The phenotypic reversion of cancer: Experimental evidences on cancer reversibility through epigenetic mechanisms (Review).

Different experimental models reveal that malignant cancer cells can be induced to change their phenotype into a benign one. This phenotypic transformation, confirmed both in vitro and in vivo, currently is known as 'tumor reversion'. This evidence raises a radical question among current cancer models: Is cancer reversible? How do genetic and epigenetic alterations hierarchically relate? Understanding the mechanisms of 'tumor reversion' represents a key point in order to evolve the actual cancer models and develop new heuristic models that can possibly lead to drugs that target epigenetic mechanisms, for example epigenetic drugs. Even though evidence of tumor reversion dates back to the 1950s, this remains a completely new field of research recently re­discovered thanks to the interest in cell reprogramming research, developmental biology and the increasing understanding of epigenetic mechanisms. In the current review, a comprehensive review of all the main experimental models on tumor reversion was presented.

Technological grandparents: how communication technologies can improve the well-being of the elderly?

The ageing of the population is one of the most significant social transformations that the twenty first century is showcasing and a challenge that impacts society at large. The elderly, inasmuch as everybody else, are confronted with continuous transformations that are induced by technology, although they seldom benefit from the opportunities that technology entails. The digital divide amongst various segments of the population is often age-related and due to different reasons, including biological, psychological, social and financial ones. There is an ongoing reflection pertaining to the factors that hinders the full adoption of ICTs by the elderly and a question regarding what can be done to overcome their poor involvement in technology. This article, based on the results of a recent research, which has been conducted in Italy, aims at highlighting the importance of engaging the elderly in the use of technology as a key to building bridges between generations.

Reuniting philosophy and science to advance cancer research.

Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer.

Is Cancer Reversible? Rethinking Carcinogenesis Models-A New Epistemological Tool.

A growing number of studies shows that it is possible to induce a phenotypic transformation of cancer cells from malignant to benign. This process is currently known as "tumor reversion". However, the concept of reversibility hardly fits the current cancer models, according to which gene mutations are considered the primary cause of cancer. Indeed, if gene mutations are causative carcinogenic factors, and if gene mutations are irreversible, how long should cancer be considered as an irreversible process? In fact, there is some evidence that intrinsic plasticity of cancerous cells may be therapeutically exploited to promote a phenotypic reprogramming, both in vitro and in vivo. Not only are studies on tumor reversion highlighting a new, exciting research approach, but they are also pushing science to look for new epistemological tools capable of better modeling cancer.

Thinking in 3 dimensions: philosophies of the microenvironment in organoids and organs-on-chip.

Organoids and organs-on-a-chip are currently the two major families of 3D advanced organotypic in vitro culture systems, aimed at reconstituting miniaturized models of physiological and pathological states of human organs. Both share the tenets of the so-called "three-dimensional thinking", a Systems Physiology approach focused on recapitulating the dynamic interactions between cells and their microenvironment. We first review the arguments underlying the "paradigm shift" toward three-dimensional thinking in the in vitro culture community. Then, through a historically informed account of the technical affordances and the epistemic commitments of these two approaches, we highlight how they embody two distinct experimental cultures. We finally argue that the current systematic effort for their integration requires not only innovative "synergistic" engineering solutions, but also conceptual integration between different perspectives on biological causality.

Stem Cells and the Microenvironment: Reciprocity with Asymmetry in Regenerative Medicine.

Much of the current research in regenerative medicine concentrates on stem-cell therapy that exploits the regenerative capacities of stem cells when injected into different types of human tissues. Although new therapeutic paths have been opened up by induced pluripotent cells and human mesenchymal cells, the rate of success is still low and mainly due to the difficulties of managing cell proliferation and differentiation, giving rise to non-controlled stem cell differentiation that ultimately leads to cancer. Despite being still far from becoming a reality, these studies highlight the role of physical and biological constraints (e.g., cues and morphogenetic fields) placed by tissue microenvironment on stem cell fate. This asks for a clarification of the coupling of stem cells and microenvironmental factors in regenerative medicine. We argue that extracellular matrix and stem cells have a causal reciprocal and asymmetric relationship in that the 3D organization and composition of the extracellular matrix establish a spatial, temporal, and mechanical control over the fate of stem cells, which enable them to interact and control (as well as be controlled by) the cellular components and soluble factors of microenvironment. Such an account clarifies the notions of stemness and stem cell regeneration consistently with that of microenvironment.

Breaking down calcium timing in heterogenous cells populations.

Calcium controls a large number of cellular processes at different scales. Decades of studies have pointed out the importance of calcium signaling in regulating differentiation, apoptosis, mitosis and functions such as secretion, muscle contraction and memory. The space-time structure of calcium signaling is central to this complex regulation. In particular, cells within organisms behave as clocks beating their own biological time, although in several cases they can synchronize across long distances leading to an emergent space-time dynamics which is central for single cell and organ functioning. We use a mathematical model built on published experimental data of hepatic non-excitable cells, analyzing emerging calcium dynamics of cells clusters composed both of normally functioning cells and pathological aggregates. Calcium oscillations are investigated by varying the severity of dysfunction and size of pathological aggregate. We show how strong and localized heterogeneity in cellular properties can profoundly alter organized calcium dynamics leading to sub-populations of cells which create their own coordinated dynamical organization. Our simulations of Ca2+ signals reveal how cell behaviors differ and are related to intrinsic time signals. Such different cells clusters dynamically influence each other so that non-physiological although organized calcium patterns are generated. This new reorganization of calcium activity may possibly be a precursor of cancer initiation.

Scientific Practice in Modeling Diseases: Stances from Cancer Research and Neuropsychiatry.

In the last few decades, philosophy of science has increasingly focused on multilevel models and causal mechanistic explanations to account for complex biological phenomena. On the one hand, biological and biomedical works make extensive use of mechanistic concepts; on the other hand, philosophers have analyzed an increasing range of examples taken from different domains in the life sciences to test-support or criticize-the adequacy of mechanistic accounts. The article highlights some challenges in the elaboration of mechanistic explanations with a focus on cancer research and neuropsychiatry. It jointly considers fields, which are usually dealt with separately, and keeps a close eye on scientific practice. The article has a twofold aim. First, it shows that identification of the explananda is a key issue when looking at dynamic processes and their implications in medical research and clinical practice. Second, it discusses the relevance of organizational accounts of mechanisms, and questions whether thorough self-sustaining mechanistic explanations can actually be provided when addressing cancer and psychiatric diseases. While acknowledging the merits of the wide ongoing debate on mechanistic models, the article challenges the mechanistic approach to explanation by discussing, in particular, explanatory and conceptual terms in the light of stances from medical cases.

Co-emergence and Collapse: The Mesoscopic Approach for Conceptualizing and Investigating the Functional Integration of Organisms.

The fall of reductionist approaches to explanation leaves biology with an unescapable challenge: how to decipher complex systems. This entails a number of very critical questions, the most basic ones being: "What do we mean by 'complex'?" and "What is the system we should look for?" In complex systems, constraints belong to a higher level that the molecular one and their effect reduces and constrains the manifold of the accessible internal states of the system itself. Function is related but not deterministically imposed by the underlying structure. It is quite unlikely that such kind of complexity could be grasped by current approaches focusing on a single organization scale. The natural co-emergence of systems, parts and properties can be adopted as a hypothesis-free conceptual framework to understand functional integration of organisms, including their hierarchical or multilevel patterns, and including the way scientific practice proceeds in approaching such complexity. External, "driving" factors - order parameters and control parameters provided by the surrounding microenvironment - are always required to "push" the components' fate into well-defined developmental directions. In the negative, we see that in pathological processes such as cancer, organizational fluidity, collapse of levels and dynamic heterogeneity make it hard to even find a level of observation for a stable explanandum to persist in scientific practice. Parts and the system both lose their properties once the system is destabilized. The mesoscopic approach is our proposal to conceptualizing, investigating and explaining in biology. "Mesoscopic way of thinking" is increasingly popular in the epistemology of biology and corresponds to looking for an explanation (and possibly a prediction) where "non-trivial determinism is maximal": the "most microscopic" level of organization is not necessarily the place where "the most relevant facts do happen." A fundamental re-thinking of the concept of causality is also due for order parameters to be carefully and correctly identified. In the biological realm, entities have relational properties only, as they depend ontologically on the context they happen to be in. The basic idea of a relational ontology is that, in our inventory of the world, relations are somehow prior to the relata (i.e., entities).

Conceptual Challenges in the Theoretical Foundations of Systems Biology.

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior-both conceptually and explanatory-to entities, and that in the biological realm entities are defined primarily by the context they are embedded within-and hence by the web of relations they are part of.

Cancer and intercellular cooperation.

The major transitions approach in evolutionary biology has shown that the intercellular cooperation that characterizes multicellular organisms would never have emerged without some kind of multilevel selection. Relying on this view, the Evolutionary Somatic view of cancer considers cancer as a breakdown of intercellular cooperation and as a loss of the balance between selection processes that take place at different levels of organization (particularly single cell and individual organism). This seems an elegant unifying framework for healthy organism, carcinogenesis, tumour proliferation, metastasis and other phenomena such as ageing. However, the gene-centric version of Darwinian evolution, which is often adopted in cancer research, runs into empirical problems: proto-tumoural and tumoural features in precancerous cells that would undergo 'natural selection' have proved hard to demonstrate; cells are radically context-dependent, and some stages of cancer are poorly related to genetic change. Recent perspectives propose that breakdown of intercellular cooperation could depend on 'fields' and other higher-level phenomena, and could be even mutations independent. Indeed, the field would be the context, allowing (or preventing) genetic mutations to undergo an intra-organism process analogous to natural selection. The complexities surrounding somatic evolution call for integration between multiple incomplete frameworks for interpreting intercellular cooperation and its pathologies.

The role of coherence in emergent behavior of biological systems.

In his research activity, Emilio Del Giudice explored the possibility to move towards a unified view of some long-range dynamics in nature, ranging from quantum field theory in physics up to biology. Such a view is adopted in this contribution by discussing a mathematical model for synchronized electrical behavior of pancreatic beta cells. The stochasticity is a fundamental component of the physiological synchronized behavior of this system. On the contrary, in a pathological type I diabetes scenario, the cells are destroyed by the autoimmune system and their coherent behavior is lost. This phenomenology conceptually links to ideas of coherent dynamics in quantum physics. Possible implications both for physical sciences and for the epistemology of life sciences are outlined.

Why network approach can promote a new way of thinking in biology.

This work deals with the particular nature of network-based approach in biology. We will comment about the shift from the consideration of the molecular layer as the definitive place where causative process start to the elucidation of the among elements (at any level of biological organization they are located) interaction network as the main goal of scientific explanation. This shift comes from the intrinsic nature of networks where the properties of a specific node are determined by its position in the entire network (top-down explanation) while the global network characteristics emerge from the nodes wiring pattern (bottom-up explanation). This promotes a "middle-out" paradigm formally identical to the time honored chemical thought holding big promises in the study of biological regulation.

Breaking down levels of biological organization.

Understanding biological behaviours implies explaining the organization of living beings. Cancer compromises the normal structure and function of tissues, cells, and genes so that it appears as a multilevel phenomenon. The biology of cancer is thus giving us interesting insights on the organization of a biological system and its hierarchical phenomenology. My thesis is that understanding the dynamics of this biological system implies making explicit features of a non-univocal notion of organization and two different dimensions of the parts-whole dependence, i.e. different modes of causality in maintaining levels of organization. The argument follows the analysis of some features of the biology of cancer. Convergence of interpretative models towards an operational account of levels, i.e. through concepts that focus on the dynamic control of levels' organization, contributes to this analysis too. A multi-unity perspective replaces the parts-whole perspective to explain what conditions the hierarchical control of biological behaviours depends on and how that dependency works.

Hierarchies and causal relationships in interpretative models of the neoplastic process.

The aim of this paper is to present a critical analysis of the kind of biological systems identified in the main explanatory theories of cancer (i.e. Somatic Mutation Theory and Tissue Organization Field Theory) and how references to the hierarchical organization of these biological systems are used in their explanatory arguments. I will discuss these aspects in terms of the isolation of the "locus of control" (Bechtel and Richardson 2010); that is, the point at which decisions are made shaping the explanatory endeavour. In fact, the current view of the neoplastic process, not as a static circumstance but as an evolving molecular and cellular process, makes it evident that the choice of the right level of analysis is not self-evident. This focus clarifies some epistemological reasons for the divergence between reductionist and organicist accounts and seems to suggest that the basis for distinctions among causal relationships that scientists sometimes make can be found in the hierarchical character of complex biological systems. I will argue that these different causal relationships reflect different levels of epistemic concern.

Gene therapy and enhancement for diabetes (and other diseases): the multiplicity of considerations.

Gene therapy has reached the forefront of studies and research over the last 30 years because of its potential for curing, treating, and preventing diseases associated with DNA mutations. Type 1 and type 2 diabetes are two examples of very common polygenic and multifactorial diseases. The huge amount of scientific literature on this topic reflects a growing general interest in the possibilities of altering our genetic heritage and thus controlling the onset of diseases associated with mutations and relative risk factors. We have focussed on the new treatment opportunities and possibility of enhancing an individual's health, physical well-being, and even an individual's behaviour through technologies specially designed for therapeutic purposes, which have been presented in literature. This historical perspective shows how this type of research, however, was immediately subjected to an ethical evaluation, especially regarding the decoding of the human genome and the questions raised by the alteration of our genetic heritage through new biotechnologies. Moreover, understanding the limitations of gene therapy protocol experiments and the multifactorial nature of many diseases, which have a genetic base, also contributes to these considerations.

Towards an integrated view of the neoplastic phenomena in cancer research.

Cancer research has been at the forefront of biomedical activity in recent decades, and advances in molecular biology have provided a growing amount of information on the mechanisms involved in the etiopathogenesis of tumors. Nevertheless, despite these advances, the complexity of cancer is more evident, especially as different levels of phenomena are considered to explain the heterogeneity of the neoplastic process. A synthetic analysis of advances in cancer research illustrates these changes. In attempting to overcome the limits of epistemological reductionism, there is a move from a view of a genetic basis for cancer to a more comprehensive perspective aiming to integrate a large amount of information and to understand the neoplastic phenomenon at higher levels of biological complexity through a new interpretative framework.

The neoplastic process and the problems with the attribution of function.

Within the reductionist paradigm that has dominated the cancer research scene over the past 50 years, the definition of cancer and the explanation of its origin have always been given at the molecular genetic level. The neoplastic process is thus commonly explained as the accumulation of somatic mutations in certain genes that thus give rise to tumor cells, with consequent assignment of function to those genes involved. Nevertheless, the search for an essential definition of this disease has shifted attention from molecular components toward the functional properties of the tumor itself, which seems to present specific capabilities, emerging over the course of the disease, so that the functional test is always required to test the properties of certain genes to give tumors. The aim of this work will be to analyze how functions are attributed within the reductionist paradigm, and then proceed to the hypothesis of cancer as a phenomenon linked to loss of organic function and discuss how this notion is consistent with a number of theories already present in the literature and could provide a more unified interpretation of the neoplastic process itself. From this analysis, some elements emerge that highlight the inadequacy of the reductionist interpretation of cancer, with some reasons for the inherent contradiction deriving from the attribution of function to the parts of a biological system when one wants to explain the whole. We also suggest that the characteristics of cancer cells could be functions recovered coincident with the loss of certain functions of the organism as a whole. In this light, a different relation emerges between cancer and selective pressure.