Modulatory profiling identifies mechanisms of small molecule-induced cell death

Abstract

Cell death is a complex process that plays a vital role in development, homeostasis, and disease. Our understanding of and ability to control cell death is impeded by an incomplete characterization of the full range of cell death processes that occur in mammalian systems, especially in response to exogenous perturbations. We present here a general approach to address this problem, which we call modulatory profiling. Modulatory profiles are composed of the changes in potency and efficacy of lethal compounds produced by a second cell death-modulating agent in human cell lines. We show that compounds with the same characterized mechanism of action have similar modulatory profiles. Furthermore, clustering of modulatory profiles revealed relationships not evident when clustering lethal compounds based on gene expression profiles alone. Finally, modulatory profiling of compounds correctly predicted three previously uncharacterized compounds to be microtubule-destabilizing agents, classified numerous compounds that act nonspecifically, and identified compounds that cause cell death through a mechanism that is morphologically and biochemically distinct from previously established ones.apoptosis | chemical biology | small molecules C ell death has historically been viewed as a binary phenomenon. Cells were described to die in one of two ways-through a controlled and ordered process (apoptosis) or an unregulated and chaotic process (necrosis) (1, 2). Not only were these often considered the only two possible mechanisms, but they were also frequently viewed as morphologically and biochemically uniform (3, 4). A great deal of research in recent decades has not only shown the complexity and heterogeneity of apoptotic and necrotic signaling, but also that cells can die in physiological and nonphysiological contexts through processes morphologically and biochemically distinct from both apoptosis and necrosis.Activation of caspases, a family of cysteine proteases, is essential for producing the full morphological characteristics of apoptosis. There are at least three distinct pathways that can lead to the activation of effector caspases-the extrinsic death receptor pathway, the intrinsic mitochondrial pathway, and the Granzyme B pathway (5)-but numerous mechanisms feed into these three pathways. There is substantial evidence that necrosis, long considered to be a disorganized and unregulated process, can proceed through an evolutionarily conserved pathway in a highly orchestrated fashion. Necrosis-like morphology has been observed after death receptor stimulation (6-12), after treatment with DNA-damaging agents (13-15), and in Caenorhabditis elegans in response to a variety of stresses (16,17). These examples illustrate the heterogeneity of cell death processes resembling necrosis. A widely debated nonapoptotic, nonnecrotic cell death mechanism is autophagic cell death, which has been implicated in vivo in the involution of the salivary gland in Drosophila (18) and in death because of the hypersensitivity response in Arabidopsi...

Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis

“…These drug-induced alterations to the proteome are superimposed on presumed differences in the baseline proteome of each celltype, as suggested by transcriptome analyses (14,15). The functional consequences of drug-induced alterations have been shown by Wolpaw et al to permit classification of apoptotic drugs based on these "modulatory profiles" (16). We hypothesize that the large cell-type and drug-specific differences in kinetic patterns we observe for caspase-derived products is because of the drug treatment causing specific alterations in the proteome before activation of the caspases.…”

La ferroptose, une nouvelle forme de mort cellulaire applicable au traitement médical des cancers

“…En culture, les cellules exposées à l'érastine s'arrondissent et se décollent rapidement sans libération mitochondriale du cytochrome c, ni activation des caspases [11]. La ferroptose est prévenue par l'application d'un chélateur des ions fer, la déferoxamine (Dfx), une caractéristique qui est à l'origine de sa dénomination [8,12]. Récemment, des progrès importants ont permis de mieux comprendre les étapes de la ferroptose et d'appréhender la singularité de cette forme de mort cellulaire.…”

Peroxidation of polyunsaturated fatty acids by lipoxygenases drives ferroptosis

“…The modulatory profiling of lipids was performed as described previously (4). The concentration of each lipid is listed here: OA, 80 μM; cardiolipin, 16.6 μM; cholesterol, 40 μM; ceramide, 37.2 μM; Lyso-PC, 80 μM; LA, 80 μM; and AA, 80 μM.…”

“…Cells undergoing ferroptosis cannot be rescued by chemical or genetic inhibitors of apoptosis (such as zVAD-fmk or Bax/Bak double knockout) (3)(4)(5)(6) or inhibitors of necroptosis (such as Nec-1 or RIPK1/3 knockdown) (1,7), which indicates that ferroptosis is a distinct cell death modality. Inhibition of ferroptosis is protective in models of Huntington's disease (8), periventricular leukomalacia (8)(9)(10), and kidney dysfunction (8,11,12).…”