Comprehensive Map of the Regulated Cell Death Signaling Network: a Powerful Analytical Tool for Studying Diseases
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cancers Article Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases 1,2,3, 1, 1,4 Jean-Marie Ravel y , L. Cristobal Monraz Gomez y, Nicolas Sompairac , Laurence Calzone 1, Boris Zhivotovsky 5,6 , Guido Kroemer 7,8,9,10,11 , Emmanuel Barillot 1 , Andrei Zinovyev 1 and Inna Kuperstein 1,* 1 Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France 2 Laboratoire de génétique médicale, CHRU-Nancy, F-54000 Nancy, France 3 Inserm, NGERE, Université de Lorraine, F-54000 Nancy, France 4 Centre de Recherches Interdisciplinaires, Université Paris Descartes, 75006 Paris, France 5 Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia 6 Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden 7 Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France 8 Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France 9 Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France 10 Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou 215163, China 11 Karolinska Institute, Department of Women’s and Children’s Health, Karolinska University Hospital, 171 77 Stockholm, Sweden * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 February 2020; Accepted: 10 March 2020; Published: 17 April 2020 Abstract: The processes leading to, or avoiding cell death are widely studied, because of their frequent perturbation in various diseases. Cell death occurs in three highly interconnected steps: Initiation, signaling and execution. We used a systems biology approach to gather information about all known modes of regulated cell death (RCD). Based on the experimental data retrieved from literature by manual curation, we graphically depicted the biological processes involved in RCD in the form of a seamless comprehensive signaling network map. The molecular mechanisms of each RCD mode are represented in detail. The RCD network map is divided into 26 functional modules that can be visualized contextually in the whole seamless network, as well as in individual diagrams. The resource is freely available and accessible via several web platforms for map navigation, data integration, and analysis. The RCD network map was employed for interpreting the functional differences in cell death regulation between Alzheimer’s disease and non-small cell lung cancer based on gene expression data that allowed emphasizing the molecular mechanisms underlying the inverse comorbidity between the two pathologies. In addition, the map was used for the analysis of genomic and transcriptomic data from ovarian cancer patients that provided RCD map-based signatures of four distinct tumor subtypes and highlighted the difference in regulations of cell death molecular mechanisms. Keywords: regulated cell death; survival; signaling network; comprehensive map; biocuration; data visualization; module activity; lung cancer; Alzheimer’s disease; NaviCell Cancers 2020, 12, 990; doi:10.3390/cancers12040990 www.mdpi.com/journal/cancers Cancers 2020, 12, 990 2 of 26 1. Introduction Cell death garners special attention not only because it represents the endpoint of the cell’s life cycle, but also because the molecular mechanisms leading to cellular demise are perturbed in many different diseases [1,2]. Two major scenarios are sealing a cell’s final fate. Cells can either die from regulated cell death (RCD) or succumb to accidental cell death [3,4]. Accidental or non-regulated cell death, which is often referred to as necrosis, is a sudden process that combines cell membrane rupture and release of the cellular content into the surrounding environment [5]. In contrast, the RCD involves an active contribution by the cells and may be executed through a panoply of different pathways that include (but are not limited to) apoptosis, necroptosis, autophagy, ferroptosis, parthanatos, and pyroptosis [6,7]. One of the most studied modes of RCD is apoptosis, a ‘clean’ cell elimination process that has been thought to be non-inflammatory and non-immunogenic. However, in specific circumstances, cells dying from apoptosis may induce an immune response against dead-cell antigens [8]. Apoptosis is a highly regulated, energy-dependent process that requires ATP supply and, therefore, hinges on a functional bioenergetics metabolism. The severity of environmental stress, damage, genetic, or epigenetic perturbations dictate the choice between survival or death program and also mode of cell death execution, be it apoptosis or another lethal subroutine [9]. A challenge is to integrate all the distinct initiation, signaling and execution pathways into one seamless map. RCD is coordinated by numerous signaling pathways including trophic signals relayed by AKT and mTOR, stress kinase including ERK and JNK, or transcription factors such as NF-κB. RCD is also dependent on mitochondria and glucose metabolism that dictate the energy supply status. In addition, there is a complex post-transcriptional regulation level by non-coding RNAs including miRNAs and post-translational modifications of apoptosis-related proteins. Morphologically, apoptosis is characterized by cell shrinkage, nuclear condensation and fragmentation, cellular detachment from surrounding tissue and surface exposure of “eat-me” signals such as phosphatidylserine that facilitate removal of the dying cells by macrophages. Another well-studied form of RCD, autophagy, is activated under various stress situations, in particular in response to a shortage in energy supply in the context of starvation or scarcity of growth factors [10]. Autophagy ensures cell homeostasis by recycling cellular organelles and macromolecules, thereby, mediating cytoprotection and reducing the propensity of cells to undergo RCD. In specific circumstances, however, autophagy can be switched to a process of self-elimination leading to cell death. Necroptosis is a signaling-mediated mode of cell death with morphological features similar to necrosis. Necroptosis is accompanied by “swelling” of cells and organelles and rapid loss of plasma membrane integrity. Ferroptosis is a cell death modality induced by an accumulation of lipid peroxides due to a dysregulation of iron metabolism that facilitates the generation of reactive oxygen species (ROS) and consequent peroxidation of membrane lipids [11]. Parthanatos is a Poly [ADP-ribose] polymerase 1 (PARP1) dependent cell death mode induced mostly by intracellular inputs such as DNA damage. When activated by single-stranded DNA breaks, PARP1 synthesizes poly (ADP-ribose) chains (PAR) that are covalently attached to nuclear proteins while consuming ADP and NAD+. PAR then acts as an activating signal for other DNA-repairing enzymes. However, in the case of excessive DNA damage, DNA repair processes are overstimulated, which leads to the consumption of ATP and NAD depletion, triggering cellular execution. Parthanatos is associated with mitochondrial fission, its major phenotype [12]. Finally, pyroptosis is a caspase-1 dependent cell death modality that can be activated by extracellular signals (such as bacterial lipopolysaccharide, LPS) that bind to receptors (such as NLRC4), inducing receptor dimerization that triggers PYCARD protein recruitment and thus caspase-1 activation. This massive knowledge of RCD mechanisms is scattered through thousands of scientific publications. This situation hampers not only the holistic understanding of RCD regulation but also the application of bioinformatics and systems biology approaches. Efforts of systematic collection and knowledge formalization about molecular interactions in a structured and computer-readable format have already been applied to numerous pathway databases. Several databases contain partially Cancers 2020, 12, 990 3 of 26 overlapping collections of signaling diagrams representing different modes of cell death, mitochondria and glucose metabolism in some detail [13–17]. However, the limiting factor of this type of signaling representation is the lack of an integrated view of the pathways linking upstream inputs, such as activators of ‘death receptor’, damaging agents or intracellular stressors to the different regulated cell death modes. As an additional approach for data formalization, protein-protein interaction (PPI) networks are used to depict reciprocal effects between molecular entities. However, PPI diagrams do not represent interactions between non-protein molecular entities (such as metabolites) and the depth of process description is generally not sufficient to understand the directionality of the signal flow, regulatory effects or feedback circuitries. Cell signaling can also be depicted at the level of biochemical reactions in the form of process diagrams, thus creating a comprehensive map as has been done for RB-E2F signaling [18], mTOR signaling [19], Alzheimer’s pathogenesis [20], influenza A virus replication [21], the Atlas of Cancer Signaling Networks (ACSN) [22], and others [23]. Here, we present the construction of a comprehensive illustration of interactions among different RCD modes in the form of a seamless signaling network. The resulting map constitutes the first integrated representation of all known modes of RCD together. The map depicts inputs, the