Genetic influences on emotion/cognition interactions : from synaptic regulation to individual differences in working memory for emotional faces

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Transcriptional and translational dynamics of the human heart

Die Genexpression wurde bisher hauptsächlich auf Transkriptions- und Proteinebene untersucht, wobei der Einfluss der Translation, die die Proteinhäufigkeit direkt beeinflusst, weitgehend außer Acht gelassen wurde. Um diese Rolle besser zu verstehen, habe ich Ribosomen-Profiling-Daten (Ribo-seq) verwendet, um die Translationsregulation zu untersuchen und neue Translationsvorgänge in 65 linksventrikulären Proben von DCM-Patienten im Endstadium und 15 Nicht-DCM-Kontrollen zu identifizieren. Dieser Datensatz half dabei, die Transkriptions- und Translationsregulation zwischen erkrankten und nicht betroffenen menschlichen Herzen zu sezieren und enthüllte Gene und Prozesse, die rein unter Translationskontrolle stehen. Darüber hinaus habe ich neue kardiale Proteine vorhergesagt, die von langen nicht-kodierenden RNAs (lncRNAs) und zirkulären RNAs (circRNAs) translatiert werden. Computergestützte Analysen dieser evolutionär jungen Proteine legten eine Beteiligung an verschiedenen molekularen Prozessen nahe, mit einer besonderen Anreicherung für den mitochondrialen Energiestoffwechsel. Schließlich identifizierte ich RNA-bindende Proteine (RBPs), deren Expression die Menge der Ziel-mRNA oder die Frequenz der Translationseffizienz (TE) beeinflusst. Für eine Untergruppe von 21 RBPs habe ich die Regulation auf beiden quantitativen Merkmalen beobachtet, was zu einer unterschiedlichen mechanistischen Basis der Expressionskontrolle für unabhängige Gensätze führte. Obwohl die genaue Umschaltung der RBP-Funktion wahrscheinlich durch eine Kombination von mehreren Faktoren erreicht wird, haben wir für drei Kandidaten eine starke Abhängigkeit von der Zielgenlänge und der 5'-UTR-Struktur beobachtet. Diese Arbeit präsentiert einen Katalog von neu identifizierten Translationsereignissen und einen quantitativen Ansatz zur Untersuchung der Translationsregulation im gesunden und kranken menschlichen Herzen.Gene expression has primarily been studied on transcriptional and protein levels, largely disregarding the extent of translational regulation that directly influences protein abundance. To elucidate its role, I used ribosome profiling (Ribo-seq) data, obtained through ribosome profiling, to study translational regulation and identify novel translation events in 65 left ventricular samples of end-stage DCM patients and 15 non-DCM controls. This dataset helped dissect transcriptional and translational regulation between diseased and unaffected human hearts, revealing genes and processes purely under translational control. These would have remained undetected by only looking at the transcriptional level. Furthermore, I predicted novel cardiac proteins translated from long non-coding RNAs (lncRNAs) and circRNAs. Computational analysis of these evolutionary young proteins suggested involvement in diverse molecular processes with a particular enrichment for mitochondrial processes. Finally, I identified RNA-binding proteins (RBPs) whose expression influences target mRNA abundance or translational efficiency (TE) rates. For a subset of 21 RBPs, I have observed regulation on both quantitative traits, which resulted in different mechanistic basis expression control for independent sets of genes. Though the precise switch in RBP function is likely achieved by a combination of multiple factors, for three candidates we have observed a strong dependency on target length and 5’ UTR structure. This work presents a catalogue of newly identified translation events and a quantitative approach to study translational regulation in the healthy and failing human heart

Characterization of protein-interaction networks in tumors

<p>Abstract</p> <p>Background</p> <p>Analyzing differential-gene-expression data in the context of protein-interaction networks (PINs) yields information on the functional cellular status. PINs can be formally represented as graphs, and approximating PINs as undirected graphs allows the network properties to be characterized using well-established graph measures.</p> <p>This paper outlines features of PINs derived from 29 studies on differential gene expression in cancer. For each study the number of differentially regulated genes was determined and used as a basis for PIN construction utilizing the Online Predicted Human Interaction Database.</p> <p>Results</p> <p>Graph measures calculated for the largest subgraph of a PIN for a given differential-gene-expression data set comprised properties reflecting the size, distribution, biological relevance, density, modularity, and cycles. The values of a distinct set of graph measures, namely <it>Closeness Centrality</it>, <it>Graph Diameter</it>, <it>Index of Aggregation</it>, <it>Assortative Mixing Coefficient</it>, <it>Connectivity</it>, <it>Sum of the Wiener Number</it>, <it>modified Vertex Distance Number</it>, and <it>Eigenvalues </it>differed clearly between PINs derived on the basis of differential gene expression data sets characterizing malignant tissue and PINs derived on the basis of randomly selected protein lists.</p> <p>Conclusion</p> <p>Cancer PINs representing differentially regulated genes are larger than those of randomly selected protein lists, indicating functional dependencies among protein lists that can be identified on the basis of transcriptomics experiments. However, the prevalence of hub proteins was not increased in the presence of cancer. Interpretation of such graphs in the context of robustness may yield novel therapies based on synthetic lethality that are more effective than focusing on single-action drugs for cancer treatment.</p

Characterising LINC complex roles in 3D epithelial migration and breast cancer metastasis

Cell migration is essential for the development of multicellular organisms; with disruptions in this process contributing to diseases such as cancer, neurological disorders and musculoskeletal diseases. The LINC (Linker of Nucleoskeleton and Cytoskeleton) complex is an evolutionary conserved proteinaceous structure, critical for maintaining proper cellular migration. This multifunctional complex provides a physical connection between the nuclear interior and the cytoskeleton, with disruptions stimulating loss of directed cell migration, compromised nuclear structure and abnormal cellular signalling. As it is also noted that the nucleus in many cells is the stiffest cellular component, it is suggested that LINC complex disruptions may be key in increasing the migration potential of cells through both in vivo and in vitro 3D environments. This project aimed to investigate the roles of LINC complex disruptions on keratinocyte morphological and migratory behaviours in 2D, and both non-restrictive and space-restrictive 3D culture environments, through the application of dominant negative SUN1 mutants. Through extensive analysis, it was identified that these mutants exhibited altered cell-cell and cell-substratum attachment phenotypes, alongside increased nuclear heights. It was also demonstrated that the LINC disrupted mutants displayed a migration advantage in space-restricted 3D environments, which was attributed to a decrease in nuclear stiffness. Through fibroblast incorporation to the 3D scaffolds used, it was further shown that LINC disrupted keratinocytes displayed increased levels of differentiation markers, alongside increased cellular stacking phenotypes across scaffolds surface regions, potentially attributed to alterations in Hippo pathway signalling. The migratory phenotypes observed in DN mutants closely resemble that of high-grade cancer cells, able to migrate through space-restrictive environments during metastasis. Comprehensive protein expression and localisation analysis across a range of breast cancer cell lines and tissues suggested that several LINC complex components display altered expression levels closely linked to cancer progression, most significantly a down-regulation of lower nesprin-1/-2 isoforms was identified. As following investigations later suggested Nup88 as an upstream regulator of nesprin-2, able to bind C-terminal regions, it’s suggested that these phenotypes link closely to that observed in high-grade cancers. Together, the data presented suggests that LINC complex disruptions increase migration potential of cells through restrictive 3D environments due to a decrease in nuclear stiffness, comparable to that observed across high-grade breast cancer cell lines

Characterization of proteome-size scaling by integrative omics reveals mechanisms of proliferation control in cancer.

Almost all living cells maintain size uniformity through successive divisions. Proteins that over and underscale with size can act as rheostats, which regulate cell cycle progression. Using a multiomic strategy, we leveraged the heterogeneity of melanoma cell lines to identify peptides, transcripts, and phosphorylation events that differentially scale with cell size. Subscaling proteins are enriched in regulators of the DNA damage response and cell cycle progression, whereas super-scaling proteins included regulators of the cytoskeleton, extracellular matrix, and inflammatory response. Mathematical modeling suggested that decoupling growth and proliferative signaling may facilitate cell cycle entry over senescence in large cells when mitogenic signaling is decreased. Regression analysis reveals that up-regulation of TP53 or CDKN1A/p21CIP1 is characteristic of proliferative cancer cells with senescent-like sizes/proteomes. This study provides one of the first demonstrations of size-scaling phenomena in cancer and how morphology influences the chemistry of the cell