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Probing Cell Death with Small Molecules

Research Summary

Brent Stockwell uses chemical tools to elucidate new cell death mechanisms that are relevant to cancer and neurodegeneration.

Cell death is a fundamental biological process that is involved in the normal development of a multicellular organism. Disturbances in the mechanisms governing cell death are implicated in numerous diseases, including cancer and neurodegenerative diseases, such as Huntington's disease.

My lab uses small molecules in a genetic-like approach to probe biological systems. To understand a process, you need to perturb it; genetic tools are powerful for perturbing processes but are less effective in the study of essential genes, rapid or redundant processes, or multigenic traits. Small organic molecules are complementary to genetic tools, because such compounds act rapidly and conditionally, can target multiple paralogous proteins simultaneously, and can be readily combined for multidimensional manipulations of biochemical networks. My research group works at the interface of chemistry and biology; we are systematically using small molecules to discover mechanisms underlying cellular processes. Our interdisciplinary approach combines chemical design and synthesis with genomics, biochemistry, and cell biology. Our goal is to reveal new basic biological mechanisms and disease pathophysiology.

Figure 1: Genetic-like screens...

Cell Death: From Nonspecific to Specific Mechanisms
Cell death had been considered to occur via necrosis, through nonspecific processes, until John Kerr, Andrew Wyllie, and Alastair Currie unified a body of literature on apoptosis, a nonnecrotic death process,. Numerous researchers demonstrated that apoptosis is genetically programmed to occur in a temporally consistent fashion in model organisms and proceeds through a specific pathway; inactivation of any of several necessary genes blocks apoptosis. Thus, a type of programmed cell death that proceeds through a defined, specific pathway was revealed.

Nonapoptotic Programmed Cell Death
Genetically programmed cell death is an essential feature of development in metazoans, required for sculpting the nervous system, major organs, muscle, skeletal structure, and digits of the extremities. Some, but not all, programmed cell death occurs via apoptosis. For example, interdigital cell death occurs through both apoptotic and nonapoptotic mechanisms. Nonapoptotic programmed cell death is even seen in Caenorhabditis elegans, the paradigmatic organism used to define apoptosis. Nonapoptotic pathways can be activated in disease: in Huntington disease mouse models and patients, neurons die through both apoptosis and an unusual morphology of cell death referred to as dark cell death. I seek to discover and characterize such nonapoptotic programmed cell death pathways that occur in development and disease, as well as new activation mechanisms for apoptosis.

There are cell destruction phenotypes distinct from apoptosis and necrosis that have been proposed for nonapoptotic programmed cell death, such as autophagic cell death, paraptosis, mitotic catastrophe, and Wallerian degeneration; however, the details of these processes are not defined, and their in vivo relevance is not established. Defining the mechanisms, generality, and genetic regulation of nonapoptotic programmed cell death may have as profound an impact as the understanding of apoptotic mechanisms has had. Moreover, defining new mechanisms regulating apoptosis will allow a better understanding of normal and disease processes and provide new therapeutic avenues.

The Small-Molecule Approach
Our strategy involves using small molecules to reveal protein regulators of cell death. Small molecules are rapid and conditional, can induce loss or gain of function, and can affect a single domain in a multidomain protein. This approach began with Paul Ehrlich in the early 1900s and was used with sporadic, but striking, success to identify mechanisms by which steroids, acetylcholine, and other natural compounds function. In recent years, researchers have used this approach with both natural products and synthetic compounds, revealing important new pathways and proteins, such as mTOR, HDACs, FKBPs, and cyclophilins. We have made use of this strategy for exploring biology.

Our approach is to discover new compounds regulating cell death and, by converting these compounds into suitable affinity reagents, identify the target proteins for these compounds, revealing new protein regulators of cell death. Subsequently, we use genetic and biochemical methods to elucidate interacting components of the pathway. Finally, we test whether these pathways occur in vivo, in mice, and whether they are activated in disease models.

Recently we have (1) reduced the small-molecule screening approach to exploring biology to practice by creating new tools, and (2) developed synthetic lethal chemical screening as a means of discovering new cell death mechanisms, antitumor agents, and drug targets.

We have pioneered new methods for screening compounds in cell-based and in vitro assays and for defining the mechanism of action of active compounds: we created a polymer-based microarray-screening system for cell-based assays; methods of testing millions of pairwise combinations of compounds; a synthetic lethal screening system using engineered human tumor cells; the first library of thousands of biologically active, annotated compounds for revealing mechanisms underlying cellular phenotypes; and a genome-wide RNAi collection. Because purification of target proteins for moderate potency compounds is challenging, we have developed a photolabeling strategy to identify such target proteins. We have focused on using these tools to reveal new pathways and proteins involved in cell death processes relevant to cancer and neurodegeneration.

We recently identified the target protein and mechanism of action of a novel and intriguing compound, which we named erastin, revealing a new form of oxidative cell death involving voltage-dependent anion channels. We are also applying this approach to the elusive cell death mechanisms in neurodegeneration: we have identified compounds that prevent cell death induced by mutant huntingtin protein, which is mutated in Huntington’s disease, and are defining the mechanisms of action of these compounds.

In summary, we are using chemical tools to develop a systematic approach to revealing new biological pathways. Our hope is that these studies will illuminate the fundamental mechanisms governing cell mortality. In time, they may also provide new therapeutic agents for currently intractable diseases.

Grants from the National Institutes of Health, the Arnold and Mabel Beckman Foundation, the Burroughs Wellcome Fund, and NYSTAR provided partial support for this research.

As of May 30, 2012

Scientist Profile

Early Career Scientist
Columbia University
Cell Biology, Chemical Biology