ERC FUNDED PROJECTS

Autophagy is a conserved, lysosomal-mediated pathway required for cell homeostasis and survival. It is controlled by the master regulators of energy (AMPK) and growth (TORC1) and mediated by the ATG (autophagy) proteins. Deregulation of autophagy is implicated in cancer, immunity, infection, aging and neurodegeneration. Autophagosomes form and expand using membranes from the secretory and endocytic pathways but how this occurs is not understood. ATG9, the only transmembrane ATG protein traffics through the cell in vesicles, and is essential for rapid initiation and expansion of the membranes which form the autophagosome. Crucially, how ATG9 functions is unknown. I will determine how ATG9 initiates the formation and expansion of the autophagosome by amino acid starvation through a molecular dissection of proteins resident in ATG9 vesicles which modulate the composition and property of the initiating membrane. I will employ high resolution light and electron microscopy to characterize the nucleation of the autophagosome, proximity-specific biotinylation and quantitative Mass Spectrometry to uncover the proteome required for the function of the ATG9, and optogenetic tools to acutely regulate signaling lipids. Lastly, with our tools and knowledge I will develop an in vitro reconstitution system to define at a molecular level how ATG9 vesicle proteins, membranes that interact with ATG9 vesicles, and other accessory ATG components nucleate and form an autophagosome. In vitro reconstitution of autophagosomes will be assayed biochemically, and by correlative light and cryo-EM and cryo-EM tomography, while functional reconstitution of autophagy will be tested by selective cargo recruitment. The development of a reconstituted system and identification proteins and lipids which are key components for autophagosome formation will provide a means to identify a new generation of targets for translational work leading to manipulation of autophagy for disease related therapies.

2 121 055 €

Start date: 2018-07-01, End date: 2023-06-30

The human hematopoietic system is a paradigmatic, stem cell-maintained organ with enormous cell turnover. Hundreds of billions of new blood cells are produced each day. The process is tightly regulated, and susceptible to perturbation due to genetic variation. In this project, we will explore an innovative, population-genetic approach to find regulators of blood cell formation. Unlike traditional studies on hematopoiesis in vitro or in animal models, we will exploit natural genetic variation to identify DNA sequence variants and genes that influence blood cell formation in vivo in humans. Instead of inserting artificial mutations in mice, we will read out ripples from the experiments that nature has performed during evolution. Building on our previous work, unique population-based materials, mathematical modeling, and the latest genomics and genome editing techniques, we will: 1. Develop high-resolution association data and analysis methods to find DNA sequence variants influencing human hematopoiesis, including stem- and progenitor stages. 2. Identify sequence variants and genes influencing specific stages of adult and fetal/perinatal hematopoiesis. 3. Define the function, and disease associations, of identified variants and genes. Led by the applicant, the project will involve researchers at Lund University, Royal Institute of Technology and deCODE Genetics, and will be carried out in strong environments. It has been preceded by significant preparatory work. It will provide a first detailed analysis of how genetic variation influences human hematopoiesis, potentially increasing our understanding, and abilities to control, diseases marked by abnormal blood cell formation (e.g., leukemia).

2 000 000 €

Start date: 2018-10-01, End date: 2023-09-30

During an organism’s development it must integrate internal and external information. An example in plants, whose development stretches across their lifetime, is the coordination between environmental stimuli and endogenous cues on regulating the key hormone gibberellin (GA). The present challenge is to understand how these diverse signals influence GA levels and how GA signalling leads to diverse GA responses. This challenge is deepened by a fundamental problem in hormone research: the specific responses directed by a given hormone often depend on the cell-type, timing, and amount of hormone accumulation, but hormone concentrations are most often assessed at the organism or tissue level. Our approach, based on a novel optogenetic biosensor, GA Perception Sensor 1 (GPS1), brings the goal of high-resolution quantification of GA in vivo within reach. In plants expressing GPS1, we observe gradients of GA in elongating root and shoot tissues. We now aim to understand how a series of independently tunable enzymatic and transport activities combine to articulate the GA gradients that we observe. We further aim to discover the mechanisms by which endogenous and environmental signals regulate these GA enzymes and transporters. Finally, we aim to understand how one of these signals, light, regulates GA patterns to influence dynamic cell growth and organ behavior. Our overarching goal is a systems level understanding of the signal integration upstream and growth programming downstream of GA. The groundbreaking aspect of this proposal is our focus at the cellular level, and we are uniquely positioned to carry out our multidisciplinary aims involving biosensor engineering, innovative imaging, and multiscale modelling. We anticipate that the discoveries stemming from this project will provide the detailed understanding necessary to make strategic interventions into GA dynamic patterning in crop plants for specific improvements in growth, development, and environmental responses.

1 499 616 €

Start date: 2018-01-01, End date: 2022-12-31

Humans are endowed with a number of advanced cognitive abilities not seen in other species. So what allows the human brain to stand out from the rest in these capabilities? In general, the brains of primates, including humans, have more neurons per unit volume than other mammals. But humans are also in the fortunate position of having the largest of the primate brains, making the number of neurons in the human cerebral cortex greatly expanded. Thus, the difference seems to be a matter of quantity, not quality. My laboratory is interested in understanding how neuron number, and thus brain size, is determined in human brain development. The research proposed here is aimed at taking an evolutionary approach to this question and comparing brain development in an in vitro 3D model system, cerebral organoids. This method, which relies on self-organization from differentiating pluripotent stem cells, recapitulates remarkably well the endogenous developmental program of the human brain. Having previously established the brain organoid approach, and more recently improved upon it with the application of bioengineering, my laboratory is in a unique position to carry out functional studies of human brain development. I propose to use this approach to compare developing human brain tissue to that of other hominid species and tease apart unique features of human neural stem cells and progenitors that allow them to generate more neurons and therefore a greater cerebral cortical size. Furthermore, we will perform transcriptomic and functional screening to identify factors underlying this expansion, followed by careful genetic substitution to test the contributions of putative evolutionary changes. In this way, we will functionally test putative human evolutionary changes in a manner not previously possible.

1 444 911 €

Start date: 2018-07-01, End date: 2023-06-30