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BACKGROUND: MicroRNAs are required for maintenance of pluripotency as well as differentiation,but since more microRNAs have been computationally predicted in genome than have been found,there are likely to be undiscovered microRNAs expressed early in stem cell differentiation. METHODOLOGY/PRINCIPAL FINDINGS: SOLiD ultra-deep sequencing identified textgreater10(7) unique small RNAs from human embryonic stem cells (hESC) and neural-restricted precursors that were fit to a model of microRNA biogenesis to computationally predict 818 new microRNA genes. These predicted genomic loci are associated with chromatin patterns of modified histones that are predictive of regulated gene expression. 146 of the predicted microRNAs were enriched in Ago2-containing complexes along with 609 known microRNAs,demonstrating association with a functional RISC complex. This Ago2 IP-selected subset was consistently expressed in four independent hESC lines and exhibited complex patterns of regulation over development similar to previously-known microRNAs,including pluripotency-specific expression in both hESC and iPS cells. More than 30% of the Ago2 IP-enriched predicted microRNAs are new members of existing families since they share seed sequences with known microRNAs. CONCLUSIONS/SIGNIFICANCE: Extending the classic definition of microRNAs,this large number of new microRNA genes,the majority of which are less conserved than their canonical counterparts,likely represent evolutionarily recent regulators of early differentiation. The enrichment in Ago2 containing complexes,the presence of chromatin marks indicative of regulated gene expression,and differential expression over development all support the identification of 146 new microRNAs active during early hESC differentiation. View Publication

BACKGROUND Pluripotency,the property of a cell to differentiate into all cellular types of a given organism,is central to the development of stem cell-based therapies and regenerative medicine. Stem cell pluripotency is the result of the orchestrated activation of a complex transcriptional network characterized by the expression of a set of transcription factors including the master regulators of pluripotency Nanog and Oct4. Recently,it has been shown that pluripotency can be induced in somatic cells by viral-mediated expression of the transcription factors Oct3/4,Sox2,Klf4,and c-Myc. RESULTS Here we show that 5-Aminoimidazole-4-carboxamide-1-b-riboside (AICAR) is able to activate the molecular circuitry of pluripotency in mouse embryonic stem cells (mESC) and maintain Nanog and Oct4 expression in mESC exposed to the differentiating agent retinoic acid. We also show that AICAR is able to induce Klf4,Klf2 and Myc expression in both mESC and murine fibroblasts. CONCLUSION AICAR is able to activate the molecular circuitry of pluripotency in mESC and to induce the expression of several key regulators of pluripotency in somatic cells. AICAR is therefore a useful pharmacological entity for studying small molecule mediated induction of pluripotency. View Publication

Neural stem cell differentiation and the determination of lineage decision between neuronal and glial fates have important implications in the study of developmental,pathological,and regenerative processes. Although small molecule chemicals with the ability to control neural stem cell fate are considered extremely useful tools in this field,few were reported. AICAR is an adenosine analog and extensively used to activate AMP-activated protein kinase (AMPK),a metabolic fuel gauge" of the biological system. In the present study� View Publication

BACKGROUND/AIMS [corrected] Embryonic stem cells (ES cells) have the capacity to propagate indefinitely,maintain pluripotency,and differentiate into any cell type under defined conditions. As a result,they are considered to be the best model system for research into early embryonic development. AICA ribonucleotide (AICAR) is an activator of AMP-activated protein kinase (AMPK) that is thought to affect ES cell function,but its role in ES cell fate decision is unclear. METHODS In this study,we performed microarray analysis to investigate AICAR downstream targets and further understand its effect on ES cells. RESULTS Our microarray data demonstrated that AICAR can significantly up-regulate pluripotency-associated genes and down-regulate differentiation-associated transcription factors. Although AICAR cannot maintain ES cell identity without LIF,it can antagonize the action of RA-induced differentiation. Using those differentially expressed genes identified,we performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis with the Database for Annotation,Visualization and Integrated Discovery (DAVID) online system. AICAR was not only shown to influence the AMPK pathway,but also act on other signaling pathways such as BMP,MAPK and TGF-β,to maintain the stemness of J1 ES cells. Furthermore,AICAR modulated ES cell epigenetic modification by altering the expression of epigenetic-associated proteins,including Dnmt3a,Dnmt3b,Smarca2,Mbd3,and Arid1a,or through regulating the transcription of long intervening non-coding RNA (lincRNA). CONCLUSION Taken together,our work suggests that AICAR is capable of maintaining ES cell self-renewal and pluripotency,which could be useful in future medical treatment. View Publication

The chemical approach to controlling stem cell fates is emerging as a powerful tool,holding great promise in tissue engineering and regenerative medicine. Various small molecules have been demonstrated capable of modulating stem cell differentiation. In this paper,we studied the effects of 5-aminoimidazole-4-carboxamide-1-ß-riboside (AICAR),an activator of AMP-activated protein kinase (AMPK),on mesenchymal stem cells (MSCs). AICAR at high concentrations (1.0-2.0 mM) significantly inhibited proliferation of both human amnion-derived MSCs (hAMSCs) and rabbit bone marrow-derived MSCs (BM-MSCs). Most importantly,AICAR efficiently promoted the osteogenic differentiation of hAMSCs and BM-MSCs in both growth medium and osteogenic medium. However,Metformin,another AMPK activator,showed no such effects. Meanwhile,AICAR significantly inhibited adipogenic differentiation of hAMSCs and BM-MSCs. Our data suggests that AICAR represents a potent molecule,which can be applied in bone tissue regeneration. View Publication

Human-induced airway basal cells (hiBCs) derived from human-induced pluripotent stem cells (hiPSCs) offer a promising cell model for studying lung diseases,regenerative medicine,and developing new gene therapy methods. We analyzed existing differentiation protocols and proposed our own protocol for obtaining hiBCs,which involves step-by-step differentiation of hiPSCs into definitive endoderm,anterior foregut endoderm,NKX2.1+ lung progenitors,and cultivation on basal cell medium with subsequent cell sorting using the surface marker CD271 (NGFR). We derived hiBCs from two healthy cell lines and three cell lines with cystic fibrosis (CF). The obtained hiBCs,expressing basal cell markers (NGFR,KRT5,and TP63),could differentiate into lung organoids (LOs). We demonstrated that LOs derived from hiBCs can assess cystic fibrosis transmembrane conductance regulator (CFTR) channel function using the forskolin-induced swelling (FIS) assay. We also carried out non-viral (electroporation) and viral (recombinant adeno-associated virus (rAAV)) serotypes 6 and 9 and recombinant adenovirus (rAdV) serotype 5 transgene delivery to hiBCs and showed that rAAV serotype 6 is most effective against hiBCs,potentially applicable for gene therapy research. View Publication

Chronic obstructive pulmonary disease (COPD) is a highly prevalent,chronic inflammatory lung disease with limited existing therapeutic options. While modulation of peroxisome proliferator-activating receptor (PPAR)-$$ activity can modify inflammatory responses in several models of lung injury,the relevance of the PPARG pathway in COPD pathogenesis has not been previously explored. Mice lacking Pparg specifically in airway epithelial cells displayed increased susceptibility to chronic cigarette smoke (CS)-induced emphysema,with excessive macrophage accumulation associated with increased expression of chemokines,Ccl5,Cxcl10,and Cxcl15. Conversely,treatment of mice with a pharmacological PPAR$$ activator attenuated Cxcl10 and Cxcl15 expression and macrophage accumulation in response to CS. In vitro,CS increased lung epithelial cell chemokine expression in a PPAR$$ activation-dependent fashion. The ability of PPAR$$ to regulate CS-induced chemokine expression in vitro was not specifically associated with peroxisome proliferator response element (PPRE)-mediated transactivation activity but was correlated with PPAR$$-mediated transrepression of NF-$$B activity. Pharmacological or genetic activation of PPAR$$ activity abrogated CS-dependent induction of NF-$$B activity. Regulation of NF-$$B activity involved direct PPAR$$-NF-$$B interaction and PPAR$$-mediated effects on IKK activation,I$$B$$ degradation,and nuclear translocation of p65. Our data indicate that PPARG represents a disease-relevant pathophysiological and pharmacological target in COPD. Its activation state likely contributes to NF-$$B-dependent,CS-induced chemokine-mediated regulation of inflammatory cell accumulation. View Publication

Alveolar macrophages (AMs) are functionally important innate cells involved in lung homeostasis and immunity and whose diversity in health and disease is a subject of intense investigations. Yet,it remains unclear to what extent conditions like smoking or chronic obstructive pulmonary disease (COPD) trigger changes in the AM compartment. Here,we aimed to explore heterogeneity of human AMs isolated from healthy nonsmokers,smokers without COPD,and smokers with COPD by analyzing BAL fluid cells by flow cytometry and bulk and single-cell RNA sequencing. We found that subpopulations of BAL fluid CD206+ macrophages could be distinguished based on their degree of autofluorescence in each subject analyzed. CD206+ autofluorescenthigh AMs were identified as classical,self-proliferative AM,whereas autofluorescentlow AMs were expressing both monocyte and classical AM-related genes,supportive of a monocytic origin. Of note,monocyte-derived autofluorescentlow AMs exhibited a functionally distinct immunoregulatory profile,including the ability to secrete the immunosuppressive cytokine IL-10. Interestingly,single-cell RNA-sequencing analyses showed that transcriptionally distinct clusters of classical and monocyte-derived AM were uniquely enriched in smokers with and without COPD as compared with healthy nonsmokers. Of note,such smoking-associated clusters exhibited gene signatures enriched in detoxification,oxidative stress,and proinflammatory responses. Our study independently confirms previous reports supporting that monocyte-derived macrophages coexist with classical AM in the airways of healthy subjects and patients with COPD and identifies smoking-associated changes in the AM compartment that may favor COPD initiation or progression. View Publication

Segmentation is required to quantify cellular structures in microscopic images. This typically requires their fluorescent labeling. Convolutional neural networks (CNNs) can detect these structures also in only transmitted light images. This eliminates the need for transgenic or dye fluorescent labeling,frees up imaging channels,reduces phototoxicity and speeds up imaging. However,this approach currently requires optimized experimental conditions and computational specialists. Here,we introduce “aiSEGcell” a user-friendly CNN-based software to segment nuclei and cells in bright field images. We extensively evaluated it for nucleus segmentation in different primary cell types in 2D cultures from different imaging modalities in hand-curated published and novel imaging data sets. We provide this curated ground-truth data with 1.1 million nuclei in 20,000 images. aiSEGcell accurately segments nuclei from even challenging bright field images,very similar to manual segmentation. It retains biologically relevant information,e.g. for demanding quantification of noisy biosensors reporting signaling pathway activity dynamics. aiSEGcell is readily adaptable to new use cases with only 32 images required for retraining. aiSEGcell is accessible through both a command line,and a napari graphical user interface. It is agnostic to computational environments and does not require user expert coding experience. Author summaryFluorescence microscopy is the most widely used method to monitor cellular structures in space and time. Fluorescently labeling cellular structures is typically required to localize (“segment”) them in electronic images for subsequent quantification. Deep learning approaches can detect these structures also in only bright field images. This eliminates the need for a fluorescent label,frees up imaging channels,speeds up imaging,and reduces the harmful effects of exposing cells to high intensity light. However,label free segmentation currently requires optimized experimental conditions and computational specialists. Therefore,we developed “aiSEGcell” a user-friendly deep learning-based software to segment nuclei and cells in only bright field images. We extensively evaluated aiSEGcell on different common experimental conditions and showed that biologically even sensitive relevant information is retained. Furthermore,we demonstrated that aiSEGcell is adaptable by retraining to new applications with very little required data. We make it accessible for users with no required expert coding experience in a wide range of computational environments. Finally,we openly share our very large imaging data sets to further the development of other segmentation approaches. View Publication

Reticular dysgenesis (RD) is a rare genetic disorder caused by mutations in the adenylate kinase 2 ( AK2 ) gene. It is characterized by a T − B − severe combined immunodeficiency,agranulocytosis,and sensorineural deafness. We established and characterized a haematopoiesis‐specific conditional Ak2 ‐knockout mouse model to provide a model system to study the molecular pathophysiology of RD. As expected from the human phenotype of RD,haematopoiesis‐specific AK2‐deficient embryos had a small,atrophic thymus consisting mainly of epithelial cells. No recognizable T‐cell component was observed,but B‐cell lineage precursor cells were present in the foetal liver. The effects of AK2 deficiency on myelopoiesis were less severe in mice than in humans. The absolute numbers of monocytes,macrophages,granulocytes and megakaryocytes in foetal liver as well as colony‐forming precursors were not reduced. In contrast to humans,haematopoiesis‐specific Ak2 ‐knockout mice exhibit embryonic lethality between E13 and E15 due to severe anaemia caused by an early block in definitive erythropoiesis. Murine erythroid progenitors mainly express AK2 and only low levels of functionally related kinases,which are unable to compensate for AK2 deficiency,in contrast to human erythroid progenitors. View Publication