Identification of control targets in Boolean molecular network models via computational algebra

Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The potential control targets can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. Experimentally, node manipulation requires technology to completely repress or fully activate a particular gene product while edge manipulations only require a drug that inactivates the interaction between two gene products. Results: This paper presents a method for the identification of potential intervention targets in Boolean molecular network models using algebraic techniques. The approach exploits an algebraic representation of Boolean networks to encode the control candidates in the network wiring diagram as the solutions of a system of polynomials equations, and then uses computational algebra techniques to find such controllers. The control methods in this paper are validated through the identification of combinatorial interventions in the signaling pathways of previously reported control targets in two well studied systems, a p53-mdm2 network and a blood T cell lymphocyte granular leukemia survival signaling network.Comment: 12 pages, 4 figures, 2 table

Review- Cancer: Some genetic considerations

Malignant transformation of normal cells to cancer cells represents an enigmatic phenomenon because of the many ambiguous controversies embodied within most of its aspects. Within a clinical context, cancer, with very few exceptions, is a dreadful disease that ends lethally. Within a biological context, however, cancer is a peculiar biosystem that has its own rules that regulate the actions/interactions/structure and behavior of its components. Unfortunately, the majority of these rules are, still, unknown.The current disappointing situation as regards research trials aiming at constructing effective treatments for cancer might be attributed, in part, to incomplete recognition of the significant differences between these two contexts of malignant transformation. Although the peculiar characteristics of cancer as a self-dependent biosystem are well studied and well defined, the basic dilemma of malignant transformation continues to exist: we know, largely, how things happen but we do not know, to any extent, why they happen.Though the logic that motivates researches aiming at formulating genetic therapies for cancer is quite reasonable, as cancer is primarily a genetic alteration, lack of essential basic knowledge regarding the different aspects of this alteration adjourn successful radical cure of cancer. Till comprehensive disclosure of the underlying mechanisms regulating growth/progression/metastasis and survival of malignant cells is attained, treatments of cancer based on different strategic concepts, viz. proteomic therapies rather than genetic therapies, might, hopefully, be the best approaches available in the fight against cancer in the current as well as in the coming era.Keywords: Cancer; Temporal imprinting; Malignant transformation; Malignant phenotype; Genomic reprograming; Genomic involution; Evolutionary paradox; Metastasis; Oncoproteome; Cancer therapy; Oncogenom

In vivo genetic manipulation of inner ear connexin expression by bovine adeno-Associated viral vectors

We have previously shown that in vitro transduction with bovine adeno-associated viral (BAAV) vectors restores connexin expression and rescues gap junction coupling in cochlear organotypic cultures from connexin-deficient mice that are models DFNB1 nonsyndromic hearing loss and deafness. The aims of this study were to manipulate inner ear connexin expression in vivo using BAAV vectors, and to identify the optimal route of vector delivery. Injection of a BAAV vector encoding a bacterial Cre recombinase via canalostomy in adult mice with floxed connexin 26 (Cx26) alleles promoted Cre/LoxP recombination, resulting in decreased Cx26 expression, decreased endocochlear potential, increased hearing thresholds, and extensive loss of outer hair cells. Injection of a BAAV vector encoding GFP-tagged Cx30 via canalostomy in P4 mice lacking connexin 30 (Cx30) promoted formation of Cx30 gap junctions at points of contacts between adjacent non-sensory cells of the cochlear sensory epithelium. Levels of exogenous Cx30 decayed over time, but were still detectable four weeks after canalostomy. Our results suggest that persistence of BAAV-mediated gene replacement in the cochlea is limited by the extensive remodeling of the organ of Corti throughout postnatal development and associated loss of non-sensory cells

mTOR Complex 1 Content and Regulation Is Adapted to Animal Longevity

Decreased content and activity of the mechanistic target of rapamycin (mTOR) signalling pathway, as well as the mTOR complex 1 (mTORC1) itself, are key traits for animal species and human longevity. Since mTORC1 acts as a master regulator of intracellular metabolism, it is respon sible, at least in part, for the longevous phenotype. Conversely, increased content and activity of mTOR signalling and mTORC1 are hallmarks of ageing. Additionally, constitutive and aberrant activity of mTORC1 is also found in age-related diseases such as Alzheimer’s disease (AD) and cancer. The downstream processes regulated through this network are diverse, and depend upon nutrient availability. Hence, multiple nutritional strategies capable of regulating mTORC1 activity and, consequently, delaying the ageing process and the development of age-related diseases, are under continuous study. Among these, the restriction of calories is still the most studied and ro bust intervention capable of downregulating mTOR signalling and feasible for application in the human population.Research by the authors was supported by the Spanish Ministry of Science, Innovation, and Universities (Ministerio de Ciencia, Innovación y Universidades, co-financed by FEDER funds from the European Union ‘A way to build Europe’, grant RTI2018-099200-B-I00), the IRBLleida-Diputació de Lleida (PIRS2021), and the Generalitat of Catalonia: Agency for Management of University and Research Grants (2017SGR696) to R.P. IRBLleida is a CERCA Programme/Generalitat of Cataloni

Regulation of excitation-contraction coupling in mouse cardiac myocytes: integrative analysis with mathematical modelling

<p>Abstract</p> <p>Background</p> <p>The cardiomyocyte is a prime example of inherently complex biological system with inter- and cross-connected feedback loops in signalling, forming the basic properties of intracellular homeostasis. Functional properties of cells and tissues have been studied e.g. with powerful tools of genetic engineering, combined with extensive experimentation. While this approach provides accurate information about the physiology at the endpoint, complementary methods, such as mathematical modelling, can provide more detailed information about the processes that have lead to the endpoint phenotype.</p> <p>Results</p> <p>In order to gain novel mechanistic information of the excitation-contraction coupling in normal myocytes and to analyze sophisticated genetically engineered heart models, we have built a mathematical model of a mouse ventricular myocyte. In addition to the fundamental components of membrane excitation, calcium signalling and contraction, our integrated model includes the calcium-calmodulin-dependent enzyme cascade and the regulation it imposes on the proteins involved in excitation-contraction coupling. With the model, we investigate the effects of three genetic modifications that interfere with calcium signalling: 1) ablation of phospholamban, 2) disruption of the regulation of L-type calcium channels by calcium-calmodulin-dependent kinase II (CaMK) and 3) overexpression of CaMK. We show that the key features of the experimental phenotypes involve physiological compensatory and autoregulatory mechanisms that bring the system to a state closer to the original wild-type phenotype in all transgenic models. A drastic phenotype was found when the genetic modification disrupts the regulatory signalling system itself, i.e. the CaMK overexpression model.</p> <p>Conclusion</p> <p>The novel features of the presented cardiomyocyte model enable accurate description of excitation-contraction coupling. The model is thus an applicable tool for further studies of both normal and defective cellular physiology. We propose that integrative modelling as in the present work is a valuable complement to experiments in understanding the causality within complex biological systems such as cardiac myocytes.</p

Quantifying cancer epithelial-mesenchymal plasticity and its association with stemness and immune response

Cancer cells can acquire a spectrum of stable hybrid epithelial/mesenchymal (E/M) states during epithelial-mesenchymal transition (EMT). Cells in these hybrid E/M phenotypes often combine epithelial and mesenchymal features and tend to migrate collectively commonly as small clusters. Such collectively migrating cancer cells play a pivotal role in seeding metastases and their presence in cancer patients indicates an adverse prognostic factor. Moreover, cancer cells in hybrid E/M phenotypes tend to be more associated with stemness which endows them with tumor-initiation ability and therapy resistance. Most recently, cells undergoing EMT have been shown to promote immune suppression for better survival. A systematic understanding of the emergence of hybrid E/M phenotypes and the connection of EMT with stemness and immune suppression would contribute to more effective therapeutic strategies. In this review, we first discuss recent efforts combining theoretical and experimental approaches to elucidate mechanisms underlying EMT multi-stability (i.e. the existence of multiple stable phenotypes during EMT) and the properties of hybrid E/M phenotypes. Following we discuss non-cell-autonomous regulation of EMT by cell cooperation and extracellular matrix. Afterwards, we discuss various metrics that can be used to quantify EMT spectrum. We further describe possible mechanisms underlying the formation of clusters of circulating tumor cells. Last but not least, we summarize recent systems biology analysis of the role of EMT in the acquisition of stemness and immune suppression.Comment: 50 pages, 6 figure

Animal models of exercise therapy: mechanisms of activity-induced angiogenesis

Skeletal muscle is spatially heterogeneous in muscle fibre type composition and microvascular supply. The capacity to quantify this heterogeneity in skeletal muscle is not routinely performed for it’s a laborious and time consuming technique. We have developed a high throughput data pipeline that utilises the simultaneous immunohistochemical labelling of muscle fibre type and microvascular supply, as an input for a semi-automated analysis software package that allows for the analysis of fine morphometric indices of fibre type composition and the interactions with microvascular supply. We have successfully shown that regional variation in fibre type composition impacts the functional characteristics of a muscle. After successful characterisation of regional heterogeneity in both structure and function we sought to establish their influence in physiological (adaptive) angiogenesis. Utilising animal angiogenic models we have shown that shear stress driven angiogenesis is principally a stochastic response that does not promote improved oxygen delivery when we analyse the spatial heterogeneity of the neovasculature. Conversely, skeletal muscle overload (abluminal stretch of microvasculature) increases the homogeneity of the oxygen supply area of the capillary bed, suggesting a tissue driven angiogenic response that is not evident in shear stress. Spinal cord injury induced rarefaction of the capillary bed attempts to maintain a homogeneous distribution of fibre size and capillary supply. The combination therapy of epidural stimulation and locomotor training can ameliorate the phenotypic change and rarefied capillary bed seen with spinal cord injury to that of intact levels. Endurance and resistance exercise have a largely similar global genomic response following a chronic training regime, which we are able to replicate in animal models of exercise through indirect electrical stimulation. The shear stress and muscle overload driven angiogenic response have distinctly different angiogenic pathways that contain no commonly expressed networks

Animal models of exercise therapy: mechanisms of activity-induced angiogenesis

Skeletal muscle is spatially heterogeneous in muscle fibre type composition and microvascular supply. The capacity to quantify this heterogeneity in skeletal muscle is not routinely performed for it’s a laborious and time consuming technique. We have developed a high throughput data pipeline that utilises the simultaneous immunohistochemical labelling of muscle fibre type and microvascular supply, as an input for a semi-automated analysis software package that allows for the analysis of fine morphometric indices of fibre type composition and the interactions with microvascular supply. We have successfully shown that regional variation in fibre type composition impacts the functional characteristics of a muscle. After successful characterisation of regional heterogeneity in both structure and function we sought to establish their influence in physiological (adaptive) angiogenesis. Utilising animal angiogenic models we have shown that shear stress driven angiogenesis is principally a stochastic response that does not promote improved oxygen delivery when we analyse the spatial heterogeneity of the neovasculature. Conversely, skeletal muscle overload (abluminal stretch of microvasculature) increases the homogeneity of the oxygen supply area of the capillary bed, suggesting a tissue driven angiogenic response that is not evident in shear stress. Spinal cord injury induced rarefaction of the capillary bed attempts to maintain a homogeneous distribution of fibre size and capillary supply. The combination therapy of epidural stimulation and locomotor training can ameliorate the phenotypic change and rarefied capillary bed seen with spinal cord injury to that of intact levels. Endurance and resistance exercise have a largely similar global genomic response following a chronic training regime, which we are able to replicate in animal models of exercise through indirect electrical stimulation. The shear stress and muscle overload driven angiogenic response have distinctly different angiogenic pathways that contain no commonly expressed networks