How do genes control animal development and behavior? To answer that question, we use the experimentally tractable nematode Caenorhabditis elegans to identify and analyze molecular and cellular pathways for these important aspects of biology, with the goal of discovering fundamental biological mechanisms and revealing insights into human diseases. Our research defined the evolutionarily conserved pathway for programmed cell death (apoptosis) and the heterochronic pathway that led to the discovery of microRNAs. We also helped define the Ras signal transduction pathway key in cancer biology. We identified founding members of the POU and LIM families of transcription factors, homologs of which play important roles in the mammalian immune system and stem cell biology; of the RGS protein family, which regulates signaling from G-protein coupled receptors; and of the EGLN family of dioxygenases, which control the HIF-VHL pathway that is vital in cellular and organismic oxygen sensing and is a therapeutic target in cancer. We also discovered a novel class of neurotransmitter receptors, chloride channels gated by biogenic amines, and a new neurotransmitter, tyramine. Our research has generated findings of fundamental and broad significance to biology and medicine. The descriptions below exemplify some of our current projects.
Programmed Cell Death
Diverse developmental events involve naturally-occurring or “programmed” cell deaths. The loss of the tadpole tail during metamorphosis into a frog, the sculpting of human fingers and toes in utero, and the elimination of self-reactive cells in the immune system all provide examples. Abnormalities in programmed cell death are causally involved in numerous human diseases, including certain neurodegenerative disorders and cancer. We discovered that the 131 programmed cell deaths that occur during C. elegans development are controlled by a specific set of killer and protector genes, and we defined the canonical molecular genetic pathway for programmed cell death. This pathway of cellular suicide subsequently proved to be conserved in other animals, including humans, and the human homologs of genes we discovered are now being pursued as therapeutic targets for human diseases. One of the C. elegans killer genes, ced-3, encodes the founding member of a family of proteases known as caspases, key drivers of apoptotic cell death.
We recently discovered that in C. elegans several programmed cell deaths can occur independently of all caspases. Some of these caspase-independent cell deaths involve dying cells being extruded from the developing embryo rather than being engulfed by neighboring cells. Although apoptotic, these deaths are driven by a completely distinct molecular mechanism involving a conserved kinase cascade with homologs involved in human cancer. We are analyzing the mechanism of this novel form of cell death.
We are also exploring how caspase-dependent and caspase-independent cell-death pathways are coordinated within single cells; how specific cells decide whether to live or die; how neighboring cells recognize and engulf dying cells to eliminate them; and how caspase activation kills cells, a major problem in this field.
Cell Lineage and Cell Fate
Animal development begins with the fertilized egg and proceeds through multiple cell divisions to generate many cell types. How cell diversity is generated during development is a fundamental issue in biology. C. elegans has only 959 somatic cells and a known cell lineage, facilitating analyses of development at the single-cell level. We defined mechanisms that make daughter cells different from mother cells or sister cells different from each other and discovered evolutionarily conserved transcription factors that determine specific cell fates and signal transduction pathways through which some cells determine the fates of other cells. In recent studies of developmental origins of bilateral asymmetry, we determined how an early developmental decision is transduced through multiple cell divisions to ultimately define the epigenetic landscape that makes left and right developmentally homologous cells different from each other. We also are examining other aspects of cell lineage and cell fate. For example, most neurons are generated from ectodermal cell lineages, and most muscles are generated from mesodermal cell lineages. However, there are exceptions. We recently discovered that the C. elegans homolog of the mammalian transcription factor ASCL1 functions to generate neurons from a mesodermal cell lineage. Ascl1 is being used to transdifferentiate mammalian fibroblasts into neurons, suggesting that new factors we discover in these studies will be useful in neuroregenerative medicine.
To explore the molecular, cellular and circuit bases of nervous system function, we are analyzing the coordinately controlled C. elegans behaviors of feeding, egg laying and locomotion. We discovered that worms can “taste” light: light inhibits feeding behavior by generating a novel chemical taste stimulus, likely H2O2, that activates gustatory receptors in the feeding organ. We showed that this response to light is controlled by three separate neural circuits; one transforms swallowing into spitting (the response to a noxious taste), a behavior not previously observed. We are now determining how a neural circuit can cause a muscular pump to reverse the direction of its output.
We are analyzing the gene egl-9, which we discovered while studying C. elegans egg-laying behavior. EGL-9 is the founding member of a family of prolyl hydroxylase domain (PHD) enzymes that act as intracellular sensors for O2 and regulate the hypoxia-inducible transcription factor HIF to mediate responses to hypoxic experience key in many aspects of human physiology and disease. The EGL-9/HIF pathway is now a major therapeutic target in cancer. Nonetheless, little is known about effectors of this pathway or about how this pathway affects behavior. We showed that the EGL-9/HIF pathway modulates C. elegans egg laying and, in an ischemia-reperfusion model, locomotion and have discovered a number of new downstream targets, including a cytochrome P450. We are now seeking other proteins that act downstream of the EGL-9/HIF pathway to control C. elegans behavior. We predict that cytochrome P450 enzymes and homologs of other proteins we discover will prove to control responses to ischemia-reperfusion in mammals and define novel therapeutic targets.
Amyotrophic lateral sclerosis (ALS).
We have long studied the human neurodegenerative disease ALS. We are now analyzing the C. elegans ortholog of the human gene C9orf72, in which disease alleles cause both ALS and frontotemporal dementia.
Grants from the National Institutes of Health and the ALS Therapy Alliance provided support for some of the studies described.
As of February 25, 2016