Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network

Hypoxia induces the expression of genes that alter metabolism through the hypoxia-inducible factor (HIF). A theoretical model based on differential equations of the hypoxia response network has been previously proposed in which a sharp response to changes in oxygen concentration was observed but not quantitatively explained. That model consisted of reactions involving 23 molecular species among which the concentrations of HIF and oxygen were linked through a complex set of reactions. In this paper, we analyze this previous model using a combination of mathematical tools to draw out the key components of the network and explain quantitatively how they contribute to the sharp oxygen response. We find that the switch-like behavior is due to pathway-switching wherein HIF degrades rapidly under normoxia in one pathway, while the other pathway accumulates HIF to trigger downstream genes under hypoxia. The analytic technique is potentially useful in studying larger biomedical networks

Structural Analysis to Determine the Core of Hypoxia Response Network

The advent of sophisticated molecular biology techniques allows to deduce the structure of complex biological networks. However, networks tend to be huge and impose computational challenges on traditional mathematical analysis due to their high dimension and lack of reliable kinetic data. To overcome this problem, complex biological networks are decomposed into modules that are assumed to capture essential aspects of the full network's dynamics. The question that begs for an answer is how to identify the core that is representative of a network's dynamics, its function and robustness. One of the powerful methods to probe into the structure of a network is Petri net analysis. Petri nets support network visualization and execution. They are also equipped with sound mathematical and formal reasoning based on which a network can be decomposed into modules. The structural analysis provides insight into the robustness and facilitates the identification of fragile nodes. The application of these techniques to a previously proposed hypoxia control network reveals three functional modules responsible for degrading the hypoxia-inducible factor (HIF). Interestingly, the structural analysis identifies superfluous network parts and suggests that the reversibility of the reactions are not important for the essential functionality. The core network is determined to be the union of the three reduced individual modules. The structural analysis results are confirmed by numerical integration of the differential equations induced by the individual modules as well as their composition. The structural analysis leads also to a coarse network structure highlighting the structural principles inherent in the three functional modules. Importantly, our analysis identifies the fragile node in this robust network without which the switch-like behavior is shown to be completely absent

Genomic insights into ayurvedic and western approaches to personalized medicine

Ayurveda, an ancient Indian system of medicine documented and practised since 1500 B.C., follows a systems approach that has interesting parallels with contemporary personalized genomic medicine approaches to the understanding and management of health and disease. It is based on the trisutra, which are the three aspects of causes, features and therapeutics that are interconnected through a common organizing principle termed ‘tridosha’. Tridosha comprise three ascertainable physiological entities; vata (kinetic), pitta (metabolic) and kapha (potential) that are pervasive across systems, work in conjunction with each other, respond to the external environment and maintain homeostasis. Each individual is born with a specific proportion of tridosha that are not only genetically determined but also influenced by the environment during foetal development. Jointly they determine a person’s basic constitution, which is termed their ‘prakriti’. Development and progression of different diseases with their subtypes are thought to depend on the origin and mechanism of perturbation of the doshas, and the aim of therapeutic practice is to ensure that the doshas retain their homeostatic state. Similarly, western systems biology epitomized by translational P4 medicine envisages the integration of multiscalar genetic, cellular, physiological and environmental networks to predict phenotypic outcomes of perturbations. In this perspective article, we aim to outline the shape of a unifying scaffold that may allow the two intellectual traditions to enhance one another. Specifically, we illustrate how a unique integrative ‘Ayurgenomics’ approach can be used to integrate the trisutra concept of Ayurveda with genomics. We observe biochemical and molecular correlates of prakriti and show how these differ significantly in processes that are linked to intermediate patho-phenotypes, known to take different course in diseases. We also observe a significant enrichment of the highly connected hub genes which could explain differences in prakriti, focussing on EGLN1, a key oxygen sensor that differs between prakriti types and is linked to high altitude adaptation. Integrating our observation with the current literature, we demonstrate how EGLN1 could qualify as a molecular equivalent of tridosha that can modulate different phenotypic outcomes, where hypoxia is a cause or a consequence both during health and diseased states. Our studies affirm that integration of the trisutra framework through Ayurgenomics can guide the identification of predisposed groups of individuals and enable discovery of actionable therapeutic points in an individualized manner

The Nefarious Nexus of Noncoding RNAs in Cancer

The past decade has witnessed enormous progress, which has seen the noncoding RNAs (ncRNAs) turn from the so called dark matter RNA to critical functional molecules, influencing most physiological processes in development and disease contexts. Many ncRNAs interact with each other and are part of networks that influence the cell transcriptome and proteome and consequently the outcome of biological processes. The regulatory circuits controlled by ncRNAs have become increasingly more relevant in cancer. Further understanding of these complex network interactions and how ncRNAs are regulated, is paving the way for the identification of better therapeutic strategies in cancer

VEGF and Sympathetic Perivascular Nerves Contribute to Hypoxic Remodeling of Ovine Cranial Arteries

Chronic hypoxia complicates many pregnancies and can result in postnatal pathologies that include compromised fetal cardiovascular structure and function. Mechanisms involved remain unclear. Because hypoxia increases production of VEGF, known to modulate smooth muscle (SM) phenotype, this thesis explored the hypothesis that VEGF contributes to hypoxic fetal vascular remodeling through direct effects on SM cells and indirectly through perivascular nerves. Using a chronic hypoxia sheep model, this work demonstrated that: 1) hypoxia potently upregulates VEGF receptor expression but not endogenous VEGF level in fetal ovine carotid arteries; 2) both chronic hypoxia and VEGF exert similar effects on smooth muscle contractile proteins; 3) both chronic hypoxia and VEGF exert similar effects on contractile protein colocalizations; and lastly, sympathetic autonomic nerves contribute to hypoxic reorganization of structure and function of vascular contractile proteins. Together, these findings advance understanding of how hypoxia precipitates fetal vascular remodeling and offer an essential first step toward finding new treatments for infants that survive in-utero hypoxia

The application of autofluorescence lifetime metrology to the study of heart failure models and heart disease

Autofluorescence spectroscopy offers a promising label-free approach to characterise biological samples and has already shown diagnostic potential in a number of medical applications, although study of myocardium has been relatively limited. A number of myocardial molecules display autofluorescence, including those involved in energetics, e.g. NADH and flavoproteins, as well as structural molecules, e.g. collagen. This thesis discusses the application of a custom-built single point fibre-optic probe-based instrumentation for time-resolved spectrofluorometry utilising spectrally resolved time-correlated single photon counting detection (TCSPC) and white light reflectometry to the investigation of models of heart failure, both ex vivo and in vivo. Heart failure (HF) is a pathophysiological state in which an abnormality of cardiac function causes failure of the heart to pump blood at a rate commensurate with the requirements of the metabolising tissues. It affects 1-2% of the population rising to greater than 10% aged over 70 years. Despite recent therapeutic advances, annualized mortality can still approach 10%. HF results from a myocardial injury (e.g. myocardial infarction, chemotherapy) causing loss of myocytes, and maladaptive changes in surviving myocytes and extracellular matrix by ‘pathological remodelling’. That HF is characterized by structural and energetic changes was the principal motivation for the creation of an instrument to investigate changes in myocardial autofluorescence signature in disease states in vivo. If the signatures associated with known pathological diagnoses could be ascertained, such a technique could perform ‘virtual biopsy’ to aid diagnosis. This thesis describes the application of autofluorescence technique to an ex vivo Langendorff-heart to characterise the changes in autofluorescence signature with controlled insults of glucose deprivation and hypoxia. Additionally, it reports for the first-time the characterization of the autofluorescence lifetime signature in vivo at different time points in an established rat post-myocardial infarction heart failure. The thesis describes development of in vivo intravenous doxorubicin chemotherapy-cardiomyopathy heart failure model (DOX-HF) and subsequent characterization of in vivo autofluorescence signature. This investigation prompted development of a clinically viable instrument and the progress to date is described.Open Acces