EngramSeq: a new technology for mapping engram networks in mice

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My lab studies how the brain encodes, stores and uses information. One arm of my research program examines how memory goes wrong in disease states (e.g., Alzheimer's disease or PTSD) and is funded by CIHR. The second arm focuses on fundamental basic processes underlying information processing. This arm has been continuously supported by NSERC since I began my lab in 2005. My recently completed NSERC Discovery grant supported the development and test-driving of an open-source mini-endoscope that allows neuronal activity to be visualized in the brain of freely-behaving mice as they learn and remember. With this technology, we can literally "watch the brain of a mouse as it remembers". I am gratified that many of the diverse trainees involved in this project have gone on to further careers in science (Google Deep Mind, two biotech start-ups, and an Assistant Professor). In the current proposal, we will also develop a new open-source tool. EngramSeq will allow us to visualize where specific memory "engram" cells project in the brain. The brain is likely one of the most complex objects in the universe. The human brain contains roughly 100 billion neurons linked together by some 100 trillion synaptic connections while the mouse brain contains roughly 70 million neurons. Fundamental brain functions including memory likely derive from the patterns of connections between neurons. However, our knowledge of the overall brain wiring diagram is limited. To better understand the brain in all of its complexity, it is important to unravel the vast tangle of different neuronal projections. Recently, a technique was developed that exploits high-throughput DNA sequencing to allow the projection profile of thousands of individual neurons to be analyzed in the same mouse brain (Kebschull et al., 2016). This technique, called MAPseq (multiplexed analysis of projections by sequencing), uses unique RNA "barcodes" to identify the projection patterns of thousands of neurons at a time. Although MAPseq is a powerful tool, it has two limitations that preclude its use in our (and likely many) studies. First, the viral vector used to express the barcode is toxic and kills infected neurons within 3 days. Second, it is not possible to "target" barcode expression to specific neurons of interest. To address these limitations, we will develop EngramSeq to examine the specific projections of different individual engram neurons. This multidisciplinary project is ideal for training highly-qualified personnel as trainees will gain expertise in molecular biology, sequencing, mouse brain surgery, mouse behaviour, and big data analysis. Importantly EngramSeq will be a versatile tool that can be applied not only to our research questions (where do different engram neurons project?), but also be applied to other questions posed by the broader neuroscientific community. Our goal is that our new open-science tool will also be valuable to the neuroscience research community at large.