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Marucci, L.

Publications and source records attributed to Marucci, L..

23 records · Page 2Linked to original sources

Canonical Wnt pathway controls mESCs self-renewal through inhibition of spontaneous differentiation via β-catenin/TCF/LEF functions

The Wnt/{beta}-catenin signalling pathway is a key regulator of embryonic stem cell self-renewal and differentiation. Constitutive activation of this pathway has been shown to significantly increase mouse embryonic stem cell (mESC) self-renewal and pluripotency marker expression. In this study, we generated a novel {beta}-catenin knock-out model in mESCs by using CRISPR/Cas9 technology to delete putatively functional N-terminally truncated isoforms observed in previous knock-out models. While we showed that aberrant N-terminally truncated isoforms are not functional in mESCS, we observed that canonical Wnt signalling is not active in mESCs, as {beta}-catenin ablation does not alter mESC transcriptional profile in LIF-enriched culture conditions; on the other hand, Wnt signalling activation represses mESC spontaneous differentiation. We also showed that transcriptionally silent {beta}-catenin ({Delta}C) isoforms can rescue {beta}-catenin knock-out self-renewal defects in mESCs, cooperating with TCF1 and LEF1 in the inhibition of mESC spontaneous differentiation in a Gsk3 dependent manner.

cell biology↗

A low cost, open source Turbidostat design for in-vivo control experiments in Synthetic Biology

To characterise the dynamics of new engineered systems in Synthetic biology, continuous culture platforms are required. In this paper, after a brief review of the existing machines present in literature, we describe the design and the implementation of a new flexible and low cost turbidostat for in-vivo control experiments. Then, the results of a 3 hours long experiment of control of the Optical Density is reported. Since the foundation of our design is flexibility, in this work we also discuss some possible extensions of our design, with particular attention to their application to validate in-vivo multicellular control design.

synthetic biology↗

Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: insightsfrom an agent-based model

Intestinal crypts are responsible for the total cell renewal of the lining of the intestines, occurring every 4-7 days in humans. This rapid turnover is governed by the complex interplay between signalling pathways and the cell cycle within individual cells in the crypts. The role of Wnt signalling in governing cell proliferation and differentiation in the intestinal crypt has been extensively studied, with increased signalling found towards the lower regions of the crypt. Recent studies have shown that the Wnt signalling gradient found within the crypt may arise as a result of division-based spreading from a Wnt reservoir at the crypt base. The discovery of the Hippo pathways involvement in maintaining crypt homeostasis is more recent; a mechanistic understanding of Hippo pathway dynamics, and its possible cross-talk with the Wnt pathway, remains lacking. To explore how the interplay between these pathways may control crypt homeostasis and dysplasia we developed and analysed a mathematical model coupling an ordinary differential equation description of Wnt and Hippo signalling with a cell-based description of cell movement, proliferation and contact inhibition. Furthermore, we compared an imposed Wnt gradient with a division-based Wnt gradient model. Our results suggest that Hippo signalling affects the Wnt pathway by reducing the presence of free cytoplasmic {beta}-catenin, causing cell cycle arrest. This process slows the rate of crypt turnover, previously attributed only to mutations in Wnt pathway components commonly observed in colorectal cancers. We also show that a division-based spreading of Wnt can form a Wnt gradient, resulting in proliferative dynamics comparable to imposed-gradient models. This suggests that imposed-gradient models are a reasonable approximation of experimentally observed Wnt gradients, however they provide little insight into the source of Wnt. Finally, a simulated APC double mutant, with misregulated Wnt and Hippo signalling activity, is predicted to be capable of completing a more rapid monoclonal conversion of the crypt than a Wnt-only mutant.\n\nAuthor summaryColorectal cancer is the fourth leading cause of cancer death worldwide. It is generally established that colorectal cancer occurs upon disruption of the dynamics of crypts, tubular indentations lining the walls of the gastrointestinal tract that are responsible for renewal of the intestinal epithelium. Thus, understanding the mechanisms that regulate intestinal crypt dynamics is instrumental to understand how colorectal cancer can emerge. We used mathematical modelling to explore how crypt dynamics emerge from the interactions across several biological scales, including mutations that cause an abnormal cell response to changes at the cell or tissue level, cell proliferation and motility within the crypt. Our model describes, in each cell within the crypt, levels and dynamics of genes involved in two signalling pathways - the canonical Wnt and Hippo pathways - relevant for cell proliferation and adhesion. In simulations, we predict how the crosstalk between these pathways affects crypt dynamics in both healthy and dysplastic cases. Furthermore, our simulations match recent biological evidence of a novel mechanism, based on cell division, causing heterogeneous and graded localisation of different cell types (dividing or not) within the crypt. Our results suggest the possibility of combined disease treatment, targeting both the Wnt and Hippo pathways.

systems biology↗

A tunable dual-input system for on-demand dynamic geneexpression regulation.

Cellular systems have evolved numerous mechanisms to finely control signalling pathway activation and properly respond to changing environmental stimuli. This is underpinned by dynamic spatiotemporal patterns of gene expression. Indeed, in addition to gene transcription and translation regulation, modulation of protein levels, dynamics and localization are also essential checkpoints that govern cell functions. The introduction of tetracycline-inducible promoters has allowed gene expression control using orthogonal small molecules, facilitating rapid and reversible manipulation to study gene function in biological systems. However, differing protein stabilities means this solely transcriptional regulation is insufficient to allow precise ON-OFF dynamics, thus hindering generation of temporal profiles of protein levels seen in vivo. We developed an improved Tet-On based system augmented with conditional destabilising elements at the post-translational level that permits simultaneous control of gene expression and protein stability. Integrating these properties to control expression of a fluorescent protein in mouse Embryonic Stem Cells (mESCs), we found that adding protein stability control allows faster response times to changes in small molecules, fully tunable and enhanced dynamic range, and vastly improved microfluidic-based in-silico feedback control of gene expression. Finally, we highlight the effectiveness of our dual-input system to finely modulate levels of signalling pathway components in stem cells.

synthetic biology↗

Designing Genomes using Design-Simulate-Test Cycles

In the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a very simple functional assay, the cell can either replicate or not. We used the first (and currently only published) whole-cell model, for the bacterium Mycoplasma genitalium 1. Our computational design-simulate-test cycles discovered novel in-silico minimal genomes smaller than JCVI-Syn3.0 2, a bacterial cell with the currently known smallest genome that can be grown in pure culture. In the process, we identified 10 low essentiality genes, 18 high essentiality genes 3, and produced evidence for at least two minimal genomes for Mycoplasma genitalium in-silico. This work brings combined computational and laboratory genome design and construction a step closer.

synthetic biology↗