tat with TAR RNA, and acetylation of lysine 50 (K50) mediated by p300/KAT3B, a later process that dissociates the complex formed by Tat, TAR RNA and the cyclin T1 subunit of the positive transcription elongation factor b (P-TEFb). We find K51 monomethylation inhibited in synthetic Tat peptides carrying an acetyl group at K50 while acetylation can occur in methylated peptides, albeit at a reduced rate. To examine whether Tat is subject to sequential monomethylation and acetylation in cells, we performed mass spectrometry on immunoprecipitated Tat proteins and generated new modification-specific Tat antibodies against monomethylated/acetylated Tat. No bimodified Tat protein was detected in cells pointing to a demethylation step during the Tat transactivation cycle. We identify lysine-specific demethylase 1 (LSD1/KDM1) as a Tat K51-specific demethylase, which is required for the activation of HIV transcription in latently infected T cells. LSD1/KDM1 and its cofactor CoREST associates with the HIV promoter in vivo and activate Tat transcriptional activity in a K51-dependent manner. In addition, small hairpin RNAs directed against LSD1/KDM1 or inhibition of its activity with the monoamine oxidase inhibitor phenelzine suppresses the activation of HIV transcription in latently infected T cells. Our data support the model that a LSD1/KDM1/CoREST complex, normally known as a transcriptional suppressor, acts as a novel activator of HIV transcription through demethylation of K51 in Tat. Small molecule inhibitors of LSD1/KDM1 show therapeutic promise by enforcing HIV latency in infected T cells
    Type of Publication: Journal article published
    PubMed ID: 21876670
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  • 26
    Keywords: APOPTOSIS ; EXPRESSION ; CELL ; THERAPY ; DISEASE ; MICE ; SKIN ; signal transduction ; LYMPHOCYTES ; ALPHA-INDUCED APOPTOSIS ; TOLL-LIKE RECEPTORS ; C3H/HEJ MICE ; AUTOIMMUNITY ; IMMUNE-SYSTEM ; HAIR LOSS ; ALOPECIA-AREATA ; myeloid-derived suppressor cells ; MEMBRANE PERMEABILIZATION ; CHRONIC CONTACT ECZEMA ; Delayed type hypersensitivity
    Abstract: Mild but efficient treatments of autoimmune diseases are urgently required. One such therapy, long-term maintenance of chronic delayed type hypersensitivity, has been described for alopecia areata (AA), a hair follicle-affecting autoimmune disease. The molecular mechanisms underlying the therapeutic efficacy are unknown, but may involve myeloid-derived suppressor cells (MDSCs). AA-affected mice were treated with squaric acid dibutyl ester (SADBE). The immunoreactivity of SADBE-treated AA lymphocytes and of AA lymphocytes co-cultured with SADBE-induced MDSCs was analyzed. The curative effect of SADBE was abolished by all-transretinoic acid, which drives MDSCs into differentiation, confirming a central role for MDSCs in therapeutic SADBE treatment. SADBE and SADBE-induced MDSCs strongly interfered with sustained autoreactive T-cell proliferation in response to AA skin lysate (autoantigen), which was accompanied by weak zeta-chain down-regulation and strongly impaired Lck activation. In contrast, activation of the mitochondrial apoptosis pathway and blockade of the anti-apoptotic PI3K/Akt pathway by SADBE-induced MDSCs did not require T-cell receptor engagement. Apoptosis induction correlated with high TNF-alpha expression in SADBE-induced MDSCs and elevated TNFRI levels in AA lymphocytes. SADBE-induced MDSCs interfere with persisting autoreactive T-cell proliferation and promote apoptosis of these T cells, which qualifies MDSCs induced and maintained by chronic delayed type hypersensitivity reactions as promising therapeutics in organ-related autoimmune diseases
    Type of Publication: Journal article published
    PubMed ID: 21728175
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  • 27
    Keywords: CELL ; PROTEIN ; PROTEINS ; MECHANISM ; PHOSPHORYLATION ; IDENTIFICATION ; ELECTROSPRAY ; fragmentation ; DISSOCIATION ; posttranslational modification ; TYROSINE SULFATION ; Negative ion CID ; Phosphotyrosine ; Sulfotyrosine ; THREONINE
    Abstract: Unambiguous differentiation between isobaric sulfated and phosphorylated tyrosine residues (sTyr and pTyr) of proteins by mass spectrometry is challenging, even using high resolution mass spectrometers. Here we show that upon negative ion mode collision-induced dissociation (CID), pTyr- and sTyr-containing peptides exhibit entirely different modification-specific fragmentation patterns leading to a rapid discrimination between the isobaric covalent modifications using the tandem mass spectral data. This study reveals that the ratio between the relative abundances of [M-H-80](-) and [M-H-98](-) fragment ions in ion-trap CID and higher energy collision dissociation (HCD) spectra of singly deprotonated +80 Da Tyr-peptides can be used as a reliable indication of the Tyr modification group nature. For multiply deprotonated +80 Da Tyr-peptides, CID spectra of sTyr- and pTyr-containing sequences can be readily distinguished based on the presence/absence of the [M-nH-79]((n-1)-) and [M-nH-79-NL]((n-1)-) (n=2, 3) fragment ions (NL=neutral loss).
    Type of Publication: Journal article published
    PubMed ID: 21952787
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  • 28
    Keywords: brain ; CELLS ; EXPRESSION ; CELL ; PROTEINS ; ACTIVATION ; COMPLEX ; DNA ; DOMAIN ; BINDING ; SUSCEPTIBILITY ; BREAST-CANCER ; CREB ; ESTROGEN ; COACTIVATOR ; CITED1 ; TOX3
    Abstract: TOX3 is a nuclear protein containing a high mobility group (HMG)-box domain, which regulates Ca2+-dependent transcription in neurons through interaction with the cAMP-response-element-binding protein (CREB). TOX3 appears to be associated with breast cancer susceptibility and was previously shown to be expressed downstream of a cytoprotective cascade together with CITED1, a transcriptional regulator that does not bind directly to DNA. In the present study we show that TOX3 is predominantly expressed in the brain, forms homodimers and interacts with CITED1. TOX3 overexpression protects neuronal cells from cell death caused by endoplasmic reticulum stress or BAX overexpression through the induction of anti-apoptotic transcripts and repression of pro-apoptotic transcripts, which correlates with enhanced transcription involving isolated estrogen-responsive elements and estrogen-responsive promoters. However, both functions cannot be inhibited with the anti-estrogen fulvestrant and are only attenuated by mutation of estrogen-responsive elements. TOX3 also interacts with native CREB and induces the CREB-responsive BCL-2 promoter, which can be inhibited by coexpression of CITED1. Coexpression of CREB, by contrast, abolishes TOX3-mediated transcription from the estrogen-responsive complement C3 promoter. Our results suggest that TOX3 can enhance transcriptional activation from different cytoprotective promoters and that this is dependent on the predominance of either phosphorylated CREB or CITED1 within the transcriptionally active complex
    Type of Publication: Journal article published
    PubMed ID: 21172805
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  • 29
    Keywords: CANCER ; EXPRESSION ; CELL ; SKIN ; human hair follicle ; INNER-ROOT-SHEATH ; FACTOR-BETA ; DIRECT BINDING ; ORGANOTYPIC COCULTURE ; EPITHELIAL KERATINS
    Abstract: The mechanism by which transforming growth factor-beta (TGF beta) regulates differentiation in human epidermal keratinocytes is still poorly understood. To assess the role of Smad signaling, we engineered human HaCaT keratinocytes either expressing small interfering RNA against Smads2, 3, and 4 or overexpressing Smad7 and verified impaired Smad signaling as decreased Smad phosphorylation, aberrant nuclear translocation, and altered target gene expression. Besides abrogation of TGF beta-dependent growth inhibition in conventional cultures, epidermal morphogenesis and differentiation in organotypic cultures were disturbed, resulting in altered tissue homeostasis with suprabasal proliferation and hyperplasia upon TGF beta treatment. Neutralizing antibodies against TGF beta, similar to blocking the actions of EGF-receptor or keratinocyte growth factor, caused significant growth reduction of Smad7-overexpressing cells, thereby demonstrating that epithelial hyperplasia was attributed to TGF beta-induced "dermis"-derived growth promoting factors. Furthermore impaired Smad signaling not only blocked the epidermal differentiation process or caused epidermal-to-mesenchymal transition but induced a switch to a complex alternative differentiation program, best characterized as mucous/intestinal-type epithelial differentiation. As the same alternative phenotype evolved from both modes of Smad-pathway interference, and reduction of Smad7-overexpression caused reversion to epidermal differentiation, our data suggest that functional TGF beta/Smad signaling, besides regulating epidermal tissue homeostasis, is not only essential for terminal epidermal differentiation but crucial in programming different epithelial differentiation routes
    Type of Publication: Journal article published
    PubMed ID: 21289094
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  • 30
    Keywords: ENDOTHELIAL-CELLS ; CELL ; IN-VIVO ; DIFFERENTIATION ; PROGENITOR CELLS ; microenvironment ; MOBILIZATION ; SELF-RENEWAL ; MAINTENANCE ; DORMANT ; HEMATOPOIETIC-STEM
    Abstract: Stem cell niches are defined as the cellular and molecular microenvironments that regulate stem cell function together with stem cell autonomous mechanisms. This includes control of the balance between quiescence, self-renewal, and differentiation, as well as the engagement of specific programs in response to stress. In mammals, the best understood niche is that harboring bone marrow hematopoietic stem cells (HSCs). Recent studies have expanded the number of cell types contributing to the HSC niche. Perivascular mesenchymal stem cells and macrophages now join the previously identified sinusoidal endothelial cells, sympathetic nerve fibers, and cells of the osteoblastic lineage to form similar, but distinct, niches that harbor dormant and self-renewing HSCs during homeostasis and mediate stem cell mobilization in response to granulocyte colony-stimulating factor
    Type of Publication: Journal article published
    PubMed ID: 21402747
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  • 31
    Keywords: IN-VITRO ; CELL ; SYSTEM ; ESCHERICHIA-COLI ; cytoskeleton ; vimentin ; FIBRILLARY ACIDIC PROTEIN ; HEAD DOMAIN ; BINDING-PROTEIN ; COILED-COIL ; TAIL DOMAIN ; CELL ARCHITECTURE ; bacterial cytoskeleton ; Caulobacter crescentus ; CAULOBACTER-CRESCENTUS ; cell curvature ; crescentin
    Abstract: Crescentin is a bacterial filament-forming protein that exhibits domain organization features found in metazoan intermediate filament (IF) proteins. Structure-function studies of eukaryotic IFs have been hindered by a lack of simple genetic systems and easily quantifiable phenotypes. Here we exploit the characteristic localization of the crescentin structure along the inner curvature of Caulobacter crescentus cells and the loss of cell curvature associated with impaired crescentin function to analyze the importance of the domain organization of crescentin. By combining biochemistry and ultrastructural analysis in vitro with cellular localization and functional studies, we show that crescentin requires its distinctive domain organization, and furthermore that different structural elements have distinct structural and functional contributions. The head domain can be functionally subdivided into two subdomains; the first (amino-terminal) is required for function but not assembly, while the second is necessary for structure assembly. The rod domain is similarly required for structure assembly, and the linker L1 appears important to prevent runaway assembly into nonfunctional aggregates. The data also suggest that the stutter and the tail domain have critical functional roles in stabilizing crescentin structures against disassembly by monovalent cations in the cytoplasm. This study suggests that the IF-like behavior of crescentin is a consequence of its domain organization, implying that the IF protein layout is an adaptable cytoskeletal motif, much like the actin and tubulin folds, that is broadly exploited for various functions throughout life from bacteria to humans. (C) 2011 Wiley-Liss, Inc
    Type of Publication: Journal article published
    PubMed ID: 21360832
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  • 32
    Keywords: CELLS ; EXPRESSION ; IN-VITRO ; SURVIVAL ; CELL ; IN-VIVO ; GENERATION ; PROTEIN ; PROTEINS ; ANTIGEN ; DENDRITIC CELLS ; MATURATION ; HEAT-SHOCK ; MARKERS ; VACCINES ; innate immunity ; STRATEGIES ; IMMUNOTHERAPY ; ADAPTIVE IMMUNITY ; HYPERTHERMIA ; CYTOTOXIC T-LYMPHOCYTES ; HSP70 ; cytotoxic T lymphocytes
    Abstract: Dendritic cell (DC)-based immunotherapy has been shown to be a promising strategy for anti-cancer therapy. Nevertheless, only a low overall clinical response rate has been observed in vaccinated patients with advanced cancer and therefore methods to improve DC immuno-stimulatory functions are currently under intense investigation. In this respect, we exposed human monocyte-derived DCs to a physiological temperature stress of 40 degrees C for up to 24 h followed by analysis for (i) expression of different heat shock proteins, (ii) survival, (iii) cell surface maturation markers, (iv) cytokine secretion, and (v) migratory capacity. Furthermore, we examined the ability of heat-shocked DCs to prime naive CD8(+) T cells after loading with MelanA peptide, by transfection with MelanA RNA, or by transduction with MelanA by an adenovirus vector. The results clearly indicate that in comparison to control DCs, which remained at 37 degrees C, heat-treated cells revealed no differences concerning the survival rate or their migratory capacity. However, DCs exposed to thermal stress showed a time-dependent enhanced expression of the immune-chaperone heat shock protein 70A and both an up-regulation of co-stimulatory molecules such as CD80, CD83, and CD86 and of the inflammatory cytokine TNF-alpha. Moreover, these cells had a markedly improved capacity to prime autologous naive CD8(+) T cells in vitro in an antigen-specific manner, independent of the method of antigen-loading. Thus, our strategy of heat treatment of DCs offers a promising means to improve DC functions during immune activation which, as a physical method, facilitates straight-forward applications in clinical DC vaccination protocols
    Type of Publication: Journal article published
    PubMed ID: 21846195
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  • 33
    Keywords: EXPRESSION ; GROWTH ; CELL ; DISEASE ; GENE ; PROTEIN ; DIFFERENTIATION ; BIOMARKERS ; IN-SITU ; MALIGNANT-MELANOMA ; ORIGIN ; SERUM ; BURDEN ; MELANOMA INHIBITORY-ACTIVITY
    Abstract: Background: Neurofibromatosis type 1 (NF1) is a frequent genetic disease characterized by multiple benign tumours with increased risk for malignancy. There is currently no biomarker for tumour load in NF1 patients. Methods: In situ hybridization and quantitative real-time polymerase reaction were applied to investigate expression of cartilage-specific genes in mice bearing conditional inactivation of NF1 in the developing limbs. These mice do not develop tumours but recapitulate aspects of NF1 bone dysplasia, including deregulation of cartilage differentiation. It has been recently shown that NF1 tumours require for their growth the master regulator of cartilage differentiation SOX9. We thus hypothesized that some of the cartilage-specific genes deregulated in an Nf1Prx1 mouse model might prove to be relevant biomarkers of NF1 tumours. We tested this hypothesis by analyzing expression of the SOX9 target gene product melanoma-inhibitory activity/cd-rap (MIA) in tumour and serum samples of NF1 patients. Results: Increased expression of Mia was found in Nf1-deficient cartilage in mice. In humans, MIA was expressed in all NF1-related tumours and its serum levels were significantly higher in NF1 patients than in healthy controls. Among NF1 patients, MIA serum levels were significantly higher in those with plexiform neurofibromas and in those with large number of cutaneous (〉 1,000) or subcutaneous (〉 100) neurofibromas than in patients without such tumours. Most notably, MIA serum levels correlated significantly with internal tumour burden. Conclusions: MIA is a potential serum biomarker of tumour load in NF1 patients which could be useful in following the disease course and monitoring the efficacy of therapies
    Type of Publication: Journal article published
    PubMed ID: 21726432
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  • 34
    Keywords: SURVIVAL ; CELL ; RISK ; TARGET ; ABERRATIONS ; 13Q14
    Type of Publication: Journal article published
    PubMed ID: 21972210
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  • 35
    Keywords: IN-VITRO ; CELL ; INHIBITION ; KINASE ; transcription ; ACTIVATION ; PHOSPHORYLATION ; ADHESION ; multiplex ; ALPHA-CATENIN
    Abstract: beta-catenin plays multiple roles in the canonical Wnt signaling pathway and in cell-cell adhesion complexes. In addition, beta-catenin is a proto-oncogene and activating beta-catenin mutations are relevant in the genesis of colorectal, hepatocellular and other common cancers. Different functions of beta-catenin as transcriptional co-activator or cell adhesion molecule are orchestrated by changes in concentration and phosphorylation as well as its ability to complex with proteins such as cadherins or transcription factors. Detailed quantitative and time-resolved analysis of beta-catenin, based on the evaluation of the changes in the Wnt pathway, enable greater insights into health- and disease-related beta-catenin function. The present paper describes a novel suspension bead array assay panel for beta-catenin, which requires minimal amounts of sample and is able to relatively quantify total beta-catenin, the extent of phosphorylation at multiple sites and the ratio of complexed and free beta-catenin. This is the first study to combine three biochemical methods--sandwich immunoassay, co-immunoprecipitation, and protein-protein interaction assay--in one suspension bead assay panel. The assay was used to measure changes in the concentration of eight different beta-catenin forms in HEK293 cells in a time-resolved manner. In contrast to the general consensus, our study demonstrates an increase in beta-catenin phosphorylated at Ser-45 upon treatment of cells with rWnt3a or a GSK3 inhibition; we also link C-terminal phosphorylation of beta-catenin on Ser-552 and Ser-675 with canonical Wnt signaling.
    Type of Publication: Journal article published
    PubMed ID: 21378377
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  • 36
    Keywords: EXPRESSION ; CELL ; PATHWAY ; ACTIVATION ; AXIS FORMATION ; JNK ; LAEVIS ; CONVERGENT EXTENSION MOVEMENTS ; gastrulation movements ; MORPHOGEN GRADIENT ; WNT5a ; ROR2 ; Wnt/PCP signaling ; Dishevelled ; Wnt11 ; Frizzled7 ; ATF2 ; PLANAR CELL-POLARITY ; VERTEBRATE GASTRULATION
    Abstract: Non-canonical/planar cell polarity (PCP) Wnt signaling plays important roles in embryonic development and tissue homeostasis, and is implicated in human disease. Monitoring Wnt/PCP signaling relies mostly on semi-quantitative bioassays or biochemical analysis. Here we describe a luciferase reporter assay based on an ATF2 response element, which faithfully monitors non-canonical Wnt signaling in Xenopus embryos. The assay is simple, quantitative, and robust. It can be used to detect non-canonical Wnt signaling changes following gain and loss of function of pathway components, including Wnt, Frizzled, Ror2, Disheveled, Rac1, MKK7, and JNK. Wnt/PCP signaling has recently been implicated in left-right asymmetry and our reporter assay suggests that in gastrula embryos there is a right-ward bias in Wnt/PCP signaling. We also mapped Wnt/PCP signaling in the early Xenopus embryo and find that it peaks in the dorso-vegetal region, paralleling Wnt/beta-catenin signaling. Developmental Dynamics, 2011. copyright 2010 Wiley-Liss, Inc.
    Type of Publication: Journal article published
    PubMed ID: 21128306
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  • 37
    Keywords: EXPRESSION ; CELL ; MOLECULES ; ESCHERICHIA-COLI ; MHC CLASS-I ; ENDOPLASMIC-RETICULUM ; TRANSPORTER ; IMMUNE EVASION ; INFECTED CELLS ; ANTIGEN-PROCESSING TAP ; HEAVY-CHAINS ; US6 GLYCOPROTEIN
    Abstract: Major histocompatibility complex class I (MHC I) molecules present antigenic peptides for CD8(+) T-cell recognition. Prior to cell surface expression, proper MHC I loading is conducted by the peptide-loading complex (PLC), composed of the MHC I heavy chain (HC) and beta(2)-microglobulin (beta(2)m), the peptide transporter TAP, and several chaperones, including tapasin. Tapasin connects peptide-receptive MHC I molecules to the PLC, thereby facilitating loading of high-affinity peptides onto MHC I. To cope with CD8(+) T-cell responses, human cytomegalovirus (HCMV) encodes several posttranslational strategies inhibiting peptide transport and MHC I biogenesis which have been studied extensively in transfected cells. Here we analyzed assembly of the PLC in naturally HCMV-infected fibroblasts throughout the protracted replication cycle. MHC I incorporation into the PLC was absent early in HCMV infection. Subsequently, tapasin neosynthesis became strongly reduced, while tapasin steady-state levels diminished only slowly in infected cells, revealing a blocked synthesis rather than degradation. Tapasin mRNA levels were continuously downregulated during infection, while tapasin transcripts remained stable and long-lived. Taking advantage of a novel method by which de novo transcribed RNA is selectively labeled and analyzed, an immediate decline of tapasin transcription was seen, followed by downregulation of TAP2 and TAP1 gene expression. However, upon forced expression of tapasin in HCMV-infected cells, repair of MHC I incorporation into the PLC was relatively inefficient, suggesting an additional level of HCMV interference. The data presented here document a two-pronged coordinated attack on tapasin function by HCMV
    Type of Publication: Journal article published
    PubMed ID: 21248040
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  • 38
    Keywords: CELLS ; EXPRESSION ; CELL ; GENE ; PROTEINS ; COMPLEX ; TRANSCRIPTION FACTOR ; ACTIVATED PROTEIN-KINASE ; IDENTIFICATION ; BINDING-PROTEIN ; GENE-REGULATION ; nonsense-mediated decay ; p38 ; POLY(A)-BINDING PROTEIN
    Abstract: mRNA turnover is a critical step in the control of gene expression. In mammalian cells, a subset of mRNAs regulated at the level of mRNA turnover contain destabilizing AU-rich elements (AREs) in their 3' untranslated regions. These transcripts are bound by a suite of ARE-binding proteins (AUBPs) that receive information from cell signaling events to modulate rates of ARE mRNA decay. Here we show that a key destabilizing AUBP, tristetraprolin (TTP), is repressed by the p38 mitogen-activated protein kinase (MAPK)-activated kinase MK2 due to the inability of phospho-TTP to recruit deadenylases to target mRNAs. TTP is tightly associated with cytoplasmic deadenylases and promotes rapid deadenylation of target mRNAs both in vitro and in cells. TTP can direct the deadenylation of substrate mRNAs when tethered to a heterologous mRNA, yet its ability to do so is inhibited upon phosphorylation by MK2. Phospho-TTP is not impaired in mRNA binding but does fail to recruit the major cytoplasmic deadenylases. These observations suggest that phosphorylation of TTP by MK2 primarily affects mRNA decay downstream of RNA binding by preventing recruitment of the deadenylation machinery. Thus, TTP may remain poised to rapidly reactivate deadenylation of bound transcripts to downregulate gene expression once the p38 MAPK pathway is deactivated
    Type of Publication: Journal article published
    PubMed ID: 21078877
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  • 39
    Keywords: CANCER ; CANCER CELLS ; CELLS ; CELL ; prognosis ; PHOSPHORYLATION ; PROGRESSION ; ABERRATIONS ; DAMAGE ; LOCALIZATION ; XENOPUS ; RECRUITMENT ; DUPLICATION ; REPLICATION ; CDK2-CYCLIN ; AURORA-A ; MAINTENANCE ; DNA-DAMAGE RESPONSE
    Abstract: Centrosomes are central regulators of mitosis that are often amplified in cancer cells. Centrosomes function both as organizers of the mitotic spindle and as reaction centers to trigger activation of Cdk1 and G(2)/M transition in the cell cycle, but their functional organization remains incomplete. Recent proteomic studies have identified novel components of the human centrosome including Cep63, a protein of unknown function that Xenopus studies have implicated in mitotic spindle assembly and spindle inactivation after DNA damage. Here, we report that human Cep63 binds to and recruits Cdk1 to centrosomes, and thereby regulates mitotic entry. RNAi-mediated Cep63 depletion in U2OS cancer cells induced polyploidization through mitotic skipping. Elicitation of this phenotype was associated with downregulation of centrosomal Cdk1, mimicking the phenotype induced by direct depletion of Cdk1. In contrast, Cep63 overexpression induced de novo centrosome amplification during cell-cycle interphase. Induction of this phenotype was suppressible by cell treatment with the Cdk inhibitor roscovitine. In a survey of 244 neuroblastoma cases, Cep63 mRNA overexpression was associated with MYCN oncogene amplification and poor prognosis. In cultured cells, Cep63 overexpression was associated with an enhancement in replication-induced DNA breakage. Together, our findings define human Cep63 as a centrosomal recruitment factor for Cdk1 that is essential for mitotic entry, providing a physical link between the centrosome and the cell-cycle machinery.
    Type of Publication: Journal article published
    PubMed ID: 21406398
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    Keywords: EXPRESSION ; CELL ; GENE-EXPRESSION ; DIFFERENTIATION ; XENOPUS ; NUCLEAR FACTOR ; EMBRYONIC STEM-CELLS ; ANTERIOR-POSTERIOR AXIS ; gastrulation ; MESODERM INDUCTION ; pluripotency ; CAUDAL GENES ; Cdx1 ; CELL FATE SPECIFICATION ; EARLY XENOPUS EMBRYOGENESIS ; FGF signaling ; germ layers ; Oct3/4 ; ORPHAN RECEPTOR ; SPEMANNS-ORGANIZER
    Abstract: Gastrulation marks the onset of germ layer formation from undifferentiated precursor cells maintained by a network including the Pou5f1 gene, Oct3/4. Negative regulation of the undifferentiated state is a prerequisite for germ layer formation and subsequent development. A novel cross-regulatory network was characterized including the Pou5f1 and Cdx1 genes as part of the signals controlling the onset of gastrulation. Of particular interest was the observation that, preceding gastrulation, the Xenopus Oct3/4 factors, Oct60, Oct25, and Oct91, positively regulate Cdx1 expression through FGF signaling, and during gastrulation the Oct3/4 factors become repressors of Cdx1. Cdx1 negatively regulates the Pou5f1 genes during gastrulation, thus contributing to the repression of the network maintaining the undifferentiated state and promoting the onset of gastrulation. These regulatory interactions suggest that Oct3/4 initiates its own negative autoregulation through Cdx1 up-regulation to begin the repression of pluripotency in preparation for the onset of gastrulation and germ layer differentiation.
    Type of Publication: Journal article published
    PubMed ID: 21360791
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    Keywords: GROWTH ; CELL ; GENE ; GENES ; GENOME ; YEAST ; Drosophila ; CAENORHABDITIS-ELEGANS ; CYCLIN-E ; SCREENS ; SYNTHETIC LETHALITY ; EPISTASIS ; INTERACTION NETWORK
    Abstract: BACKGROUND: Systematic measurement of genetic interactions by combinatorial RNAi (co-RNAi) is a powerful tool for mapping functional modules and discovering components. It also provides insights into the role of epistasis on the way from genotype to phenotype. The interpretation of co-RNAi data requires computational and statistical analysis in order to detect interactions reliably and sensitively. RESULTS: We present a comprehensive approach to the analysis of univariate phenotype measurements, such as cell culture size. The method is based on a quantitative model and is demonstrated on two example Drosophila data sets. We discuss adjustment for technical variability, data quality assessment, model parameter fitting and fit diagnostics, choice of scale, and assessment of statistical significance. CONCLUSIONS: As a result, we obtain quantitative genetic interactions and interaction networks reflecting known biological relationships between the target genes. The reliable extraction of presence, absence, and strength of interactions provides insights into molecular mechanisms.
    Type of Publication: Journal article published
    PubMed ID: 21849035
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    Keywords: regulatory T cells ; SUPPRESSOR-CELLS ; T-CELL ; T-CELLS ; CELLS ; GROWTH ; CELL ; MELANOMA ; PHENOTYPE
    Type of Publication: Meeting abstract published
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    Keywords: TARGET ; CELL-LINE ; LINE ; ONCOLOGY ; GENES ; GENE ; CELL ; GENERATION ; TARGET GENES
    Type of Publication: Meeting abstract published
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