How do cells control the temporal dynamics of autophagy?

Nutrients like amino acids, lipids, and glucose and related sugars are simple organic compounds that are involved in biochemical reactions that produce energy or that function as building blocks for growth and development of organisms. During their lifetime, all organisms will at some point be confronted with changes in the nutrient supply. At the cellular level, when a cell detects a loss of nutrients in its environment, it responds by altering its metabolism to save energy and to produce alternative nutrient sources. One key element of the response to nutrient starvation is activation of a process called autophagy. Autophagy, which literally means 'self-eating' is a process in which the cell degrades non-essential parts of itself to free up nutrients that are required for sustaining essential cellular processes. Autophagy is not only required for normal development of cells and organisms, but it has also been found to play an major role in a wide array of human diseases. Underscoring the importance of this process, the 2016 Nobel Prize in Physiology or Medicine was awarded for the discovery of autophagy. Despite the fact that autophagy has been studied extensively over the past decade, we still know relatively little about how cells regulate this process. It is very important to understand how autophagy is regulated by the cell, because failure to control this process (both positively and negatively) can have grave consequences for the organism. In this project, we are studying the upstream regulatory mechanisms that control the activity of autophagy. In the past year we have systematically interrogated nearly all genes in the yeast genome for their effect on autophagy using high-content microscopy. We collected approximately 20Tb of data. To analyze this dataset we needed to develop novel bioinformatics methods, which make use of machine learning and neural networks-based methodology. These analyses resulted in the identification of numerous genes that affect activation as well as inactivation/dampenening of the autophagic response. We have recently published an article in which we describe how cells dampen noise in intracellular signaling pathways, which is critical for maintenance of homeostasis. Furthermore, we have completed processing of large-scale datasets and are now preparing several manuscripts where we will present a map of the genome-wide landscape of autophagy; i.e. how cell integrate different pathways and processes to control autophagy. We will also publish articles in which we describe novel assays and bioinformatics methods to study autophagy in single cells within the context of entire cell populations. Finally, we have initiated a new NFR-sponsored study where we follow up several key findings of this NFR project.

This basic research project will mainly have impact for other researchers in the field. In particular, we developed several bioinformatics tools that will be widely applicable in cell biology, such as machine learning tools for analysis of large-scale microscopy datasets. The ability to generate large datasets has greatly increased over the years, but development of methods and tools to analyze such datasets has lagged, and it is crucial that such methods are developed for optimal use of data. In addition, our study has provided numerous starting points for follow-up studies, which will be a great resource for the field.

Nutrients like amino acids, lipids, and glucose and related sugars are simple organic compounds that are involved in biochemical reactions that produce energy or that constitute cellular biomass. Maintaining cellular homeostasis in the face of changes in nutrient supply is essential for the growth and development of all organisms, from unicellular microorganisms to higher eukaryotes. When a cell detects a loss of its nutrient supply, it activates signal transduction pathways that elicit integrated responses that alter cell metabolism (reducing biosynthesis and increasing catabolism) and that mobilize alternative nutrient sources. One key element of the response to nutrient starvation is activation of autophagy, which is a catabolic process that recycles cytoplasmic components through lysosomal degradation, thereby generating nutrients to sustain essential cellular processes. However, the upstream pathways that activate autophagy are only partially understood; moreover, the mechanisms that switch off autophagy when nutrient status has improved have hardly been explored. Clearly, there is a gap in our knowledge of how this important process is regulated. We have recently identified a large collection of novel factors that either positively or negatively regulate autophagy. Here, we present a comprehensive research plan to elucidate at the molecular level how cells dynamically control autophagy during changing nutrient conditions. Initially, we will use the model organism Saccharaomyces cerevisiae as a model. At the later stages of the project we will expand the scope of our studies to include mammalian cells and the model organism Drosophila melanogaster. Upon completion of this project we expect to have (i) identified several novel pathways that dynamically regulate autophagy under fluctuating nutrient conditions, and (ii) determined the physiological relevance of these pathways on homeostasis and development.