Differential miRNA and IncRNA expression in embryonic stem cells lacking the Notch1 receptor

Embryonic stem (ES) cells-derived cardiomyocytes represent an attractive source of cells in cell replacement therapies for heart disease. However, controlled cardiogenic differentiation of ES cells requires a complete understanding of the complex molecular mechanisms regulating the differentiation process. We have previously shown that differentiation of ES cells into cardiomyocytes is favored by inactivation of the Notch 1 receptor pathway. In the present study, we therefore compared two ES cell lines, one with normal Notchl expression and one carrying deleted Notchl receptor alleles (Notchl-deleted ES cells) in order to identify genes responsible for the increased propensity of Notchl-deleted ES cells to produce cardiomyocytes. Using RNA-sequencing, we found approximately 300 coding and noncoding transcripts, which are differently expressed in undifferentiated Notchl-deleted ES cells. Since accumulating evidences indicate that long noncoding RNAs (IncRNAs) play important roles in ES cell pluripotency and differentiation, we focused our analysis on modulated IncRNAs. In particular, two IncRNAs, named here lnc 1230 and lnc 1335, are highly induced in the absence of Notchl receptor expression. These represent therefore prime candidates that could favor cardiogenic commitment in undifferentiated ES cells. Indeed, we demonstrate that forced expression of these two IncRNAs in wild-type ES cells result in a significant increase of the number of cardiac progenitor cells and cardiomyocytes in the differentiated progeny of these ES cells. Furthermore, we also identify several microRNAs that are differentially modulated in absence of Notchl expression. Among these are miR-142-5p and miR- 381-3p. Interestingly, both lncl230 and lncl335 are targets of these two microRNAs. Altogether, these data suggest that Notchl-dependent noncoding gene networks, implicating microRNAs and IncRNAs, control embryonic stem cell commitment into the mesodermal and cardiac lineages already at the undifferentiated state. - Les cardiomyocytes issus cellules souches embryonnaires sont une source très prometteuse pour les thérapies cellulaire de remplacement dans le cadre des maladies cardiaques. Cependant, l'utilisation de telles cellules requiert une compréhension poussée des mécanismes moléculaire régulant la différenciation. Nous avons par le passé démontré que la différenciation des cellules souches embryonnaires en cardiomyocytes est favorisée par l'inactivation de la voie d'activation intracellulaire dépendante du récepteur Notch 1. Nous avons donc comparé deux lignées de cellules souches embryonnaires, une présentant une voie d'activation Notchl normale et une chez laquelle les allèles codant pour le récepteur Notchl avaient été invalidés, de façon à identifier les gènes impliqués dans la capacité augmentée des cellules déficientes à produire des cardiomyocytes. En utilisant du séquençage d'ARN à haut débit, nous avons trouvé environ 300 gènes différemment exprimés dans les cellules déficientes pour Notchl. Par ailleurs, des évidences de plus en plus nombreuses suggèrent qu'une nouvelle classe de molécules appelée « long noncoding RNAs » joue un rôle prépondérant dans la maintenance de l'état non différencié et de la capacité de différenciation des cellules souches embryonnaires. Nous avons trouvé que plusieurs « long noncoding RNAs » étaient modulés en l'absence de Notchl, et en particulier deux molécules que nous avons appelées lncl230 et lncl335. Ces derniers représentent des candidats potentiels devant permettre de favoriser la production de cardiomyocytes. Nous avons en effet démontré que la surexpression de ces deux candidats dans des cellules souches embryonnaires résultait en une surproduction de cardiomyocytes. De plus, nous avons également identifié plusieurs microRNAs dont l'expression était modulée dans les cellules souches embryonnaires déficientes dans la voie Notchl. De façon intéressante, parmi ces microRNAs, le miR-142-5p et le miR-381-3p sont capables de cibler lncl230 and lncl335. Dans l'ensemble, ces résultats indiquent donc que des réseaux d'interaction dépendant de la voie d'activation Notch 1 et impliquant des ARNs non codant existent dans les cellules souches embryonnaires pour réguler leur différenciation en différent types cellulaires spécifiques.

A PiggyBac-mediated approach for muscle gene transfer or cell therapy.

An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable gene expression when transferred to cultured mesoangioblasts and into murine muscles. Without selection, up to 8% of the mesoangioblasts expressed the transgene from 1 to 2 genomic copies of the piggyBac vector. Integration occurred mostly in intergenic genomic DNA and transgene expression was stable in vitro. Intramuscular transplantation of mouse Tibialis anterior muscles with mesoangioblasts containing the transposon led to sustained myofiber GFP expression in vivo. In contrast, the direct electroporation of the transposon-donor plasmids in the mouse Tibialis muscles in vivo did not lead to sustained transgene expression despite molecular evidence of piggyBac transposition in vivo. Together these findings provide a proof-of-principle that piggyBac transposon may be considered for mesoangioblast cell-based therapies of muscular dystrophies.

Ochratoxin A at nanomolar concentration perturbs the homeostasis of neural stem cells in highly differentiated but not in immature three-dimensional brain cell cultures.

Ochratoxin A (OTA), a fungal contaminant of basic food commodities, is known to be highly cytotoxic, but the pathways underlying adverse effects at subcytotoxic concentrations remain to be elucidated. Recent reports indicate that OTA affects cell cycle regulation. Therefore, 3D brain cell cultures were used to study OTA effects on mitotically active neural stem/progenitor cells, comparing highly differentiated cultures with their immature counterparts. Changes in the rate of DNA synthesis were related to early changes in the mRNA expression of neural stem/progenitor cell markers. OTA at 10nM, a concentration below the cytotoxic level, was ineffective in immature cultures, whereas in mature cultures it significantly decreased the rate of DNA synthesis together with the mRNA expression of key transcriptional regulators such as Sox2, Mash1, Hes5, and Gli1; the cell cycle activator cyclin D2; the phenotypic markers nestin, doublecortin, and PDGFRα. These effects were largely prevented by Sonic hedgehog (Shh) peptide (500ngml(-1)) administration, indicating that OTA impaired the Shh pathway and the Sox2 regulatory transcription factor critical for stem cell self-renewal. Similar adverse effects of OTA in vivo might perturb the regulation of stem cell proliferation in the adult brain and in other organs exhibiting homeostatic and/or regenerative cell proliferation.

Emerging paradigms and questions on pro-angiogenic bone marrow-derived myelomonocytic cells.

Cancer-related inflammation has emerged in recent years as a major event contributing to tumor angiogenesis, tumor progression and metastasis formation. Bone marrow-derived and inflammatory cells promote tumor angiogenesis by providing endothelial progenitor cells that differentiate into mature endothelial cells, and by secreting pro-angiogenic factors and remodeling the extracellular matrix to stimulate angiogenesis though paracrine mechanisms. Several bone marrow-derived myelonomocytic cells, including monocytes and macrophages, have been identified and characterized by several laboratories in recent years. While the central role of these cells in promoting tumor angiogenesis, tumor progression and metastasis is nowadays well established, many questions remain open and new ones are emerging. These include the relationship between their phenotype and function, the mechanisms of pro-angiogenic programming, their contribution to resistance to anti-angiogenic treatments and to metastasis and their potential clinical use as biomarkers of angiogenesis and anti-angiogenic therapies. Here, we will review phenotypical and functional aspects of bone marrow-derived myelonomocytic cells and discuss some of the current outstanding questions.

CD103 marks a subset of human CD34(+)-derived langerin(+) dendritic cells that induce T-regulatory cells via indoleamine 2,3-dioxygenase-1.

Indoleamine 2,3-dioxygenase 1 (IDO1) is an immunosuppressive molecule expressed in some subsets of normal and neoplastic cells. Mature human dendritic cells (DCs) have been shown to express IDO1, but little is known about its expression and function during DC differentiation from bone marrow hematopoietic stem/progenitor cells (HSPCs). Here, we show that during in vitro differentiation along the myeloid DC lineage, CD34(+) HSPCs acquire IDO1 expression, which acts in a tolerogenic manner by inducing a population of fully functional CD4(+)CD25(+) FOXP3(+) T-regulatory cells. Phenotypically, CD1a(+)CD14(-) HPSC-derived DCs expressed IDO1, langerin, CD11b, and CD1c. Cell-sorting experiments demonstrated that IDO1 expression is found in a subset of CD1a(+)CD14(-)langerin(+) cells, expressing CD103, which is capable of inducing T-regulatory cells in an IDO1-dependent manner. In conclusion, DC differentiation from CD34(+) HSPCs results in the expression of a functionally active IDO1 protein in CD1a(+)langerin(+), CD103-expressing DCs. These data point toward IDO1 expression as part of a tolerogenic signature during DC development.

Taurine increases hippocampal neurogenesis in aging mice.

Aging is associated with increased inflammation and reduced hippocampal neurogenesis, which may in turn contribute to cognitive impairment. Taurine is a free amino acid found in numerous diets, with anti-inflammatory properties. Although abundant in the young brain, the decrease in taurine concentration with age may underlie reduced neurogenesis. Here, we assessed the effect of taurine on hippocampal neurogenesis in middle-aged mice. We found that taurine increased cell proliferation in the dentate gyrus through the activation of quiescent stem cells, resulting in increased number of stem cells and intermediate neural progenitors. Taurine had a direct effect on stem/progenitor cells proliferation, as observed in vitro, and also reduced activated microglia. Furthermore, taurine increased the survival of newborn neurons, resulting in a net increase in adult neurogenesis. Together, these results show that taurine increases several steps of adult neurogenesis and support a beneficial role of taurine on hippocampal neurogenesis in the context of brain aging.

Exosomes for Intramyocardial Intercellular Communication.

Cross-talk between different cell types plays central roles both in cardiac homeostasis and in adaptive responses of the heart to stress. Cardiomyocytes (CMs) send biological messages to the other cell types present in the heart including endothelial cells (ECs) and fibroblasts. In turn, CMs receive messages from these cells. Recent evidence has now established that exosomes, nanosized secreted extracellular vesicles, are crucial mediators of such messages. CMs, ECs, cardiac fibroblasts, and cardiac progenitor cells (CPCs) release exosomes carrying nonrandom subsets of proteins, lipids, and nucleic acids present in their cells of origin. Exosomes secreted from CMs are internalized by fibroblasts and regulate gene expression in these cells as well as in ECs. CPC-derived exosomes protect CMs against apoptosis while also stimulating angiogenesis. They are rich in cardioprotective and proangiogenic microRNAs such as miR-146, miR-210, and miR-132. When injected into infracted hearts in vivo, CPC-derived exosomes reduce infarct size and improve cardiac function. Thus, exosomes are emerging both as key mediators of intercellular communication in the heart and as therapeutic candidates for heart disease.

Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease.

The key information processing units within gene regulatory networks are enhancers. Enhancer activity is associated with the production of tissue-specific noncoding RNAs, yet the existence of such transcripts during cardiac development has not been established. Using an integrated genomic approach, we demonstrate that fetal cardiac enhancers generate long noncoding RNAs (lncRNAs) during cardiac differentiation and morphogenesis. Enhancer expression correlates with the emergence of active enhancer chromatin states, the initiation of RNA polymerase II at enhancer loci and expression of target genes. Orthologous human sequences are also transcribed in fetal human hearts and cardiac progenitor cells. Through a systematic bioinformatic analysis, we identified and characterized, for the first time, a catalog of lncRNAs that are expressed during embryonic stem cell differentiation into cardiomyocytes and associated with active cardiac enhancer sequences. RNA-sequencing demonstrates that many of these transcripts are polyadenylated, multi-exonic long noncoding RNAs. Moreover, knockdown of two enhancer-associated lncRNAs resulted in the specific downregulation of their predicted target genes. Interestingly, the reactivation of the fetal gene program, a hallmark of the stress response in the adult heart, is accompanied by increased expression of fetal cardiac enhancer transcripts. Altogether, these findings demonstrate that the activity of cardiac enhancers and expression of their target genes are associated with the production of enhancer-derived lncRNAs.

Enhancement of human adipose-derived stem cell expansion and stability for clinical use

Co-culture techniques associating both dermal fibroblasts and epidermal keratinocytes have shown to have better clinical outcome than keratinocyte culture alone for the treatment of severe burns. Since fat grafting has been shown to improve scar remodelling, new techniques such as cell-therapy-assisted surgical reconstruction with isolated and expanded autologous adipose-derived stem cells (ASCs) would be of benefit to increase graft acceptation. Therefore, integrating ASCs into standardized procedures for cultured skin grafting could be of benefit for the patient if cell quality and quantity could be maintained. The purpose of this study was to evaluate ASC processing from adult tissue with simple isolation (without enzymatic steps), expansion (low density of 325-3,000 cells/cm2) and storage conditions to assure methods to enhance the cellular resistance when transferred back to the patient. Co-culture with cell-banked skin progenitor cells (FE002-SK2) showed an increase of 40-50% ASCs yield at high passages alongside with a better preservation of morphology, proper adipogenic and osteogenic differentiation and efficient biocompatibility with 3D collagen scaffolds. ASCs can be considered as a valuable additional cell source to be delivered in biological bandages to the patient in a need of tissue reconstruction such as burn patients.