Chromatin accessibility profiling of HSPC-derived erythroblast differentiation [ATAC-seq]

A prime goal of regenerative medicine is to replace dysfunctional cells in the body. To design protocols for producing target cells in the laboratory, one may need to consider exponentially large combinations of culture components. Here, we tested the potential of iteratively approximating the target phenotype by quantifying the distance between chromatin profiles (ATAC-seq) of differentiating cells in vitro and their in-vivo counterparts. We tested this approach on the well-studied generation of erythroblasts from haematopoietic stem cells, evaluating a fixed number of components over two sequential differentiation rounds (8x8 protocols). We found that the most erythroblast-like cells upon the first round yielded the most erythroblast-like cells at the second round, suggesting that greedy selection by chromatin approximation can be a viable optimisation strategy. Furthermore, by targeting transcriptional regulators linked to chromatin regions that were incompletely reprogrammed even after two rounds of differentiation, we could make a data-driven selection of additions to the protocol that further improved erythropoiesis. In future, our methodology can help craft notoriously difficult cells in vitro, such as B cells. Overall design: 165 ATAC-seq datasets from two round of differentiation with different treatment combinations: 16 from pilot experiment (8 combinations round 1 only) + 135 full experiment (8 combinations round 1; 8x8 combinations round 2) + 15 validation experiment with adapted treatment protocols (+TGFB or IL4); 2-3 replicates per condition, low-quality samples removed