Systems biology of ion channels and transporters in tumor angiogenesis: An omics view

AbstractSolid tumors require the formation of new blood vessels to support their growth, invasiveness and metastatic potential. Tumor neovascularization is achieved by vasculogenesis from endothelial precursors and by sprouting angiogenesis from preexisting vessels. The complex sequence of events driving these processes, including endothelial activation, proliferation, migration and differentiation, is associated with fluxes of ions, water and other small molecules mediated by a great pool of ion channels and transporters (ICT). This ‘transportome’ is regulated by environmental factors as well as intracellular signaling molecules. In turn, ICT play a prominent role in the response to angiogenesis-related stimuli through canonical and ‘unconventional’ activities: indeed, there is an increasing recognition of the multifunctionality of several ion channels that could also be annotated as receptors, enzymes, scaffolding proteins, mechanical and chemical sensors.The investigation of ICT structure and function has been far from the experimental oncology for long time and these two domains converged only very recently. Furthermore, the systems biology viewpoint has not received much attention in the biology of cancer transportome. Modulating angiogenesis by interference with membrane transport has a great potential in cancer treatment and the application of an ‘omics’ logic will hopefully contribute to the overall advancement in the field.This review is an attempt to apply the systems biology approach to the analysis of ICT involved in tumor angiogenesis, with a particular focus on endothelial transportome diversity. This article is part of a Special Issue entitled: Membrane channels and transporters in cancers

MULTISCALE COMPLEXITY OF CALCIUM SIGNALING: MODELING ANGIOGENESIS

Intracellular calcium signaling is a universal, evolutionary conserved and versatile regulator of cell biochemistry. The complexity of calcium signaling and related cell machinery can be investigated by the use of experimental strategies, as well as by computational approaches. Vascular endothelium is a fascinating model to study the specific properties and roles of calcium signals at multiple biological levels. During the past 20 years, live cell imaging, patch clamp and other techniques have allowed us to detect and interfere with calcium signaling in endothelial cells (ECs), providing a huge amount of information on the regulation of vascularization (angiogenesis) in normal and tumoral tissues. These data range from the spatiotemporal dynamics of calcium within difffferent cell microcompartments to those in entire multicellular and organized EC networks. Beside experimental strategies, in silico endothelial models, specifically designed for simulating calcium signaling, are contributing to our knowledge of vascular physiology and pathology. They help to investigate and predict the quantitative features of proangiogenic events moving through subcellular, cellular and supracellular levels. This review focuses on some recent developments of computational approaches for proangiogenic endothelial calcium signaling. In particular, we discuss the creation of hybrid simulation environments, which combine and integrate discrete Cellular Potts Models. They are able to capture the phenomenological mechanisms of cell morphological reorganization, migration, and intercellular adhesion, with single-cell spatiotemporal models, based on reaction-diffffusion equations that describe the agonist-induced intracellular calcium events

Computational approaches for translational oncology: Concepts and patents

Background: Cancer is a heterogeneous disease, which is based on an intricate network of processes at different spatiotemporal scales, from the genome to the tissue level. Hence the necessity for the biomedical and pharmaceutical research to work in a multiscale fashion. In this respect, a significant help derives from the collaboration with theoretical sciences. Mathematical models can in fact provide insights into tumor-related processes and support clinical oncologists in the design of treatment regime, dosage, schedule and toxicity. Objective and Method: The main objective of this article is to review the recent computational-based patents which tackle some relevant aspects of tumor treatment. We first analyze a series of patents concerning the purposing the purposing or repurposing of anti-tumor compounds. These approaches rely on pharmacokinetics and pharmacodynamics modules, that incorporate data obtained in the different phases of clinical trials. Similar methods are also at the basis of other patents included in this paper, which deal with treatment optimization, in terms of maximizing therapy efficacy while minimizing side effects on the host. A group of patents predicting drug response and tumor evolution by the use of kinetics graphs are commented as well. We finally focus on patents that implement informatics tools to map and screen biological, medical, and pharmaceutical knowledge. Results and Conclusions: Despite promising aspects (and an increasing amount of the relative literature), we found few computational-based patents: There is still a significant effort to do for allowing modelling approaches to become an integral component of the pharmaceutical research

MULTISCALE MODEL OF TUMOR-DERIVED CAPILLARY-LIKE NETWORK FORMATION

Solid tumors recruit and form blood vessels, used for maintenance and growth as well as for formation and spread of metastases. Vascularization is therefore a pivotal switch in cancer malignancy: an accurate analysis of its driving processes is a big issue for the development of treatments. In vitro experiments have demonstrated that cultured tumor-derived endothelial cells (TECs) are able to organize in a connected network, which mimics an in vivo capillary-plexus. The process, called tubulogenesis, is promoted by the activity of soluble peptides (such as VEGFs), as well as by the following intracellular calcium signals. We here propose a multilevel approach, reproducing selected features of the experimental system: it incorporates a continuous model of microscopic VEGF-induced events in a discrete mesoscopic Cellular Potts Model (CPM). The two components are interfaced, producing a multiscale framework characterized by a constant ux of information from ner to coarser levels. The simulation results, in agreement with experimental analysis, allow to identify the key mechanisms of network formation. In particular, we provide evidence that the nascent pattern is characterized by precise topological properties, regulated by the initial cell density in conjunction with the degree of the chemotactic response and the directional persistence of cell migration

A cellular Potts model analyzing differentiated cell behavior during in vivo vascularization of a hypoxic tissue

Angiogenesis, the formation of new blood vessel networks from existing capillary or post-capillary venules, is an intrinsically multiscale process occurring in several physio-pathological conditions. In particular, hypoxic tissue cells activate downstream cascades culminating in the secretion of a wide range of angiogenic factors, including VEGF isoforms. Such diffusive chemicals activate the endothelial cells (ECs) forming the external walls of the nearby vessels that chemotactically migrate toward the hypoxic areas of the tissue as multicellular sprouts. A functional network eventually emerges by further branching and anastomosis processes. We here propose a CPM-based approach reproducing selected features of the angiogenic progression necessary for the reoxygenation of a hypoxic tissue. Our model is able to span the different scale involved in the angiogenic progression as it incorporates reaction-diffusion equations for the description of the evolution of microenvironmental variables in a discrete mesoscopic cellular Potts model (CPM) that reproduces the dynamics of the vascular cells. A key feature of this work is the explicit phenotypic differentiation of the ECs themselves, distinguished in quiescent, stalk and tip. The simulation results allow identifying a set of key mechanisms underlying tissue vascularization. Further, we provide evidence that the nascent pattern is characterized by precise topological properties. Finally, we link abnormal sprouting angiogenesis with alteration in selected cell behavior

A multiscale hybrid approach for vasculogenesis and related potential blocking therapies

Solid tumors must recruit and form new blood vessels for maintenance, growth and detachments of metastases. Discovering drugs that block malignant angiogenesis is thus an important approach in cancer treatment and has given rise to multiple in vitro and in silico models. The present hybrid individual cell-based model incorporates some underlying biochemical events relating more closely the classical Cellular Potts Model (CPM) parameters to subcellular mechanisms and to the activation of specific signaling pathways. The model spans the three fundamental biological levels: at the extracellular level a continuous model describes secretion, diffusion, uptake and decay of the autocrine VEGF; at the cellular level, an extended lattice CPM, based on a system energy reduction, reproduces cell dynamics such as migration, adhesion and chemotaxis; at the subcellular level, a set of reaction-diffusion equations describes a simplified VEGF-induced calcium-dependent intracellular pathway. The results agree with the known interplay between calcium signals and VEGF dynamics and with their role in malignant vasculogenesis. Moreover, the analysis of the link between the microscopic subcellular dynamics and the macroscopic cell behaviors confirms the efficiency of some pharmacological interventions that are currently in use and, more interestingly, proposes some new therapeutic approaches, that are counter-intuitive but potentially effective

Alternative strategies to inhibit tumor vascularization

Endothelial cells present in tumors show different origin, phenotype, and genotype with respect to the normal counterpart. Various mechanisms of intra-tumor vasculogenesis sustain the complexity of tumor vasculature, which can be further modified by signals deriving from the tumor microenvironment. As a result, resistance to anti-VEGF therapy and activation of compensatory pathways remain a challenge in the treatment of cancer patients, revealing the need to explore alternative strategies to the classical anti-angiogenic drugs. In this review, we will describe some alternative strategies to inhibit tumor vascularization, including targeting of antigens and signaling pathways overexpressed by tumor endothelial cells, the development of endothelial vaccinations, and the use of extracellular vesicles. In addition, anti-angiogenic drugs with normalizing effects on tumor vessels will be discussed. Finally, we will present the concept of endothelial demesenchymalization as an alternative approach to restore normal endothelial cell phenotype

A multiscale hybrid model for pro-angiogenic calcium signals in a vascular endothelial cell

Cytosolic calcium machinery is one of the principal signaling mechanisms by which endothelial cells (ECs) respond to external stimuli during several biological processes, including vascular progression in both physiological and pathological conditions. Low concentrations of angiogenic factors (such as VEGF) activate in fact complex pathways involving, among others, second messengers arachidonic acid (AA) and nitric oxide (NO), which in turn control the activity of plasma membrane calcium channels. The subsequent increase in the intracellular level of the ion regulates fundamental biophysical properties of ECs (such as elasticity, intrinsic motility, and chemical strength), enhancing their migratory capacity. Previously, a number of continuous models have represented cytosolic calcium dynamics, while EC migration in angiogenesis has been separately approached with discrete, lattice-based techniques. These two components are here integrated and interfaced to provide a multiscale and hybrid Cellular Potts Model (CPM), where the phenomenology of a motile EC is realistically mediated by its calcium-dependent subcellular events. The model, based on a realistic 3-D cell morphology with a nuclear and a cytosolic region, is set with known biochemical and electrophysiological data. In particular, the resulting simulations are able to reproduce and describe the polarization process, typical of stimulated vascular cells, in various experimental conditions.Moreover, by analyzing the mutual interactions between multilevel biochemical and biomechanical aspects, our study investigates ways to inhibit cell migration: such strategies have in fact the potential to result in pharmacological interventions useful to disrupt malignant vascular progressio

Osteogenic differentiation modulates the cytokine, chemokine, and growth factor profile of ASCs and SHED

Great efforts have been made to improve bone regeneration techniques owing to a growing variety of sources of stem cells suitable for autologous transplants. Specifically, adipose-derived stem cells (ASCs) and stems cells from human exfoliated deciduous teeth (SHED) hold great potential for bone tissue engineering and cell therapy. After a preliminary characterization of the main biomolecules ASCs and SHED released in their conditioned media, cells were kept both in normal and osteo-inducing conditions. Conventional assays were performed to prove their osteogenic potential such as quantitative real-time polymerase chain reaction (qRT-PCR) (for RUNX-2, collagen type I, osteopontin and osteonectin), alkaline phosphatase activity, osteocalcin production, and von Kossa staining. Conditioned media were tested again after the osteogenic induction and compared to maintaining condition both at base line and after 14 days of culture. The osteogenic condition inhibited the release of all the biomolecules, with the exception, concerning SHED, of growth-regulated alpha protein precursor (GRO\u3b1), and, to a lesser extent, interleukin (IL)-8. In conclusion, our data support that undifferentiated ASCs and SHED may be preferable to committed ones for general cell therapy approaches, due to their higher paracrine activity. Osteoinduction significantly affects the cytokine, chemokine, and growth factor profile in a differential way, as SHED kept a more pronounced pro-angiogenic signature than ASCs