TY - JOUR A1 - Feldheim, Jonas A1 - Kessler, Almuth F. A1 - Feldheim, Julia J. A1 - Schmitt, Dominik A1 - Oster, Christoph A1 - Lazaridis, Lazaros A1 - Glas, Martin A1 - Ernestus, Ralf-Ingo A1 - Monoranu, Camelia M. A1 - Löhr, Mario A1 - Hagemann, Carsten T1 - BRMS1 in gliomas — an expression analysis JF - Cancers N2 - The metastatic suppressor BRMS1 interacts with critical steps of the metastatic cascade in many cancer entities. As gliomas rarely metastasize, BRMS1 has mainly been neglected in glioma research. However, its interaction partners, such as NFκB, VEGF, or MMPs, are old acquaintances in neurooncology. The steps regulated by BRMS1, such as invasion, migration, and apoptosis, are commonly dysregulated in gliomas. Therefore, BRMS1 shows potential as a regulator of glioma behavior. By bioinformatic analysis, in addition to our cohort of 118 specimens, we determined BRMS1 mRNA and protein expression as well as its correlation with the clinical course in astrocytomas IDH mutant, CNS WHO grade 2/3, and glioblastoma IDH wild-type, CNS WHO grade 4. Interestingly, we found BRMS1 protein expression to be significantly decreased in the aforementioned gliomas, while BRMS1 mRNA appeared to be overexpressed throughout. This dysregulation was independent of patients’ characteristics or survival. The protein and mRNA expression differences cannot be finally explained at this stage. However, they suggest a post-transcriptional dysregulation that has been previously described in other cancer entities. Our analyses present the first data on BRMS1 expression in gliomas that can provide a starting point for further investigations. KW - glioblastoma KW - metastasis KW - suppressor KW - behavior KW - mRNA KW - protein Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-319225 SN - 2072-6694 VL - 15 IS - 11 ER - TY - JOUR A1 - Feldheim, Jonas A1 - Wend, David A1 - Lauer, Mara J. A1 - Monoranu, Camelia M. A1 - Glas, Martin A1 - Kleinschnitz, Christoph A1 - Ernestus, Ralf-Ingo A1 - Braunger, Barbara M. A1 - Meybohm, Patrick A1 - Hagemann, Carsten A1 - Burek, Malgorzata T1 - Protocadherin Gamma C3 (PCDHGC3) is strongly expressed in glioblastoma and its high expression is associated with longer progression-free survival of patients JF - International Journal of Molecular Sciences N2 - Protocadherins (PCDHs) belong to the cadherin superfamily and represent the largest subgroup of calcium-dependent adhesion molecules. In the genome, most PCDHs are arranged in three clusters, α, β, and γ on chromosome 5q31. PCDHs are highly expressed in the central nervous system (CNS). Several PCDHs have tumor suppressor functions, but their individual role in primary brain tumors has not yet been elucidated. Here, we examined the mRNA expression of PCDHGC3, a member of the PCDHγ cluster, in non-cancerous brain tissue and in gliomas of different World Health Organization (WHO) grades and correlated it with the clinical data of the patients. We generated a PCDHGC3 knockout U343 cell line and examined its growth rate and migration in a wound healing assay. We showed that PCDHGC3 mRNA and protein were significantly overexpressed in glioma tissue compared to a non-cancerous brain specimen. This could be confirmed in glioma cell lines. High PCDHGC3 mRNA expression correlated with longer progression-free survival (PFS) in glioma patients. PCDHGC3 knockout in U343 resulted in a slower growth rate but a significantly faster migration rate in the wound healing assay and decreased the expression of several genes involved in WNT signaling. PCDHGC3 expression should therefore be further investigated as a PFS-marker in gliomas. However, more studies are needed to elucidate the molecular mechanisms underlying the PCDHGC3 effects. KW - glioblastoma multiforme KW - glioma KW - astrocytoma KW - recurrence KW - relapse KW - mRNA KW - protein KW - brain KW - expression KW - PCDHGC3 KW - WNT signaling Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-284433 SN - 1422-0067 VL - 23 IS - 15 ER - TY - JOUR A1 - El Mouali, Youssef A1 - Gerovac, Milan A1 - Mineikaitė, Raminta A1 - Vogel, Jörg T1 - In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid JF - Nucleic Acids Research N2 - FinO-domain proteins represent an emerging family of RNA-binding proteins (RBPs) with diverse roles in bacterial post-transcriptional control and physiology. They exhibit an intriguing targeting spectrum, ranging from an assumed single RNA pair (FinP/traJ) for the plasmid-encoded FinO protein, to transcriptome-wide activity as documented for chromosomally encoded ProQ proteins. Thus, the shared FinO domain might bear an unusual plasticity enabling it to act either selectively or promiscuously on the same cellular RNA pool. One caveat to this model is that the full suite of in vivo targets of the assumedly highly selective FinO protein is unknown. Here, we have extensively profiled cellular transcripts associated with the virulence plasmid-encoded FinO in Salmonella enterica. While our analysis confirms the FinP sRNA of plasmid pSLT as the primary FinO target, we identify a second major ligand: the RepX sRNA of the unrelated antibiotic resistance plasmid pRSF1010. FinP and RepX are strikingly similar in length and structure, but not in primary sequence, and so may provide clues to understanding the high selectivity of FinO-RNA interactions. Moreover, we observe that the FinO RBP encoded on the Salmonella virulence plasmid controls the replication of a cohabitating antibiotic resistance plasmid, suggesting cross-regulation of plasmids on the RNA level. KW - antisense RNA KW - Escherichia coli KW - chromosomal genes KW - protein KW - chaperone KW - virulence KW - family KW - HFQ KW - specificity KW - inhibition Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-261072 VL - 49 IS - 9 ER - TY - JOUR A1 - Tolay, Nazife A1 - Buchberger, Alexander T1 - Comparative profiling of stress granule clearance reveals differential contributions of the ubiquitin system JF - Life Science Alliance N2 - Stress granules (SGs) are cytoplasmic condensates containing untranslated mRNP complexes. They are induced by various proteotoxic conditions such as heat, oxidative, and osmotic stress. SGs are believed to protect mRNPs from degradation and to enable cells to rapidly resume translation when stress conditions subside. SG dynamics are controlled by various posttranslationalmodifications, but the role of the ubiquitin system has remained controversial. Here, we present a comparative analysis addressing the involvement of the ubiquitin system in SG clearance. Using high-resolution immuno-fluorescence microscopy, we found that ubiquitin associated to varying extent with SGs induced by heat, arsenite, H2O2, sorbitol, or combined puromycin and Hsp70 inhibitor treatment. SG-associated ubiquitin species included K48- and K63-linked conjugates, whereas free ubiquitin was not significantly enriched. Inhibition of the ubiquitin activating enzyme, deubiquitylating enzymes, the 26S proteasome and p97/VCP impaired the clearance of arsenite- and heat-induced SGs, whereas SGs induced by other stress conditions were little affected. Our data underline the differential involvement of the ubiquitin system in SG clearance, a process important to prevent the formation of disease-linked aberrant SGs. KW - phase transition KW - quality control KW - protein KW - inhibition KW - complexity KW - separation KW - diversity KW - autophagy KW - ALS KW - P97 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-259810 VL - 4 IS - 5 ER - TY - JOUR A1 - Feldheim, Jonas A1 - Kessler, Almuth F. A1 - Schmitt, Dominik A1 - Salvador, Ellaine A1 - Monoranu, Camelia M. A1 - Feldheim, Julia J. A1 - Ernestus, Ralf-Ingo A1 - Löhr, Mario A1 - Hagemann, Carsten T1 - Ribosomal Protein S27/Metallopanstimulin-1 (RPS27) in Glioma — A New Disease Biomarker? JF - Cancers N2 - Despite its significant overexpression in several malignant neoplasms, the expression of RPS27 in the central nervous system (CNS) is widely unknown. We identified the cell types expressing RPS27 in the CNS under normal and disease conditions. We acquired specimens of healthy brain (NB), adult pilocytic astrocytoma (PA) World Health Organization (WHO) grade I, anaplastic PA WHO grade III, gliomas WHO grade II/III with or without isocitrate dehydrogenase (IDH) mutation, and glioblastoma multiforme (GBM). RPS27 protein expression was examined by immunohistochemistry and double-fluorescence staining and its mRNA expression quantified by RT-PCR. Patients’ clinical and tumor characteristics were collected retrospectively. RPS27 protein was specifically expressed in tumor cells and neurons, but not in healthy astrocytes. In tumor tissue, most macrophages were positive, while this was rarely the case in inflamed tissue. Compared to NB, RPS27 mRNA was in mean 6.2- and 8.8-fold enhanced in gliomas WHO grade II/III with (p < 0.01) and without IDH mutation (p = 0.01), respectively. GBM displayed a 4.6-fold increased mean expression (p = 0.02). Although RPS27 expression levels did not affect the patients’ survival, their association with tumor cells and tumor-associated macrophages provides a rationale for a future investigation of a potential function during gliomagenesis and tumor immune response. KW - glioblastoma multiforme KW - low-grade glioma KW - astrocytoma KW - recurrence KW - relapse KW - mRNA KW - protein KW - brain KW - expression KW - MPS1 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-203648 SN - 2072-6694 VL - 12 IS - 5 ER - TY - JOUR A1 - Hoffmann, Linda S A1 - Schmidt, Peter M A1 - Keim, Yvonne A1 - Hoffmann, Carsten A1 - Schmidt, Harald H H W A1 - Stasch, Johannes-Peter T1 - Fluorescence Dequenching Makes Haem-Free Soluble Guanylate Cyclase Detectable in Living Cells JF - PLOS ONE N2 - In cardiovascular disease, the protective NO/sGC/cGMP signalling-pathway is impaired due to a decreased pool of NO-sensitive haem-containing sGC accompanied by a reciprocal increase in NO-insensitive haem-free sGC. However, no direct method to detect cellular haem-free sGC other than its activation by the new therapeutic class of haem mimetics, such as BAY 58-2667, is available. Here we show that fluorescence dequenching, based on the interaction of the optical active prosthetic haem group and the attached biarsenical fluorophor FlAsH can be used to detect changes in cellular sGC haem status. The partly overlap of the emission spectrum of haem and FlAsH allows energy transfer from the fluorophore to the haem which reduces the intensity of FlAsH fluorescence. Loss of the prosthetic group, e. g. by oxidative stress or by replacement with the haem mimetic BAY 58-2667, prevented the energy transfer resulting in increased fluorescence. Haem loss was corroborated by an observed decrease in NO-induced sGC activity, reduced sGC protein levels, and an increased effect of BAY 58-2667. The use of a haem-free sGC mutant and a biarsenical dye that was not quenched by haem as controls further validated that the increase in fluorescence was due to the loss of the prosthetic haem group. The present approach is based on the cellular expression of an engineered sGC variant limiting is applicability to recombinant expression systems. Nevertheless, it allows to monitor sGC's redox regulation in living cells and future enhancements might be able to extend this approach to in vivo conditions. KW - spontaneously hypersensitive-rats KW - nitric-oxide KW - down-regulation KW - energy-transfer KW - cyclic-gmp KW - protein KW - activation KW - identification KW - in-vivo KW - no Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-139631 VL - 6 IS - 8 ER - TY - JOUR A1 - Zanucco, Emanuele A1 - Götz, Rudolf A1 - Potapenko, Tamara A1 - Carraretto, Irene A1 - Ceteci, Semra A1 - Ceteci, Fatih A1 - Seeger, Werner A1 - Savai, Rajkumar A1 - Rapp, Ulf R. T1 - Expression of B-RAF V600E in Type II Pneumocytes Causes Abnormalities in Alveolar Formation, Airspace Enlargement and Tumor Formation in Mice JF - PLOS ONE N2 - Growth factor induced signaling cascades are key regulatory elements in tissue development, maintenance and regeneration. Perturbations of these cascades have severe consequences, leading to developmental disorders and neoplastic diseases. As a major function in signal transduction, activating mutations in RAF family kinases are the cause of human tumorigenesis, where B-RAF V600E has been identified as the prevalent mutant. In order to address the oncogenic function of B-RAF V600E, we have generated transgenic mice expressing the activated oncogene specifically in lung alveolar epithelial type II cells. Constitutive expression of B-RAF V600E caused abnormalities in alveolar epithelium formation that led to airspace enlargements. These lung lesions showed signs of tissue remodeling and were often associated with chronic inflammation and low incidence of lung tumors. The inflammatory cell infiltration did not precede the formation of the lung lesions but was rather accompanied with late tumor development. These data support a model where the continuous regenerative process initiated by oncogenic B-RAF-driven alveolar disruption provides a tumor-promoting environment associated with chronic inflammation. KW - obstructive pulmonary-disease KW - lung-cancer KW - somatic mutations KW - epithelial-cells KW - mouse models KW - protein KW - kinase KW - inflammation KW - activation KW - pathway Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-137061 VL - 6 IS - 12 ER - TY - JOUR A1 - Harrington, John M. A1 - Scelsi, Chris A1 - Hartel, Andreas A1 - Jones, Nicola G. A1 - Engstler, Markus A1 - Capewell, Paul A1 - MacLeod, Annette A1 - Hajduk, Stephen T1 - Novel African Trypanocidal Agents: Membrane Rigidifying Peptides JF - PLoS One N2 - The bloodstream developmental forms of pathogenic African trypanosomes are uniquely susceptible to killing by small hydrophobic peptides. Trypanocidal activity is conferred by peptide hydrophobicity and charge distribution and results from increased rigidity of the plasma membrane. Structural analysis of lipid-associated peptide suggests a mechanism of phospholipid clamping in which an internal hydrophobic bulge anchors the peptide in the membrane and positively charged moieties at the termini coordinate phosphates of the polar lipid headgroups. This mechanism reveals a necessary phenotype in bloodstream form African trypanosomes, high membrane fluidity, and we suggest that targeting the plasma membrane lipid bilayer as a whole may be a novel strategy for the development of new pharmaceutical agents. Additionally, the peptides we have described may be valuable tools for probing the biosynthetic machinery responsible for the unique composition and characteristics of African trypanosome plasma membranes. KW - depth KW - trypanosome lytic factor KW - signal peptides KW - cell surface KW - protein KW - brucei KW - environment KW - bilayers KW - binding KW - probes Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-135179 VL - 7 IS - 9 ER - TY - JOUR A1 - Worku, Netsanet A1 - Stich, August A1 - Daugschies, Arwid A1 - Wenzel, Iris A1 - Kurz, Randy A1 - Thieme, Rene A1 - Kurz, Susanne A1 - Birkenmeier, Gerd T1 - Ethyl Pyruvate Emerges as a Safe and Fast Acting Agent against Trypanosoma brucei by Targeting Pyruvate Kinase Activity JF - PLoS ONE N2 - Background Human African Trypanosomiasis (HAT) also called sleeping sickness is an infectious disease in humans caused by an extracellular protozoan parasite. The disease, if left untreated, results in 100% mortality. Currently available drugs are full of severe drawbacks and fail to escape the fast development of trypanosoma resistance. Due to similarities in cell metabolism between cancerous tumors and trypanosoma cells, some of the current registered drugs against HAT have also been tested in cancer chemotherapy. Here we demonstrate for the first time that the simple ester, ethyl pyruvate, comprises such properties. Results The current study covers the efficacy and corresponding target evaluation of ethyl pyruvate on T. brucei cell lines using a combination of biochemical techniques including cell proliferation assays, enzyme kinetics, phasecontrast microscopic video imaging and ex vivo toxicity tests. We have shown that ethyl pyruvate effectively kills trypanosomes most probably by net ATP depletion through inhibition of pyruvate kinase (Ki = 3.0\(\pm\)0.29 mM). The potential of ethyl pyruvate as a trypanocidal compound is also strengthened by its fast acting property, killing cells within three hours post exposure. This has been demonstrated using video imaging of live cells as well as concentration and time dependency experiments. Most importantly, ethyl pyruvate produces minimal side effects in human red cells and is known to easily cross the blood-brain-barrier. This makes it a promising candidate for effective treatment of the two clinical stages of sleeping sickness. Trypanosome drug-resistance tests indicate irreversible cell death and a low incidence of resistance development under experimental conditions. Conclusion Our results present ethyl pyruvate as a safe and fast acting trypanocidal compound and show that it inhibits the enzyme pyruvate kinase. Competitive inhibition of this enzyme was found to cause ATP depletion and cell death. Due to its ability to easily cross the blood-brain-barrier, ethyl pyruvate could be considered as new candidate agent to treat the hemo-lymphatic as well as neurological stages of sleeping sickness. KW - human african trypanosomiasis KW - glycolysis KW - transport KW - protein KW - cruzi KW - chemotherapy KW - metabolism KW - in vitro KW - drugs KW - sleeping sickness Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-150002 VL - 10 IS - 9 ER - TY - JOUR A1 - Vieira, Jacqueline A1 - Jones, Alex R. A1 - Danon, Antoine A1 - Sakuma, Michiyo A1 - Hoang, Nathalie A1 - Robles, David A1 - Tait, Shirley A1 - Heyes, Derren J. A1 - Picot, Marie A1 - Yoshii, Taishi A1 - Helfrich-Förster, Charlotte A1 - Soubigou, Guillaume A1 - Coppee, Jean-Yves A1 - Klarsfeld, André A1 - Rouyer, Francois A1 - Scrutton, Nigel S. A1 - Ahmad, Margaret T1 - Human Cryptochrome-1 Confers Light Independent Biological Activity in Transgenic Drosophila Correlated with Flavin Radical Stability JF - PLoS One N2 - Cryptochromes are conserved flavoprotein receptors found throughout the biological kingdom with diversified roles in plant development and entrainment of the circadian clock in animals. Light perception is proposed to occur through flavin radical formation that correlates with biological activity in vivo in both plants and Drosophila. By contrast, mammalian (Type II) cryptochromes regulate the circadian clock independently of light, raising the fundamental question of whether mammalian cryptochromes have evolved entirely distinct signaling mechanisms. Here we show by developmental and transcriptome analysis that Homo sapiens cryptochrome - 1 (HsCRY1) confers biological activity in transgenic expressing Drosophila in darkness, that can in some cases be further stimulated by light. In contrast to all other cryptochromes, purified recombinant HsCRY1 protein was stably isolated in the anionic radical flavin state, containing only a small proportion of oxidized flavin which could be reduced by illumination. We conclude that animal Type I and Type II cryptochromes may both have signaling mechanisms involving formation of a flavin radical signaling state, and that light independent activity of Type II cryptochromes is a consequence of dark accumulation of this redox form in vivo rather than of a fundamental difference in signaling mechanism. KW - arabidopsi KW - dependent magnetosensitvity KW - protein KW - clock KW - gene KW - mechanism KW - rhythm KW - oscillator KW - circadian photoreception KW - mammalian CRY1 Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134513 VL - 7 IS - 3 ER - TY - JOUR A1 - Molochnikov, Leonid A1 - Rabey, Jose M. A1 - Dobronevsky, Evgenya A1 - Bonuccelli, Ubaldo A1 - Ceravolo, Roberto A1 - Frosini, Daniela A1 - Grünblatt, Edna A1 - Riederer, Peter A1 - Jacob, Christian A1 - Aharon-Peretz, Judith A1 - Bashenko, Yulia A1 - Youdim, Moussa B. H. A1 - Mandel, Silvia A. T1 - A molecular signature in blood identifies early Parkinson's disease JF - Molecular Neurodegeneration N2 - Background: The search for biomarkers in Parkinson's disease (PD) is crucial to identify the disease early and monitor the effectiveness of neuroprotective therapies. We aim to assess whether a gene signature could be detected in blood from early/mild PD patients that could support the diagnosis of early PD, focusing on genes found particularly altered in the substantia nigra of sporadic PD. Results: The transcriptional expression of seven selected genes was examined in blood samples from 62 early stage PD patients and 64 healthy age-matched controls. Stepwise multivariate logistic regression analysis identified five genes as optimal predictors of PD: p19 S-phase kinase-associated protein 1A (odds ratio [OR] 0.73; 95% confidence interval [CI] 0.60-0.90), huntingtin interacting protein-2 (OR 1.32; CI 1.08-1.61), aldehyde dehydrogenase family 1 subfamily A1 (OR 0.86; 95% CI 0.75-0.99), 19 S proteasomal protein PSMC4 (OR 0.73; 95% CI 0.60-0.89) and heat shock 70-kDa protein 8 (OR 1.39; 95% CI 1.14-1.70). At a 0.5 cut-off the gene panel yielded a sensitivity and specificity in detecting PD of 90.3 and 89.1 respectively and the area under the receiving operating curve (ROC AUC) was 0.96. The performance of the five-gene classifier on the de novo PD individuals alone composing the early PD cohort (n = 38), resulted in a similar ROC with an AUC of 0.95, indicating the stability of the model and also, that patient medication had no significant effect on the predictive probability (PP) of the classifier for PD risk. The predictive ability of the model was validated in an independent cohort of 30 patients at advanced stage of PD, classifying correctly all cases as PD (100% sensitivity). Notably, the nominal average value of the PP for PD (0.95 (SD = 0.09)) in this cohort was higher than that of the early PD group (0.83 (SD = 0.22)), suggesting a potential for the model to assess disease severity. Lastly, the gene panel fully discriminated between PD and Alzheimer's disease (n = 29). Conclusions: The findings provide evidence on the ability of a five-gene panel to diagnose early/mild PD, with a possible diagnostic value for detection of asymptomatic PD before overt expression of the disorder. KW - cerebrospina KW - magnetic-resonance-spectroscopy KW - protein KW - biomarkers KW - E3 ubiquitin ligase KW - SCF KW - SKP1 KW - heat shock protein Hsc-70 KW - early diagnosis KW - fluid KW - alpha-synuclein KW - dehydrogenases KW - Alzheimer's disease KW - sporadic Parkinson's disease KW - blood biomarker KW - CSF KW - multiple system atrophy KW - clinical diagnosis KW - substantia nigra KW - gene expression Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-134508 VL - 7 IS - 26 ER - TY - JOUR A1 - Tessmer, Ingrid A1 - Melikishvili, Manana A1 - Fried, Michael G. T1 - Cooperative cluster formation, DNA bending and base-flipping by O\(^6\)-alkylguanine-DNA alkyltransferase JF - Nucleic Acids Research N2 - O\(^6\)-Alkylguanine-DNA alkyltransferase (AGT) repairs mutagenic O\(^6\)-alkylguanine and O\(^4\)-alkylthymine adducts in DNA, protecting the genome and also contributing to the resistance of tumors to chemotherapeutic alkylating agents. AGT binds DNA cooperatively, and cooperative interactions are likely to be important in lesion search and repair. We examined morphologies of complexes on long, unmodified DNAs, using analytical ultracentrifugation and atomic force microscopy. AGT formed clusters of 11 proteins. Longer clusters, predicted by the McGhee-von Hippel model, were not seen even at high [protein]. Interestingly, torsional stress due to DNA unwinding has the potential to limit cluster size to the observed range. DNA at cluster sites showed bend angles (similar to 0, similar to 30 and similar to 60 degrees) that are consistent with models in which each protein induces a bend of similar to 30 degrees. Distributions of complexes along the DNA are incompatible with sequence specificity but suggest modest preference for DNA ends. These properties tell us about environments in which AGT may function. Small cooperative clusters and the ability to accommodate a range of DNA bends allow function where DNA topology is constrained, such as near DNA-replication complexes. The low sequence specificity allows efficient and unbiased lesion search across the entire genome. KW - inactivation KW - nucleotide excision-repair KW - atomic-force microscopy KW - noncooperative binding KW - restricition enzymes KW - complex stability KW - stranded DNAs KW - protein KW - chemotherapy KW - AGT Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-133949 VL - 40 IS - 17 ER - TY - JOUR A1 - Fernández-Rodríguez, Juana A1 - Quiles, Francisco A1 - Blanco, Ignacio A1 - Teulé, Alex A1 - Feliubadaló, Lídia A1 - del Valle, Jesús A1 - Salinas, Mónica A1 - Izquierdo, Ángel A1 - Darder, Esther A1 - Schindler, Detlev A1 - Capellá, Gabriel A1 - Brunet, Joan A1 - Lázaro, Conxi A1 - Angel Pujana, Miguel T1 - Analysis of SLX4/FANCP in non-BRCA1/2-mutated breast cancer families JF - BMC Cancer N2 - Background: Genes that, when mutated, cause Fanconi anemia or greatly increase breast cancer risk encode for proteins that converge on a homology-directed DNA damage repair process. Mutations in the SLX4 gene, which encodes for a scaffold protein involved in the repair of interstrand cross-links, have recently been identified in unclassified Fanconi anemia patients. A mutation analysis of SLX4 in German or Byelorussian familial cases of breast cancer without detected mutations in BRCA1 or BRCA2 has been completed, with globally negative results. Methods: The genomic region of SLX4, comprising all exons and exon-intron boundaries, was sequenced in 94 Spanish familial breast cancer cases that match a criterion indicating the potential presence of a highly-penetrant germline mutation, following exclusion of BRCA1 or BRCA2 mutations. Results: This mutational analysis revealed extensive genetic variation of SLX4, with 21 novel single nucleotide variants; however, none could be linked to a clear alteration of the protein function. Nonetheless, genotyping 10 variants (nine novel, all missense amino acid changes) in a set of controls (138 women and 146 men) did not detect seven of them. Conclusions: Overall, while the results of this study do not identify clearly pathogenic mutations of SLX4 contributing to breast cancer risk, further genetic analysis, combined with functional assays of the identified rare variants, may be warranted to conclusively assess the potential link with the disease. KW - SLX4 KW - Holliday junction reolvass KW - Fanconi-anemia subtype KW - susceptibility gene KW - helicase BRIP1 KW - ovarian cancer KW - DNA repair KW - mutations KW - protein KW - RAD51C Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131772 VL - 12 IS - 84 ER - TY - JOUR A1 - Gassen, Alwine A1 - Brechtefeld, Doris A1 - Schandry, Niklas A1 - Arteaga-Salas, J. Manuel A1 - Israel, Lars A1 - Imhof, Axel A1 - Janzen, Christian J. T1 - DOT1A-dependent H3K76 methylation is required for replication regulation in Trypanosoma brucei JF - Nucleic Acids Research N2 - Cell-cycle progression requires careful regulation to ensure accurate propagation of genetic material to the daughter cells. Although many cell-cycle regulators are evolutionarily conserved in the protozoan parasite Trypanosoma brucei, novel regulatory mechanisms seem to have evolved. Here, we analyse the function of the histone methyltransferase DOT1A during cell-cycle progression. Over-expression of DOT1A generates a population of cells with aneuploid nuclei as well as enucleated cells. Detailed analysis shows that DOT1A over-expression causes continuous replication of the nuclear DNA. In contrast, depletion of DOT1A by RNAi abolishes replication but does not prevent karyokinesis. As histone H3K76 methylation has never been associated with replication control in eukaryotes before, we have discovered a novel function of DOT1 enzymes, which might not be unique to trypanosomes. KW - variants KW - cell-cycle regulation KW - blood-stream forms KW - african trypanosomes KW - mammalian cells KW - DNA replication KW - DOT1 KW - protein KW - transcription KW - cultivation Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131449 VL - 40 IS - 20 ER - TY - JOUR A1 - Buga, Ana-Maria A1 - Scholz, Claus Jürgen A1 - Kumar, Senthil A1 - Herndon, James G. A1 - Alexandru, Dragos A1 - Cojocaru, Gabriel Radu A1 - Dandekar, Thomas A1 - Popa-Wagner, Aurel T1 - Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke JF - PLoS One N2 - Background: Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions. Methodology/Principal Findings: We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats. The correspondence, heat map, and dendrogram analyses independently suggest a differential, age-group-specific behaviour of major gene clusters after stroke. Overall, the pattern of gene expression strongly suggests that the response of the aged rat brain is qualitatively rather than quantitatively different from the young, i.e. the total number of regulated genes is comparable in the two age groups, but the aged rats had great difficulty in mounting a timely response to stroke. Our study indicates that four genes related to neuropathic syndrome, stress, anxiety disorders and depression (Acvr1c, Cort, Htr2b and Pnoc) may have impaired response to stroke in aged rats. New therapeutic options in aged rats may also include Calcrl, Cyp11b1, Prcp, Cebpa, Cfd, Gpnmb, Fcgr2b, Fcgr3a, Tnfrsf26, Adam 17 and Mmp14. An unexpected target is the enzyme 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 in aged rats, a key enzyme in the cholesterol synthesis pathway. Post-stroke axonal growth was compromised in both age groups. Conclusion/Significance: We suggest that a multi-stage, multimodal treatment in aged animals may be more likely to produce positive results. Such a therapeutic approach should be focused on tissue restoration but should also address other aspects of patient post-stroke therapy such as neuropathic syndrome, stress, anxiety disorders, depression, neurotransmission and blood pressure. KW - gamma KW - corticotropin-releasing hormone KW - colony-stimulating factor KW - cerebral ischemia KW - receptor KW - brain KW - protein KW - inhibitor KW - mouse KW - differentiation Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130657 VL - 7 IS - 12 ER - TY - JOUR A1 - Stepniak, Beata A1 - Kästner, Anne A1 - Poggi, Giulia A1 - Mitjans, Marina A1 - Begemann, Martin A1 - Hartmann, Annette A1 - Van der Auwera, Sandra A1 - Sananbenesi, Farahnaz A1 - Krüger-Burg, Dilja A1 - Matuszko, Gabriela A1 - Brosi, Cornelia A1 - Homuth, Georg A1 - Völzke, Henry A1 - Benseler, Fritz A1 - Bagni, Claudia A1 - Fischer, Utz A1 - Dityatev, Alexander A1 - Grabe, Hans-Jörgen A1 - Rujescu, Dan A1 - Fischer, Andre A1 - Ehrenreich, Hannelore T1 - Accumulated common variants in the broader fragile X gene family modulate autistic phenotypes JF - EMBO Molecular Medicine N2 - Fragile X syndrome (FXS) is mostly caused by a CGG triplet expansion in the fragile X mental retardation 1 gene (FMR1). Up to 60% of affected males fulfill criteria for autism spectrum disorder (ASD), making FXS the most frequent monogenetic cause of syndromic ASD. It is unknown, however, whether normal variants (independent of mutations) in the fragile X gene family (FMR1, FXR1, FXR2) and in FMR2 modulate autistic features. Here, we report an accumulation model of 8 SNPs in these genes, associated with autistic traits in a discovery sample of male patients with schizophrenia (N = 692) and three independent replicate samples: patients with schizophrenia (N = 626), patients with other psychiatric diagnoses (N = 111) and a general population sample (N = 2005). For first mechanistic insight, we contrasted microRNA expression in peripheral blood mononuclear cells of selected extreme group subjects with high-versus low-risk constellation regarding the accumulation model. Thereby, the brain-expressed miR-181 species emerged as potential "umbrella regulator", with several seed matches across the fragile X gene family and FMR2. To conclude, normal variation in these genes contributes to the continuum of autistic phenotypes. KW - permutation KW - miR-181 KW - PGAS KW - FXR2 KW - FXR1 KW - FMR2 KW - FMR1 KW - identification KW - protein KW - fraxe mental retardation KW - CGG repeat KW - CPG Island KW - schizophrenia KW - expression KW - males Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-136893 VL - 7 IS - 12 ER - TY - JOUR A1 - Rodrigues, Lénia A1 - Popov, Nikita A1 - Kaye, Kenneth M. A1 - Simas, J. Pedro T1 - Stabilization of Myc through Heterotypic Poly-Ubiquitination by mLANA Is Critical for \(\gamma\)-Herpesvirus Lymphoproliferation JF - PLoS PATHOGENS N2 - Host colonization by lymphotropic \(\gamma\)-herpesviruses depends critically on expansion of viral genomes in germinal center (GC) B-cells. Myc is essential for the formation and maintenance of GCs. Yet, the role of Myc in the pathogenesis of \(\gamma\)-cherpesviruses is still largely unknown. In this study, Myc was shown to be essential for the lymphotropic \(\gamma\)-herpesvirus MuHV- 4 biology as infected cells exhibited increased expression of Myc signature genes and the virus was unable to expand in Myc defficient GC B- cells. We describe a novel strategy of a viral protein activating Myc through increased protein stability resulting in increased progression through the cell cycle. This is acomplished by modulating a physiological posttranslational regulatory pathway of Myc. The molecular mechanism involves Myc heterotypic poly- ubiquitination mediated via the viral E3 ubiquitin- ligase mLANA protein. \(EC_5S^{mLANA}\) modulates cellular control of Myc turnover by antagonizing \(SCF^{Fbw7}\) mediated proteasomal degradation of Myc, mimicking \(SCF^{\beta-TrCP}\). The findings here reported reveal that modulation of Myc is essential for \(\gamma\)-herpesvirus persistent infection, establishing a link between virus induced lymphoproliferation and disease. KW - latency KW - murine gammaherpesvirus 68 KW - Epstein-Barr-virus KW - C-MYC KW - nuclear antigen KW - germinal center KW - B lymphocytes KW - protein KW - cells KW - beta-TRCP Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131227 VL - 9 IS - 8 ER - TY - JOUR A1 - Karle, Kathrin N. A1 - Schüle, Rebecca A1 - Klebe, Stephan A1 - Otto, Susanne A1 - Frischholz, Christian A1 - Liepelt-Scarfone, Inga A1 - Schöls, Ludger T1 - Electrophysiological characterisation of motor and sensory tracts in patients with hereditary spastic paraplegia (HSP) JF - Orphanet Journal of Rare Diseases N2 - Background: Hereditary spastic paraplegias (HSPs) are characterised by lower limb spasticity due to degeneration of the corticospinal tract. We set out for an electrophysiological characterisation of motor and sensory tracts in patients with HSP. Methods: We clinically and electrophysiologically examined a cohort of 128 patients with genetically confirmed or clinically probable HSP. Motor evoked potentials (MEPs) to arms and legs, somato-sensory evoked potentials of median and tibial nerves, and nerve conduction studies of tibial, ulnar, sural, and radial nerves were assessed. Results: Whereas all patients showed clinical signs of spastic paraparesis, MEPs were normal in 27% of patients and revealed a broad spectrum with axonal or demyelinating features in the others. This heterogeneity can at least in part be explained by different underlying genotypes, hinting for distinct pathomechanisms in HSP subtypes. In the largest subgroup, SPG4, an axonal type of damage was evident. Comprehensive electrophysiological testing disclosed a more widespread affection of long fibre tracts involving peripheral nerves and the sensory system in 40%, respectively. Electrophysiological abnormalities correlated with the severity of clinical symptoms. Conclusions: Whereas HSP is primarily considered as an upper motoneuron disorder, our data suggest a more widespread affection of motor and sensory tracts in the central and peripheral nervous system as a common finding in HSP. The distribution patterns of electrophysiological abnormalities were associated with distinct HSP genotypes and could reflect different underlying pathomechanisms. Electrophysiological measures are independent of symptomatic treatment and may therefore serve as a reliable biomarker in upcoming HSP trials. KW - motor evoked potential (MEP) KW - amyotrophic-lateral-sclerosis KW - somatosensory-evoked-potentials KW - Silver-syndrome KW - gene mutations KW - SPG4 KW - mouse model KW - ALSIN gene KW - neuropathy KW - paraparesis KW - protein KW - electrophysiology KW - hereditary spastic paraplegia (HSP) Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-124763 SN - 1750-1172 VL - 8 IS - 158 ER - TY - JOUR A1 - Farag, Heba Gamal A1 - Froehler, Sebastian A1 - Oexle, Konrad A1 - Ravindran, Ethiraj A1 - Schindler, Detlev A1 - Staab, Timo A1 - Huebner, Angela A1 - Kraemer, Nadine A1 - Chen, Wei A1 - Kaindl, Angela M. T1 - Abnormal centrosome and spindle morphology in a patient with autosomal recessive primary microcephaly type 2 due to compound heterozygous WDR62 gene mutation JF - Orphanet Journal of Rare Diseases N2 - Background: Autosomal recessive primary microcephaly (MCPH) is a rare neurodevelopmental disease with severe microcephaly at birth due to a pronounced reduction in brain volume and intellectual disability. Biallelic mutations in the WD repeat-containing protein 62 gene WDR62 are the genetic cause of MCPH2. However, the exact underlying pathomechanism of MCPH2 remains to be clarified. Methods/results: We characterized the clinical, radiological, and cellular features that add to the human MCPH2 phenotype. Exome sequencing followed by Sanger sequencing in a German family with two affected daughters with primary microcephaly revealed in the index patient the compound heterozygous mutations c. 1313G>A (p.R438H) / c.2864-2867delACAG (p.D955Afs*112) of WDR62, the second of which is novel. Radiological examination displayed small frontal lobes, corpus callosum hypoplasia, simplified hippocampal gyration, and cerebellar hypoplasia. We investigated the cellular phenotype in patient-derived lymphoblastoid cells and compared it with that of healthy female controls. WDR62 expression in the patient's immortalized lymphocytes was deranged, and mitotic spindle defects as well as abnormal centrosomal protein localization were apparent. Conclusion: We propose that a disruption of centrosome integrity and/or spindle organization may play an important role in the development of microcephaly in MCPH2. KW - cell division KW - intellectual disability KW - missense mutations KW - protein KW - malformations KW - establishment KW - cytokinesis KW - genome KW - midbody KW - database KW - maintenance KW - families KW - microcephaly KW - WDR62 mutation Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-123505 SN - 1750-1172 VL - 8 IS - 178 ER - TY - JOUR A1 - Piteau, Marianne A1 - Papatheodorou, Panagiotis A1 - Schwan, Carsten A1 - Schlosser, Andreas A1 - Aktories, Klaus A1 - Schmidt, Gudula T1 - Lu/BCAM Adhesion Glycoprotein Is a Receptor for Escherichia coli Cytotoxic Necrotizing Factor 1 (CNF1) JF - PLoS Pathogens N2 - The Cytotoxic Necrotizing Factor 1 (CNF1) is a protein toxin which is a major virulence factor of pathogenic Escherichia coli strains. Here, we identified the Lutheran (Lu) adhesion glycoprotein/basal cell adhesion molecule (BCAM) as cellular receptor for CNF1 by co-precipitation of cell surface molecules with tagged toxin. The CNF1-Lu/BCAM interaction was verified by direct protein-protein interaction analysis and competition studies. These studies revealed amino acids 720 to 1014 of CNF1 as the binding site for Lu/BCAM. We suggest two cell interaction sites in CNF1: first the N-terminus, which binds to p37LRP as postulated before. Binding of CNF1 to p37LRP seems to be crucial for the toxin's action. However, it is not sufficient for the binding of CNF1 to the cell surface. A region directly adjacent to the catalytic domain is a high affinity interaction site for Lu/BCAM. We found Lu/BCAM to be essential for the binding of CNF1 to cells. Cells deficient in Lu/BCAM but expressing p37LRP could not bind labeled CNF1. Therefore, we conclude that LRP and Lu/BCAM are both required for toxin action but with different functions. Author Summary We study a crucial virulence factor produced by pathogenic Escherichia coli strains, the Cytotoxic Necrotizing Factor 1 (CNF1). More than 80% of urinary tract infections (UTIs), which are counted among the most common bacterial infections of humans, are caused by Uropathogenic Escherichia coli (UPEC) strains. We and others elucidated the molecular mechanism of the E. coli toxin CNF1. It constitutively activates Rho GTPases by a direct covalent modification. The toxin enters mammalian cells by receptor-mediated endocytosis. Here, we identified the protein receptor for CNF1 by co-precipitation of cell surface molecules with the tagged toxin and subsequent Maldi-TOF analysis. We identified the Lutheran (Lu) adhesion glycoprotein/basal cell adhesion molecule (BCAM) as receptor for CNF1 and located its interaction site to the C-terminal part of the toxin. We performed direct protein-protein interaction analysis and competition studies. Moreover, cells deficient in Lu/BCAM could not bind labeled CNF1. The identification of a toxin's cellular receptor and receptor binding region is an important task for understanding the pathogenic function of the toxin and, moreover, to make the toxin accessible for its use as a cellbiological and pharmacological tool, for example for the generation of immunotoxins. KW - laminin receptor KW - factor-I KW - toxin KW - RHO KW - cells KW - activation KW - protein KW - domain KW - translocation KW - membrane Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-117987 SN - 1553-7374 VL - 10 IS - 1 ER - TY - JOUR A1 - Groeneweg, Femke L. A1 - van Royen, Martin E. A1 - Fenz, Susanne A1 - Keizer, Veer I. P. A1 - Geverts, Bart A1 - Prins, Jurrien A1 - de Kloet, E. Ron A1 - Houtsmuller, Adriaan B. A1 - Schmidt, Thomas S. A1 - Schaaf, Marcel J. M. T1 - Quantitation of Glucocorticoid Receptor DNA-Binding Dynamics by Single-Molecule Microscopy and FRAP JF - PLOS ONE N2 - Recent advances in live cell imaging have provided a wealth of data on the dynamics of transcription factors. However, a consistent quantitative description of these dynamics, explaining how transcription factors find their target sequences in the vast amount of DNA inside the nucleus, is still lacking. In the present study, we have combined two quantitative imaging methods, single-molecule microscopy and fluorescence recovery after photobleaching, to determine the mobility pattern of the glucocorticoid receptor (GR) and the mineralocorticoid receptor (MR), two ligand-activated transcription factors. For dexamethasone-activated GR, both techniques showed that approximately half of the population is freely diffusing, while the remaining population is bound to DNA. Of this DNA-bound population about half the GRs appeared to be bound for short periods of time (similar to 0.7 s) and the other half for longer time periods (similar to 2.3 s). A similar pattern of mobility was seen for the MR activated by aldosterone. Inactive receptors (mutant or antagonist-bound receptors) show a decreased DNA binding frequency and duration, but also a higher mobility for the diffusing population. Likely, very brief (<= 1 ms) interactions with DNA induced by the agonists underlie this difference in diffusion behavior. Surprisingly, different agonists also induce different mobilities of both receptors, presumably due to differences in ligand-induced conformational changes and receptor complex formation. In summary, our data provide a consistent quantitative model of the dynamics of GR and MR, indicating three types of interactions with DNA, which fit into a model in which frequent low-affinity DNA binding facilitates the search for high-affinity target sequences. KW - NF-KAPPA-B KW - image correlation spectroscopy KW - human mineralocorticoid receptor KW - nuclear-pore complexes KW - in-vivo KW - living cells KW - mobility KW - transcription KW - protein KW - reveals Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-117085 VL - 9 IS - 3 ER - TY - JOUR A1 - Fagan, Jeremy K. A1 - Dollar, Gretchen A1 - Lu, Qiuheng A1 - Barnett, Austen A1 - Jorge, Joaquin Pechuan A1 - Schlosser, Andreas A1 - Pfleger, Cathie A1 - Adler, Paul A1 - Jenny, Andreas T1 - Combover/CG10732, a Novel PCP Effector for Drosophila Wing Hair Formation JF - PLOS ONE N2 - The polarization of cells is essential for the proper functioning of most organs. Planar Cell Polarity (PCP), the polarization within the plane of an epithelium, is perpendicular to apical-basal polarity and established by the non-canonical Wnt/Fz-PCP signaling pathway. Within each tissue, downstream PCP effectors link the signal to tissue specific readouts such as stereocilia orientation in the inner ear and hair follicle orientation in vertebrates or the polarization of ommatidia and wing hairs in Drosophila melanogaster. Specific PCP effectors in the wing such as Multiple wing hairs (Mwh) and Rho Kinase (Rok) are required to position the hair at the correct position and to prevent ectopic actin hairs. In a genome-wide screen in vitro, we identified Combover (Cmb)/CG10732 as a novel Rho kinase substrate. Overexpression of Cmb causes the formation of a multiple hair cell phenotype (MHC), similar to loss of rok and mwh. This MHC phenotype is dominantly enhanced by removal of rok or of other members of the PCP effector gene family. Furthermore, we show that Cmb physically interacts with Mwh, and cmb null mutants suppress the MHC phenotype of mwh alleles. Our data indicate that Cmb is a novel PCP effector that promotes to wing hair formation, a function that is antagonized by Mwh. KW - planar cell polarity KW - RHO-associated kinease KW - convergent extension movements KW - ROK-alpha KW - protein KW - phosphorylation KW - actin KW - gene KW - morphogenesis KW - localization Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-115394 SN - 1932-6203 VL - 9 IS - 9 ER - TY - JOUR A1 - Norrmen, Camilla A1 - Figlia, Gianluca A1 - Lebrun-Julien, Frederic A1 - Pereira, Jorge A. A1 - Trötzmüller, Martin A1 - Köfeler, Harald C. A1 - Rantanen, Ville A1 - Wessig, Carsten A1 - van Deijk, Anne-Lieke F. A1 - Smit, August B. A1 - Verheijen, Mark H. G. A1 - Rüegg, Markus A. A1 - Hall, Michael N. A1 - Suter, Ueli T1 - mTORC1 Controls PNS Myelination along the mTORC1-RXR gamma-SREBP-Lipid Biosynthesis Axis in Schwann Cells JF - Cell Reports N2 - Myelin formation during peripheral nervous system (PNS) development, and reformation after injury and in disease, requires multiple intrinsic and extrinsic signals. Akt/mTOR signaling has emerged as a major player involved, but the molecular mechanisms and downstream effectors are virtually unknown. Here, we have used Schwann-cell-specific conditional gene ablation of raptor and rictor, which encode essential components of the mTOR complexes 1 (mTORC1) and 2 (mTORC2), respectively, to demonstrate that mTORC1 controls PNS myelination during development. In this process, mTORC1 regulates lipid biosynthesis via sterol regulatory element-binding proteins (SREBPs). This course of action is mediated by the nuclear receptor RXRg, which transcriptionally regulates SREBP1c downstream of mTORC1. Absence of mTORC1 causes delayed myelination initiation as well as hypomyelination, together with abnormal lipid composition and decreased nerve conduction velocity. Thus, we have identified the mTORC1-RXR gamma-SREBP axis controlling lipid biosynthesis as a major contributor to proper peripheral nerve function. KW - axonal integrity KW - peripheral nervous-system KW - COMPLEX 1 KW - rat hepatocytes KW - SREBP KW - mice KW - growth KW - protein KW - element KW - CNS Myelination Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114847 SN - 2211-1247 VL - 9 IS - 2 ER - TY - JOUR A1 - Senecal, Jean-Luc A1 - Isabelle, Catherine A1 - Fritzler, Marvin J. A1 - Targoff, Ira N. A1 - Goldstein, Rose A1 - Gagne, Michel A1 - Raynauld, Jean-Pierre A1 - Joyal, France A1 - Troyanov, Yves A1 - Dabauvalle, Marie-Christine T1 - An Autoimmune Myositis-Overlap Syndrome Associated With Autoantibodies to Nuclear Pore Complexes Description and Long-Term Follow-up of the Anti-Nup Syndrome JF - Medicine N2 - Autoimmune myositis encompasses various myositis-overlap syndromes, each being identified by the presence of serum marker autoantibodies. We describe a novel myositis-overlap syndrome in 4 patients characterized by the presence of a unique immunologic marker, autoantibodies to nuclear pore complexes. The clinical phenotype was characterized by prominent myositis in association with erosive, anti-CCP, and rheumatoid factor-positive arthritis, trigeminal neuralgia, mild interstitial lung disease, Raynaud phenomenon, and weight loss. The myositis was typically chronic, relapsing, and refractory to corticosteroids alone, but remitted with the addition of a second immuno-modulating drug. There was no clinical or laboratory evidence for liver disease. The prognosis was good with 100% long-term survival (mean follow-up 19.5 yr). By indirect immunofluorescence on HEp-2 cells, sera from all 4 patients displayed a high titer of antinuclear autoantibodies (ANA) with a distinct punctate peripheral (rim) fluorescent pattern of the nuclear envelope characteristic of nuclear pore complexes. Reactivity with nuclear pore complexes was confirmed by immunoelectron microscopy. In a cohort of 100 French Canadian patients with autoimmune myositis, the nuclear pore complex fluorescent ANA pattern was restricted to these 4 patients (4%). It was not observed in sera from 393 adult patients with systemic sclerosis (n = 112), mixed connective tissue disease (n = 35), systemic lupus (n = 94), rheumatoid arthritis (n = 45), or other rheumatic diseases (n = 107), nor was it observed in 62 normal adults. Autoantibodies to nuclear pore complexes were predominantly of IgG isotype. No other IgG autoantibody markers for defined connective tissue diseases or overlap syndromes were present, indicating a selective and highly focused immune response. In 3 patients, anti-nuclear pore complex autoantibody titers varied in parallel with myositis activity, suggesting a pathogenic link to pathophysiology. The nuclear pore complex proteins, that is, nucleoporins (nup), recognized by these sera were heterogeneous and included Nup358/RanBP2 (n = 2 patients), Nup90 (n = 1), Nup62 (n = 1), and gp210 (n = 1). Taken together the data suggest that nup autoantigens themselves drive the anti-nup autoimmune response. Immunogenetically, the 4 patients shared the DQA1*0501 allele associated with an increased risk for autoimmune myositis. In conclusion, we report an apparent novel subset of autoimmune myositis in our population of French Canadian patients with connective tissue diseases. This syndrome is recognized by the presence of a unique immunologic marker, autoantibodies to nuclear pore complexes that react with nups, consistent with an "anti-nupsyndrome.'' KW - idiopathic inflammatory myopathies KW - primary biliary-cirrhosis KW - transfer RNA-synthetases KW - major histocompatibility complex KW - systemic sclerosis KW - French-Canadian patients KW - protein KW - predictive factors KW - envelope KW - antibodies Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114829 SN - 0025-7974 VL - 93 IS - 24 ER - TY - THES A1 - Pinkert, Stefan T1 - The human proteome is shaped by evolution and interactions T1 - Das menschliche Proteom ist geformt durch Evolution und Interaktion N2 - Das menschliche Genom ist seit 2001 komplett sequenziert. Ein Großteil der Proteine wurde mittlerweile beschrieben und täglich werden bioinformatische Vorhersagen praktisch bestätigt. Als weiteres Großprojekt wurde kürzlich die Sequenzierung des Genoms von 1000 Menschen gestartet. Trotzdem ist immer noch wenig über die Evolution des gesamten menschlichen Proteoms bekannt. Proteindomänen und ihre Kombinationen sind teilweise sehr detailliert erforscht, aber es wurden noch nicht alle Domänenarchitekturen des Menschen in ihrer Gesamtheit miteinander verglichen. Der verwendete große hochqualitative Datensatz von Protein-Protein-Interaktionen und Komplexen stammt aus dem Jahr 2006 und ermöglicht es erstmals das menschliche Proteom mit einer vorher nicht möglichen Genauigkeit analysieren zu können. Hochentwickelte Cluster Algorithmen und die Verfügbarkeit von großer Rechenkapazität befähigen uns neue Information über Proteinnetzwerke ohne weitere Laborarbeit zu gewinnen. Die vorliegende Arbeit analysiert das menschliche Proteom auf drei verschiedenen Ebenen. Zuerst wurde der Ursprung von Proteinen basierend auf ihrer Domänenarchitektur analysiert, danach wurden Protein-Protein-Interaktionen untersucht und schließlich erfolgte Einteilung der Proteine nach ihren vorhandenen und fehlenden Interaktionen. Die meisten bekannten Proteine enthalten mindestens eine Domäne und die Proteinfunktion ergibt sich aus der Summe der Funktionen der einzelnen enthaltenen Domänen. Proteine, die auf der gleichen Domänenarchitektur basieren, das heißt die die gleichen Domänen in derselben Reihenfolge besitzen, sind homolog und daher aus einem gemeinsamen ursprünglichen Protein entstanden. Die Domänenarchitekturen der ursprünglichen Proteine wurden für 750000 Proteine aus 1313 Spezies bestimmt. Die Gruppierung von Spezies und ihrer Proteine ergibt sich aus taxonomischen Daten von NCBI-Taxonomy, welche mit zusätzlichen Informationen basierend auf molekularen Markern ergänzt wurden. Der resultierende Datensatz, bestehend aus 5817 Domänen und 32868 Domänenarchitekturen, war die Grundlage für die Bestimmung des Ursprungs der Proteine aufgrund ihrer Domänenarchitekturen. Es wurde festgestellt, dass nur ein kleiner Teil der neu evolvierten Domänenarchitekturen eines Taxons gleichzeitig auch im selben Taxon neu entstandene Proteindomänen enthält. Ein weiteres Ergebnis war, dass Domänenarchitekturen im Verlauf der Evolution länger und komplexer werden, und dass so verschiedene Organismen wie der Fadenwurm, die Fruchtfliege und der Mensch die gleiche Menge an unterschiedlichen Proteinen haben, aber deutliche Unterschiede in der Anzahl ihrer Domänenarchitekturen aufweisen. Der zweite Teil beschäftigt sich mit der Frage wie neu entstandene Proteine Bindungen mit dem schon bestehenden Proteinnetzwerk eingehen. In früheren Arbeiten wurde gezeigt, dass das Protein-Interaktions-Netzwerk ein skalenfreies Netz ist. Skalenfreie Netze, wie zum Beispiel das Internet, bestehen aus wenigen Knoten mit vielen Interaktionen, genannt Hubs, und andererseits aus vielen Knoten mit wenigen Interaktionen. Man vermutet, dass zwei Mechanismen zur Entstehung solcher Netzwerke führen. Erstens müssen neue Proteine um auch Teil des Proteinnetzwerkes zu werden mit Proteinen interagieren, die bereits Teil des Netzwerkes sind. Zweitens interagieren die neuen Proteine, gemäß der Theorie der bevorzugten Bindung, mit höherer Wahrscheinlichkeit mit solchen Proteinen im Netzwerk, die schon an zahlreichen weiteren Protein-Interaktionen beteiligt sind. Die Human Protein Reference Database stellt ein auf Informationen aus in-vivo Experimenten beruhendes Proteinnetzwerk für menschliche Proteine zur Verfügung. Basierend auf den in Kapitel I gewonnenen Informationen wurden die Proteine mit dem Ursprungstaxon ihrer Domänenarchitekturen versehen. Dadurch wurde gezeigt, dass ein Protein häufiger mit Proteinen, die im selben Taxon entstanden sind, interagiert, als mit Proteinen, die in anderen Taxa neu aufgetreten sind. Es stellte sich heraus, dass diese Interaktionsraten für alle Taxa deutlich höher waren, als durch das Zufallsmodel vorhergesagt wurden. Alle Taxa enthalten den gleichen Anteil an Proteinen mit vielen Interaktionen. Diese zwei Ergebnisse sprechen dagegen, dass die bevorzugte Bindung der alleinige Mechanismus ist, der zum heutigen Aufbau des menschlichen Proteininteraktion-Netzwerks beigetragen hat. Im dritten Teil wurden Proteine basierend auf dem Vorhandensein und der Abwesenheit von Interaktionen in Gruppen eingeteilt. Proteinnetzwerke können in kleine hoch vernetzte Teile zerlegt werden, die eine spezifische Funktion ausüben. Diese Gruppen können mit hoher statistischer Signifikanz berechnet werden, haben meistens jedoch keine biologische Relevanz. Mit einem neuen Algorithmus, welcher zusätzlich zu Interaktionen auch Nicht-Interaktionen berücksichtigt, wurde ein Datensatz bestehend aus 8,756 Proteinen und 32,331 Interaktionen neu unterteilt. Eine Einteilung in elf Gruppen zeigte hohe auf Gene Ontology basierte Werte und die Gruppen konnten signifikant einzelnen Zellteilen zugeordnet werden. Eine Gruppe besteht aus Proteinen, welche wenige Interaktionen miteinander aber viele Interaktionen zu zwei benachbarten Gruppen besitzen. Diese Gruppe enthält eine signifikant erhöhte Anzahl an Transportproteinen und die zwei benachbarten Gruppen haben eine erhöhte Anzahl an einerseits extrazellulären und andererseits im Zytoplasma und an der Membran lokalisierten Proteinen. Der Algorithmus hat damit unter Beweis gestellt das die Ergebnisse nicht bloß statistisch sondern auch biologisch relevant sind. Wenn wir auch noch weit vom Verständnis des Ursprungs der Spezies entfernt sind, so hat diese Arbeit doch einen Beitrag zum besseren Verständnis der Evolution auf dem Level der Proteine geleistet. Im Speziellen wurden neue Erkenntnisse über die Beziehung von Proteindomänen und Domänenarchitekturen, sowie ihre Präferenzen für Interaktionspartner im Interaktionsnetzwerk gewonnen. N2 - The human genome has been sequenced since 2001. Most proteins have been characterized now and with everyday more bioinformatical predictions are experimentally verified. A project is underway to sequence thousand humans. But still, little is known about the evolution of the human proteome itself. Domains and their combinations are analysed in detail but not all of the human domain architectures at once. Like no one before, we have large datasets of high quality human protein-protein-protein interactions and complexes available which allow us to characterize the human proteome with unmatched accuracy. Advanced clustering algorithms and computing power enable us to gain new information about protein interactions without touching a pipette. In this work, the human proteome is analysed at three different levels. First, the origin of the different types of proteins was analysed based on their domain architectures. The second part focuses on the protein-protein interactions. Finally, in the third part, proteins are clustered based on their interactions and non-interactions. Most proteins are built of domains and their function is the sum of their domain functions. Proteins that share the same domain architecture, the linear order of domains are homologues and should have originated from one common ancestral protein. This ancestor was calculated for roughly 750 000 proteins from 1313 species. The relations between the species are based on the NCBI Taxonomy and additional molecular data. The resulting data set of 5817 domains and 32868 domain architectures was used to estimate the origin of these proteins based on their architectures. It could be observed, that new domain architectures are only in a small fraction composed of domains arisen at the same taxon. It was also found that domain architectures increase in length and complexity in the course of evolution and that different organisms like worm, and human share nearly the same amount of proteins but differ in their number of distinct domain architectures. The second part of this thesis focuses on protein-protein interactions. This chapter addresses the question how new evolved proteins form connections within the existing network. The network built of protein-protein interactions was shown to be scale free. Scale free networks, like the internet, consist of few hubs with many connections and many nodes with few connections. They are thought to arise by two mechanisms. First, newly emerged proteins interact with proteins of the network. Second, according to the theory of preferential attachment, new proteins have a higher chance to interact with already interaction rich proteins. The Human Protein Reference Database provides an on in-vivo interaction data based network for human. With the data obtained from chapter one, proteins were marked with their taxon of origin based on their domain architectures. The interaction ratio of proteins of the same taxa compared to all interactions was calculated and higher values than the random model showed for nearly every taxa. On the other hand, there was no enrichment of proteins originated at the taxon of cellular organisms for the node degree found. The node degree is the number of links for this node. According to the theorie of preferential attachment the oldest nodes should have the most interactions and newly arisen proteins should be preferably attached to them not together. Both could not be shown in this analysis, preferential attachment could therefore not be the only explanation for the forming of the human protein interaction network. Finally in part three, proteins and all their interactions in the network are analysed. Protein networks can be divided into smaller highly interacting parts carrying out specific functions. This can be done with high statistical significance but still, it does not reflect the biological significance. Proteins were clustered based on their interactions and non-interactions with other proteins. A version with eleven clusters showed high gene ontology based ratings and clusters related to specific cell parts. One cluster consists of proteins having very few interactions together but many to proteins of two other clusters. This first cluster is significantly enriched with transport proteins and the two others are enriched with extracellular and cytoplasm/membrane located proteins. The algorithm seems therefore well suited to reflect the biological importance behind functional modules. Although we are still far from understanding the origin of species, this work has significantly contributed to a better understanding of evolution at the protein level and has, in particular, shown the relation of protein domains and protein architectures and their preferences for binding partners within interaction networks. KW - Evolution KW - Protein KW - Domäne KW - Interaktion KW - evolution KW - protein KW - interaction KW - domain Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-35566 ER - TY - THES A1 - Qiu, Liyan T1 - Structural and functional analysis of crossveinless 2 / BMP-2 /Chordin interaction N2 - No abstract available KW - structure KW - protein KW - BMP Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-29249 ER -