Final Report Summary - BRAINCELL (Charting the landscape of brain development by large-scale single-cell transcriptomics and phylogenetic lineage reconstruction)
We have pursued the two main themes of my proposal. First, to determine cellular lineage using somatic mutations. Second, to determine cellular identity ("cell type") using large-scale single-cell transcriptomics.
The lineage project has resulted in some successes; notably we have used somatic mutations in myelodysplastic syndrome (MDS) to prove unequivocally that the hematopoietic stem cell is the cell of origin of the tumor (collaboration with Sten-Eirik Jacobsen; paper published in Cancer Cell). However, we have found that the natural somatic mutation rate even in such repeats is too low to be practically useful for high resolution lineage discovery in non-tumor cells. We have thus instead developed synthetic constructs in transgenic mice, currently based on a lentiviral barcoding strategy. This approach will not reveal complete lineage trees, but will label sublineages stochastically. We will use in utero injection to label radial glia (or neuroepithelial stem cells). This project is still ongoing.
The single-cell transcriptomics project has been very successful. We have greatly exceeded the main goal of the whole ERC grant, namely to analyze 10,000 single cells from mouse brain; in total we now have a high-quality dataset of more than 25,000 single cells, covering mouse brain and some other tissues (notably hair follicles, a key model of adult stem cells). We have published two landmark papers. One in Nature Neuroscience where we completed a classification of peripheral sensory neurons based on 800+ single cells from dorsal root ganglia. The other in Science, where we classified >3,000 neurons, glia and vascular cells in cortex and hippocampus. We are preparing publications from additional brain regions amygdala, dentate gyrus, midbrain, hypothalamus, zona incerta, spinal cord, and more.
The lineage project has resulted in some successes; notably we have used somatic mutations in myelodysplastic syndrome (MDS) to prove unequivocally that the hematopoietic stem cell is the cell of origin of the tumor (collaboration with Sten-Eirik Jacobsen; paper published in Cancer Cell). However, we have found that the natural somatic mutation rate even in such repeats is too low to be practically useful for high resolution lineage discovery in non-tumor cells. We have thus instead developed synthetic constructs in transgenic mice, currently based on a lentiviral barcoding strategy. This approach will not reveal complete lineage trees, but will label sublineages stochastically. We will use in utero injection to label radial glia (or neuroepithelial stem cells). This project is still ongoing.
The single-cell transcriptomics project has been very successful. We have greatly exceeded the main goal of the whole ERC grant, namely to analyze 10,000 single cells from mouse brain; in total we now have a high-quality dataset of more than 25,000 single cells, covering mouse brain and some other tissues (notably hair follicles, a key model of adult stem cells). We have published two landmark papers. One in Nature Neuroscience where we completed a classification of peripheral sensory neurons based on 800+ single cells from dorsal root ganglia. The other in Science, where we classified >3,000 neurons, glia and vascular cells in cortex and hippocampus. We are preparing publications from additional brain regions amygdala, dentate gyrus, midbrain, hypothalamus, zona incerta, spinal cord, and more.