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Transitions in cell states are controlled by combinatorial actions of transcription factors. BLIMP1, the key regulator of primordial germ cell (PGC) specification, apparently acts together with PRDM14 and AP2γ. To investigate their individual and combinatorial functions, we first sought an in vitro system for transcriptional readouts and chromatin immunoprecipitation sequencing analysis. We then integrated this data with information from single-cell transcriptome analysis of normal and mutant PGCs. Here we show that BLIMP1 binds directly to repress somatic and cell proliferation genes. It also directly induces AP2γ, which together with PRDM14 initiates the PGC-specific fate. We determined the occupancy of critical genes by AP2γ—which, when computed altogether with those of BLIMP1 and PRDM14 (both individually and cooperatively), reveals a tripartite mutually interdependent transcriptional network for PGCs. We also demonstrate that, in principle, BLIMP1, AP2γ and PRDM14 are sufficient for PGC specification, and the unprecedented resetting of the epigenome towards a basal state. Surani and colleagues use single-cell transcriptomics analysis in a model of mouse primordial germ cell specification to analyse the collaboration between three transcription factors, BLIMP1, PRDM14 and AP2γ, in determining germ cell fate. They find that BLIMP1 binds directly to repress somatic and cell proliferation genes, and at the same time induces AP2γ, which acts together with PRDM14. The three factors are sufficient for specification and form a tripartite interdependent transcriptional network.

T cells develop in the thymus and are critical for adaptive immunity. Natural killer (NK) lymphocytes constitute an essential component of the innate immune system in tumor surveillance, reproduction, and defense against microbes and viruses. Here, we show that the transcription factor Bcl11b was expressed in all T cell compartments and was indispensable for T lineage development. When Bcl11b was deleted, T cells from all developmental stages acquired NK cell properties and concomitantly lost or decreased T cell-associated gene expression. These induced T-to-natural killer (ITNK) cells, which were morphologically and genetically similar to conventional NK cells, killed tumor cells in vitro, and effectively prevented tumor metastasis in vivo. Therefore, ITNKs may represent a new cell source for cell-based therapies.

IntroductionThe epicardium is a heterogeneous cell layer covering the mammalian heart. During embryogenesis, the epicardial lineage is essential to heart and vascular development, yielding cardiac fibroblasts and coronary vascular smooth muscle cells. The epicardium also has a trophic effect on developing cardiomyocytes. It is quiescent in adulthood but reactivates post-injury to a limited degree to yield cardiac fibroblasts, which allows fast healing, yet also causes fibrosis. Epicardial functional heterogeneity remains incompletely characterised.MethodsThe Sinha group has derived a robust model of human epicardium (hpsc-epi) from human pluripotent stem cells; this was used for single-cell RNA sequencing (scRNA-seq). Immunohistochemistry and immunocytochemistry were used to validate scRNA-seq results in primary human foetal tissue. The candidate gene BNC1 has been investigated by siRNA-mediated knockdown studies in vitro. ResultsSingle-cell RNA-seq identified two main epicardial subpopulations in hpsc-epi: WT1high/BNC1high/TCF21low and WT1low/BNC1low/TCF21high. Here we show validation of our scRNA-seq data in human foetal epicardium by immunohistochemistry in cryosections and human foetal epicardial explants, confirming our hpsc-epi model is representative of the in vivo situation. We show preliminary data from siRNA-mediated knockdown of BNC1, which indicate this gene may play a role in epicardial function, possibly in regulating cell migration in a model of epithelial-to-mesenchymal transition.ImplicationsImproved understanding of developmental epicardial regulation could pave the way towards harnessing epicardial potential in prospective strategies to aid revascularisation and regeneration of the injured heart.

The histone H3 Lys27-specific demethylase UTX (or KDM6A) is targeted by loss-of-function mutations in multiple cancers. Here, we demonstrate that UTX suppresses myeloid leukemogenesis through noncatalytic functions, a property shared with its catalytically inactive Y-chromosome paralog, UTY (or KDM6C). In keeping with this, we demonstrate concomitant loss/mutation of KDM6A ( UTX ) and UTY in multiple human cancers. Mechanistically, global genomic profiling showed only minor changes in H3K27me3 but significant and bidirectional alterations in H3K27ac and chromatin accessibility; a predominant loss of H3K4me1 modifications; alterations in ETS and GATA-factor binding; and altered gene expression after Utx loss. By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML. Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs. This study shows that UTX (KDM6A) suppresses myeloid leukemogenesis through noncatalytic functions. UTX loss leads to alterations in H3K27ac, H3K4me1 and chromatin accessibility, and in gene-regulatory programs mediated by ETS and GATA transcription factors.

The transcription factor RUNX1 is essential to establish the haematopoietic gene expression programme; however, the mechanism of how it activates transcription of haematopoietic stem cell (HSC) genes is still elusive. Here, we obtained novel insights into RUNX1 function by studying regulation of the human CD34 gene, which is expressed in HSCs. Using transgenic mice carrying human CD34 PAC constructs, we identified a novel downstream regulatory element (DRE), which is bound by RUNX1 and is necessary for human CD34 expression in long‐term (LT)‐HSCs. Conditional deletion of Runx1 in mice harbouring human CD34 promoter–DRE constructs abrogates human CD34 expression. We demonstrate by chromosome conformation capture assays in LT‐HSCs that the DRE physically interacts with the human CD34 promoter. Targeted mutagenesis of RUNX binding sites leads to perturbation of this interaction and decreased human CD34 expression in LT‐HSCs. Overall, our in vivo data provide novel evidence about the role of RUNX1 in mediating interactions between distal and proximal elements of the HSC gene CD34 . This study reveals molecular details of RUNX1 function in haematopoiesis. Employing various in vivo genetic models and chromatin conformation capture (3C) assays in HSCs, RUNX1 is shown to regulate CD34 expression by looping of a newly characterized distal regulatory element to the core promoter.

T cells develop in the thymus and are critical for adaptive immunity.

Doc number: P50

Doc number: P59

Recent lineage tracing single-cell techniques (LT-scSeq), e.g., the Lineage And RNA RecoverY (LARRY) barcoding system, have enabled clonally resolved interpretation of differentiation trajectories. However, the heterogeneity of clone-specific kinetics remains understudied, both quantitatively and in terms of interpretability, thus limiting the power of bar-coding systems to unravel how heterogeneous stem cell clones drive overall cell population dynamics. Here, we present CLADES, a NeuralODE-based framework to faithfully estimate clone-specific kinetics of cell states from newly generated and publicly available human cord blood LARRY LT-scSeq data. By incorporating a stochastic simulation algorithm (SSA) and differential expression gene (DEGs) analysis, CLADES yields cell division dynamics across differentiation timecourses and fate bias predictions for the early progenitor cells. Moreover, clone-level quantitative behaviours can be grouped into characteristic types by pooling individual clones into meta-clones. By benchmarking with CoSpar, we found that CLADES improves fate bias prediction accuracy at the meta-clone level. In conclusion, we report a broadly applicable approach to robustly quantify differentiation kinetics using meta-clones while providing valuable insights into the fate bias of cellular populations for any organ system maintained by a pool of heterogeneous stem and progenitor cells.