1,274 research outputs found
Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition
Epithelial-to-mesenchymal transition (EMT), a fundamental transdifferentiation process in development, produces diverse phenotypes in different physiological or pathological conditions. Many genes involved in EMT have been identified to date, but mechanisms contributing to the phenotypic diversity and those governing the coupling between the dynamics of epithelial (E) genes and that of the mesenchymal (M) genes are unclear. In this study, we employed combinatorial perturbations to mammary epithelial cells to induce a series of EMT phenotypes by manipulating two essential EMT-inducing elements, namely TGF-ÎČ and ZEB1. By measuring transcriptional changes in more than 700 E-genes and M-genes, we discovered that the M-genes exhibit a significant diversity in their dependency to these regulatory elements and identified three groups of M-genes that are controlled by different regulatory circuits. Notably, functional differences were detected among the M-gene clusters in motility regulation and in survival of breast cancer patients. We computationally predicted and experimentally confirmed that the reciprocity and reversibility of EMT are jointly regulated by ZEB1. Our integrative analysis reveals the key roles of ZEB1 in coordinating the dynamics of a large number of genes during EMT, and it provides new insights into the mechanisms for the diversity of EMT phenotypes
Jefferson Digital Commons quarterly report: October-December 2018
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Topological and semantic Web based method for analyzing TGF-ÎČ signaling pathways
International audienceTargeting the deleterious effects of Transforming Growth Factor TGF-ÎČ without affecting its physiological role is the common goal of therapeutic strategies aiming at curing fibrosis, the final outcome of all chronic liver disease. The pleiotropic effects of TGF-ÎČ are linked to the complex nature of its activation and signaling net- works which understanding requires modeling approaches. Our group recently developed a model of TGF-beta signal propagation based on guarded transitions (ref, Andrieux et al, 2014). In this initial work, we explored the combinatorial complexity of cell signaling, developing a discrete formalism based on guarded transitions. We imported the whole database Pathway Interaction Database into a single unified model of signal transduction. We detected 16,000 chains of reactions linking TGF-ÎČ to at least one of 159 target genes in the nucleus. The size and complexity of this model place it beyond current understanding. Its analysis requires automated tools for identifying general patterns.Currently, we focus on designing one reasoning method based on Semantic Web technologies for the analysis of signaling pathways. Our method aims at leveraging external domain knowledge represented in biomedical ontologies and linked databases to rank these candidates. We consider a signaling pathway as a set of proteins involved in the respons of a cell to an external stimulus and influencing at least one gene. The underlying reasoning methods are based on graph topological analysis, formal concepts analysis (FCA) and semantic similarity and particularity measures. First, we determine the formal concepts, maximal bi-cliques, between proteins sets and genes. Then, to determine the biological relevance of theses gene clusters, we calculate a similarity score for each cluster based on Wang semantic similarity. Using such approaches, we identify groups of genes sharing signaling networks.Cibler les effets dĂ©lĂ©tĂšres du Transforming Growth Factor, TGF-ÎČ, sans affecter son rĂŽle physiologique est lâobjectif commun des stratĂ©gies thĂ©rapeutiques visant Ă guĂ©rir la fibrose, la consĂ©quence finale de toutes les maladies chroniques du foie. Les effets plĂ©iotropiques du TGF-ÎČ sont liĂ©s Ă la nature complexe de son activation et du rĂ©seaux de signalisation quâil induit, et dont la comprĂ©hension nĂ©cessite des approches de modĂ©lisation. Notre Ă©quipe a dĂ©veloppĂ© un modĂšle de la propagation du signal induit par le TGF-ÎČ base Ì sur les transitions gardĂ©es. Le dĂ©veloppement dâun formalisme discret base Ì sur les transitions gardĂ©es permet dâĂ©tudier la complexitĂ© combinatoire de la signalisation cellulaire. Nous avons formalise Ì lâintĂ©gralitĂ© de la base de donnĂ©es Pathway Interaction Database en un unique modĂšle de la propagation du signal. Nous avons dĂ©tectĂ© 16 000 chaines de rĂ©actions reliant le TGF-ÎČ Ă au moins lâun des 159 gĂšnes cibles dâintĂ©rĂȘt Pour identifier des propriĂ©tĂ©s au sein de ces rĂ©sultats il est nĂ©cessaire dâutiliser des outils automatisĂ©s.Nous dĂ©veloppons actuellement une mĂ©thode basĂ©e sur le Web sĂ©mantique pour lâanalyse des voies de signalisation. Cette mĂ©thode vise Ă tirer parti des connaissances de domaine externe reprĂ©sentĂ©es dans les ontologies biomĂ©dicales et des bases de donnĂ©es pour classer ces candidats. Nous considĂ©rons quâune voie de signalisation est un ensemble des protĂ©ines impliquĂ©es dans la rĂ©action dâune cellule Ă un stimulus externe et qui influence au moins un gĂšne. Les mĂ©thodes de raisonnement sous-jacentes sont basĂ©es sur lâanalyse topologique, lâanalyse formelle de concepts et les mesures de similaritĂ© et de particularitĂ© sĂ©mantique. Tout dâabord, nous dĂ©terminons les concepts formels, câest-Ă -dire les bi-cliques maximales, entre les ensembles de protĂ©ines et les gĂšnes. Puis, afin de dĂ©terminer la pertinence biologique de ces groupes de gĂšnes, nous calculons un score de similaritĂ© pour chacun des groupes, base Ì sur la mesure de Wang. La finalitĂ© est dâidentifier des groupes de gĂšnes similaires influencĂ©s par un mĂȘme ensemble de voies de signalisation
The tumour ecology of quiescence: Niches across scales of complexity
Quiescence is a state of cell cycle arrest, allowing cancer cells to evade anti-proliferative cancer therapies. Quiescent cancer stem cells are thought to be responsible for treatment resistance in glioblastoma, an aggressive brain cancer with poor patient outcomes. However, the regulation of quiescence in glioblastoma cells involves a myriad of intrinsic and extrinsic mechanisms that are not fully understood. In this review, we synthesise the literature on quiescence regulatory mechanisms in the context of glioblastoma and propose an ecological perspective to stemness-like phenotypes anchored to the contemporary concepts of niche theory. From this perspective, the cell cycle regulation is multiscale and multidimensional, where the niche dimensions extend to extrinsic variables in the tumour microenvironment that shape cell fate. Within this conceptual framework and powered by ecological niche modelling, the discovery of microenvironmental variables related to hypoxia and mechanosignalling that modulate proliferative plasticity and intratumor immune activity may open new avenues for therapeutic targeting of emerging biological vulnerabilities in glioblastoma
Colorectal Cancer Through Simulation and Experiment
Colorectal cancer has continued to generate a huge amount of research interest over several decades, forming a canonical example of tumourigenesis since its use in Fearon and Vogelsteinâs linear model of genetic mutation. Over time, the field has witnessed a transition from solely experimental work to the inclusion of mathematical biology and computer-based modelling. The fusion of these disciplines has the potential to provide valuable insights into oncologic processes, but also presents the challenge of uniting many diverse perspectives. Furthermore, the cancer cell phenotype defined by the âHallmarks of Cancerâ has been extended in recent times and provides an excellent basis for future research. We present a timely summary of the literature relating to colorectal cancer, addressing the traditional experimental findings, summarising the key mathematical and computational approaches, and emphasising the role of the Hallmarks in current and future developments. We conclude with a discussion of interdisciplinary work, outlining areas of experimental interest which would benefit from the insight that mathematical and computational modelling can provide
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Impaired neurodevelopmental pathways in autism spectrum disorder: a review of signaling mechanisms and crosstalk.
BackgroundThe development of an autistic brain is a highly complex process as evident from the involvement of various genetic and non-genetic factors in the etiology of the autism spectrum disorder (ASD). Despite being a multifactorial neurodevelopmental disorder, autistic patients display a few key characteristics, such as the impaired social interactions and elevated repetitive behaviors, suggesting the perturbation of specific neuronal circuits resulted from abnormal signaling pathways during brain development in ASD. A comprehensive review for autistic signaling mechanisms and interactions may provide a better understanding of ASD etiology and treatment.Main bodyRecent studies on genetic models and ASD patients with several different mutated genes revealed the dysregulation of several key signaling pathways, such as WNT, BMP, SHH, and retinoic acid (RA) signaling. Although no direct evidence of dysfunctional FGF or TGF-ÎČ signaling in ASD has been reported so far, a few examples of indirect evidence can be found. This review article summarizes how various genetic and non-genetic factors which have been reported contributing to ASD interact with WNT, BMP/TGF-ÎČ, SHH, FGF, and RA signaling pathways. The autism-associated gene ubiquitin-protein ligase E3A (UBE3A) has been reported to influence WNT, BMP, and RA signaling pathways, suggesting crosstalk between various signaling pathways during autistic brain development. Finally, the article comments on what further studies could be performed to gain deeper insights into the understanding of perturbed signaling pathways in the etiology of ASD.ConclusionThe understanding of mechanisms behind various signaling pathways in the etiology of ASD may help to facilitate the identification of potential therapeutic targets and design of new treatment methods
A computational modelling of cellular and supra-cellular networks to unravel the control of EMT
"Over the last decade, Epithelial-to-Mesenchymal Transition (EMT) has gained the
attention of cancer researchers due to its potential to promote cancer migration
and metastasis. However, the complexity of EMT intertwined regulation and the
involvement of multiple signals in the tumour microenvironment have been
limiting the understanding of how this process can be controlled. Cell-cell
adhesion and focal adhesion dynamics are two critical properties that change
during EMT, which provide a simple way to characterize distinct modes of cancer
migration. Therefore, the main focus of this thesis is to provide a framework to
predict critical microenvironment and de-regulations in cancer that drive interconversion
between adhesion phenotypes, accounting for main
microenvironment signals and signalling pathways in EMT. Here, we address this
issue through a systems approach using the logical modelling framework to
generate new testable predictions for the field.(...)"Instituto Gulbenkian de CiĂȘncia (FCG-IGC
Advanced technologies to target cardiac cell fate plasticity for heart regeneration
The adult human heart can only adapt to heart diseases by starting a myocardial remodeling process to compensate for the loss of functional cardiomyocytes, which ultimately develop into heart failure. In recent decades, the evolution of new strategies to regenerate the injured myocardium based on cellular reprogramming represents a revolutionary new paradigm for cardiac repair by targeting some key signaling molecules governing cardiac cell fate plasticity. While the indirect reprogramming routes require an in vitro engineered 3D tissue to be transplanted in vivo, the direct cardiac reprogramming would allow the administration of reprogramming factors directly in situ, thus holding great potential as in vivo treatment for clinical applications. In this framework, cellular reprogramming in partnership with nanotechnologies and bioengineering will offer new perspectives in the field of cardiovascular research for disease modeling, drug screening, and tissue engineering applications. In this review, we will summarize the recent progress in developing innovative therapeutic strategies based on manipulating cardiac cell fate plasticity in combination with bioengineering and nanotechnology-based approaches for targeting the failing heart
Evolutionary underpinnings of microgeographic adaptation in song sparrows distributed along a steep climate gradient
2021 Summer.Includes bibliographical references.Understanding how evolutionary processes interact to maintain adaptive variation in natural populations has been a fundamental goal of evolutionary biology. Yet, despite adaptation remaining at the forefront of evolutionary theory and empirical studies, there remains a lack of consensus about the evolutionary conditions that enable adaptation to persist in natural populations, especially when considering complex phenotypes in response to multivariate selection regimes. In my dissertation, I disentangle the evolutionary mechanisms that shape adaptive divergence in song sparrows (Melospiza melodia) distributed along a climate gradient on the California Channel Islands and nearby coastal California. First, I found evidence that climate, and neither vegetation nor selection for increased foraging efficiency, likely drive adaptive divergence in bill morphology among insular populations. Second, I used an integrated population and landscape genomics approach to infer that bill variation is indicative of microgeographic local adaptation to temperature. Lastly, I tested whether the distinct climate gradient facilitates adaptative divergence in other thermoregulatory traits and found evidence to support environmental temperatures result in fixed population differences in many complementary phenotypes, including plumage color, feather microstructure, and thermal physiology. Collectively, these results find support for microgeographic climate adaptation in a suite of complex phenotypes and demonstrate the utility of integrative approaches to infer local adaptation in natural populations. Finally, by developing a more holistic understanding of climate adaptation in natural populations, my results inform conservation management of this species of special concern
Reconstructing equations of motion for cell phenotypic transitions: integration of data science and dynamical systems theory
Dynamical systems theory has long been fruitfully applied to describe
cellular processes, while a main challenge is lack of quantitative information
for constraining models. Advances of quantitative approaches, especially single
cell techniques, have accelerated the emergence of a new direction of
reconstructing the equations of motion of a cellular system from quantitative
single cell data, thus places studies under the framework of dynamical systems
theories, as compared to the currently dominant statistics-based approaches.
Here I review a selected number of recent studies using live- and fixed- cell
data, and provide my perspective on the future development.Comment: 18 pages, 4 figure
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