EMBL Seminars

Abstract
The brain is a highly complex and fascinating organ and we are interested in understanding how cellular heterogeneity emerges during brain development and how brain cells can regenerate upon injury. We are tackling these questions by applying and further developing integrative, multi-modal single-cell technologies. 

In the first part of my talk, I will present our work on human pluripotent stem cell (PSC) derived organoids that model human brain development in vitro. We generated a data set of paired single-cell transcriptome and accessible chromatin profiling over a dense time course of human brain organoid development, which we utilized to infer a gene regulatory network of human brain organoid development. We then used pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoid and identified an important role of GLI3 during human telencephalon dorso-ventral patterning. Further, we have developed single-cell methodologies to directly track developmental lineages in brain organoids and could identify clonality of brain organoid regions as well as a temporal window of regional fate specification. Finally, we are working towards engineering diverse human neuronal populations in vitro using morphogen screening approaches.

In the second part of my talk, I will present our work on understanding the organization and regeneration of the telencephalon in the axolotl salamander using single-cell genomics. We first generated a single-cell multiomic atlas of the axolotl telencephalon, identified evolutionary conservation of neuronal cell types and reconstructed trajectories of post-embryonic neurogenesis. We then showed that upon major injury, all neuronal cell types reemerge through regenerative neurogenesis and neuronal projections to other brain regions are re-established. Finally, we identified a regeneration specific state of neural progenitor cells that is characterized by expression of wound healing genes.

Together, our work highlights the power of single-cell technologies to understand the gene regulatory logic underlying brain development and regeneration.

Abstract
Development is driven by a sequence of molecularly interconnected transcriptional, epigenetic, and metabolic changes. Specific metabolites, like α-ketoglutarate (αKG), function as signalling molecules affecting the activity of chromatin modifying enzymes. It remains unclear, how such non-canonical function of metabolism coordinates specific cell-state changes especially in early development. Here we uncover that when naive human embryonic stem cells (nESC) are induced towards human trophoblast stem cells (hiTSC) a significant metabolic rewiring occurs, characterised by the accumulation of αKG. Published in vivo transcriptomic data further confirmed that metabolic rewiring likely takes place in the nascent trophectoderm (TE). We show that the intracellular αKG level is an important regulator of TE fate acquisition. Indeed, a dimethyl-αKG (dm-αKG) treatment of nESC increases their competence towards TE-like cells during hiTSC induction. Moreover, dm-αKG also increases the robustness of blastoid polarisation and TE maturation. Surprisingly, dm-αKG treatment does not affect global histone methylation levels in nESC, but rather leads to decreased acetyl-CoA levels, reduced histone acetyltransferase (HAT) activity and weakening of the pluripotency network. Further functional assays confirmed that both HAT inhibition and increased αKG level promote nESC competence towards TE but not other lineages e.g. primitive endoderm. We propose that an increased αKG level regulates pluripotency by reducing acetylation, thus creating a positive feedback loop promoting the induction of TE fate.

Abstract

Groups of cells of all kinds work together as part of multicellular behaviors ranging from collective migration to development. These behaviors are coordinated at the level of single cells, where information about other cells and the environment are encoded in intracellular signaling dynamics that then drive cellular and multicellular-level behaviors. Understanding how these complex behaviors are coordinated in nature is challenging because natural environments perturb signaling and behaviors but make it difficult to visualize behaviors. To identify how natural environments shape multicellular coordination and thus behaviors, we have designed a naturalistic soil model environment where we can visualize how cells interact with environments to affect collective outcomes. We focus on a cellular slime mold, Dictyostelium discoideum, that uses a biochemical environmental signal during starvation to coordinate aggregation into multicellular groups for continued survival. Our current findings suggest that the single-cell and population-wide signaling dynamics that coordinate development are robust in highly complex, three-dimensional environments, and that there are also other important cellular properties driving new behaviors we do not yet fully understand required for success in nature.

Abstract
Drastic epigenetic reprogramming occurs during mammalian early embryogenesis. Deciphering the molecular events underlying these processes is crucial for understanding how epigenetic information is transmitted between generations and how life really begins. Probing these questions was previously hindered by the scarce experimental materials that are available in early development. By developing a set of ultra-sensitive chromatin analysis technologies, we investigated chromatin reprogramming during early mouse development for chromatin accessibility, histone modifications, and 3D architecture. These studies unveiled highly dynamic and non-canonical chromatin regulation during maternal-to-zygotic transition and zygotic genome activation (ZGA). However, how ZGA is kickstarted and how the early development program is progressively driven by transcription factors (TFs) remain enigmatic. Recently, we identified key TFs that act at the onset of ZGA, and those that connect ZGA to the first cell fate commitment. In this talk, I will discuss how TFs and epigenetic factors cooperatively establish embryonic program and restore the embryonic epigenomes when the life begins.