Mutant p53 Gain-of-Function in Cancer

In its wild-type form, p53 is a major tumor suppressor whose function is critical for protection against cancer. Many human tumors carry missense mutations in the TP53 gene, encoding p53. Typically, the affected tumor cells accumulate excessive amounts of the mutant p53 protein. Various lines of evidence indicate that, in addition to abrogating the tumor suppressor functions of wild-type p53, the common types of cancer-associated p53 mutations also endow the mutant protein with new activities that can contribute actively to various stages of tumor progression and to increased resistance to anticancer treatments. Collectively, these activities are referred to as mutant p53 gain-of-function. This article addresses the biological manifestations of mutant p53 gain-of-function, the underlying molecular mechanisms, and their possible clinical implications.Mutations in the TP53 gene, encoding the p53 tumor suppressor, are arguably the most frequent type of gene-specific alterations in human cancer. This attests to the centrality of p53 as a major mainstay in the body’s built-in anticancer defense mechanisms. Not surprisingly, this pivotal role of the wild-type p53 (wtp53) protein in tumor suppression has attracted many researchers to study it in detail, resulting in an avalanche of information and publications. One might expect that, similar to other tumor suppressor genes, the sole outcome of mutations in the TP53 gene will be loss of wtp53 function, characteristically manifested as total lack of p53 expression or production of unstable or truncated mutant proteins. Yet, quite strikingly, the vast majority of cancer-associated p53 mutations actually lead to production of full length protein, typically with only a single amino acid substitution, which tends to accumulate in the tumor cells and reach steady-state levels that greatly exceed those of wtp53 in noncancerous cells (Rotter 1983). This remarkable feature has suggested early on in p53 research that cancer-associated mutant p53 (mutp53) isoforms may be more than just relics of wtp53 inactivation, and may instead play distinctive roles in the tumor cells.In principle, emergence of a p53 mutation within a cell might have three, not mutually exclusive, types of outcome (Michalovitz et al. 1991; Sigal and Rotter 2000; Weisz et al. 2007b). First, such mutation is expected to abrogate the tumor suppressor function of the affected TP53 allele, reducing the overall capacity of the cell to mount a proper p53 response; if both alleles eventually become mutated, or if the remaining allele is lost, such cells will be totally deprived of anticancer protection by p53. Second, many common mutp53 isoforms can exert dominant–negative effects over coexpressed wtp53, largely by forming mixed tetramers that are incapable of DNA binding and transactivation. Hence, even if one wt allele is retained, the cell may be rendered practically devoid of wtp53 function through such mechanism, particularly if the mutant protein is expressed in excess over its wt counterpart. Third, and most relevant for this article, the emergent mutp53 protein might possess activities of its own, often not present in the original wtp53 protein, which can actively contribute to various aspects of tumor progression. Such activities, commonly described as mutp53 gain-of-function (GOF), are the subject of this article. Several recent reviews address in detail the various aspects of mutp53 GOF (Brosh and Rotter 2009; Donzelli et al. 2008; Lozano 2007; Olivier et al. 2009; Peart and Prives 2006; Petitjean et al. 2007; Song and Xu 2007; Strano et al. 2007; Weisz et al. 2007b). Therefore, we focus here mainly on general principles as well as on some of the more recent findings.     

Metabolic Stress in Autophagy and Cell Death Pathways

Growth factors and oncogenic kinases play important roles in stimulating cell growth during development and transformation. These processes have significant energetic and synthetic requirements and it is apparent that a central function of growth signals is to promote glucose metabolism to support these demands. Because metabolic pathways represent a fundamental aspect of cell proliferation and survival, there is considerable interest in targeting metabolism as a means to eliminate cancer. A challenge, however, is that molecular links between metabolic stress and cell death are poorly understood. Here we review current literature on how cells cope with metabolic stress and how autophagy, apoptosis, and necrosis are tightly linked to cell metabolism. Ultimately, understanding of the interplay between nutrients, autophagy, and cell death will be a key component in development of new treatment strategies to exploit the altered metabolism of cancer cells.Although single-celled organisms grow and proliferate based on nutrient availability, metazoan cells rely on growth factor input to promote nutrient uptake, regulate growth and proliferation, and survive (Raff 1992; Rathmell et al. 2000). Access and competition for these signals are critical in developmental patterning and to maintain homeostasis of mature tissues. Cells that do not receive proper growth factor signals typically atrophy, lose the ability to uptake and use extracellular nutrients, and instead induce the self-digestive process of autophagy as an intracellular energy source before ultimately undergoing programmed cell death. Cancer cells, in contrast, often become independent of extracellular growth signals by gaining mutations or expressing oncogenic kinases to drive intrinsic growth signals that mimic growth factor input, which can be the source of oncogene addiction. Growth factor input or oncogenic signals often drive highly elevated glucose uptake and metabolism (Rathmell et al. 2000; DeBerardinis et al. 2008; Michalek and Rathmell 2010). First described in cancer by Warburg in the 1920s, this highly glycolytic metabolic program is termed aerobic glycolysis and is a general feature of many nontransformed proliferative cells (Warburg 1956; DeBerardinis et al. 2008).Nutrient uptake and aerobic glycolysis induced by growth signals play key roles in cell survival (Vander Heiden et al. 2001). Manipulating cell metabolism as a means to promote the death of inappropriately dividing cells, therefore, is a promising new avenue to treat disease. Targeting the altered metabolism of cancer cells in particular is of great interest. It is still unclear at the molecular level, however, how inhibiting or modulating cell metabolism leads to apoptosis, and how these pathways may best be exploited (Dang et al. 2009; Wise and Thompson 2010).Growth factor or oncogenic kinases promote multiple metabolic pathways that are essential to prevent metabolic stress and may be targets in efforts to link metabolism and cell death (Vander Heiden et al. 2001). Decreased glucose metabolism on loss of growth signals leads to decreased ATP generation as well as loss in generation of many biosynthetic precursor molecules, including nucleic acids, fatty acids, and acetyl-CoA for acetylation (Zhao et al. 2007; Wellen et al. 2009; Coloff et al. 2011). Glucose is also important as a precursor for the hexosamine pathway, to allow proper glycosylation and protein folding in the endoplasmic reticulum (Dennis et al. 2009; Kaufman et al. 2010). If glucose metabolism remains insufficient or disrupted, the cells can switch to rely on mitochondrial oxidation of fatty acids and amino acids, which are energy rich but do not readily support cell growth and can lead to potentially dangerous levels of reactive oxygen species (Wellen and Thompson 2010). Amino acid deficiency can directly inhibit components of the signaling pathways downstream from growth factors and activate autophagy (Lynch 2001; Beugnet et al. 2003; Byfield et al. 2005; Nobukuni et al. 2005). Finally, hypoxia induces a specific pathway to increase nutrient uptake and metabolism via the hypoxia-inducible factor (HIF1/2α) that promotes adaptation to anaerobic conditions, but may lead to apoptosis if hypoxia is severe (Saikumar et al. 1998; Suzuki et al. 2001; Fulda and Debatin 2007).Typically a combination of metabolic stresses rather than loss of a single nutrient input occur at a given time (Degenhardt et al. 2006) and autophagy is activated to mitigate damage and provide nutrients for short-term survival (Bernales et al. 2006; Tracy et al. 2007; Altman et al. 2011; Guo et al. 2011). Autophagy is a cellular process of bulk cytoplasmic and organelle degradation common to nearly all eukaryotes. Unique double-membraned vesicles known as autophagosomes engulf cellular material and fuse with lysosomes to promote degradation of the contents (Kelekar 2005). Described in greater detail below, autophagy can reduce sources of stress, such as protein aggregates and damaged or dysfunctional intracellular organelles, and provide nutrients during times of transient and acute nutrient withdrawal.Despite the protective effects of autophagy, cells deprived of growth signals, nutrients, or oxygen for prolonged times will eventually succumb to cell death. Apoptosis is the initial death response on metabolic stress and is regulated by Bcl-2 family proteins. In healthy cells, antiapoptotic Bcl-2 family proteins, such as Bcl-2, Bcl-xl, and Mcl-1, bind and inhibit the multidomain proapoptotic proteins Bax and Bak (van Delft and Huang 2006; Walensky 2006; Chipuk et al. 2010). In metabolic stress, proapoptotic “BH3-only” proteins of the Bcl-2 family are induced or activated and bind to and inhibit the antiapoptotic Bcl-2 family proteins to allow activation of the proapoptotic Bax and Bak (Galonek and Hardwick 2006). The BH3-only proteins Bim, Bid, and Puma can also directly bind and activate Bax and Bak (Letai et al. 2002; Ren et al. 2010). Active Bax and Bak disrupt the outer mitochondrial membrane (termed mitochondrial outer-membrane permeabilization, or MOMP) and release several proapoptotic factors including cytochrome-C that activate the apoptosome that in turn activates effector caspases to cleave a variety of cellular proteins and drive apoptosis (Schafer and Kornbluth 2006). In cases in which these apoptotic pathways are suppressed, metabolic stress can instead lead to necrotic cell death (Jin et al. 2007).     

Cadherin-mediated Intercellular Adhesion and Signaling Cascades Involving Small GTPases

Epithelia form physical barriers that separate the internal milieu of the body from its external environment. The biogenesis of functional epithelia requires the precise coordination of many cellular processes. One of the key events in epithelial biogenesis is the establishment of cadherin-dependent cell–cell contacts, which initiate morphological changes and the formation of other adhesive structures. Cadherin-mediated adhesions generate intracellular signals that control cytoskeletal reorganization, polarity, and vesicle trafficking. Among such signaling pathways, those involving small GTPases play critical roles in epithelial biogenesis. Assembly of E-cadherin activates several small GTPases and, in turn, the activated small GTPases control the effects of E-cadherin-mediated adhesions on epithelial biogenesis. Here, we focus on small GTPase signaling at E-cadherin-mediated epithelial junctions.Cell–cell adhesions are involved in a diverse range of physiological processes, including morphological changes during tissue development, cell scattering, wound healing, and synaptogenesis (Adams and Nelson 1998; Gumbiner 2000; Halbleib and Nelson 2006; Takeichi 1995; Tepass et al. 2000). In epithelial cells, cell–cell adhesions are classified into three kinds of adhesions: adherens junction, tight junction, and desmosome (for more details, see Meng and Takeichi 2009, Furuse 2009, and Delva et al. 2009, respectively). A key event in epithelial polarization and biogenesis is the establishment of cadherin-dependent cell–cell contacts. Cadherins belong to a large family of adhesion molecules that require Ca²⁺ for their homophilic interactions (Adams and Nelson 1998; Blanpain and Fuchs 2009; Gumbiner 2000; Hartsock and Nelson 2008; Takeichi 1995; Tepass et al. 2000). Cadherins form transinteraction on the surface of neighboring cells (for details, see Shapiro and Weis 2009). For the development of strong and rigid adhesions, cadherins are clustered concomitantly with changes in the organization of the actin cytoskeleton (Tsukita et al. 1992). Classical cadherins are required, but not sufficient, to initiate cell–cell contacts, and other adhesion protein complexes subsequently assemble (for details, see Green et al. 2009). These complexes include the tight junction, which controls paracellular permeability, and desmosomes, which support the structural continuum of epithelial cells. A fundamental problem is to understand how these diverse cellular processes are regulated and coordinated. Intracellular signals, generated when cells attach with one another, mediate these complicated processes.Several signaling pathways upstream or downstream of cadherin-mediated cell–cell adhesions have been identified (Perez-Moreno et al. 2003) (see also McCrea et al. 2009). Among these pathways, small GTPases including the Rho and Ras family GTPases play critical roles in epithelial biogenesis and have been studied extensively. Many key morphological and functional changes are induced when these small GTPases act at epithelial junctions, where they mediate an interplay between cell–cell adhesion molecules and fundamental cellular processes including cytoskeletal activity, polarity, and vesicle trafficking. In addition to these small GTPases, Ca²⁺ signaling and phosphorylation of cadherin complexes also play pivotal roles in the formation and maintenance of cadherin-mediated adhesions. Here, we focus on signaling pathways involving the small GTPases in E-cadherin-mediated cell–cell adhesions. Other signaling pathways are described in recent reviews (Braga 2002; Fukata and Kaibuchi 2001; Goldstein and Macara 2007; McLachlan et al. 2007; Tsukita et al. 2008; Yap and Kovacs 2003; see also McCrea et al. 2009).     

Biology of the TAM Receptors

The TAM receptors—Tyro3, Axl, and Mer—comprise a unique family of receptor tyrosine kinases, in that as a group they play no essential role in embryonic development. Instead, they function as homeostatic regulators in adult tissues and organ systems that are subject to continuous challenge and renewal throughout life. Their regulatory roles are prominent in the mature immune, reproductive, hematopoietic, vascular, and nervous systems. The TAMs and their ligands—Gas6 and Protein S—are essential for the efficient phagocytosis of apoptotic cells and membranes in these tissues; and in the immune system, they act as pleiotropic inhibitors of the innate inflammatory response to pathogens. Deficiencies in TAM signaling are thought to contribute to chronic inflammatory and autoimmune disease in humans, and aberrantly elevated TAM signaling is strongly associated with cancer progression, metastasis, and resistance to targeted therapies.The name of the TAM family is derived from the first letter of its three constituents—Tyro3, Axl, and Mer (Prasad et al. 2006). As detailed in Figure 1, members of this receptor tyrosine kinase (RTK) family were independently identified by several different groups and appear in the early literature under multiple alternative names. However, Tyro3, Axl, and Mer (officially c-Mer or MerTK for the protein, Mertk for the gene) have now been adopted as the NCBI designations. The TAMs were first grouped into a distinct RTK family (the Tyro3/7/12 cluster) in 1991, through PCR cloning of their kinase domains (Lai and Lemke 1991). The isolation of full-length cDNAs for Axl (O''Bryan et al. 1991), Mer (Graham et al. 1994), and Tyro3 (Lai et al. 1994) confirmed their segregation into a structurally distinctive family of orphan RTKs (Manning et al. 2002b). The two ligands that bind and activate the TAMs—Gas6 and Protein S (Pros1)—were identified shortly thereafter (Ohashi et al. 1995; Stitt et al. 1995; Mark et al. 1996; Nagata et al. 1996).Open in a separate windowFigure 1.TAM receptors and ligands. The TAM receptors (red) are Tyro3 (Lai and Lemke 1991; Lai et al. 1994)—also designated Brt (Fujimoto and Yamamoto 1994), Dtk (Crosier et al. 1994), Rse (Mark et al. 1994), Sky (Ohashi et al. 1994), and Tif (Dai et al. 1994); Axl (O''Bryan et al. 1991)—also designated Ark (Rescigno et al. 1991), Tyro7 (Lai and Lemke 1991), and Ufo (Janssen et al. 1991); and Mer (Graham et al. 1994)—also designated Eyk (Jia and Hanafusa 1994), Nyk (Ling and Kung 1995), and Tyro12 (Lai and Lemke 1991). The TAMs are widely expressed by cells of the mature immune, nervous, vascular, and reproductive systems. The TAM ligands (blue) are Gas6 and Protein S (Pros1). The carboxy-terminal SHBG domains of the ligands bind to the immunoglobulin (Ig) domains of the receptors, induce dimerization, and activate the TAM tyrosine kinases. When γ-carboxylated in a vitamin-K-dependent reaction, the amino-terminal Gla domains of the dimeric ligands bind to the phospholipid phosphatidylserine expressed on the surface on an apposed apoptotic cell or enveloped virus. See text for details. (From Lemke and Burstyn-Cohen 2010; adapted, with permission, from the authors.)Subsequent progress on elucidating the biological roles of the TAM receptors was considerably slower and ultimately required the derivation of mouse loss-of-function mutants (Camenisch et al. 1999; Lu et al. 1999). The fact that Tyro3^−/−, Axl^−/−, and Mer^−/− mice are all viable and fertile permitted the generation of a complete TAM mutant series that included all possible double mutants and even triple mutants that lack all three receptors (Lu et al. 1999). Remarkably, these Tyro3^−/−Axl^−/−Mer^−/− triple knockouts (TAM TKOs) are viable, and for the first 2–3 wk after birth, superficially indistinguishable from their wild-type counterparts (Lu et al. 1999). Because many RTKs play essential roles in embryonic development, even single loss-of-function mutations in RTK genes often result in an embryonic-lethal phenotype (Gassmann et al. 1995; Lee et al. 1995; Soriano 1997; Arman et al. 1998). The postnatal viability of mice in which an entire RTK family is ablated completely—the TAM TKOs can survive for more than a year (Lu et al. 1999)—is therefore highly unusual. Their viability notwithstanding, the TAM mutants go on to develop a plethora of phenotypes, some of them debilitating (Camenisch et al. 1999; Lu et al. 1999; Lu and Lemke 2001; Scott et al. 2001; Duncan et al. 2003; Prasad et al. 2006). Almost without exception, these phenotypes are degenerative in nature and reflect the loss of TAM signaling activities in adult tissues that are subject to regular challenge, renewal, and remodeling. These activities are the subject of this review.     

Imaging the Dynamics of Endocytosis in Live Mammalian Tissues

In mammalian cells, endocytosis plays a pivotal role in regulating several basic cellular functions. Up to now, the dynamics and the organization of the endocytic pathways have been primarily investigated in reductionist model systems such as cell and organ cultures. Although these experimental models have been fully successful in unraveling the endocytic machinery at a molecular level, our understanding of the regulation and the role of endocytosis in vivo has been limited. Recently, advancements in intravital microscopy have made it possible to extend imaging in live animals to subcellular structures, thus revealing new aspects of the molecular machineries regulating membrane trafficking that were not previously appreciated in vitro. Here, we focus on the use of intravital microscopy to study endocytosis in vivo, and discuss how this approach will allow addressing two fundamental questions: (1) how endocytic processes are organized in mammalian tissues, and (2) how they contribute to organ physiopathology.Endocytosis is a fundamental process used by the cell to internalize molecules from the plasma membrane (Mellman 1996; Doherty and McMahon 2009), and its dysregulation is the cause of several pathological conditions, such as cancer and neurodegenerative, metabolic, and storage diseases (Lanzetti and Di Fiore 2008; Mosesson et al. 2008; Ballabio and Gieselmann 2009).In mammals, endocytosis has been primarily studied in cell culture, which has been instrumental in identifying various endocytic pathways and elucidating the trafficking of internalized molecules throughout the endolysosomal system (Conner and Schmid 2003; Maxfield and McGraw 2004; Donaldson et al. 2009; Hurley and Stenmark 2011). The degree of complexity in the organization and the regulation of the endocytic processes have been shown to substantially increase in polarized cells (Mostov et al. 2003; Folsch et al. 2009) and in organ cultures (Dunn et al. 1980; Kandimalla et al. 2009; Khandelwal et al. 2010), which recapitulate some of the architectural features of the intact tissue. The scenario is further complicated in live animals, where tissues are continuously exposed to a specific combination of cues coming from the vasculature, the central nervous system, and the extracellular environment, which are difficult to reconstitute accurately in vitro. Therefore, although our knowledge of the molecular machineries controlling mammalian endocytosis has substantially increased in the last decades, there are still fundamental issues that have not been explored yet, such as how endocytic pathways are organized and regulated in mammalian tissues. Specifically, it is fundamental to establish whether in vivo cells show the same regulation of endocytic pathways that has been reported in vitro, or how molecules are internalized and trafficked in the presence of physiological levels of ligands and regulatory molecules. Another question is what is the contribution of the endocytic pathways to the physiopathology of a specific tissue or organ. For example, it is of paramount importance to determine whether and how endocytic pathways are altered in epithelial and stromal cells during tumor development and progression, and which specific cell function is affected by their dysregulation.Investigations of endocytosis in live mammals (i.e., rodents) were extensively performed during the 1980s and 1990s by using conventional techniques (e.g., biochemical assays, EM, and indirect immunofluorescence). However, the advent of the green fluorescent protein (GFP) technology, which has enabled imaging subcellular organelles in real time, has significantly shifted the focus toward cell cultures.The recent advancements in intravital microscopy (IVM), which encompasses a series of light microscopy–based techniques, have now made possible imaging biological processes in live animals at a subcellular resolution (Weigert et al. 2013). In this perspective, we focus on reviewing most of the recent data on IVM and endocytosis and try to convey to the reader a sense of the potential, challenges, and limitations of this approach. However, before discussing the “heart of the matter,” we start by briefly pointing out the advantages of using animal models versus the more popular and well-established in vitro model systems.     

Molecular Bases of Cell–Cell Junctions Stability and Dynamics

Epithelial cell–cell junctions are formed by apical adherens junctions (AJs), which are composed of cadherin adhesion molecules interacting in a dynamic way with the cortical actin cytoskeleton. Regulation of cell–cell junction stability and dynamics is crucial to maintain tissue integrity and allow tissue remodeling throughout development. Actin filament turnover and organization are tightly controlled together with myosin-II activity to produce mechanical forces that drive the assembly, maintenance, and remodeling of AJs. In this review, we will discuss these three distinct stages in the lifespan of cell–cell junctions, using several developmental contexts, which illustrate how mechanical forces are generated and transmitted at junctions, and how they impact on the integrity and the remodeling of cell–cell junctions.Cell–cell junction formation and remodeling occur repeatedly throughout development. Epithelial cells are linked by apical adherens junctions (AJs) that rely on the cadherin-catenin-actin module. Cadherins, of which epithelial E-cadherin (E-cad) is the most studied, are Ca²⁺-dependent transmembrane adhesion proteins forming homophilic and heterophilic bonds in trans between adjacent cells. Cadherins and the actin cytoskeleton are mutually interdependent (Jaffe et al. 1990; Matsuzaki et al. 1990; Hirano et al. 1992; Oyama et al. 1994; Angres et al. 1996; Orsulic and Peifer 1996; Adams et al. 1998; Zhang et al. 2005; Pilot et al. 2006). This has long been attributed to direct physical interaction of E-cad with β-catenin (β-cat) and of α-catenin (α-cat) with actin filaments (for reviews, see Gumbiner 2005; Leckband and Prakasam 2006; Pokutta and Weis 2007). Recently, biochemical and protein dynamics analyses have shown that such a link may not exist and that instead, a constant shuttling of α-cat between cadherin/β-cat complexes and actin may be key to explain the dynamic aspect of cell–cell adhesion (Drees et al. 2005; Yamada et al. 2005). Regardless of the exact nature of this link, several studies show that AJs are indeed physically attached to actin and that cadherins transmit cortical forces exerted by junctional acto-myosin networks (Costa et al. 1998; Sako et al. 1998; Pettitt et al. 2003; Dawes-Hoang et al. 2005; Cavey et al. 2008; Martin et al. 2008; Rauzi et al. 2008). In addition, physical association depends in part on α-cat (Cavey et al. 2008) and additional intermediates have been proposed to represent alternative missing links (Abe and Takeichi 2008) (reviewed in Gates and Peifer 2005; Weis and Nelson 2006). Although further work is needed to address the molecular nature of cadherin/actin dynamic interactions, association with actin is crucial all throughout the lifespan of AJs. In this article, we will review our current understanding of the molecular mechanisms at work during three different developmental stages of AJs biology: assembly, stabilization, and remodeling, with special emphasis on the mechanical forces controlling AJs integrity and development.     

The Regulation of the p53-mediated Stress Response by MDM2 and MDM4

Exquisite control of the activity of p53 is necessary for mammalian survival. Too much p53 is lethal, whereas too little permits tumorigenesis. MDM2 and MDM4 are structurally related proteins critical for the control of p53 activity during development, homeostasis, and the response to stress. These two essential proteins regulate both the activation of p53 in response to stress and the recovery of cells following resolution of the damage, yet both are oncogenic when overexpressed. Thus, multiple regulatory circuits ensure that their activities are fine-tuned to promote tumor-free survival. Numerous diverse stressors activate p53, and much research has gone into trying to find commonalities between them that would explain the mechanism by which p53 becomes active. It is now clear that although these diverse stressors activate p53 by different biochemical pathways, one common feature is the effort they direct, through a variety of means, toward disrupting the functions of both MDM2 and MDM4. This article provides an overview of the relationship between MDM2 and MDM4, features the various biochemical mechanisms by which p53 is activated through inhibition of their functions, and proposes some emerging areas for investigation of the p53-mediated stress response.Regulation of the p53-mediated stress response by the essential inhibitory proteins MDM2 and MDM4 is critical for survival. In response to stressors such as ionizing radiation, p53 induces a number of potentially lethal but tumor-suppressive processes, including cell cycle arrest, senescence, and apoptosis (reviewed by Horn and Vousden 2007). Both MDM2 and MDM4 are critical to surviving the p53-mediated stress response to whole body ionizing irradiation as mice with reduced levels of either protein undergo p53-dependent death after exposure to doses of radiation that are sublethal to wild-type mice (Mendrysa et al. 2003; Terzian et al. 2007). MDM2 and MDM4 are also required to control p53 function during development, as shown by the early embryonic death of mice lacking either MDM2 or MDM4, unless they also lack p53 (Jones et al. 1995; Montes de Oca Luna et al. 1995; Parant et al. 2001; Migliorini et al. 2002).Although both MDM2 and MDM4 are essential for development, they are detrimental to long-term survival when in excess, because both are oncogenic. Both MDM2 and MDM4 confer the tumorigenic phenotype on cultured cells when experimentally overexpressed (Fakharzadeh et al. 1991; Danovi et al. 2004). In addition, targeted expression of MDM2 in the mammary gland results in tumorigenesis (Lundgren et al. 1997). In people, single nucleotide polymorphisms that reduce expression of either of the orthologs of MDM2 or MDM4 (also referred to as Hdm2 and Hdm4) correlate with increased risk for breast cancer (Bond et al. 2004; Atwal et al. 2009). Approximately 10% of human tumors have been found to overexpress either MDM2 or MDM4 and many of these express wild-type p53 (reviewed in Toledo and Wahl 2006). Because the majority of human cancers express mutant forms of p53, overexpression of MDM2 and MDM4 in the subset of tumors expressing wild-type p53 supports the notion that excessive MDM2 and MDM4 promote tumorigenesis, at least in part, by blocking p53 function. Thus, limiting the activities of MDM2 and MDM4 is important to prevent cancer.     

Origin and Evolution of the Self-Organizing Cytoskeleton in the Network of Eukaryotic Organelles

The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here, the dynamic properties of the prokaryotic and eukaryotic cytoskeleton are compared, and how these relate to function and evolution of organellar networks is discussed. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing “active gel,” the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming.The eukaryotic cytoskeleton organizes space on the cellular scale and this organization influences almost every process in the cell. Organization depends on the mechanochemical properties of the cytoskeleton that dynamically maintain cell shape, position organelles, and macromolecules by trafficking, and drive locomotion via actin-rich cellular protrusions, ciliary beating, or ciliary gliding. The eukaryotic cytoskeleton is best described as an “active gel,” a cross-linked network of polymers (gel) in which many of the links are active motors that can move the polymers relative to each other (Karsenti et al. 2006). Because prokaryotes have only cytoskeletal polymers but lack motor proteins, this “active gel” property clearly sets the eukaryotic cytoskeleton apart from prokaryotic filament systems.Prokaryotes contain elaborate systems of several cytomotive filaments (Löwe and Amos 2009) that share many structural and dynamic features with eukaryotic actin filaments and microtubules (Löwe and Amos 1998; van den Ent et al. 2001). Prokaryotic cytoskeletal filaments may trace back to the first cells and may have originated as higher-order assemblies of enzymes (Noree et al. 2010; Barry and Gitai 2011). These cytomotive filaments are required for the segregation of low copy number plasmids, cell rigidity and cell-wall synthesis, cell division, and occasionally the organization of membranous organelles (Komeili et al. 2006; Thanbichler and Shapiro 2008; Löwe and Amos 2009). These functions are performed by dynamic filament-forming systems that harness the energy from nucleotide hydrolysis to generate forces either via bending or polymerization (Löwe and Amos 2009; Pilhofer and Jensen 2013). Although the identification of actin and tubulin homologs in prokaryotes is a major breakthrough, we are far from understanding the origin of the structural and dynamic complexity of the eukaryotic cytoskeleton.Advances in genome sequencing and comparative genomics now allow a detailed reconstruction of the cytoskeletal components present in the last common ancestor of eukaryotes. These studies all point to an ancestrally complex cytoskeleton, with several families of motors (Wickstead and Gull 2007; Wickstead et al. 2010) and filament-associated proteins and other regulators in place (Jékely 2003; Richards and Cavalier-Smith 2005; Rivero and Cvrcková 2007; Chalkia et al. 2008; Eme et al. 2009; Fritz-Laylin et al. 2010; Eckert et al. 2011; Hammesfahr and Kollmar 2012). Genomic reconstructions and comparative cell biology of single-celled eukaryotes (Raikov 1994; Cavalier-Smith 2013) allow us to infer the cellular features of the ancestral eukaryote. These analyses indicate that amoeboid motility (Fritz-Laylin et al. 2010; although, see Cavalier-Smith 2013), cilia (Cavalier-Smith 2002; Mitchell 2004; Jékely and Arendt 2006; Satir et al. 2008), centrioles (Carvalho-Santos et al. 2010), phagocytosis (Cavalier-Smith 2002; Jékely 2007; Yutin et al. 2009), a midbody during cell division (Eme et al. 2009), mitosis (Raikov 1994), and meiosis (Ramesh et al. 2005) were all ancestral eukaryotic cellular features. The availability of functional information from organisms other than animals and yeasts (e.g., Chlamydomonas, Tetrahymena, Trypanosoma) also allow more reliable inferences about the ancestral functions of cytoskeletal components (i.e., not only their ancestral presence or absence) and their regulation (Demonchy et al. 2009; Lechtreck et al. 2009; Suryavanshi et al. 2010).The ancestral complexity of the cytoskeleton in eukaryotes leaves a huge gap between prokaryotes and the earliest eukaryote we can reconstruct (provided that our rooting of the tree is correct) (Cavalier-Smith 2013). Nevertheless, we can attempt to infer the series of events that happened along the stem lineage, leading to the last common ancestor of eukaryotes. Meaningful answers will require the use of a combination of gene family history reconstructions (Wickstead and Gull 2007; Wickstead et al. 2010), transition analyses (Cavalier-Smith 2002), and computer simulations relevant to cell evolution (Jékely 2008).     

Wnt Signaling in Vertebrate Axis Specification

The Wnt pathway is a major embryonic signaling pathway that controls cell proliferation, cell fate, and body-axis determination in vertebrate embryos. Soon after egg fertilization, Wnt pathway components play a role in microtubule-dependent dorsoventral axis specification. Later in embryogenesis, another conserved function of the pathway is to specify the anteroposterior axis. The dual role of Wnt signaling in Xenopus and zebrafish embryos is regulated at different developmental stages by distinct sets of Wnt target genes. This review highlights recent progress in the discrimination of different signaling branches and the identification of specific pathway targets during vertebrate axial development.Wnt pathways play major roles in cell-fate specification, proliferation and differentiation, cell polarity, and morphogenesis (Clevers 2006; van Amerongen and Nusse 2009). Signaling is initiated in the responding cell by the interaction of Wnt ligands with different receptors and coreceptors, including Frizzled, LRP5/6, ROR1/2, RYK, PTK7, and proteoglycans (Angers and Moon 2009; Kikuchi et al. 2009; MacDonald et al. 2009). Receptor activation is accompanied by the phosphorylation of Dishev-elled (Yanagawa et al. 1995), which appears to transduce the signal to both the cell membrane and the nucleus (Cliffe et al. 2003; Itoh et al. 2005; Bilic et al. 2007). Another common pathway component is β-catenin, an abundant component of adherens junctions (Nelson and Nusse 2004; Grigoryan et al. 2008). In response to signaling, β-catenin associates with T-cell factors (TCFs) and translocates to the nucleus to stimulate Wnt target gene expression (Behrens et al. 1996; Huber et al. 1996; Molenaar et al. 1996).This β-catenin-dependent activation of specific genes is often referred to as the “canonical” pathway. In the absence of Wnt signaling, β-catenin is destroyed by the protein complex that includes Axin, GSK3, and the tumor suppressor APC (Clevers 2006; MacDonald et al. 2009). Wnt proteins, such as Wnt1, Wnt3, and Wnt8, stimulate Frizzled and LRP5/6 receptors to inactivate this β-catenin destruction complex, and, at the same time, trigger the phosphorylation of TCF proteins by homeodomain-interacting protein kinase 2 (HIPK2) (Hikasa et al. 2010; Hikasa and Sokol 2011). Both β-catenin stabilization and the regulation of TCF protein function by phosphorylation appear to represent general strategies that are conserved in multiple systems (Sokol 2011). Thus, the signaling pathway consists of two branches that together regulate target gene expression (Fig. 1).Open in a separate windowFigure 1.Conserved Wnt pathway branches and components. In the absence of Wnt signals, glycogen synthase kinase 3 (GSK3) binds Axin and APC to form the β-catenin destruction complex. Some Wnt proteins, such as Wnt8 and Wnt3a, stimulate Frizzled and LRP5/6 receptors to inhibit GSK3 activity and stabilize β-catenin (β-cat). Stabilized β-cat forms a complex with T-cell factors (e.g., TCF1/LEF1) to activate target genes. Moreover, GSK3 inhibition leads to target gene derepression by promoting TCF3 phosphorylation by homeodomain-interacting protein kinase 2 (HIPK2) through an unknown mechanism, for which β-catenin is required as a scaffold. This phosphorylation results in TCF3 removal from target promoters and gene activation. Other Wnt proteins, such as Wnt5a and Wnt11, use distinct receptors such as ROR2 and RYK, in addition to Frizzled, to control the the cytoskeletal organization through core planar cell polarity (PCP) proteins, small GTPases (Rho/Rac/Cdc42), and c-Jun amino-terminal kinase (JNK).Other Wnt proteins, such as Wnt5a or Wnt11, strongly affect the cytoskeletal organization and morphogenesis without stabilizing β-catenin (Torres et al. 1996; Angers and Moon 2009; Wu and Mlodzik 2009). These “noncanonical” ligands do not influence TCF3 phosphorylation (Hikasa and Sokol 2011), but may use distinct receptors such as ROR1/2 and RYK instead of or in addition to Frizzled (Hikasa et al. 2002; Lu et al. 2004; Mikels and Nusse 2006; Nishita et al. 2006, 2010; Schambony and Wedlich 2007; Grumolato et al. 2010; Lin et al. 2010; Gao et al. 2011). In such cases, signaling mechanisms are likely to include planar cell polarity (PCP) components, such as Vangl2, Flamingo, Prickle, Diversin, Rho GTPases, and c-Jun amino-terminal kinases (JNKs), which do not directly affect β-catenin stability (Fig. 1) (Sokol 2000; Schwarz-Romond et al. 2002; Schambony and Wedlich 2007; Komiya and Habas 2008; Axelrod 2009; Itoh et al. 2009; Tada and Kai 2009; Sato et al. 2010; Gao et al. 2011). This simplistic dichotomy of the Wnt pathway does not preclude some Wnt ligands from using both β-catenin-dependent and -independent routes in a context-specific manner.Despite the existence of many pathway branches, only the β-catenin-dependent branch has been implicated in body-axis specification. Recent experiments in lower vertebrates have identified additional pathway components and targets and provided new insights into the underlying mechanisms.     

Replicating Damaged DNA in Eukaryotes

DNA damage is one of many possible perturbations that challenge the mechanisms that preserve genetic stability during the copying of the eukaryotic genome in S phase. This short review provides, in the first part, a general introduction to the topic and an overview of checkpoint responses. In the second part, the mechanisms of error-free tolerance in response to fork-arresting DNA damage will be discussed in some detail.Before eukaryotic cells divide, the successful completion of DNA replication during S phase is essential to preserve genomic integrity from one generation to the next. During this process, the replication apparatus traverses in the form of bidirectionally moving forks to synthesize new daughter strands. Cells use several means to ensure faithful copying of the parental strands—first, by means of regulatory mechanisms a correctly coordinated replication apparatus is established, and second, a high degree of fidelity during DNA synthesis is maintained by replicative polymerases (Kunkel and Bebenek 2000; Reha-Krantz 2010). However, under several stressful circumstances, endogenously or exogenously induced, the replication apparatus can stall (Tourriere and Pasero 2007). Mostly, structural deformations in the form of lesions or special template-specific features arrest the replication process, activate checkpoint pathways and set in motion repair or tolerance mechanisms to counter the stalling (Branzei and Foiani 2009; Zegerman and Diffley 2009). Basic replication mechanism, its regulatory pathways and means to tolerate DNA damage are largely conserved across eukaryotic species (Branzei and Foiani 2010; Yao and O’Donnell 2010). Understanding the mechanisms involved may enable therapeutic intervention to several human conditions arising from an incomplete replication or from the inability to tolerate perturbations (Ciccia et al. 2009; Preston et al. 2010; Abbas et al. 2013). Enhanced replication stress has also been commonly identified in precancerous lesions, and the inactivation of checkpoint responses coping with this presumably oncogene-induced condition is considered necessary to establish the fully malignant phenotype (Bartkova et al. 2005; Negrini et al. 2010).It is not possible to treat this topic in a comprehensive manner in the allotted space; the reader is referred to excellent recent reviews for more details (Branzei and Foiani 2010; Jones and Petermann 2012). We will attempt to provide an overview of the various strategies that a eukaryotic cell invokes to avoid problems caused by replication stress related to DNA damage and, if problems arise, to tolerate damage without endangering the entire process of genome duplication. In this context, we will only give a brief outline of checkpoint responses that are discussed in more detail in Sirbu and Cortez (2013) and Marechal and Zou (2013). Also, a detailed discussion of translesion synthesis can be reviewed in Sale (2013).     

Endocytosis,Signaling, and Beyond

The endocytic network comprises a vast and intricate system of membrane-delimited cell entry and cargo sorting routes running between biochemically and functionally distinct intracellular compartments. The endocytic network caters to the organization and redistribution of diverse subcellular components, and mediates appropriate shuttling and processing of materials acquired from neighboring cells or the extracellular milieu. Such trafficking logistics, despite their importance, represent only one facet of endocytic function. The endocytic network also plays a key role in organizing, mediating, and regulating cellular signal transduction events. Conversely, cellular signaling processes tightly control the endocytic pathway at different steps. The present article provides a perspective on the intimate relationships that exist between particular endocytic and cellular signaling processes in mammalian cells, within the context of understanding the impact of this nexus on integrated physiology.Molecular mechanisms governing the remarkable diversity of endocytic routes and trafficking steps are described elsewhere in the literature (see Bissig and Gruenberg 2013; Henne et al. 2013; Burd and Cullen 2014; Gautreau et al. 2014; Kirchhausen et al. 2014; Mayor et al. 2014; Merrifield and Kaksonen 2014; Piper et al. 2014). Moreover, these have been the focus of many studies in the last 30 years, and the topic has been covered by many excellent reviews, making it unnecessary for us to dwell on this aspect any further here (see, for instance, Howes et al. 2010; McMahon and Boucrot 2011; Sandvig et al. 2011; Parton and del Pozo 2013). Herein, we will instead concentrate our attention on how cellular regulatory mechanisms control endocytosis, as well as on how endocytic events impinge on cell functions. Emphasis will be placed, although not exclusively, on studies that analyze cellular networks using holistic approaches and in vivo analysis. Our aim is to give the reader a flavor of the deep embedding of endocytic processes within cellular programs, a concept we refer to as the endocytic matrix (Scita and Di Fiore 2010).     

p53-based Cancer Therapy

Inactivation of p53 functions is an almost universal feature of human cancer cells. This has spurred a tremendous effort to develop p53 based cancer therapies. Gene therapy using wild-type p53, delivered by adenovirus vectors, is now in widespread use in China. Other biologic approaches include the development of oncolytic viruses designed to replicate and kill only p53 defective cells and also the development of siRNA and antisense RNA''s that activate p53 by inhibiting the function of the negative regulators Mdm2, MdmX, and HPV E6. The altered processing of p53 that occurs in tumor cells can elicit T-cell and B-cell responses to p53 that could be effective in eliminating cancer cells and p53 based vaccines are now in clinical trial. A number of small molecules that directly or indirectly activate the p53 response have also reached the clinic, of which the most advanced are the p53 mdm2 interaction inhibitors. Increased understanding of the p53 response is also allowing the development of powerful drug combinations that may increase the selectivity and safety of chemotherapy, by selective protection of normal cells and tissues.Thirty years of research on p53 have produced a detailed understanding of its structure and function. The almost universal loss of p53 activity in tumors has spurred an enormous effort to develop new cancer treatments based on this fact. Sophisticated animal models have shown that activation of the p53 response in even advanced tumors can be curative (Martins et al. 2006; Ventura et al. 2007; Xue et al. 2007). The p53 gene therapy, Gendicine, is approved in China and its US counterpart, Advexin, has shown activity in number of clinical trials. The p53 protein level is raised in many tumors by virtue of an increase in the protein''s half life and this tumor specific alteration in p53 processing has attracted tumor immunologists, who are now testing a number of p53 based vaccines in cancer patients (Speetjens et al. 2009).In more conventional approaches a range of small druglike molecules targeting the p53 system have been developed and several are now in clinical trials. Of critical importance has been the development of small-molecule inhibitors of the p53–Mdm2 protein interaction such as the Nutlins (Vassilev et al. 2004), which have shown activity against human xenografts in preclinical models. Advanced structural approaches have provided compelling support for the idea that some mutant p53 proteins can be targets for small molecules that would cause them to regain wild-type function (Joerger et al. 2006). Cell based screening methods have identified small molecules that can activate both mutant and wild-type p53 proteins in tumor cells to induce apoptosis. These screens, and RNAi based approaches, have revealed many new targets for therapy in the p53 pathway. In an exciting new approach, that has been validated in other tumor suppressor pathways, the search is on for targets in pathways that will show synthetic lethal interactions with loss of p53 function. Finally drug combinations have been developed that can selectively kill cancer cells that lack p53 function while protecting normal cells (Sur et al. 2009). The next few years hold out the prospect of new p53 based therapies that will be of wide application in cancer and other diseases.     

Functional Differentiation of Adult-Born Neurons along the Septotemporal Axis of the Dentate Gyrus

Over the past several decades, the proliferation and integration of adult-born neurons into existing hippocampal circuitry has been implicated in a wide range of behaviors, including novelty recognition, pattern separation, spatial learning, anxiety behaviors, and antidepressant response. In this review, we suggest that the diversity in behavioral requirements for new neurons may be partly caused by separate functional roles of individual neurogenic niches. Growing evidence shows that the hippocampal formation can be compartmentalized not only along the classic trisynaptic circuit, but also along a longitudinal septotemporal axis. We suggest that subpopulations of hippocampal adult-born neurons may be specialized for distinct mnemonic- or mood-related behavioral tasks. We will examine the literature supporting a functional and anatomical dissociation of the hippocampus along the longitudinal axis and discuss techniques to functionally dissect the roles of adult-born hippocampal neurons in these distinct subregions.Since the presence of dividing cells in the mostly postmitotic adult brain was first described (Altman and Das 1965), the generation of new neurons in adulthood has been proposed to be involved in a variety of behaviors (Doetsch and Hen 2005; Becker and Wojtowicz 2007; Sahay and Hen 2007; Deng et al. 2010; Ming and Song 2011; Miller and Hen 2014). Adult neurogenesis in the healthy mammalian brain is consistently seen in the subventricular zone (SVZ) of the lateral ventricles and the subgranular zone (SGZ) of the hippocampal dentate gyrus (DG). Recent studies have implicated hippocampal neurogenesis in learning- and memory-related tasks, such as contextual discrimination and spatial navigation and, specifically, in behavioral pattern separation (Clelland et al. 2009; Sahay et al. 2011; Nakashiba et al. 2012; Niibori et al. 2012; see also reviews in Deng et al. 2010; Ming and Song 2011; Marin-Burgin and Schinder 2012), but also in some behavioral effects of antidepressants (Santarelli et al. 2003; see also reviews in Sahay and Hen 2007; Kheirbek et al. 2012; Tanti and Belzung 2013). However, the exact role of adult hippocampal neurogenesis in some of these behaviors has been debated as some studies have shown no effects of altering adult neurogenesis on spatial navigation or antidepressant response. Proposed explanations have included differences in the behavioral tasks used to measure cognition or emotion, motivational state of subjects, species differences, or in how neurogenesis is defined, either as proliferation, survival, or differentiation (see reviews in Zhao et al. 2008; Aimone et al. 2011; Petrik et al. 2012b; Miller and Hen 2014).It must also be noted, however, that these hippocampal neurons are not born into a singular structure. Work in the past several decades has shown that the hippocampus can be divided, not only along the classic trisynaptic loop, but also longitudinally along a septotemporal axis. The septal (dorsal in rodents; posterior in primates) and temporal (ventral in rodents; anterior in primates) poles, as well as potential intermediate zones of the hippocampus, have different anatomic connections and electrophysiological properties, express a gradient of molecular markers, and play different functional roles, such as performance in spatial learning tasks and stress responses (see reviews in Moser and Moser 1998; Fanselow and Dong 2010). Consequently, adult-born neurons in the hippocampal DG may also be segregated along this longitudinal axis, and conflicting functional roles for neurogenesis may be a result of attempting to examine hippocampal neurogenesis as a unitary phenomenon. It is possible that there are intrinsic, cell-autonomous differences in adult-born neurons generated at opposite poles of the DG. An alternative, although not mutually exclusive, hypothesis is that progenitor cells are initially identical, but differentiate in a dissimilar manner as a result of integration into distinct network circuitry. We will, therefore, first discuss heterogeneity of the hippocampus along its longitudinal axis before reviewing differences in neurogenesis between the septal and temporal poles of the DG. As these topics have been reviewed extensively elsewhere (Moser and Moser 1998; Deng et al. 2010; Fanselow and Dong 2010; Koehl and Abrous 2011; Samuels and Hen 2011; Kheirbek et al. 2012; Petrik et al. 2012b), we will not try to exhaustively cover all the current literature. Rather, we attempt to gather key studies examining a septotemporal gradient of the hippocampus and hippocampal neurogenesis. We will then suggest possible approaches to examine neurogenesis in specific subregions of the hippocampal DG. Finally, a short section will examine segregation of the DG along its transverse axis.     

Relevance of Mitochondrial Genetics and Metabolism in Cancer Development

Cancer cells are characterized in general by a decrease of mitochondrial respiration and oxidative phosphorylation, together with a strong enhancement of glycolysis, the so-called Warburg effect. The decrease of mitochondrial activity in cancer cells may have multiple reasons, related either to the input of reducing equivalents to the electron transfer chain or to direct alterations of the mitochondrial respiratory complexes. In some cases, the depression of respiratory activity is clearly the consequence of disruptive mitochondrial DNA (mtDNA) mutations and leads as a consequence to enhanced generation of reactive oxygen species (ROS). By acting both as mutagens and cellular mitogens, ROS may contribute directly to cancer progression. On the basis of our experimental evidence, we suggest a deep implication of the supercomplex organization of the respiratory chain as a missing link between oxidative stress, energy failure, and tumorigenesis. We speculate that under conditions of oxidative stress, a dissociation of mitochondrial supercomplexes occurs, with destabilization of complex I and secondary enhanced generation of ROS, thus leading to a vicious circle amplifying mitochondrial dysfunction. An excellent model to dissect the role of pathogenic, disassembling mtDNA mutations in tumor progression and their contribution to the metabolic reprogramming of cancer cells (glycolysis vs. respiration) is provided by an often underdiagnosed subset of tumors, namely, the oncocytomas, characterized by disruptive mutations of mtDNA, especially of complex I subunits. Such mutations almost completely abolish complex I activity, which slows down the Krebs cycle, favoring a high ratio of α-ketoglutarate/succinate and consequent destabilization of hypoxia inducible factor 1α (HIF1α). On the other hand, if complex I is partially defective, the levels of NAD⁺ may be sufficient to implement the Krebs cycle with higher levels of intermediates that stabilize HIF1α, thus favoring tumor malignancy. The threshold model we propose, based on the population-like dynamics of mitochondrial genetics (heteroplasmy vs. homoplasmy), implies that below threshold complex I is present and functioning correctly, thus favoring tumor growth, whereas above threshold, when complex I is not assembled, tumor growth is arrested. We have therefore termed “oncojanus” the mtDNA genes whose disruptive mutations have such a double-edged effect.Cancer cells are characterized by uncontrolled proliferation due to gain-of-function of oncogenes and loss of function of tumor-suppressor genes. Among the hallmarks of the cancer phenotype, there is a metabolic reprogramming (DeBerardinis et al. 2008). Cancer cells are characterized in general by a decrease of mitochondrial respiration and oxidative phosphorylation, together with a strong enhancement of glycolysis, the so-called Warburg effect, first reported by Otto Warburg (Warburg 1956). Owing to space limitations, for this particular topic we refer you to recent excellent reviews (Moreno-Sanchez et al. 2007; Mayevsky 2009; Mathupala et al. 2010; Koppenol et al. 2011). Nevertheless, it is not clear which of the two processes (i.e., decreased respiration and enhanced glycolysis) is the primary event, or even if they are concomitant consequences of a common causal event.Although the decrease of mitochondrial oxidative phosphorylation is considered by many investigators as a universal feature of neoplastic cells, there are numerous publications in which cancer cells have been reported to show normal or even high respiratory activity (Zu and Guppy 2004; Weinberg and Chandel 2009). This apparent paradox can be explained by the hypothesis advanced by Smolkova et al (2010) that cancer progression is characterized by waves of gene expression, where initial waves suppressing mitochondrial function and stimulating glycolysis are followed by a resumption of mitochondrial oxidative phosphorylation when glutamine becomes the leading substrate for energy production and the major carbon source for anabolic processes. Each malignant tumor is characterized by a distinct metabolic phenotype reflecting the history of the different waves during the sequence of carcinogenic mutations.The enhanced aerobic glycolysis characterizing cancer cells (and, in general, highly proliferating cells) at least in some periods of their progression toward malignancy may be vital to provide, besides energy, also the starting materials for active biosynthetic processes (Cuezva et al. 2009). Indeed, it was recognized early that incomplete activity of the Krebs cycle allows the use of citrate as a starting intermediate for the synthesis of fatty acids and cholesterol (Parlo and Coleman 1986; Kuhajda et al. 1994), whereas glycolysis may provide the majority of energy required for the anabolic processes. The supply of citrate for lipid biosynthetic processes may be provided by reductive carboxylation of α-ketoglutarate by reversal of the isocitrate dehydrogenase reaction when the major carbon source is glutamine (Holleran et al. 1995; Yoo et al. 2008) and pyruvate dehydrogenase activity is depressed by the activation of pyruvate dehydrogenase kinase (Kim et al. 2006).During the cell cycle, the genes for glycolytic enzymes are overexpressed at the time of active DNA synthesis (Klevecz et al. 2004). Likewise, several oncogenes (such as c-myc, HIF1α, Akt) or tumor suppressors (p53) are involved in the transactivation of glycolytic enzymes (Cuezva et al. 2009). The activation of these genes may involve mitochondrial dysregulation, for example, through unbalance of Krebs cycle intermediates (see below).