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  • DKFZ Publication Database  (1,990)
  • PROTEIN  (1,990)
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  • Articles  (2)
  • DKFZ Publication Database  (1,990)
Keywords
  • 1
    Keywords: PROTEIN ; COLORECTAL-CANCER ; SQUAMOUS-CELL CARCINOMA ; MALIGNANT-TUMORS ; ANTI-P53 ANTIBODIES ; HUMORAL IMMUNE-RESPONSE ; TUMOR-ASSOCIATED ANTIGEN ; POTENTIAL BIOMARKER ; PROTEOMICS-BASED IDENTIFICATION ; P53 ANTIBODY
    Abstract: Antibodies against tumor-associated antigens have been found in serum of patients with various types of cancers and may serve as biomarkers for early detection of gastric cancer as well. This systematic review aims to give an overview about known autoantibodies and their diagnostic value in gastric cancer. We conducted a systematic literature search in two databases to identify studies which performed serological testing for autoantibodies in gastric cancer patients and controls. Data on study characteristics and results were extracted independently by two reviewers. Overall, 39 articles reporting the detection of 34 different autoantibodies met the inclusion criteria for this review. The most common antibody detection method was enzyme-linked immunosorbent assay and the most frequently assessed autoantibody was anti-p53, which was tested in 13 studies. Most antibodies were assessed in only one study and only few authors have evaluated the diagnostic value of combinations of multiple autoantibodies. For single autoantibodies, specificity was generally very high (median: 99.15%), but sensitivity was mostly rather low (median: 12.35%). For some autoantibody combinations, substantially higher sensitivity at reasonably high levels of specificity could be achieved. Development of extended and optimized multimarker panels of autoantibodies might be a promising approach for gastric cancer early detection.
    Type of Publication: Journal article published
    PubMed ID: 24615018
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  • 2
    Keywords: EXPRESSION ; GROWTH ; PROTEIN ; ACTIVATION ; PHOSPHORYLATION ; INTERACTS ; FAS ; EMT ; TUMOR-FORMATION ; CANCER STEM-CELLS
    Abstract: Cancer stem cells (CSCs) have been implicated in the initiation and maintenance of tumour growth as well as metastasis. Recent reports link stemness to epithelial-mesenchymal transition (EMT) in cancer. However, there is still little knowledge about the molecular markers of those events. In silico analysis of RNA profiles of 36 pancreatic ductal adenocarcinomas (PDAC) reveals an association of the expression of CD95 with EMT and stemness that was validated in CSCs isolated from PDAC surgical specimens. CD95 expression was also higher in metastatic pancreatic cells than in primary PDAC. Pharmacological inhibition of CD95 activity reduced PDAC growth and metastasis in CSC-derived xenografts and in a murine syngeneic model. On the mechanistic level, Sck was identified as a novel molecule indispensable for CD95's induction of cell cycle progression. This study uncovers CD95 as a marker of EMT and stemness in PDAC. It also addresses the molecular mechanism by which CD95 drives tumour growth and opens tantalizing therapeutic possibilities in PDAC.
    Type of Publication: Journal article published
    PubMed ID: 25613377
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  • 3
    Keywords: PROTEIN ; AMPLIFICATION ; MUTATIONS ; RECRUITMENT ; centrosome ; SCAFFOLD ; HUMAN-CELLS ; Plk4 ; MEDIATED DEGRADATION ; procentriole formation
    Abstract: Duplication of centrioles, namely the formation of a procentriole next to the parental centriole, is regulated by the polo-like kinase Plk4. Only a few other proteins, including STIL (SCL/TAL1 interrupting locus, SIL) and Sas-6, are required for the early step of centriole biogenesis. Following Plk4 activation, STIL and Sas-6 accumulate at the cartwheel structure at the initial stage of the centriole assembly process. Here, we show that STIL interacts with Plk4 in vitro and in vivo. Both the conserved STAN motif and the coiled-coil domain of STIL are required for Plk4 binding. Furthermore, we find that STIL is phosphorylated by Plk4. We identified Plk4 specific phosphorylation sites within the C-terminal domain of STIL and show that phosphorylation of STIL by Plk4 is required to trigger centriole duplication.
    Type of Publication: Journal article published
    PubMed ID: 25701666
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  • 4
    Keywords: RECEPTOR ; PROTEIN ; RESPONSES ; INFECTION ; DENDRITIC CELLS ; DOWN-REGULATION ; LINE ; EPSTEIN-BARR-VIRUS ; rituximab ; DEC-205
    Abstract: The treatment of non-Hodgkin lymphomas has benefited enormously from the introduction of monoclonal antibody-based therapies. However, the efficacy of these treatments varies with lymphoma subtypes and typically decreases with subsequent relapses. Here, we report on antigen-armed antibodies (AgAbs) as a potential treatment of B-cell lymphoma. AgAbs include antigens from ubiquitous pathogens, such as Epstein-Barr virus (EBV), that persist in their host and elicit strong lifelong T-cell responses. They act as vectors by introducing antigen directly into tumor cells to induce an antigen-specific CD4(+) T-cell response against these cells. We have fused antibodies targeting human B-cell surface receptors (CD19-22) to immunodominant T-cell antigens from EBV proteins, including EBNA1, EBNA3B, and EBNA3C. Exposure of EBV-transformed B cells and of Burkitt lymphoma cells to AgAbs led to antigen presentation, T-cell recognition, and target cell killing. The efficiency of AgAb action paralleled the abundance of the targeted molecules on lymphoma cells as well as their HLA class II expression levels. AgAbs can also induce activation and proliferation of EBV-specific memory CD4(+) T cells ex vivo. These studies show the potential of AgAbs as an effective therapeutic strategy against B-cell lymphomas.
    Type of Publication: Journal article published
    PubMed ID: 25568348
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  • 5
    Keywords: DISEASE ; MORTALITY ; PROTEIN ; MARKERS ; antioxidants ; inflammation ; OLDER-ADULTS ; PHYSICAL PERFORMANCE BATTERY ; CARDIOVASCULAR HEALTH ; GRIP STRENGTH
    Abstract: Background: Oxidative stress (OS) and inflammatory biomarkers have been postulated to be important factors in the development of age-related diseases. While causes of frailty are complex and multidimensional based on the interaction of genetic, biological, physical, and environmental factors, the biological basis of frailty has been difficult to establish. Objective: In this study, we aimed to assess the possible association between different OS and inflammatory biomarkers and frailty. Methods: This cross-sectional analysis was performed among 2,518 subjects participating in a large population-based cohort study on aging conducted in Germany. Frailty was assessed as proposed by Fried et al. [J Gerontol A Biol Sci Med Sci 2001; 56: M146-M156]. OS biomarkers, biological antioxidant potential (BAP), derivate of reactive oxygen metabolites (d-ROM) and total thiol levels (TTL), and an established biomarker of inflammation Creactive protein (CRP) were measured by spectrophotometry and immunoturbidimetry. Logistic regression models were performed to assess the relationship between the OS biomarkers and frailty status. Odds ratios (OR) and 95% confidence intervals (CI) were calculated to quantify the associations. Results: Mean levels of d-ROM, TTL, and CRP differed between frail and non-frail participants (p values 〈0.0001). Comparing highest and lowest quartiles of the biomarkers, statistically significant positive associations with frailty were observed for d-ROM (OR: 2.02, 95% CI: 1.25-3.25) and CRP (OR: 3.15, 95% CI: 2.00-4.96), respectively, after controlling for age and sex. An inverse statistically significant association with frailty was observed for TTL (OR: 0.42, 95% CI: 0.25-0.69). Conclusion: The strong associations with OS biomarkers and CRP support a major role of OS and inflammation in the development of frailty, which should be followed up in further longitudinal studies on frailty.
    Type of Publication: Journal article published
    PubMed ID: 25924722
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  • 6
    Keywords: EXPRESSION ; GENE ; PROTEIN ; DIFFERENTIATION ; METASTASIS ; DISSEMINATED TUMOR-CELLS ; micrometastasis ; MAMMARY-GLAND ; SELF-RENEWAL ; CTBP
    Abstract: Regulatory pathways that drive early hematogenous dissemination of tumor cells are insufficiently defined. Here, we used the presence of disseminated tumor cells (DTC) in the bone marrow to define patients with early disseminated breast cancer and identified low retinoic acid-induced 2 (RAI2) expression to be significantly associated with DTC status. Low RAI2 expression was also shown to be an independent poor prognostic factor in 10 different cancer datasets. Depletion of RAI2 protein in luminal breast cancer cell lines resulted in dedifferentiation marked by downregulation of ERalpha, FOXA1, and GATA3, together with increased invasiveness and activation of AKT signaling. Functional analysis of the previously uncharacterized RAI2 protein revealed molecular interaction with CtBP transcriptional regulators and an overlapping function in controlling the expression of a number of key target genes involved in breast cancer. These results suggest that RAI2 is a new metastasis-associated protein that sustains differentiation of luminal breast epithelial cells. SIGNIFICANCE: We identified downregulation of RAI2 as a novel metastasis-associated genetic alteration especially associated with early occurring bone metastasis in ERalpha-positive breast tumors. We specified the role of the RAI2 protein to function as a transcriptional regulator that controls the expression of several key regulators of breast epithelial integrity and cancer. Cancer Discov; 5(5); 506-19. (c)2015 AACR. See related commentary by Esposito and Kang, p. 466 This article is highlighted in the In This Issue feature, p. 453.
    Type of Publication: Journal article published
    PubMed ID: 25716347
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  • 7
    Keywords: RECEPTOR ; EXPRESSION ; MODELS ; PROTEIN ; DIFFERENTIATION ; DOMAIN ; MIGRATION ; CD34 ; INHIBITS SPROUTING ANGIOGENESIS ; EXHIBIT
    Abstract: Given the need for robust and cost-efficient in vitro models to study angiogenesis and reproducibly analyze potential pro- and antiangiogenic compounds in preclinical studies, we developed a 3-dimensional in vitro angiogenesis assay that is based on collagen gel-embedded, size-defined spheroids generated from cultured human umbilical vein endothelial cells (HUVECs). Despite its wide distribution, limitations, sensitivity, robustness, and improvements, the capacity of this assay for functional screening purposes has not been elucidated thus far. By using time-lapse video microscopy, we show that tip cells lead the formation of capillary-like and partially lumenized sprouts originating from the spheroids. Angiogenic sprouting from spheroids generated from 5 different primary cultured human endothelial cell types was induced by physiologic concentrations of vascular endothelial cell growth factor 165. Based on this assay system, we determined the capacity of 880 approved drugs to interfere with or boost angiogenic sprouting, thereby assessing their putative angiogenesis-related side effects or novel applications. However, although this assay allowed for a rapid and reproducible determination of functional IC50 values of individual compounds, the sprouting results were partially affected by the HUVEC passage number and donor variability. To overcome this limitation, immortalized HUVECs (iHUVECs) showing a more homogenous response in terms of proliferation and sprouting over multiple population doublings were used in the course of this study. Collectively, the spheroid-based angiogenesis assay provides a sensitive and versatile tool to study the impact of pro- and antiangiogenic determinants on multiple steps of the angiogenic cascade. It is compatible with different endothelial cell types and allows use of iHUVECs to improve its overall robustness.-Heiss, M., Hellstrom, M., Kalen, M., May, T., Weber, H., Hecker, M., Augustin, H. G., Korff, T. Endothelial cell spheroids as a versatile tool to study angiogenesis in vitro.
    Type of Publication: Journal article published
    PubMed ID: 25857554
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  • 8
    Keywords: DISEASE ; RISK ; PROTEIN ; POLYMORPHISMS ; PATHOGENESIS ; CLINICAL-FEATURES ; GENETIC SUSCEPTIBILITY ; MANIFESTATIONS ; AICARDI-GOUTIERES SYNDROME ; TRIM39
    Abstract: Cutaneous lupus erythematosus (CLE) is a chronic autoimmune disease of the skin with typical clinical manifestations. Here, we genotyped 906 600 single nucleotide polymorphisms (SNPs) in 183 CLE cases and 1288 controls of Central European ancestry. Replication was performed for 13 SNPs in 219 case subjects and 262 controls from Finland. Association was particularly pronounced at 4 loci, all with genomewide significance (P 〈 5 x 10(-8) ): rs2187668 (PGWAS = 1.4 x 10(-12) ), rs9267531 (PGWAS = 4.7 x 10(-10) ), rs4410767 (PGWAS = 1.0 x 10(-9) ) and rs3094084 (PGWAS = 1.1 x 10(-9) ). All mentioned SNPs are located within the major histocompatibility complex (MHC) region of chromosome 6 and near genes of known immune functions or associations with other autoimmune diseases such as HLA-DQ alpha chain 1 (HLA-DQA1), MICA, MICB, MSH5, TRIM39 and RPP21. For example, TRIM39/RPP21 read through transcript is a known mediator of the interferon response, a central pathway involved in the pathogenesis of CLE and systemic lupus erythematosus (SLE). Taken together, this genomewide analysis of disease association of CLE identified candidate genes and genomic regions that may contribute to pathogenic mechanisms in CLE via dysregulated antigen presentation (HLA-DQA1), apoptosis regulation, RNA processing and interferon response (MICA, MICB, MSH5, TRIM39 and RPP21).
    Type of Publication: Journal article published
    PubMed ID: 25827949
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  • 9
    Keywords: IN-VITRO ; PROTEIN ; PHOSPHORYLATION ; NERVOUS-SYSTEM ; SUBUNIT ; INTERMEDIATE-FILAMENTS ; TAIL DOMAIN ; NF-H ; SIDEARMS ; BRUSHES
    Abstract: Neuronal cytoplasmic intermediate filaments are principal structural and mechanical elements of the axon. Their expression during embryonic development follows a differential pattern, while their unregulated expression is correlated to neurodegenerative diseases. The largest neurofilament proteins of medium (NF-M) and high molecular weight (NF-H) were shown to modulate the axonal architecture and inter-filament spacing. However, the individual roles of the remaining alpha-internexin (alpha-Inx) and neurofilament of low molecular weight (NF-L) proteins in composite filaments remained elusive. In contrast to previous predictions, we show that when co-assembled with NF-M, the shortest and the least charged alpha-Inx protein increases inter-filament spacing. These findings suggest a novel structural explanation for the expression pattern of neurofilament proteins during embryonic development. We explain our results by an analysis of ionic cross-links between the disordered polyampholytic C-terminal tails and suggest that a collapsed conformation of the alpha-Inx tail domain interferes with tail cross-linking near the filament backbone.
    Type of Publication: Journal article published
    PubMed ID: 26100609
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  • 10
    Keywords: APOPTOSIS ; PROTEIN ; INDUCTION ; ASSOCIATION ; CERVICAL-CANCER ; p53 ; POSITIVE CANCER-CELLS ; NUCLEAR-LOCALIZATION ; E6-MEDIATED DEGRADATION ; AGGRESOMES
    Abstract: Oncogenic types of human papillomaviruses (HPVs) cause cervical cancer and other malignancies in humans. The HPV E6 oncoprotein is considered to be an attractive therapeutic target since its inhibition can lead to the apoptotic cell death of HPV-positive cancer cells. The HPV type 16 (HPV16) E6-binding peptide pep11, and variants thereof, induce cell death specifically in HPV16-positive cancer cells. Although they do not encompass the LxxLL binding motif found in cellular HPV16 E6 interaction partners, such as E6AP, the pep11 variants strongly bind to HPV16 E6 by contacting the recently identified E6AP binding pocket. Thus, these peptides can serve as prototype E6-inhibitory molecules which target the E6AP pocket. We here analyzed their intracellular interaction with HPV16 E6. By comprehensive intracellular binding studies and GST pull-down assays, we show that E6-binding competent pep11 variants induce the formation of a trimeric complex, consisting of pep11, HPV16 E6 and p53. These findings indicate that peptides, which do not contain the LxxLL motif, can reshape E6 to enable its interaction with p53. The formation of the trimeric HPV16 E6 / peptide / p53 complex was associated with an increase of endogenous HPV16 E6 protein amounts. Yet, total cellular p53 amounts were also increased, indicating that the E6 / E6AP-mediated degradation of p53 is blocked. These findings suggest that inhibition of oncogenic activities by targeting the E6AP pocket on HPV16 E6 could be a strategy for therapeutic intervention.
    Type of Publication: Journal article published
    PubMed ID: 26151636
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  • 11
    Keywords: RECEPTOR ; ENDOTHELIAL-CELLS ; EXPRESSION ; PROTEIN ; LYMPHOCYTES ; B-CELLS ; STOMATITIS-VIRUS GLYCOPROTEIN ; EFFICIENT GENE-TRANSFER ; LYSE TARGET-CELLS ; IMMUNORECEPTOR
    Abstract: Playing a central role in both innate and adaptive immunity, CD4(+) T cells are a key target for genetic modifications in basic research and immunotherapy. In this article, we describe novel lentiviral vectors (CD4-LV) that have been rendered selective for human or simian CD4(+) cells by surface engineering. When applied to PBMCs, CD4-LV transduced CD4(+) but not CD4(-) cells. Notably, also unstimulated T cells were stably genetically modified. Upon systemic or intrasplenic administration into mice reconstituted with human PBMCs or hematopoietic stem cells, reporter gene expression was predominantly detected in lymphoid organs. Evaluation of GFP expression in organ-derived cells and blood by flow cytometry demonstrated exclusive gene transfer into CD4(+) human lymphocytes. In bone marrow and spleen, memory T cells were preferentially hit. Toward therapeutic applications, we also show that CD4-LV can be used for HIV gene therapy, as well as for tumor therapy, by delivering chimeric Ag receptors. The potential for in vivo delivery of the FOXP3 gene was also demonstrated, making CD4-LV a powerful tool for inducible regulatory T cell generation. In summary, our work demonstrates the exclusive gene transfer into a T cell subset upon systemic vector administration opening an avenue toward novel strategies in immunotherapy.
    Type of Publication: Journal article published
    PubMed ID: 26232436
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  • 12
    Keywords: EXPRESSION ; DISEASE ; GENE ; GENOME ; PROTEIN ; CHROMATIN ; C-MYC ; X-CHROMOSOME ; LONG NONCODING RNA ; LANDSCAPE
    Abstract: Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long noncoding RNAs (lncRNAs), on MYC ability to influence the cellular transcriptome. Here, we have intersected RNA-sequencing data from two MYC-inducible cell lines and a cohort of 91 B-cell lymphomas with or without genetic variants resulting in MYC overexpression. We identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated in the same direction by MYC in the model cell lines. Among them, we focused on a lncRNA that we named MYC-induced long noncoding RNA (MINCR), showing a strong correlation with MYC expression in MYC-positive lymphomas. To understand its cellular role, we performed RNAi and found that MINCR knockdown is associated with an impairment in cell cycle progression. Differential gene expression analysis after RNAi showed a significant enrichment of cell cycle genes among the genes down-regulated after MINCR knockdown. Interestingly, these genes are enriched in MYC binding sites in their promoters, suggesting that MINCR acts as a modulator of the MYC transcriptional program. Accordingly, MINCR knockdown was associated with a reduction in MYC binding to the promoters of selected cell cycle genes. Finally, we show that down-regulation of Aurora kinases A and B and chromatin licensing and DNA replication factor 1 may explain the reduction in cellular proliferation observed on MINCR knockdown. We, therefore, suggest that MINCR is a newly identified player in the MYC transcriptional network able to control the expression of cell cycle genes.
    Type of Publication: Journal article published
    PubMed ID: 26351698
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  • 13
    Keywords: GENE-EXPRESSION ; PROTEIN ; TRANSCRIPTION FACTOR ; CANCER-CELLS ; CARCINOMAS ; CHRONIC LYMPHOCYTIC-LEUKEMIA ; B-CELL LYMPHOMAS ; SOMATIC MUTATIONS ; HISTONE METHYLTRANSFERASE ; CODING GENOME
    Abstract: BACKGROUND: Splenic marginal zone lymphoma (SMZL) is an indolent B-cell non-Hodgkin lymphoma and represents the most common primary malignancy of the spleen. Its precise molecular pathogenesis is still unknown and specific molecular markers for diagnosis or possible targets for causal therapies are lacking. METHODS: We performed whole exome sequencing (WES) and copy number analysis from laser-microdissected tumor cells of two primary SMZL discovery cases. Selected somatic single nucleotide variants (SNVs) were analyzed using pyrosequencing and Sanger sequencing in an independent validation cohort. RESULTS: Overall, 25 nonsynonymous somatic SNVs were identified, including known mutations in the NOTCH2 and MYD88 genes. Twenty-three of the mutations have not been associated with SMZL before. Many of these seem to be subclonal. Screening of 24 additional SMZL for mutations at the same positions found mutated in the WES approach revealed no recurrence of mutations for ZNF608 and PDE10A, whereas the MYD88 L265P missense mutation was identified in 15 % of cases. An analysis of the NOTCH2 PEST domain and the whole coding region of the transcription factor SMYD1 in eight cases identified no additional case with a NOTCH2 mutation, but two additional cases with SMYD1 alterations. CONCLUSIONS: In this first WES approach from microdissected SMZL tissue we confirmed known mutations and discovered new somatic variants. Recurrence of MYD88 mutations in SMZL was validated, but NOTCH2 PEST domain mutations were relatively rare (10 % of cases). Recurrent mutations in the transcription factor SMYD1 have not been described in SMZL before and warrant further investigation.
    Type of Publication: Journal article published
    PubMed ID: 26498442
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  • 14
    Keywords: THERAPY ; PROTEIN ; T-CELLS ; leukemia ; NATURAL-KILLER-CELLS ; CANCER-IMMUNOTHERAPY ; PROTOONCOGENE ; CYTOTOXIC ACTIVITY ; LINE NK-92 ; ERBB-2 RECEPTOR
    Abstract: Natural killer (NK) cells are an important effector cell type for adoptive cancer immunotherapy. Similar to T cells, NK cells can be modified to express chimeric antigen receptors (CARs) to enhance antitumor activity, but experience with CAR-engineered NK cells and their clinical development is still limited. Here, we redirected continuously expanding and clinically usable established human NK-92 cells to the tumor-associated ErbB2 (HER2) antigen. Following GMP-compliant procedures, we generated a stable clonal cell line expressing a humanized CAR based on ErbB2-specific antibody FRP5 harboring CD28 and CD3? signaling domains (CAR 5.28.z). These NK-92/5.28.z cells efficiently lysed ErbB2-expressing tumor cells in vitro and exhibited serial target cell killing. Specific recognition of tumor cells and antitumor activity were retained in vivo, resulting in selective enrichment of NK-92/5.28.z cells in orthotopic breast carcinoma xenografts, and reduction of pulmonary metastasis in a renal cell carcinoma model, respectively. ?-irradiation as a potential safety measure for clinical application prevented NK cell replication, while antitumor activity was preserved. Our data demonstrate that it is feasible to engineer CAR-expressing NK cells as a clonal, molecularly and functionally well-defined and continuously expandable cell therapeutic agent, and suggest NK-92/5.28.z cells as a promising candidate for use in adoptive cancer immunotherapy.Molecular Therapy (2014); doi:10.1038/mt.2014.219.
    Type of Publication: Journal article published
    PubMed ID: 25373520
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  • 15
    Keywords: RECEPTOR ; CANCER ; PROTEIN ; DIFFERENTIATION ; TUMORS ; SKIN ; MUTATIONS ; beta-catenin ; LESSONS
    Abstract: Pilomatricoma is a tumour derived from hair matrix cells, which shows progressive keratin expression. Tumorigenesis is frequently associated with activating mutations in beta-catenin gene inducing nuclear expression of beta-catenin protein. The present study analysed the role of transforming growth factor-beta1 (TGF-beta1) and four-and-a-half LIM domain protein 2 (FHL2) in pilomatricoma in synopsis with their expression patterns in human anagen hair. Human anagen hair showed TGF-beta1 and nuclear FHL2 expression in the outer root sheath layer separated from nuclear beta-catenin staining, which was observed in cells of matrix and inner root sheath layers. Correspondingly, 41 out of 50 pilomatricomas showed co-labelling of TGF-beta1 and nuclear FHL2 in tumour cells, which mostly lacked nuclear beta-catenin expression. Tumoural proliferation (ki67) was associated with nuclear beta-catenin staining but not with expression of nuclear FHL2. In early pilomatricomas, TGF-beta1 expression was observed in few peripheral tumour cells showing absent or faint nuclear FHL2 co-staining. TGF-beta1 expression extended in growing tumours going along with strong nuclear FHL2 co-labelling as well as progressive keratin 14 and keratin 1 expression. In vitro, cultured human keratinocytes showed weak to marked autocrine TGF-beta1 expression; in case of enhanced TGF-beta1 expression associated with keratin 10 staining. TGF-beta1-treatment of cultured human keratinocytes induced nuclear and cytoplasmatic FHL2 staining as well as keratin 14 staining. Accordingly, siRNA-mediated FHL2 knockdown of TGF-beta1-stimulated keratinocytes reduced keratin 14 staining. In conclusion, tumoural TGF-beta1 secretion seems to induce nuclear translocation of co-factor FHL2 mediating progressive keratin expression in pilomatricoma.
    Type of Publication: Journal article published
    PubMed ID: 25477051
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  • 16
    Keywords: PROTEIN ; LIVING CELLS ; STRUCTURAL INSIGHTS ; ANEMONE STICHODACTYLA-HELIANTHUS ; SEA-ANEMONE ; CELL PLASMA-MEMBRANE ; EQUINATOXIN-II ; PARTICLE TRACKING ; STICHOLYSIN-I ; TRANSMEMBRANE PORE
    Abstract: alpha-Pore-forming toxins (alpha-PFTs) are ubiquitous defense tools that kill cells by opening pores in the target cell membrane. Despite their relevance in host/pathogen interactions, very little is known about the pore stoichiometry and assembly pathway leading to membrane permeabilization. Equinatoxin II (EqtII) is a model alpha-PFT from sea anemone that oligomerizes and forms pores in sphingomyelin-containing membranes. Here, we determined the spatiotemporal organization of EqtII in living cells by single molecule imaging. Surprisingly, we found that on the cell surface EqtII did not organize into a unique oligomeric form. Instead, it existed as a mixture of oligomeric species mostly including monomers, dimers, tetramers, and hexamers. Mathematical modeling based on our data supported a new model in which toxin clustering happened in seconds and proceeded via condensation of EqtII dimer units formed upon monomer association. Furthermore, altering the pathway of EqtII assembly strongly affected its toxic activity, which highlights the relevance of the assembly mechanism on toxicity.
    Type of Publication: Journal article published
    PubMed ID: 25525270
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  • 17
    Keywords: PROTEIN ; SEQUENCE ; ASSOCIATION ; TYPE-16 ; bioinformatics ; PREDICTION ; HPV-16 E6 ; INDIAN WOMEN ; NATURAL VARIANTS ; HPV16 E6
    Abstract: The infection with high-risk human papillomavirus (HR-HPV) is the most important risk factor for development of cervical cancer. The intra-type variations of HPV have different biological and pathological consequences with respect to disease progression. In the present study, six major Indian variants were experimentally identified in E6 gene of HPV-16 and showed their impact on immunogenicity by in silico methods. Four different phylogenetic lineages were observed in sequences including European (E) prototype, European variant, Asian and American Asian variant classes and complete absence of African phylogenetic lineages. On the prediction of B- and T-cell epitopes, 18 and 23 potent epitopes for MHC-II alleles, 10 potent MHC-I and 15 B-cell epitopes in each reference and variant sequence were identified. Interestingly, the presence of variation H78Y and L83V result in creation of four new epitopes for the HLA-DQA1*0101/DQB1*0501. Out of 15 B-cell predicted epitopes, three most potent epitopes were identified in both reference and variant sequence. Notably the amino acid stretch from amino acid 16-60 and 76-94 are very important for the immunological properties of E6 protein because these regions contain majority of the predicted epitopes. In future, this could control the cervical cancer by targeting these amino acid stretches for the development of HPV-16 vaccine.
    Type of Publication: Journal article published
    PubMed ID: 25800725
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  • 18
    Keywords: carcinoma ; PROTEIN ; CARCINOGENESIS ; CELL-LINES ; CERVICAL-CANCER ; DEGRADATION ; HUMAN-PAPILLOMAVIRUS TYPE-16 ; CPG METHYLATION ; INTEGRATION ; E2 BINDING-SITES
    Abstract: BACKGROUND: The human papillomavirus (HPV) E2 protein is a transcriptional repressor of the oncogenes E6/E7 and loss of E2 function is considered a key step in carcinogenesis. Integration of HPV into the host genome may disrupt the E2 gene. Furthermore, methylation of CpG dinucleotides in E2-binding sites (E2BSs) in the HPV upstream regulatory region may interfere with transcriptional repression of E6 and E7 by E2. The authors hypothesized that the CpG methylation status of E2BS identifies subtypes of HPV type 16 (HPV16)-associated oropharyngeal squamous cell cancers (OPSCC) in association with E2 gene integrity and viral integration. METHODS: Methylation of 10 CpG dinucleotides within the upstream regulatory region, encompassing E2BSs 1, 2, 3, and 4, was quantitatively analyzed by bisulfite pyrosequencing in 57 HPV16-associated OPSCC cases. E2 status was analyzed by gene amplification and quantitative real-time reverse transcriptase-polymerase chain reaction. Viral integration was determined by integration-specific polymerase chain reaction methods. RESULTS: Three subgroups with differential methylation at E2BS3 and E2BS 4 were identified: 1) complete methylation (〉80%) associated with the presence of integrated HPV genomes with an intact E2 gene; 2) intermediate methylation levels (20%-80%) with predominantly episomal HPV genomes with intact E2; and 3) no methylation (〈20%) with a disrupted E2 gene. Patients with high methylation levels tended to have a worse 5-year overall survival compared with patients with intermediate methylation (hazard ratio, 3.23; 95% confidence interval, 1.13-9.24 [P = .06]). CONCLUSIONS: Methylation of E2BS3 and E2BS4 in OPSCC is associated with E2 integrity and viral physical status. It might explain deregulated viral oncogene expression in the presence of E2. The prognostic significance of E2BS methylation for patients with HPV-associated OPSCC needs to be analyzed further. Cancer 2015;121:1966-1976. (c) 2015 American Cancer Society.
    Type of Publication: Journal article published
    PubMed ID: 25731880
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  • 19
    Keywords: RECEPTOR ; KINASE ; PROTEIN ; DOWN-REGULATION ; fibroblasts ; BONE-MARROW ; STROMAL CELLS ; INTERNATIONAL-SOCIETY ; THERAPY POSITION STATEMENT ; GENOME-WIDE RNAI
    Abstract: Mesenchymal stem cells (MSCs) are promising candidates for cellular therapies ranging from tissue repair in regenerative medicine to immunomodulation in graft versus host disease after allogeneic transplantation or in autoimmune diseases. Nonetheless, progress has been hampered by their enormous phenotypic as well as functional heterogeneity and the lack of uniform standards and guidelines for quality control. In this study, we describe a method to perform cellular phenotyping by high-throughput RNA interference in primary human bone marrow MSCs. We have shown that despite heterogeneity of MSC populations, robust functional assays can be established that are suitable for high-throughput and high-content screening. We profiled primary human MSCs against human fibroblasts. Network analysis showed a kinome fingerprint that differs from human primary fibroblasts as well as fibroblast cell lines. In conclusion, this study shows that high-throughput screening in primary human MSCs can be reliably used for kinome fingerprinting.
    Type of Publication: Journal article published
    PubMed ID: 26120366
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  • 20
    Keywords: PROTEIN ; AAV ; SITE-SPECIFIC INTEGRATION ; VECTOR INTEGRATION ; DNA HELICASE ACTIVITY
    Abstract: High-throughput integration site (IS) analysis of wild-type adeno-associated virus type 2 (wtAAV2) in human dermal fibroblasts (HDFs) and HeLa cells revealed that juxtaposition of a Rep binding site (RBS) and terminal resolution site (trs)-like motif leads to a 4-fold-increased probability of wtAAV integration. Electrophoretic mobility shift assays (EMSAs) confirmed binding of Rep to off-target RBSs. For the first time, we show Rep protein off-target nicking activity, highlighting the importance of the nicking substrate for Rep-mediated integration.
    Type of Publication: Journal article published
    PubMed ID: 25972561
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  • 21
    Keywords: INHIBITION ; PROTEIN ; REGION ; NUCLEAR-LOCALIZATION ; HEPATITIS-C VIRUS ; AMINO-ACID ; MUTATIONAL ANALYSIS ; HELICASE ; WEST-NILE-VIRUS ; DEPENDENT RNA-POLYMERASE
    Abstract: Dengue virus (DENV) infection causes the most prevalent arthropod-borne viral disease worldwide. Approved vaccines are not available, and targets suitable for the development of antiviral drugs are lacking. One possible drug target is nonstructural protein 4B (NS4B), because it is absolutely required for virus replication; however, its exact role in the DENV replication cycle is largely unknown. With the aim of mapping NS4B determinants critical for DENV replication, we performed a reverse genetic screening of 33 NS4B mutants in the context of an infectious DENV genome. While the majority of these mutations were lethal, for several of them, we were able to select for second-site pseudoreversions, most often residing in NS4B and restoring replication competence. To identify all viral NS4B interaction partners, we engineered a fully viable DENV genome encoding an affinity-tagged NS4B. Mass spectrometry-based analysis of the NS4B complex isolated from infected cells identified the NS3 protease/helicase as a major interaction partner of NS4B. By combining the genetic complementation map of NS4B with a replication-independent expression system, we identified the NS4B cytosolic loop-more precisely, amino acid residue Q134-as a critical determinant for NS4B-NS3 interaction. An alanine substitution at this site completely abrogated the interaction and DENV RNA replication, and both were restored by pseudoreversions A69S and A137V. This strict correlation between the degree of NS4B-NS3 interaction and DENV replication provides strong evidence that this viral protein complex plays a pivotal role during the DENV replication cycle, hence representing a promising target for novel antiviral strategies. IMPORTANCE: With no approved therapy or vaccine against dengue virus infection, the viral nonstructural protein 4B (NS4B) represents a possible drug target, because it is indispensable for virus replication. However, little is known about its precise structure and function. Here, we established the first comprehensive genetic interaction map of NS4B, identifying amino acid residues that are essential for virus replication, as well as second-site mutations compensating for their defects. Additionally, we determined the NS4B viral interactome in infected cells and identified the NS3 protease/helicase as a major interaction partner of NS4B. We mapped residues in the cytosolic loop of NS4B as critical determinants for interaction with NS3, as well as RNA replication. The strong correlation between NS3-NS4B interaction and RNA replication provides strong evidence that this complex plays a pivotal role in the viral replication cycle, hence representing a promising antiviral drug target.
    Type of Publication: Journal article published
    PubMed ID: 25926641
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  • 22
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    Annalen der Physik 527 (7-8), 423- 
    Keywords: PROTEIN ; DIFFRACTION RESOLUTION LIMIT ; STIMULATED-EMISSION ; BREAKING ; GROUND-STATE-DEPLETION ; SINGLE MOLECULES ; DIAMOND ; FIELD FLUORESCENCE MICROSCOPY ; OPTICAL NANOSCOPY ; COLOR-CENTERS
    Abstract: Stefan W. Hell received the Nobel Prize in Chemistry in 2014 for the development of super-resolved fluorescence microscopy, together with Eric Betzig and William Moerner. With the invention of STED (Stimulated Emission Depletion) microscopy experimentally realized in 1999, he has revolutionized light microscopy, overcoming the resolution limit of conventional optical microscopes - a breakthrough that has enabled new ground-breaking discoveries in biological and medical research.
    Type of Publication: Journal article published
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  • 23
    Keywords: PROTEIN ; NEPHRIN ; NEPHROTIC SYNDROME ; kidney development ; ZEBRAFISH ; CELL BIOLOGY ; WT1 ; SELF-ASSOCIATION ; GLOMERULAR-FILTRATION BARRIER ; DENYS-DRASH SYNDROME
    Abstract: The Wilms' tumor suppressor gene 1 (WT1) encodes a zinc finger transcription factor. Mutation of WT1 in humans leads to Wilms' tumor, a pediatric kidney tumor, or other kidney diseases, such as Denys-Drash and Frasier syndromes. We showed previously that inactivation of WT1 in podocytes of adult mice results in proteinuria, foot process effacement, and glomerulosclerosis. However, the WT1-dependent transcriptional network regulating podocyte development and maintenance in vivo remains unknown. Here, we performed chromatin immunoprecipitation followed by high-throughput sequencing with glomeruli from wild-type mice. Additionally, we performed a cDNA microarray screen on an inducible podocyte-specific WT1 knockout mouse model. By integration of cistromic and transcriptomic analyses, we identified the WT1 targetome in mature podocytes. To further analyze the function and targets of WT1 in podocyte maturation, we used an Nphs2-Cre model, in which WT1 is deleted during podocyte differentiation. These mice display anuria and kidney hemorrhage and die within 24 hours after birth. To address the evolutionary conservation of WT1 targets, we performed functional assays using zebrafish as a model and identified Nphs2, Mafb, and Magi2 as novel WT1 target genes required for podocyte development. Our data also show that both Mafb and Magi2 are required for normal development of the embryonic zebrafish kidney. Collectively, our work provides insights into the transcriptional networks controlled by WT1 and identifies novel WT1 target genes that mediate the function of WT1 in podocyte differentiation and maintenance.
    Type of Publication: Journal article published
    PubMed ID: 25556170
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  • 24
    Keywords: CANCER ; CELLS ; EXPRESSION ; GROWTH ; PATHWAY ; NETWORK ; PROTEIN ; IDENTIFICATION ; DATABASE ; HEPATITIS-B
    Abstract: Hepatocellular carcinoma (HCC) is the most common type of liver cancer worldwide and mostly occurs in viral hepatitis endemic areas such as China. Knowledge of HCC-related genes may lead to an early detection of HCC and develop molecularly targeted therapeutics, reducing mortality and improving a patient's prognosis significantly. Therefore, it is valuable and important for us to identify common characters of HCC related genes. In this study, we proposed a computational method to predict HCC related genes based on Gene Ontology terms and KEGG terms using Random Forest (RF), in which features were optimized by maximum relevance minimum redundancy (mRMR) and incremental feature selection (IFS). 224 HCC gene candidates were compiled from some databases, while 11,200non-HCC gene candidates were randomly selected from Ensemble database. 10 candidate datasets were constructed by dividing non-HCC gene candidates into 10 groups. Each gene in datasets was encoded by 13,126 features including 12,887 Gene Ontology enrichment scores and 239 KEGG enrichment scores. Finally, an optimal feature set including 615 GO terms and 11 KEGG pathways was discovered. Through analysis, we found these features were closely related to HCC, which means our method is effective for discovering HCC related genes, and it is hopeful that it can also be used to predict and analyze genes for other types of cancer.
    Type of Publication: Journal article published
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  • 25
    Keywords: CANCER ; PROTEIN ; MALIGNANT-MELANOMA ; relapse ; biomarker ; S100 ; RELEVANCE ; MicroRNAs ; LACTATE-DEHYDROGENASE ; TUMOR-MARKERS
    Abstract: Abstract Background: Melanoma is the most aggressive skin cancer and, despite recent advances in therapy, about 20% of the patients die of their disease. Early relapse detection and monitoring of therapy response are crucial for efficient treatment of advanced melanoma. Thus, there is a need for blood-based biomarkers in melanoma management. Serum-derived U2 small nuclear RNA fragments (RNU2-1f) were previously shown to be blood-based biomarkers for gastrointestinal and gynecologic malignancies. Here we examined whether RNU2-1f may also serve as diagnostic biomarker in advanced melanoma. METHODS: Circulating RNU2-1f levels were quantified by comparative reverse transcription PCR in a training cohort of patients with metastatic melanoma (n=33, thereof regionally metastasized to skin and lymph nodes, n=23, and distantly metastasized, n=10) vs. patients with benign naevi (n=16) vs. healthy controls (n=39). RESULTS were validated in an independent patient cohort with distant metastasis (n=16) vs. controls (n=18). RESULTS: Circulating RNU2-1f levels in the training cohort were significantly increased in serum of regionally and distantly metastatic patients, compared with patients with benign naevi or healthy controls (p〈0.0001) and allowed accurate detection of regional (AUC 0.80) as well as distant (AUC 0.84) metastasis. In the validation cohort, increased RNU2-1f levels were confirmed and enabled highly specific detection of distant metastasis (sensitivity 81%, specificity 100%, AUC 0.94). CONCLUSIONS: This is the first report to suggest a blood-based snRNA serving as a diagnostic biomarker for melanoma metastasis. Our data provide a rationale for further defining clinical utility of circulating RNU2-1f in metastasis detection in the management of melanoma patients at risk of relapse and/or with advanced disease.
    Type of Publication: Journal article published
    PubMed ID: 25741740
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  • 26
    Keywords: RECEPTOR ; carcinoma ; RISK ; PROTEIN ; SUSCEPTIBILITY LOCUS ; VARIANTS ; METAANALYSIS ; 5P15.33 ; CEP57
    Abstract: Lung cancer is the leading cause of cancer death worldwide. Although several genetic variants associated with lung cancer have been identified in the past, stringent selection criteria of genome-wide association studies (GWAS) can lead to missed variants. The objective of this study was to uncover missed variants by using the known association between lung cancer and first-degree family history of lung cancer to enrich the variant prioritization for lung cancer susceptibility regions. In this two-stage GWAS study, we first selected a list of variants associated with both lung cancer and family history of lung cancer in four GWAS (3,953 cases, 4,730 controls), then replicated our findings for 30 variants in a meta-analysis of four additional studies (7,510 cases, 7,476 controls). The top ranked genetic variant rs12415204 in chr10q23.33 encoding FFAR4 in the Discovery set was validated in the Replication set with an overall OR of 1.09 (95% CI = 1.04, 1.14, P = 1.63 x 10(-4) ). When combining the two stages of the study, the strongest association was found in rs1158970 at Ch4p15.2 encoding KCNIP4 with an OR of 0.89 (95% CI = 0.85, 0.94, P = 9.64 x 10(-6) ). We performed a stratified analysis of rs12415204 and rs1158970 across all eight studies by age, gender, smoking status, and histology, and found consistent results across strata. Four of the 30 replicated variants act as expression quantitative trait loci (eQTL) sites in 1,111 nontumor lung tissues and meet the genome-wide 10% FDR threshold.
    Type of Publication: Journal article published
    PubMed ID: 25644374
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  • 27
    Keywords: PROTEIN ; NEUROBLASTOMA-CELLS ; TRANSCRIPTION FACTOR ; PHOSPHORYLATION ; DRUG-INDUCED APOPTOSIS ; GLYCOGEN-SYNTHASE KINASE-3 ; BCL-XL ; MEMBRANE PERMEABILIZATION ; MITOTIC ARREST ; OVERCOMES RESISTANCE
    Abstract: Aberrant activation of the phosphatidylinositol 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) pathway has been reported for rhabdomyosarcoma (RMS) and is implicated in survival of tumor cells as well as therapeutic resistance. In the present study, we searched for combination therapies with the dual PI3K/mTOR inhibitor NVP-BEZ235 (BEZ235) in RMS. Here, we identify a synthetic lethal interaction of BEZ235 together with the lysosomotropic agent chloroquine (CQ), which is effective against embryonal rhabdomyosarcoma (ERMS). BEZ235 and CQ at subtoxic concentrations synergize to induce apoptosis in ERMS cells, as confirmed by calculation of combination index (CI). BEZ235 and CQ cooperate to activate caspase-9, -3 and -8, which is crucial for apoptosis induction given that the broad-range caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone (zVAD.fmk) blocks BEZ235/CQ-induced apoptosis. Additionally, pharmacological inhibition of lysosomal enzymes significantly reduces BEZ235/CQ-induced apoptosis, indicating concomitant activation of the lysosomal compartment. Importantly, BEZ235/CQ-induced apoptosis is significantly inhibited by antioxidants, implying that increased oxidative stress contributes to BEZ235/CQ-induced cell death. Importantly, our molecular studies reveal that BEZ235/CQ-induced apoptosis is mediated by cooperative downregulation of the antiapoptotic BCL-2 family protein MCL-1, since stabilization of MCL-1 by expression of a non-degradable MCL-1 phospho-defective mutant significantly decreases BEZ235/CQ-induced apoptosis. Also, overexpression of antiapoptotic BCL-2 leads to a significant reduction of BEZ235/CQ-induced apoptosis, emphasizing that an intact mitochondrial pathway of apoptosis is required for BEZ235/CQ-induced cell death. This identification of a synthetic lethality of BEZ235 and CQ has important implications for the development of molecular targeted therapies for RMS.
    Type of Publication: Journal article published
    PubMed ID: 25637161
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  • 28
    Keywords: CELL-PROLIFERATION ; PROTEIN ; POOR-PROGNOSIS ; CANCER-THERAPY ; SPINDLE CHECKPOINT ; OVARIAN-CARCINOMA ; MULTIPOLAR MITOSES ; CHROMOSOMAL PASSENGER COMPLEX ; H3 PHOSPHORYLATION ; C KINASE
    Abstract: Experimental model systems identified phosphorylation of linker histone variant H1.4 at Ser 27 (H1.4S27p) as a novel mitotic mark set by Aurora B kinase. Here, we examined expression of Aurora B and H1.4S27p in colorectal carcinoma (CRC) cell lines (HCT116, DLD1, Caco-2, HT29) and tissue specimens (n = 36), in relation to microsatellite instability (MSI) status and ploidy. In vitro, Aurora B (pro-/meta-/anaphase) and H1.4S27p (pro-/metaphase) were localized in mitotic figures. The proportion of labeled mitoses was significantly different between cell lines for Aurora B (p = 0.019) but not for H1.4S27p (p = 0.879). For Aurora B, these differences were not associated with an altered Aurora B gene copy number (FISH) or messenger RNA (mRNA) expression level (qRT-PCR). Moreover, Aurora B expression and H1.4S27 phosphorylation were no longer coordinated during metaphase in aneuploid HT29 cells (p = 0.039). In CRCs, immunoreactivity for Aurora B or H1.4S27p did not correlate with T- or N-stage, grade, or MSI status. However, metaphase labeling of H1.4S27p was significantly higher in diploid than in aneuploid CRCs (p = 0.011). Aurora B was significantly correlated with H1.4S27p-positive metaphases in MSI (p = 0.010) or diploid (p = 0.003) CRCs. Finally, combined classification of MSI status and ploidy revealed a significant positive correlation of Aurora B with H1.4S27p in metaphases of diploid/MSI (p = 0.010) and diploid/microsatellite-stable (MSS; p = 0.031) but not of aneuploid/MSS (p = 0.458) CRCs. The present study underlines the functional link of Aurora B expression and H1.4S27p during specific phases of mitosis in diploid and/or MSI-positive CRCs in vitro and in situ. Importantly, the study shows that the coordination between Aurora B expression and phosphorylation of H1.4 at Ser 27 is lost in cycling aneuploid CRC cells.
    Type of Publication: Journal article published
    PubMed ID: 25680570
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  • 29
    Keywords: EXPRESSION ; SURVIVAL ; GENE ; PROTEIN ; LYMPHOMA ; MELANOMA ; FEATURES ; HUMAN CANCER ; CLINICAL-PRACTICE ; VEMURAFENIB
    Abstract: Detection of BRAF V600E has diagnostic, prognostic, and therapeutic relevance. The recently developed BRAF V600E mutation-specific antibody has evolved into a feasible alternative to DNA analysis. The plethora of immunohistochemical protocols makes implementation tedious and, here we tested a set of manual and automated protocols and compared test performance with sequencing results. For assays, we employed formalin-fixed, in part decalcified, and paraffin-embedded tissue samples. Empiric testing of manual protocols included 10 variables in 17 protocols. Automated immunohistochemical staining and BRAF pyrosequencing served as independent test methods. Test performance measures were compared without considering 1 method as a standard. Four well-fixed samples (2WT/2Mut) were used for testing of all protocols and indicated 2 correctly classifying procedures. Practical performance assessment employed 33 independent tissue samples, composed of 27 leukemias (by pyrosequencing: 8 wild-type; 18 mutated; 1 noninformative) and 6 melanomas (V600E; V600K; wild-type, 2 each). Manual V600E staining was positive in 20 cases (19 of 20 V600E-containing samples plus the 1 sample that was noninformative), whereas all wild-type and V600K cases were immunonegative. Manual or automated staining as well as pyrosequencing would have missed an equal number of V600E-mutated cases and the correlation coefficient for these methods was 0.75 to 0.93 (substantial to almost perfect); the Youden index was 0.95. Detection of V600E-mutated BRAF at the protein level in routine and decalcified tissue samples is possible, and the presented manual protocols should expedite implementation in routine diagnostic practice. Our results indicate that both molecular techniques should be considered complementary.
    Type of Publication: Journal article published
    PubMed ID: 25611237
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  • 30
    Keywords: IN-VIVO ; PATHWAY ; PROTEIN ; NEUROBLASTOMA-CELLS ; TARGET ; resistance ; MESYLATE ; soft-tissue sarcoma ; PRECLINICAL TESTING PROGRAM ; ENDONUCLEASE-G
    Abstract: Eribulin, a novel microtubule-interfering drug, was recently shown to exhibit high antitumor activity in vivo against various pediatric cancers. Here, we identify a novel synthetic lethal interaction of Eribulin together with Polo-like kinase 1 (PLK1) inhibitors against rhabdomyosarcoma (RMS) in vitro and in vivo. Eribulin and the PLK1 inhibitor BI 2536 at subtoxic concentrations synergize to induce apoptosis in RMS cells as confirmed by calculation of combination index (CI). Also, Eribulin/BI 2536 co-treatment is significantly more effective than monotherapy to reduce cell viability and inhibit colony formation of RMS cells. Similarly, Eribulin and BI 2536 act in concert to trigger apoptosis in a primary, patient-derived ARMS culture, underscoring the clinical relevance of this combination. Importantly, Eribulin and BI 2536 cooperate to suppress tumor growth in an in vivo model of RMS. On molecular grounds, Eribulin/BI 2536 co-treatment causes profound mitotic arrest, which is critically required for synergism, since inhibition of mitotic arrest by CDK1 inhibitor RO-3306 abolishes Eribulin/BI 2536-mediated apoptosis. Eribulin and BI 2536 cooperate to activate caspase-9, -3 and -8, which is necessary for apoptosis induction, since the broad-range caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone (zVAD.fmk) reduces Eribulin/BI 2536-induced apoptosis significantly, yet partially. Intriguingly, knockdown of endonuclease G (ENDOG) also significantly inhibits Eribulin/BI 2536-triggered apoptosis, demonstrating the involvement of both caspase-dependent and -independent effector pathways. Synergistic induction of apoptosis is similarly found for Eribulin/BI 2536 co-treatment in neuroblastoma cells and for the combination of vincristine (another antimicrotubule chemotherapeutic) with Poloxin (another PLK1 inhibitor), thus pointing to a broader significance of this concomitant microtubule- and PLK1-targeting strategy for pediatric oncology. In conclusion, the identification of a novel synthetic lethality by dual targeting of mitosis using microtubule-interfering and PLK1-targeted drugs, i.e. Eribulin and BI 2536, has important implications for the development of more effective treatment strategies for RMS.
    Type of Publication: Journal article published
    PubMed ID: 25917079
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  • 31
    Keywords: CANCER ; EXPRESSION ; CELL-PROLIFERATION ; GENES ; PROTEIN ; IDENTIFICATION ; REVEALS ; MicroRNAs ; RELATIVE QUANTIFICATION ; FEEDBACK LOOP
    Abstract: LIN28B has been identified as an oncogene in various tumor entities, including neuroblastoma, a childhood cancer that originates from neural crest-derived cells, and is characterized by amplification of the MYCN oncogene. Recently, elevated LIN28B expression levels were shown to contribute to neuroblastoma tumorigenesis via let-7 dependent de-repression of MYCN. However, additional insight in the regulation of LIN28B in neuroblastoma is lacking. Therefore, we have performed a comprehensive analysis of the regulation of LIN28B in neuroblastoma, with a specific focus on the contribution of miRNAs. We show that MYCN regulates LIN28B expression in neuroblastoma tumors via two distinct parallel mechanisms. First, through an unbiased LIN28B-3'UTR reporter screen, we found that miR-26a-5p and miR-26b-5p regulate LIN28B expression. Next, we demonstrated that MYCN indirectly affects the expression of miR-26a-5p, and hence regulates LIN28B, therefore establishing an MYCN-miR-26a-5p-LIN28B regulatory axis. Second, we provide evidence that MYCN regulates LIN28B expression via interaction with the LIN28B promoter, establishing a direct MYCN-LIN28B regulatory axis. We believe that these findings mark LIN28B as an important effector of the MYCN oncogenic phenotype and underline the importance of MYCN-regulated miRNAs in establishing the MYCN-driven oncogenic process.
    Type of Publication: Journal article published
    PubMed ID: 26123663
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  • 32
    Keywords: CELLS ; INVASION ; PATHWAY ; GENE-EXPRESSION ; PROTEIN ; BREAST-CANCER ; TUMOR PROGRESSION ; HYPOXIA ; CADHERIN ; miR-200 family
    Abstract: The microRNA (miRNA) landscape changes during the progression of cancer. We defined a metastasis-associated miRNA landscape using a systematic approach. We profiled and validated miRNA and mRNA expression in a unique series of human colorectal metastasis tissues together with their matched primary tumors and corresponding normal tissues. We identified an exclusive miRNA signature that is differentially expressed in metastases. Three of these miRNAs were identified as key drivers of an EMT-regulating network acting though a number of novel targets. These targets include SIAH1, SETD2, ZEB2, and especially FOXN3, which we demonstrated for the first time as a direct transcriptional suppressor of N-cadherin. The modulation of N-cadherin expression had significant impact on migration, invasion, and metastasis in two different in vivo models. The significant deregulation of the miRNAs defining the network was confirmed in an independent patient set as well as in a database of diverse malignancies derived from more than 6,000 patients. Our data define a novel metastasis-orchestrating network based on systematic hypothesis generation from metastasis tissues. Cancer Res; 75(15); 3010-9. (c)2015 AACR.
    Type of Publication: Journal article published
    PubMed ID: 26069251
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  • 33
    Keywords: PROTEIN ; PURIFICATION ; MODEL MEMBRANES ; LIPID-COMPOSITION ; ACTINIA-EQUINA ; STICHOLYSIN-I ; PORE-FORMING TOXIN ; SEA-ANEMONE STICHODACTYLA ; CYTOLYSIN EQUINATOXIN-II ; HELIANTHUS
    Abstract: Actinoporins are pore-forming toxins (PFT) produced by sea anemones with molecular mass around 20 kDa and high affinity for sphingomyelin. The most studied atinoporins are sticholysins I and II (StI/StII) from Stichodactyla helianthus, equinatoxin II (EqtII) from Actinia equina, and fragaceatoxin C (FraC) from Actinia fragacea. Their N-terminal sequences encompassing residues 1-30 seem to be the best candidates for pore formation. This segment comprises an amphipathic alpha-helix preceded by a more or less hydrophobic segment, depending on the toxin, of around 10 amino acid residues. Although it is clear that the N-terminal is the most variable sequence in this protein family, the role of their hydrophobic segment in not fully understood. Here we show a comparison of StI, StII, EqtII, and FraC activities with that of their respective N-terminal synthetic peptides. The hemolytic and permeabilizing activity of the peptides reproduce qualitatively the behavior of their respective parental proteins and are particularly related to the hydrophobicity of the corresponding 1-10 segment. Furthermore, the dendrogram analysis of actinoporins' N-terminal sequence allows relating differences in alignment with differences in activity among the four toxins. We have also evaluated the penetration depth of the N-terminal segment of StI and StII by using Trp-containing peptide-analogs. Our data suggest that the N-terminus of StII is more deeply buried into the hydrophobic core of the bilayer than that of StI. We hypothesize that the highest activity of StII could be ascribed to a larger hydrophobic continuum, an uninterrupted sequence of non-charged mainly hydrophobic amino acid residues, of its N-terminus promoting a highest ability to partially insert in the membrane core. Moreover, as we show for four related peptides that a higher hydrophobicity contributes to increase the activity, we reinforce the notion that this property must be taken into account to design new potent membranotropic agents.
    Type of Publication: Journal article published
    PubMed ID: 26134716
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  • 34
    Keywords: EXPRESSION ; PATHWAY ; DEATH ; DISEASE ; PROTEIN ; DROSOPHILA-MELANOGASTER ; LIFE-SPAN ; MITOCHONDRIA ; HOMEOSTASIS ; Longevity
    Abstract: Mitochondrial dysfunction has been implicated in human diseases, including cancer, and proposed to accelerate aging. The Drosophila Cyclin-dependent protein kinase complex cyclin D/cyclin-dependent kinase 4 (CycD/Cdk4) promotes cellular growth by stimulating mitochondrial biogenesis. Here, we examine the neurodegenerative and aging consequences of altering CycD/Cdk4 function in Drosophila. We show that pan-neuronal loss or gain of CycD/Cdk4 increases mitochondrial superoxide, oxidative stress markers, and neurodegeneration and decreases lifespan. We find that RNAi-mediated depletion of the mitochondrial transcription factor, Tfam, can abrogate CycD/Cdk4's detrimental effects on both lifespan and neurodegeneration. This indicates that CycD/Cdk4's pathological consequences are mediated through altered mitochondrial function and a concomitant increase in reactive oxygen species. In support of this, we demonstrate that CycD/Cdk4 activity levels in the brain affect the expression of a set of 'oxidative stress' genes. Our results indicate that the precise regulation of neuronal CycD/Cdk4 activity is important to limit mitochondrial reactive oxygen species production and prevent neurodegeneration.
    Type of Publication: Journal article published
    PubMed ID: 26219626
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  • 35
    Keywords: CELLS ; tumor ; PROTEIN ; immunohistochemistry ; MUTATION ; MELANOMA ; OF-THE-LITERATURE ; LOW-GRADE GLIOMAS ; VEMURAFENIB ; INFANCY
    Abstract: AimsDesmoplastic infantile astrocytoma/ganglioglioma (DIA/DIG) is a rare primary neuroepithelial brain tumour typically affecting paediatric patients younger than 24 months. Knowledge about genetic alterations in DIA/DIG is limited. However, a previous study on BRAF V600E mutation in paediatric glioma revealed a BRAF mutation in one of two tested DIAs/DIGs. The limited number of cases in that study did not allow any conclusion about mutation frequency of BRAF in this tumour entity. MethodsWe collected a series of 18 DIAs/DIGs for testing BRAF V600E mutational status by BRAF V600E immunohistochemistry (clone VE1). Cases with sufficient DNA were tested for BRAF V600E mutation by pyrosequencing. ResultsThree out of 18 DIAs/DIGs presented with VE1 binding. A considerable proportion of BRAF V600E mutated tumour cells was detected in the cortical tumour component, whereas the pronounced leptomeningeal tumoural stroma was predominantly negative for VE1 binding. Pyrosequencing confirmed BRAF V600E mutation in two of three VE1-positive cases. ConclusionBRAF V600E mutation affects a subset of DIAs/DIGs and offers new therapeutic opportunities.
    Type of Publication: Journal article published
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  • 36
    Keywords: CELLS ; EXPRESSION ; PROTEIN ; VARIANTS ; ESTROGEN-RECEPTOR ; CONSORTIUM ; TBX3
    Abstract: In a genome-wide scan, we show that 30 variants in 25 genomic regions are associated with risk of TN breast cancer. Women carrying many of the risk variants may have 4-fold increased risk relative to women with few variants.Triple-negative (TN) breast cancer is an aggressive subtype of breast cancer associated with a unique set of epidemiologic and genetic risk factors. We conducted a two-stage genome-wide association study of TN breast cancer (stage 1: 1529 TN cases, 3399 controls; stage 2: 2148 cases, 1309 controls) to identify loci that influence TN breast cancer risk. Variants in the 19p13.1 and PTHLH loci showed genome-wide significant associations (P 〈 5 x 10(-) (8)) in stage 1 and 2 combined. Results also suggested a substantial enrichment of significantly associated variants among the single nucleotide polymorphisms (SNPs) analyzed in stage 2. Variants from 25 of 74 known breast cancer susceptibility loci were also associated with risk of TN breast cancer (P 〈 0.05). Associations with TN breast cancer were confirmed for 10 loci (LGR6, MDM4, CASP8, 2q35, 2p24.1, TERT-rs10069690, ESR1, TOX3, 19p13.1, RALY), and we identified associations with TN breast cancer for 15 additional breast cancer loci (P 〈 0.05: PEX14, 2q24.1, 2q31.1, ADAM29, EBF1, TCF7L2, 11q13.1, 11q24.3, 12p13.1, PTHLH, NTN4, 12q24, BRCA2, RAD51L1-rs2588809, MKL1). Further, two SNPs independent of previously reported signals in ESR1 [rs12525163 odds ratio (OR) = 1.15, P = 4.9 x 10(-) (4)] and 19p13.1 (rs1864112 OR = 0.84, P = 1.8 x 10(-) (9)) were associated with TN breast cancer. A polygenic risk score (PRS) for TN breast cancer based on known breast cancer risk variants showed a 4-fold difference in risk between the highest and lowest PRS quintiles (OR = 4.03, 95% confidence interval 3.46-4.70, P = 4.8 x 10(-) (69)). This translates to an absolute risk for TN breast cancer ranging from 0.8% to 3.4%, suggesting that genetic variation may be used for TN breast cancer risk prediction.
    Type of Publication: Journal article published
    PubMed ID: 24325915
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  • 37
    Keywords: IN-VIVO ; PROTEIN ; COMPLEXES ; LIVING CELLS ; ARRAY ; CAMERA ; FCS ; FRET ; MEMBRANE DYNAMICS ; LASER EXCITATION
    Abstract: Single plane illumination microscopy based fluorescence correlation spectroscopy (SPIM-FCS) is a new method for imaging FCS in 3D samples, providing diffusion coefficients, flow velocities and concentrations in an imaging mode. Here we extend this technique to two-color fluorescence cross-correlation spectroscopy (SPIM-FCCS), which allows to measure molecular interactions in an imaging mode. We present a theoretical framework for SPIM-FCCS fitting models, which is subsequently used to evaluate several test measurements of in-vitro (labeled microspheres, several DNAs and small unilamellar vesicles) and in-vivo samples (dimeric and monomeric dual-color fluorescent proteins, as well as membrane bound proteins). Our method yields the same quantitative results as the well-established confocal FCCS, but in addition provides unmatched statistics and true imaging capabilities.
    Type of Publication: Journal article published
    PubMed ID: 24663528
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  • 38
    Keywords: EXPRESSION ; SURVIVAL ; PATHWAY ; PROTEIN ; DIFFERENTIATION ; CLEAVAGE ; DEGRADATION ; BORTEZOMIB ; ANTI-APOPTOTIC MCL-1 ; NOXA
    Abstract: Myeloid cell leukemia-1 (Mcl-1, HGNC: 6943), a pro-survival member of the Bcl-2 family, plays a crucial role in Multiple Myeloma (MM) pathogenesis and drug resistance, thus representing a promising therapeutic target in MM. A novel strategy to inhibit Mcl-1 activity is the induction of ubiquitin-independent Mcl-1 degradation. Our own and other previous studies have demonstrated caspase-dependent generation of a 28kDa Mcl-1 fragment, Mcl-1(128-350), which inhibits MM cell proliferation and survival. Here, we show that similar to bortezomib, the novel proteasome inhibitors carfilzomib and ixazomib, as well as staurosporine and adaphostin, induce the generation of Mcl-1(128-350) in MM cells. Next, the molecular sequelae downstream of Mcl-1(128-350), which mediate its pro-apoptotic activity, were delineated. Surprisingly, we observed nuclear accumulation of drug-induced or exogenously overexpressed Mcl-1(128-350), followed by elevated mRNA and protein levels of c-Jun, as well as enhanced AP-1 reporter activity. Moreover, drug-induced AP-1 activity was blocked after introducing a point mutation into the highly conserved Mcl-1 caspase-cleavage site Asp127, but not Asp157. Consequently, drug-triggered cell death was significantly decreased in MM cells transfected with Mcl-1 D127A, but not with Mcl-1 D157A. Consistent with these data, treatment with bortezomib triggered c-Jun upregulation followed by apoptosis in Mcl-1(wt/wt), but not Mcl-1(Delta/null) murine embryonic fibroblasts (MEFs). Transfection of a plasmid carrying Mcl-1(wt) into Mcl-1(Delta/null) MEFs restored bortezomib-induced Mcl-1 fragmentation, c-Jun upregulation and AP-1 reporter activity. Finally, our data indicate that drug-induced generation of a pro-apoptotic Mcl-1 fragment followed by c-Jun upregulation may also be a novel therapeutic approach in other tumor entities.
    Type of Publication: Journal article published
    PubMed ID: 24120758
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  • 39
    Keywords: GENE-EXPRESSION ; PROTEIN ; transcription ; MOUSE ; CLOCK ; NUCLEUS ; DEGRADATION ; STRUCTURAL BASIS ; LYSINE DEMETHYLASE LSD1 ; MPER2
    Abstract: The circadian clock is a self-sustaining oscillator that controls daily rhythms. For the proper circadian gene expression, dynamic changes in chromatin structure are important. Although chromatin modifiers have been shown to play a role in circadian gene expression, the in vivo role of circadian signal-modulated chromatin modifiers at an organism level remains to be elucidated. Here, we provide evidence that the lysine-specific demethylase 1 (LSD1) is phosphorylated by protein kinase C alpha (PKC alpha) in a circadian manner and the phosphorylated LSD1 forms a complex with CLOCK:BMAL1 to facilitate E-box-mediated transcriptional activation. Knockin mice bearing phosphorylation-defective Lsd1(SA/SA) alleles exhibited altered circadian rhythms in locomotor behavior with attenuation of rhythmic expression of core clock genes and impaired phase resetting of circadian clock. These data demonstrate that LSD1 is a key component of the molecular circadian oscillator, which plays a pivotal role in rhythmicity and phase resetting of the circadian clock.
    Type of Publication: Journal article published
    PubMed ID: 24582500
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  • 40
    Keywords: RECEPTOR ; EXPRESSION ; KINASE ; PROTEIN ; ACTIVATION ; GLYCATION END-PRODUCTS ; OXIDATIVE STRESS ; p38 ; METHYLGLYOXAL INDUCES APOPTOSIS ; GLYOXAL
    Abstract: Tamoxifen is the standard adjuvant endocrine therapy for estrogen-receptor positive premenopausal breast cancer patients. However, tamoxifen resistance is frequently observed under therapy. A tamoxifen resistant cell line has been generated from the estrogen receptor positive mamma carcinoma cell line MCF-7 and was analyzed for putative differences in the aldehyde defence system and accumulation of advanced glycation end products (AGE). In comparison to wt MCF-7 cells, these tamoxifen resistant cells were more sensitive to the dicarbonyl compounds glyoxal and methylglyoxal and displayed increased caspase activity, p38-MAPK- and I kappa B alpha-phosphorylation. However, mRNA accumulation of the aldehyde-and AGE-defence enzymes glyoxalase-1 and -2 (GLO1, GLO2) as well as fructosamine-3-kinase (FN3K) was not significantly altered. Tamoxifen resistant cells contained less free sulfhydryl-groups (glutathione) suggesting that the increased sensitivity towards the dicarbonyls was due to a higher sensitivity towards reactive oxygen species which are associated with dicarbonyl stress. To further analyse, if these data are of more general importance, key experiments were replicated with tamoxifen resistant MCF-7 cell lines from two independent sources. These cell lines were also more sensitive to aldehydes, especially glyoxal, but were different in their cellular signalling responses to the aldehydes. In conclusion, glyoxalases and other aldehyde defence enzymes might represent a promising target for the therapy of tamoxifen resistant breast cancers.
    Type of Publication: Journal article published
    PubMed ID: 24983248
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  • 41
    Keywords: PROTEIN ; DOWN-REGULATION ; NUCLEAR-LOCALIZATION ; ANIMAL LECTINS ; SUGAR CODE ; fetuin ; SUBSTRATE ; CARBOHYDRATE-RECOGNITION DOMAIN ; PANCREATIC-CARCINOMA MODEL ; SELF-ASSOCIATION
    Abstract: Many human proteins have a modular design with receptor and structural domains. Using adhesion/growth-regulatory galectin-3 as model, we describe an interdisciplinary strategy to define the functional significance of its tail established by nine non-triple helical collagen-like repeats (I-IX) and the N-terminal peptide. Genetic engineering with sophisticated mass spectrometric product analysis provided the tools for biotesting, i.e. eight protein variants with different degrees of tail truncation. Evidently,various aspects of galectin-3 activity (cis binding and cell bridging) are affected by tail shortening in a different manner. Thus, this combined approach reveals an unsuspected complexity of structure-function relationship, encouraging further application beyond this chimera-type galectin.
    Type of Publication: Journal article published
    PubMed ID: 24909114
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  • 42
    Keywords: APOPTOSIS ; SURVIVAL ; carcinoma ; GENE-EXPRESSION ; PROTEIN ; IMMUNOHISTOCHEMICAL ANALYSIS ; FAMILY-MEMBERS ; Bcl-x(L) ; BIOLOGICAL NETWORKS ; X-L
    Abstract: INTRODUCTION: Apoptosis is a crucial pathway in tumor growth and metastatic development. Apoptotic proteins regulate the underlying molecular cascades and are thought to modulate the tumor response to chemotherapy and radiation. However, the prognostic value of the expression of apoptosis regulators in localized non-small-cell lung cancer (NSCLC) is still unclear. METHODS: We investigated the protein expression of apoptosis regulators Bcl-2, Bcl-xl, Mcl-1, and pp32/PHAPI, and the expression of the lncRNA MALAT-1 in tumor samples from 383 NSCLC patients (median age: 65.6 years; 77.5% male; paraffin-embedded tissue microarrays). For statistical analysis correlation tests, Log rank tests and Cox proportional hazard models were applied. RESULTS: Tumor histology was significantly associated with the expression of Bcl-2, Bcl-xl and Mcl-1 (all p 〈 0.001). Among the tested apoptotic markers only Bcl-2 demonstrated prognostic impact (hazard ratio = 0.64, p = 0.012). For NSCLC patients with non-adenocarcinoma histology, Bcl-2 expression was associated with increased overall survival (p = 0.036). Besides tumor histology, prognostic impact of Bcl-2 was also found to depend on MALAT-1 lncRNA expression. Gene expression analysis of A549 adenocarcinoma cells with differential MALAT-1 lncRNA expression demonstrated an influence on the expression of Bcl-2 and its interacting proteins. CONCLUSIONS: Bcl-2 expression was specifically associated with superior prognosis in localized NSCLC. An interaction of Bcl-2 with MALAT-1 lncRNA expression was revealed, which merits further investigation for risk prediction in resectable NSCLC patients.
    Type of Publication: Journal article published
    PubMed ID: 25036876
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  • 43
    Keywords: proliferation ; GENE-EXPRESSION ; PROTEIN ; EPITHELIAL-MESENCHYMAL TRANSITIONS ; TRANSCRIPTION FACTOR SNAIL ; REPRESSOR ; regeneration ; SELF-RENEWAL ; MIDGUT ; NOTCH ACTIVITY
    Abstract: Snail family transcription factors are expressed in various stem cell types, but their function in maintaining stem cell identity is unclear. In the adult Drosophila midgut, the Snail homolog Esg is expressed in intestinal stem cells (ISCs) and their transient undifferentiated daughters, termed enteroblasts (EB). We demonstrate here that loss of esg in these progenitor cells causes their rapid differentiation into enterocytes (EC) or entero-endocrine cells (EE). Conversely, forced expression of Esg in intestinal progenitor cells blocks differentiation, locking ISCs in a stem cell state. Cell type-specific transcriptome analysis combined with Dam-ID binding studies identified Esg as a major repressor of differentiation genes in stem and progenitor cells. One critical target of Esg was found to be the POU-domain transcription factor, Pdm1, which is normally expressed specifically in differentiated ECs. Ectopic expression of Pdm1 in progenitor cells was sufficient to drive their differentiation into ECs. Hence, Esg is a critical stem cell determinant that maintains stemness by repressing differentiation-promoting factors, such as Pdm1.
    Type of Publication: Journal article published
    PubMed ID: 25298397
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  • 44
    Keywords: GENE-EXPRESSION ; PROTEIN ; T-CELLS ; E7 ; CERVICAL-CANCER ; intraepithelial neoplasia ; HUMAN-PAPILLOMAVIRUS TYPE-16 ; NUCLEAR IMPORT ; II TRIAL ; GRADE 3
    Abstract: Persistent infection with the high-risk Human Papillomavirus type 16 (HPV 16) is the causative event for the development of cervical cancer and other malignant tumors of the anogenital tract and of the head and neck. Despite many attempts to develop therapeutic vaccines no candidate has entered late clinical trials. An interesting approach is a DNA based vaccine encompassing the nucleotide sequence of the E6 and E7 viral oncoproteins. Because both proteins are consistently expressed in HPV infected cells they represent excellent targets for immune therapy. Here we report the development of 8 DNA vaccine candidates consisting of differently rearranged HPV-16 E6 and E7 sequences within one molecule providing all naturally occurring epitopes but supposedly lacking transforming activity. The HPV sequences were fused to the J-domain and the SV40 enhancer in order to increase immune responses. We demonstrate that one out of the 8 vaccine candidates induces very strong cellular E6- and E7- specific cellular immune responses in mice and, as shown in regression experiments, efficiently controls growth of HPV 16 positive syngeneic tumors. This data demonstrates the potential of this vaccine candidate to control persistent HPV 16 infection that may lead to malignant disease. It also suggests that different sequence rearrangements influence the immunogenecity by an as yet unknown mechanism.
    Type of Publication: Journal article published
    PubMed ID: 25422946
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  • 45
    Keywords: PROTEIN ; MUTATIONS ; STABILITY ; ATOMIC-STRUCTURE ; ROD DOMAIN ; MOLECULAR ARCHITECTURE ; OLIGOMERIZATION STATE ; HELICAL COILED-COILS ; DISTINCT STAGES ; SALT-BRIDGES
    Abstract: Intermediate filaments (IFs) are key to the mechanical strength of metazoan cells. Their basic building blocks are dimeric coiled coils mediating hierarchical assembly of the full-length filaments. Here we use single-molecule force spectroscopy by optical tweezers to assess the folding and stability of coil 2B of the model IF protein vimentin. The coiled coil was unzipped from its N and C termini. When pulling from the C terminus, we observed that the coiled coil was resistant to force owing to the high stability of the C-terminal region. Pulling from the N terminus revealed that the N-terminal half is considerably less stable. The mechanical pulling assay is a unique tool to study and control seed formation and structure propagation of the coiled coil. We then used rigorous theory-based deconvolution for a model-free extraction of the energy landscape and local stability profiles. The data obtained from the two distinct pulling directions complement each other and reveal a tripartite stability of the coiled coil: a labile N-terminal half, followed by a medium stability section and a highly stable region at the far C-terminal end. The different stability regions provide important insight into the mechanics of IF assembly.
    Type of Publication: Journal article published
    PubMed ID: 25049381
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  • 46
    Keywords: PROTEIN ; GERM-CELLS ; centrosome ; SRC FAMILY KINASES ; F-ACTIN ; SELF-RENEWAL ; BITHORAX COMPLEX ; HEMATOPOIETIC STEM ; ABDOMINAL-B ; LAMININ-A
    Abstract: Proper niche architecture is critical for stem cell function, yet only few upstream regulators are known. Here, we report that the Hox transcription factor Abdominal-B (Abd-B), active in premeiotic spermatocytes of Drosophila testes, is essential for positioning the niche to the testis anterior by regulating integrin in neighboring somatic cyst cells. Abd-B also non-cell-autonomously controls critical features within the niche, including centrosome orientation and division rates of germline stem cells. By using genome-wide binding studies, we find that Abd-B mediates its effects on integrin localization by directly controlling at multiple levels the signaling activity of the Sev ligand Boss via its direct targets src42A and sec63, two genes involved in protein trafficking and recycling. Our data show that Abd-B, through local signaling between adjucent cell types, provides positional cues for integrin localization, which is critical for placement of the distant stem cell niche and stem cell activity.
    Type of Publication: Journal article published
    PubMed ID: 24480643
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