Alternative polyadenylation (APA) is emerging as an important regulatory mechanism of RNA and protein isoform expression by controlling 3′ untranslated region (3′-UTR) composition. The relevance of ...APA in stem cell hierarchies remains elusive. Here, we first demonstrate the requirement of the APA regulator Pabpn1 for hematopoietic stem cell (HSC) function. We then determine the genome-wide APA landscape (APAome) of HSCs and progenitors by performing low-input 3′ sequencing paired with bioinformatic pipelines. This reveals transcriptome-wide dynamic APA patterns and an overall shortening of 3′-UTRs during differentiation and upon homeostatic or stress-induced transition from quiescence to proliferation. Specifically, we show that APA regulates activation-induced Glutaminase (Gls) isoform switching by Nudt21. This adaptation of the glutamine metabolism by increasing the GAC:KGA isoform ratio fuels versatile metabolic pathways necessary for HSC self-renewal and proper stress response. Our study establishes APA as a critical regulatory layer orchestrating HSC self-renewal, behavior, and commitment.
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•Alternative polyadenylation (APA) mediated by PABPN1 is required for HSC function•3′-seq reveals distinct genome-wide APA landscapes (APAomes) of HSCs and progenitors•Global 3′-UTR shortening occurs upon HSC activation and differentiation•NUDT21-mediated Glutaminase isoform switching promotes HSC metabolism upon stress
Using 3′ sequencing, we assessed genome-wide alternative polyadenylation (APA) landscapes (APAomes) of hematopoietic stem cells (HSCs) and progenitors and characterized changes in the APAome upon differentiation and HSC activation. Our data introduce APA as a novel regulatory layer controlling HSC self-renewal and differentiation by influencing stem cell activation and metabolism.
The occurrence of clonal hematopoiesis, caused by acquired somatic mutations of leukemia-associated genes in blood stem cells is very common in the population and increases with age. Besides an ...increased risk of developing myeloid neoplasms, an unexpected causal relationship between clonal hematopoiesis and cardiovascular diseases was recently discovered. Clonal hematopoiesis presents as a new independent and strong risk factor for cardiovascular diseases, such as atherosclerosis, coronary heart disease, heart failure, aortic valve stenosis and stroke, which from a medical perspective should no longer be ignored. Worldwide intensive research for associations of clonal hematopoiesis with other age-related and infectious diseases identifies increasingly more illnesses that are influenced by the presence of mutated blood cells. Current data describe a fatal vicious circle, initiated by somatic blood cell mutations, which accelerate the progression of associated diseases in a proinflammatory way and feed-back to hematopoiesis leading to a further enlargement of the mutated blood cell clone. First experimental treatment approaches to break this vicious circle are discussed here. The causal relationship and the underlying pathomechanisms are now at the center of research interest in order to rapidly establish risk stratification and therapeutic measures for the benefit of patients in the near future.
Abstract
Aims
Identification of signatures of immune cells at single-cell level may provide novel insights into changes of immune-related disorders. Therefore, we used single-cell RNA-sequencing to ...determine the impact of heart failure on circulating immune cells.
Methods and results
We demonstrate a significant change in monocyte to T-cell ratio in patients with heart failure, compared to healthy subjects, which were validated by flow cytometry analysis. Subclustering of monocytes and stratification of the clusters according to relative CD14 and FCGR3A (CD16) expression allowed annotation of classical, intermediate, and non-classical monocytes. Heart failure had a specific impact on the gene expression patterns in these subpopulations. Metabolically active genes such as FABP5 were highly enriched in classical monocytes of heart failure patients, whereas β-catenin expression was significantly higher in intermediate monocytes. The selective regulation of signatures in the monocyte subpopulations was validated by classical and multifactor dimensionality reduction flow cytometry analyses.
Conclusion
Together this study shows that circulating cells derived from patients with heart failure have altered phenotypes. These data provide a rich source for identification of signatures of immune cells in heart failure compared to healthy subjects. The observed increase in FABP5 and signatures of Wnt signalling may contribute to enhanced monocyte activation.
Graphical Abstract
Abstract
Genetic disruptions of the forkhead box transcription factor FOXP2 in humans cause an autosomal-dominant speech and language disorder. While FOXP2 expression pattern are highly conserved, ...its role in specific brain areas for mammalian social behaviors remains largely unknown. Here we studied mice carrying a homozygous cortical Foxp2 deletion. The postnatal development and gross morphological architecture of mutant mice was indistinguishable from wildtype (WT) littermates. Unbiased behavioral profiling of adult mice revealed abnormalities in approach behavior towards conspecifics as well as in the reciprocal responses of WT interaction partners. Furthermore mutant mice showed alterations in acoustical parameters of ultrasonic vocalizations, which also differed in function of the social context. Cell type-specific gene expression profiling of cortical pyramidal neurons revealed aberrant regulation of genes involved in social behavior. In particular Foxp2 mutants showed the downregulation of Mint2 (Apba2), a gene involved in approach behavior in mice and autism spectrum disorder in humans. Taken together these data demonstrate that cortical Foxp2 is required for normal social behaviors in mice.
The mechanisms underlying haematopoietic lineage decisions remain disputed. Lineage-affiliated transcription factors with the capacity for lineage reprogramming, positive auto-regulation and mutual ...inhibition have been described as being expressed in uncommitted cell populations. This led to the assumption that lineage choice is cell-intrinsically initiated and determined by stochastic switches of randomly fluctuating cross-antagonistic transcription factors. However, this hypothesis was developed on the basis of RNA expression data from snapshot and/or population-averaged analyses. Alternative models of lineage choice therefore cannot be excluded. Here we use novel reporter mouse lines and live imaging for continuous single-cell long-term quantification of the transcription factors GATA1 and PU.1 (also known as SPI1). We analyse individual haematopoietic stem cells throughout differentiation into megakaryocytic-erythroid and granulocytic-monocytic lineages. The observed expression dynamics are incompatible with the assumption that stochastic switching between PU.1 and GATA1 precedes and initiates megakaryocytic-erythroid versus granulocytic-monocytic lineage decision-making. Rather, our findings suggest that these transcription factors are only executing and reinforcing lineage choice once made. These results challenge the current prevailing model of early myeloid lineage choice.
Hematopoietic stem cells (HSCs) are the best studied adult stem cells with enormous clinical value. Most of our knowledge about their biology relies on assays at the single HSC level. However, only ...the recent advances in developing new single cell technologies allowed the elucidation of the complex regulation of HSC fate decision control. This Review will focus on current attempts to investigate individual HSCs at molecular and functional levels. The advantages of these technologies leading to groundbreaking insights into hematopoiesis will be highlighted, and the challenges facing these technologies will be discussed. The importance of combining molecular and functional assays to enlighten regulatory networks of HSC fate decision control, ideally at high temporal resolution, becomes apparent for future studies.
Hematopoietic stem cells (HSCs) mediate regeneration of the hematopoietic system following injury, such as following infection or inflammation. These challenges impair HSC function, but whether this ...functional impairment extends beyond the duration of inflammatory exposure is unknown. Unexpectedly, we observed an irreversible depletion of functional HSCs following challenge with inflammation or bacterial infection, with no evidence of any recovery up to 1 year afterward. HSCs from challenged mice demonstrated multiple cellular and molecular features of accelerated aging and developed clinically relevant blood and bone marrow phenotypes not normally observed in aged laboratory mice but commonly seen in elderly humans. In vivo HSC self-renewal divisions were absent or extremely rare during both challenge and recovery periods. The progressive, irreversible attrition of HSC function demonstrates that temporally discrete inflammatory events elicit a cumulative inhibitory effect on HSCs. This work positions early/mid-life inflammation as a mediator of lifelong defects in tissue maintenance and regeneration.
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•HSCs fail to recover functional potency after inflammatory/infection challenge•Discrete challenges have a cumulative effect, even if separated by weeks or months•Inflammation in early life accelerates the cellular and molecular aging of HSCs•Mice exposed to inflammation develop features of aged human hematopoiesis
Inflammation and infection acutely suppress HSC function. However, the long-term ramifications of such challenges are unclear. This study demonstrates that murine HSCs fail to recover functional potency up to 1 year post-inflammatory/infection challenge, meaning that such events can have accumulative effects over a lifetime; this promotes acquisition of the aged state.
The transcription factor Meis1 drives myeloid leukemogenesis in the context of Hox gene overexpression but is currently considered undruggable. We therefore investigated whether myeloid progenitor ...cells transformed by Hoxa9 and Meis1 become addicted to targetable signaling pathways. A comprehensive (phospho)proteomic analysis revealed that Meis1 increased Syk protein expression and activity. Syk upregulation occurs through a Meis1-dependent feedback loop. By dissecting this loop, we show that Syk is a direct target of miR-146a, whose expression is indirectly regulated by Meis1 through the transcription factor PU.1. In the context of Hoxa9 overexpression, Syk signaling induces Meis1, recapitulating several leukemogenic features of Hoxa9/Meis1-driven leukemia. Finally, Syk inhibition disrupts the identified regulatory loop, prolonging survival of mice with Hoxa9/Meis1-driven leukemia.
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•Meis1 regulates expression and activation of Syk in Hoxa9-driven leukemia•Syk upregulation in Hoxa9/Meis1-driven leukemia is mediated by miR-146a•Increased Syk activity induces a Meis1 transcriptional program•In vivo, Meis1 sensitizes Hoxa9-driven leukemia to Syk inhibition
Mohr et al. identify a Meis1-dependent regulatory loop involving PU.1, miR-146a, and Syk, resulting in the addiction to Syk activity in Hoxa9/Meis1-transformed myeloid progenitor cells. Syk inhibition disrupts the regulatory loop and prolongs survival of mice with Hoxa9/Meis1-driven acute myeloid leukemia.
Quaking RNA binding protein (QKI) is essential for oligodendrocyte development as myelination requires myelin basic protein mRNA regulation and localization by the cytoplasmic isoforms (e.g., QKI-6). ...QKI-6 is also highly expressed in astrocytes, which were recently demonstrated to have regulated mRNA localization. Here, we define the targets of QKI in the mouse brain via CLIPseq and we show that QKI-6 binds 3'UTRs of a subset of astrocytic mRNAs. Binding is also enriched near stop codons, mediated partially by QKI-binding motifs (QBMs), yet spreads to adjacent sequences. Using a viral approach for mosaic, astrocyte-specific gene mutation with simultaneous translating RNA sequencing (CRISPR-TRAPseq), we profile ribosome associated mRNA from QKI-null astrocytes in the mouse brain. This demonstrates a role for QKI in stabilizing CLIP-defined direct targets in astrocytes in vivo and further shows that QKI mutation disrupts the transcriptional changes for a discrete subset of genes associated with astrocyte maturation.
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