Etablierung muriner embryonaler Stammzellen mit vorhersagbarer, regulierbarer Transgenexpression

Transgenic mice are often generated by Random Integration (RI) of the transgene into the genome of murine Embryonic Stem (mES) cells. Since the chromosomal integration site of the gene of interest has a strong impact on expression patterns in the animal (ôposition effectö), generation of transgenic mouse models is hindered by high screening efforts to identify appropriate loci. Strategies devised to circumvent the problems of RI, e.g. site specific integration by homologous recombination, suffer from various limitations like the small number of suitable integration sites currently available. Hence, the aim of this work was to screen for chromosomal loci in mES cells that allow for high and well regulated transgene expression in mice and to render them reusable via Recombinase Mediated Cassette Exchange (RMCE). The screening cassette applied for this purpose contained an autoregulatory positive feedback loop driven by the tetracycline dependent system. As autoregulated transgene expression has not yet been examined in detail on transgenic mouse level, evaluation of this mode of regulated expression was a major issue of this work. Luciferase reporter levels from two random loci and the ROSA26 reference locus revealed strong variations that seem to be specific to autoregulation. In vivo bioluminescence analyses of transgenic mice derived from the two above mentioned clones showed a strong heterogeneity of expression between individuals of the same line with some animals completely shutting off expression. As expected for the autoregulated design, luciferase expression in one transgenic mouse line could only be induced by doxycycline if the animal had previously shown detectable basal levels. For both transgenic lines activity of the cassette was restricted to certain tissues. In conclusion, proof of principle for the envisioned "tag-and-target" strategy has been provided by this work and the tools and methods have been established to start large scale screening.Transgene Mäuse werden oft durch Integration des Transgens in zufällige chromosomale Loci muriner embryonaler Stammzellen (mES Zellen) generiert. Der jeweilige Integrationsort hat einen starken Einfluss auf das Expressionsverhalten, was aufwändiges Screening nach geeigneten Loci erforderlich macht. Es gibt mehrere Möglichkeiten diesen Positionseffekt zu umgehen, z.B. durch spezifische Integration des Transgens in einen definierten Locus durch homologe Rekombination. Diese Strategien unterliegen aber einigen Beschränkungen, u. a. der geringen Anzahl zur Zeit verwendbarer Loci. Deshalb befasst sich diese Arbeit mit dem Screening nach chromosomalen Loci in mES Zellen, welche eine hohe und gut regulierte Transgenexpression erlauben. Diese Integrationsorte werden über Rekombinase vermittelten Kassetten Austausch (RMCE) wieder verwendbar gemacht. Dazu wurde eine Screening Kassette mit einem autoregulierten, Tetracyclin (Tet) abhängigen positiven Feedback Loop eingesetzt. Die Charakterisierung dieses autoregulierten, Tet abhängigen Expressionsmodus in transgenen Mäusen war ein wichtiger Aspekt dieser Arbeit. Die Luziferase Reporter Expression von zwei zufälligen Loci und vom ROSA26 Referenz Locus in mES Zellen schwankte stark, was vermutlich eine spezifische Eigenschaft der Autoregulation ist. Aus den ersten beiden Klonen wurden transgene Mäuse generiert. In vivo Biolumineszenz Analysen dieser Tiere zeigten ein sehr heterogenes Expressionsverhalten in beiden Linien; einige Mäuse unterdrückten die Expression komplett. Wie für das autoregulierte System erwartet konnte die Expression durch Gabe von Doxycyclin in einer Linie induziert werden sofern das jeweilige Tier detektierbare Basalwerte aufwies. In beiden transgenen Linien war die Aktivität der Kassette auf bestimmte Gewebe beschränkt. Zusammenfassend konnte die Funktionalität der verwendeten „tag and target“ Strategie nachgewiesen werden und die notwendigen Methoden für ein groß angelegtes Screening etabliert werden

Transcriptomic Deconvolution of Neuroendocrine Neoplasms Predicts Clinically Relevant Characteristics

Pancreatic neuroendocrine neoplasms (panNENs) are a rare yet diverse type of neoplasia whose precise clinical–pathological classification is frequently challenging. Since incorrect classifications can affect treatment decisions, additional tools which support the diagnosis, such as machine learning (ML) techniques, are critically needed but generally unavailable due to the scarcity of suitable ML training data for rare panNENs. Here, we demonstrate that a multi-step ML framework predicts clinically relevant panNEN characteristics while being exclusively trained on widely available data of a healthy origin. The approach classifies panNENs by deconvolving their transcriptomes into cell type proportions based on shared gene expression profiles with healthy pancreatic cell types. The deconvolution results were found to provide a prognostic value with respect to the prediction of the overall patient survival time, neoplastic grading, and carcinoma versus tumor subclassification. The performance with which a proliferation rate agnostic deconvolution ML model could predict the clinical characteristics was found to be comparable to that of a comparative baseline model trained on the proliferation rate-informed MKI67 levels. The approach is novel in that it complements established proliferation rate-oriented classification schemes whose results can be reproduced and further refined by differentiating between identically graded subgroups. By including non-endocrine cell types, the deconvolution approach furthermore provides an in silico quantification of panNEN dedifferentiation, optimizing it for challenging clinical classification tasks in more aggressive panNEN subtypes.Peer Reviewe

Characterisation of hepcidin response to holotransferrin treatment in CHO TRVb-1 cells

Iron overload coupled with low hepcidin levels are characteristics of hereditary haemochromatosis. To understand the role of transferrin receptor (TFR) and intracellular iron in hepcidin secretion, Chinese hamster ovary transferrin receptor variant (CHO TRVb-1) cells were used that express iron-response-element-depleted human TFRC mRNA (TFRC∆IRE). Results showed that CHO TRVb-1 cells expressed higher basal levels of cell-surface TFR1 than HepG2 cells (2.2-fold; p < 0.01) and following 5 g/L holotransferrin treatment maintained constitutive over-expression at 24h and 48 h, contrasting the HepG2 cells where the receptor levels significantly declined. Despite this, the intracellular iron content was neither higher than HepG2 cells nor increased over time under basal or holotransferrin-treated conditions. Interestingly, hepcidin secretion in CHO TRVb-1 cells exceeded basal levels at all time-points (p < 0.02) and matched levels in HepG2 cells following treatment. While TFRC mRNA expression showed expected elevation (2h, p < 0.03; 4h; p < 0.05), slc40a1 mRNA expression was also elevated (2 h, p < 0.05; 4 h, p < 0.03), unlike the HepG2 cells. In conclusion, the CHO TRVb-1 cells prevented cellular iron-overload by elevating slc40a1 expression, thereby highlighting its significance in the absence of iron-regulated TFRC mRNA. Furthermore, hepcidin response to holotransferrin treatment was similar to HepG2 cells and resembled the human physiological response

DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors.

BACKGROUND Pancreatic neuroendocrine neoplasms (PanNENs) fall into two subclasses: the well-differentiated, low- to high-grade pancreatic neuroendocrine tumors (PanNETs), and the poorly-differentiated, high-grade pancreatic neuroendocrine carcinomas (PanNECs). While recent studies suggest an endocrine descent of PanNETs, the origin of PanNECs remains unknown. METHODS We performed DNA methylation analysis for 57 PanNEN samples and found that distinct methylation profiles separated PanNENs into two major groups, clearly distinguishing high-grade PanNECs from other PanNETs including high-grade NETG3. DNA alterations and immunohistochemistry of cell-type markers PDX1, ARX, and SOX9 were utilized to further characterize PanNECs and their cell of origin in the pancreas. RESULTS Phylo-epigenetic and cell-type signature features derived from alpha, beta, acinar, and ductal adult cells suggest an exocrine cell of origin for PanNECs, thus separating them in cell lineage from other PanNENs of endocrine origin. CONCLUSIONS Our study provides a robust and clinically applicable method to clearly distinguish PanNECs from G3 PanNETs, improving patient stratification

Controlled re-activation of epigenetically silenced Tet promoter-driven transgene expression by targeted demethylation

Faithful expression of transgenes in cell cultures and mice is often challenged by locus dependent epigenetic silencing. We investigated silencing of Tet-controlled expression cassettes within the mouse ROSA26 locus. We observed pronounced DNA methylation of the Tet promoter concomitant with loss of expression in mES cells as well as in differentiated cells and transgenic animals. Strikingly, the ROSA26 promoter remains active and methylation free indicating that this silencing mechanism specifically affects the transgene, but does not spread to the host's chromosomal neighborhood. To reactivate Tet cassettes a synthetic fusion protein was constructed and expressed in silenced cells. This protein includes the enzymatic domains of ten eleven translocation methylcytosine dioxygenase 1 (TET-1) as well as the Tet repressor DNA binding domain. Expression of the synthetic fusion protein and Doxycycline treatment allowed targeted demethylation of the Tet promoter in the ROSA26 locus and in another genomic site, rescuing transgene expression in cells and transgenicmice. Thus, inducible, reversible and site-specific epigenetic modulation is a promising strategy for reactivation of silenced transgene expression, independent of the integration site

Transcriptomic Deconvolution of Neuroendocrine Neoplasms Predicts Clinically Relevant Characteristics

Pancreatic neuroendocrine neoplasms (panNENs) are a rare yet diverse type of neoplasia whose precise clinical&ndash;pathological classification is frequently challenging. Since incorrect classifications can affect treatment decisions, additional tools which support the diagnosis, such as machine learning (ML) techniques, are critically needed but generally unavailable due to the scarcity of suitable ML training data for rare panNENs. Here, we demonstrate that a multi-step ML framework predicts clinically relevant panNEN characteristics while being exclusively trained on widely available data of a healthy origin. The approach classifies panNENs by deconvolving their transcriptomes into cell type proportions based on shared gene expression profiles with healthy pancreatic cell types. The deconvolution results were found to provide a prognostic value with respect to the prediction of the overall patient survival time, neoplastic grading, and carcinoma versus tumor subclassification. The performance with which a proliferation rate agnostic deconvolution ML model could predict the clinical characteristics was found to be comparable to that of a comparative baseline model trained on the proliferation rate-informed MKI67 levels. The approach is novel in that it complements established proliferation rate-oriented classification schemes whose results can be reproduced and further refined by differentiating between identically graded subgroups. By including non-endocrine cell types, the deconvolution approach furthermore provides an in silico quantification of panNEN dedifferentiation, optimizing it for challenging clinical classification tasks in more aggressive panNEN subtypes

Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5

Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning Ache to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by Ache and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse–human comparison can be viewed at http://web.uvic.ca/~bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions

BrO and inferred Bry profiles over the western Pacific : Relevance of inorganic bromine sources and a Bry minimum in the aged tropical tropopause layer

We report measurements of bromine monoxide (BrO) and use an observationally constrained chemical box model to infer total gas-phase inorganic bromine (Bry) over the tropical western Pacific Ocean (tWPO) during the CONTRAST field campaign (January-February 2014). The observed BrO and inferred Bry profiles peak in the marine boundary layer (MBL), suggesting the need for a bromine source from sea-salt aerosol (SSA), in addition to organic bromine (CBry). Both profiles are found to be C-shaped with local maxima in the upper free troposphere (FT). The median tropospheric BrO vertical column density (VCD) was measured as 1.6×1013 molec cm-2, compared to model predictions of 0.9×1013 molec cm-2 in GEOS-Chem (CBry but no SSA source), 0.4×1013 molec cm-2 in CAM-Chem (CBry and SSA), and 2.1×1013 molec cm-2 in GEOS-Chem (CBry and SSA). Neither global model fully captures the C-shape of the Bry profile. A local Bry maximum of 3.6 ppt (2.9-4.4 ppt; 95 % confidence interval, CI) is inferred between 9.5 and 13.5 km in air masses influenced by recent convective outflow. Unlike BrO, which increases from the convective tropical tropopause layer (TTL) to the aged TTL, gas-phase Bry decreases from the convective TTL to the aged TTL. Analysis of gas-phase Bry against multiple tracers (CFC-11, H2O-O3 ratio, and potential temperature) reveals a Bry minimum of 2.7 ppt (2.3-3.1 ppt; 95 % CI) in the aged TTL, which agrees closely with a stratospheric injection of 2.6 ± 0.6 ppt of inorganic Bry (estimated from CFC-11 correlations), and is remarkably insensitive to assumptions about heterogeneous chemistry. Bry increases to 6.3 ppt (5.6-7.0 ppt; 95 % CI) in the stratospheric "middleworld" and 6.9 ppt (6.5-7.3 ppt; 95 % CI) in the stratospheric "overworld". The local Bry minimum in the aged TTL is qualitatively (but not quantitatively) captured by CAM-Chem, and suggests a more complex partitioning of gas-phase and aerosol Bry species than previously recognized. Our data provide corroborating evidence that inorganic bromine sources (e.g., SSA-derived gas-phase Bry) are needed to explain the gas-phase Bry budget in the upper free troposphere and TTL. They are also consistent with observations of significant bromide in Upper Troposphere-Lower Stratosphere aerosols. The total Bry budget in the TTL is currently not closed, because of the lack of concurrent quantitative measurements of gas-phase Bry species (i.e., BrO, HOBr, HBr, etc.) and aerosol bromide. Such simultaneous measurements are needed to (1) quantify SSA-derived Bry in the upper FT, (2) test Bry partitioning, and possibly explain the gas-phase Bry minimum in the aged TTL, (3) constrain heterogeneous reaction rates of bromine, and (4) account for all of the sources of Bry to the lower stratosphere

Ras-Mediated Deregulation of the Circadian Clock in Cancer

<div><p>Circadian rhythms are essential to the temporal regulation of molecular processes in living systems and as such to life itself. Deregulation of these rhythms leads to failures in biological processes and eventually to the manifestation of pathological phenotypes including cancer. To address the questions as to what are the elicitors of a disrupted clock in cancer, we applied a systems biology approach to correlate experimental, bioinformatics and modelling data from several cell line models for colorectal and skin cancer. We found strong and weak circadian oscillators within the same type of cancer and identified a set of genes, which allows the discrimination between the two oscillator-types. Among those genes are IFNGR2, PITX2, RFWD2, PPARγ, LOXL2, Rab6 and SPARC, all involved in cancer-related pathways. Using a bioinformatics approach, we extended the core-clock network and present its interconnection to the discriminative set of genes. Interestingly, such gene signatures link the clock to oncogenic pathways like the RAS/MAPK pathway. To investigate the potential impact of the RAS/MAPK pathway - a major driver of colorectal carcinogenesis - on the circadian clock, we used a computational model which predicted that perturbation of BMAL1-mediated transcription can generate the circadian phenotypes similar to those observed in metastatic cell lines. Using an inducible RAS expression system, we show that overexpression of RAS disrupts the circadian clock and leads to an increase of the circadian period while RAS inhibition causes a shortening of period length, as predicted by our mathematical simulations. Together, our data demonstrate that perturbations induced by a single oncogene are sufficient to deregulate the mammalian circadian clock.</p></div