Telomerase abrogates aneuploidy‐induced telomere replication stress,senescence and cell depletion

The causal role of aneuploidy in cancer initiation remains under debate since mutations of euploidy‐controlling genes reduce cell fitness but aneuploidy strongly associates with human cancers. Telomerase activation allows immortal growth by stabilizing telomere length, but its role in aneuploidy survival has not been characterized. Here, we analyze the response of primary human cells and murine hematopoietic stem cells (HSCs) to aneuploidy induction and the role of telomeres and the telomerase in this process. The study shows that aneuploidy induces replication stress at telomeres leading to telomeric DNA damage and p53 activation. This results in p53/Rb‐dependent, premature senescence of human fibroblast, and in the depletion of hematopoietic cells in telomerase‐deficient mice. Endogenous telomerase expression in HSCs and enforced expression of telomerase in human fibroblasts are sufficient to abrogate aneuploidy‐induced replication stress at telomeres and the consequent induction of premature senescence and hematopoietic cell depletion. Together, these results identify telomerase as an aneuploidy survival factor in mammalian cells based on its capacity to alleviate telomere replication stress in response to aneuploidy induction.     

Visualization of genomic aberrations using Affymetrix SNP arrays

MOTIVATION: DNA copy number aberrations are frequently found in different types of cancer. Recent developments of microarray-based approaches have broadened the knowledge on number and structure of such aberrations. High-density single nucleotide polymorphism (SNP) microarrays provide an extremely high resolution with up to 500,000 SNPs per genome. Owing to the enormous amount of data the detection of common aberrations in large datasets is a great challenge. We describe a novel open source software tool--IdeogramBrowser--which was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards. Visualization of consensus regions together with gene representation allows the explorative assessment of the data. AVAILABILITY: IdeogramBrowser and its source code are freely available under a creative commons license and can be obtained from http://www.informatik.uni-ulm.de/ni/staff/HKestler/ideo/. IdeogramBrowser is a platform independent Java application.     

VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays

Background  

Microarray experiments generate vast amounts of data. The functional context of differentially expressed genes can be assessed by querying the Gene Ontology (GO) database via GoMiner. Directed acyclic graph representations, which are used to depict GO categories enriched with differentially expressed genes, are difficult to interpret and, depending on the particular analysis, may not be well suited for formulating new hypotheses. Additional graphical methods are therefore needed to augment the GO graphical representation.     

The Listeria monocytogenesiap gene as an indicator gene for the study of PrfA-dependent regulation

The Bacillus subtilis 168 RecR protein bound to duplex DNA in the presence of ATP and divalent cations (Mg²⁺ and Zn²⁺) was visualized by electron microscopy as a nearly spherical particle. A RecR homomultimer is frequently located at the intersection of two duplex DNA strands in an interwound DNA molecule, generating DNA loops of variable length. Two individual DNA molecules bound to the same protein are seen at a very low frequency, if at all. The association of RecR with the intersection of two duplex DNA strands is more often seen in supercoiled than with relaxed or linear DNA. The RecR protein displays a slight but significant preference for negatively supercoiled over linear DNA. The minimum substrate size for RecR protein is about 150 bp in length. A possible mechanism for RecR function in DNA repair is discussed.     

Chronophin Dimerization Is Required for Proper Positioning of Its Substrate Specificity Loop

Mammalian phosphatases of the haloacid dehalogenase (HAD) superfamily have emerged as important regulators of physiology and disease. Many of these enzymes are stable homodimers; however, the role of their dimerization is largely unknown. Here, we explore the function of the obligatory homodimerization of chronophin, a mammalian HAD phosphatase known to dephosphorylate pyridoxal 5′-phosphate (PLP) and serine/threonine-phosphorylated proteins. The exchange of two residues in the murine chronophin homodimerization interface (chronophin^A194K,A195K) yields a constitutive monomer both in vitro and in cells. The catalytic activity of monomeric chronophin toward PLP is strongly impaired. X-ray crystallographic studies of chronophin^A194K,A195K revealed that dimer formation is essential for an intermolecular arginine-arginine-tryptophan stacking interaction that positions a critical histidine residue in the substrate specificity loop of chronophin for PLP coordination. Analysis of all available crystal structures of HAD hydrolases that are grouped together with chronophin in the C2a-type structural subfamily uncovered a highly conserved mode of dimerization that results in intermolecular contacts involving the substrate specificity loop. Our results explain how the dimerization of HAD hydrolases contributes to their catalytic efficiency and substrate specificity.     

Significantly improved precision of cell migration analysis in time-lapse video microscopy through use of a fully automated tracking system

Background  

Cell motility is a critical parameter in many physiological as well as pathophysiological processes. In time-lapse video microscopy, manual cell tracking remains the most common method of analyzing migratory behavior of cell populations. In addition to being labor-intensive, this method is susceptible to user-dependent errors regarding the selection of "representative" subsets of cells and manual determination of precise cell positions.     

Chromosomal Integration of Adenoviral Vector DNA In Vivo

So far there has been no report of any clinical or preclinical evidence for chromosomal vector integration following adenovirus (Ad) vector-mediated gene transfer in vivo. We used liver gene transfer with high-capacity Ad vectors in the FAH^Δexon5 mouse model to analyze homologous and heterologous recombination events between vector and chromosomal DNA. Intravenous injection of Ad vectors either expressing a fumarylacetoacetate hydrolase (FAH) cDNA or carrying part of the FAH genomic locus resulted in liver nodules of FAH-expressing hepatocytes, demonstrating chromosomal vector integration. Analysis of junctions between vector and chromosomal DNA following heterologous recombination indicated integration of the vector genome through its termini. Heterologous recombination occurred with a median frequency of 6.72 × 10⁻⁵ per transduced hepatocyte, while homologous recombination occurred more rarely with a median frequency of 3.88 × 10⁻⁷. This study has established quantitative and qualitative data on recombination of adenoviral vector DNA with genomic DNA in vivo, contributing to a risk-benefit assessment of the biosafety of Ad vector-mediated gene transfer.Recombinant adenovirus (Ad) vectors are under clinical development for different applications, including tumor therapy, vaccination, and gene therapy. Today, the largest number of clinical gene transfer trials has been based on Ad vectors (http://www.wiley.co.uk/genmed/clinical). Several Ad vectors are in phase III clinical trials, and two products have already been approved in China. The occurrence of malignancies due to retroviral integration and oncogene activation in a clinical trial for the treatment of children with SCID-X1 (10) has pointed to the need for a thorough preclinical evaluation of potential genotoxic effects due to chromosomal integration of gene transfer vectors as an important part of the overall risk-benefit analysis. Detailed information on genotoxicity following gene transfer is available for vectors derived from viruses of the Retroviridae and Parvoviridae families (2, 20, 23, 26, 46). Between 60 and 75% of integrations of retrovirus, lentivirus, or adeno-associated virus (AAV)-based vectors take place in or close to genes.Chromosomal integration of Ad vector DNA following gene transfer in cell culture has been analyzed in only a few studies, and even less is known about Ad vector integration in vivo. Since the life cycle of wild-type adenovirus is extrachromosomal, Ad vectors are perceived to be nonintegrating vectors. However, in earlier studies it was observed that injection of hamsters with wild-type adenovirus type 12 (Ad12) resulted in tumor formation due to chromosomal integration of virus DNA and expression of the E1A/E1B oncoproteins (33). Recent in vitro studies with Ad vectors with E1 deletions have demonstrated the occurrence of vector integration following transduction of transformed cell lines and primary cells, with the frequencies of homologous and heterologous recombination being between 10⁻³ and 10⁻⁶ and between 10⁻³ and 10⁻⁵ per cell, respectively, depending on the conditions used (12, 14, 28, 36, 37, 42, 43). Since clinical gene transfer trials, including prophylactic vaccination of healthy volunteers against infectious diseases, are performed with large amounts of vector (in general, between 10¹⁰ and 10¹³ particles), it is possible that substantial integration of adenoviral vector DNA might also occur in vivo even if integration rates were low. However, so far there has been no attempt to experimentally address the issue of Ad vector integration in vivo. We used the FAH^Δexon5 mouse model (8) of tyrosinemia type I (MIM 27670) to analyze potential homologous and heterologous recombination events between Ad vector DNA and chromosomal DNA in vivo. Tyrosinemia type I is caused by the lack of fumarylacetoacetate hydrolase, an enzyme that is involved in the tyrosine degradation pathway and that converts fumarylacetoacetate into fumaric acid and acetoacetic acid in hepatocytes (38). Loss of fumarylacetoacetate hydrolase (FAH) activity in hepatocytes results in the accumulation of toxic and mutagenic metabolites in a cell-autonomous fashion, leading after birth to an acute hepatopathy and later in life to a chronic hepatopathy. Liver damage can be prevented both in humans and in FAH-deficient animals by the administration of 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione (NTBC), which blocks the tyrosine degradation pathway by inhibiting 4-hydroxphenyl pyruvate dioxygenase, thereby preventing the accumulation of the toxic compounds. The murine FAH gene is located on chromosome 7, contains 14 exons, and spans 20.5 kb.The autosomal recessive FAH^Δexon5 mouse model, in which exon 5 is disrupted by the insertion of a NeoR gene (8), has been a useful system to analyze chromosomal integration of AAV, retrovirus, Sleeping Beauty transposon, and plasmid DNA in hepatocytes (13, 25, 27, 31). Similar to human tyrosinemia type I patients with spontaneous reversions of point mutations (18), FAH-expressing hepatocytes have a strong growth advantage over FAH^−/− hepatocytes, and the developing nodules, consisting of FAH-positive [FAH⁺] hepatocytes, can be easily distinguished in an environment of FAH^−/− hepatocytes. Following injection of an FAH-expressing Ad vector with the E1 deletion (30) into FAH^−/− mice, the development of FAH⁺ nodules in the livers of the experimental animals was observed, suggesting potential chromosomal integration of vector DNA. Since transgene expression from vectors with the E1 deletion is transient, in part due to viral toxicity and an immune response directed to viral proteins expressed from the vector, integration events and their characterization were not possible. We reasoned that the use of high-capacity Ad (HC-Ad) vectors (also called “helper-dependent” or “gutless” Ad vectors) (41) not expressing any viral proteins would allow reliable data on Ad vector integration in vivo to be obtained.