TGF-beta2 allows pluripotent human embryonic stem cell proliferation on E6/E7 immortalized mouse embryonic fibroblasts

Initial WNT/β-Catenin Activation Enhanced Mesoderm Commitment, Extracellular Matrix Expression, Cell Aggregation and Cartilage Tissue Yield From Induced Pluripotent Stem Cells

Mesodermal differentiation of induced pluripotent stem cells (iPSCs) in vitro and subsequent specification into mesodermal derivatives like chondrocytes is currently afflicted with a substantial cell loss that severely limits tissue yield. More knowledge on the key players regulating mesodermal differentiation of iPSCs is currently needed to drive all cells into the desired lineage and to overcome the current need for intermediate cell selection steps to remove misdifferentiated cells. Using two independent human iPSC lines, we here report that a short initial WNT/β-catenin pulse induced by the small molecule CHIR99021 (24 h) enhanced expression of mesodermal markers (PDGFRα, HAND1, KDR, and GATA4), supported the exit from pluripotency (decreased OCT4, SOX2, and LIN28A) and inhibited ectodermal misdifferentiation (reduced PAX6, TUBB3, and NES). Importantly, the initial CHIR pulse increased cell proliferation until day 14 (five-fold), adjusted expression of adhesion-related genes (CDH3 up, CDH6 down) and increased extracellular matrix (ECM)-related gene expression (COL6, COL1, COL3, COL5, DCN, NPNT, LUM, MGP, MATN2, and VTN), thus yielding more matrix-interacting progenitors with a high aggregation capability. Enhanced contribution to chondrogenic pellet formation increased the cell yield after eight weeks 200-fold compared to controls. The collagen type II and proteoglycan-positive area was enlarged in the CHIR group, indicating an increased number of cartilage-forming cells. Conclusively, short initial WNT activation improved mesoderm commitment and our data demonstrated for the first time to our knowledge that, acting via stimulation of cell proliferation, ECM expression and cell aggregation, WNT pulsing is a key step to make cell selection steps before chondrogenesis obsolete. This advanced understanding of the WNT/β-catenin function is a major step toward robust and efficient generation of high-quality mesodermal progenitors from human iPSCs and toward rescuing low tissue yield during subsequent in vitro chondrogenesis, which is highly desired for clinical cartilage regeneration, disease modeling and drug screening.

The transcriptional regulator ZNF398 mediates pluripotency and epithelial character downstream of TGF-beta in human PSCs

Human pluripotent stem cells (hPSCs) have the capacity to give rise to all differentiated cells of the adult. TGF-beta is used routinely for expansion of conventional hPSCs as flat epithelial colonies expressing the transcription factors POU5F1/OCT4, NANOG, SOX2. Here we report a global analysis of the transcriptional programme controlled by TGF-beta followed by an unbiased gain-of-function screening in multiple hPSC lines to identify factors mediating TGF-beta activity. We identify a quartet of transcriptional regulators promoting hPSC self-renewal including ZNF398, a human-specific mediator of pluripotency and epithelial character in hPSCs. Mechanistically, ZNF398 binds active promoters and enhancers together with SMAD3 and the histone acetyltransferase EP300, enabling transcription of TGF-beta targets. In the context of somatic cell reprogramming, inhibition of ZNF398 abolishes activation of pluripotency and epithelial genes and colony formation. Our findings have clear implications for the generation of bona fide hPSCs for regenerative medicine.

Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing

Alternative splicing is facilitated by accessory proteins that guide spliceosome subunits to the primary transcript. Many of these splicing factors recognize the RNA polymerase II tail, but SFPQ is a notable exception even though essential for mammalian RNA processing. This study reveals a novel role for Dido3, one of three Dido gene products, in alternative splicing. Binding of the Dido3 amino terminus to histones and to the polymerase jaw domain was previously reported, and here we show interaction between its carboxy terminus and SFPQ. We generated a mutant that eliminates Dido3 but preserves other Dido gene products, mimicking reduced Dido3 levels in myeloid neoplasms. Dido mutation suppressed SFPQ binding to RNA and increased skipping for a large group of exons. Exons bearing recognition sequences for alternative splicing factors were nonetheless included more efficiently. Reduced SFPQ recruitment may thus account for increased skipping of SFPQ-dependent exons, but could also generate a splicing factor surplus that becomes available to competing splice sites. Taken together, our data indicate that Dido3 is an adaptor that controls SFPQ utilization in RNA splicing. Distributing splicing factor recruitment over parallel pathways provides mammals with a simple mechanism to regulate exon usage while maintaining RNA splicing efficiency.

Isolation of female germline stem cells from porcine ovarian tissue and differentiation into oocyte-like cells

Historically, it had been widely accepted that the female mammalian ovary contained a limited number of oocytes that would reduce over time, without the possibility of replenishment. However, recent studies have suggested that female germline stem cells (FGSCs) could replenish the oocyte-pool in adults. The aim of this study was to isolate FGSCs from porcine ovaries and differentiate them into oocyte-like cells (OLCs). The FGSCs were successfully isolated from porcine ovarian tissue and cultured in vitro, in DMEM/F-12 medium supplemented with growth factors (EGF, FGF, GDNF, etc.) and a supplement (N21). These cells possessed spherical morphology and expressed specific germline characteristics (Vasa, Stella, Oct4, c-kit). By evaluating different conditions for in vitro differentiation of FGSCs, co-culturing the isolated FGSCs with MEF cells, under three-dimensional (3D) cell cultures, were shown to be optimal. FGSCs could successfully be differentiated into OLCs and reached about 70 µm in diameter, with a large number of surrounding somatic cells. Importantly, OLCs contained large nuclei, about 25–30 µm, with filamentous chromatin, similar to oocyte morphology, and expressed oocyte-specific markers (Gdf9, Zp2, SCP3, etc.) at the same level as oocytes. In conclusion, we successfully isolated FGSCs from porcine ovarian tissue and differentiated them into oocyte-like cells. This will provide a valuable model for studying a new, alternative source of oocytes.

Differential Proliferation Effects after Short-Term Cultivation of Mouse Spermatogonial Stem Cells on Different Feeder Layers

Objective

Spermatogonial stem cells (SSCs) provide the cellular basis for sperm production transforming the male’s genetic information to the next generation. We aimed to examine the effect of different feeder layer on proliferation of SSCs.

Materials and Methods

In this experimental study, we compared the in vitro effects of the co-culture of mouse SSCs with mouse embryonic fibroblasts (MEFs), sandos inbred mice (SIM) embryo-derived thioguanine- and ouabain- resistant (STO) feeders, and neonate and adult testicular stroma cell (TSC) feeders on the efficiency of mouse SSC proliferation and colony formation. Cells were cultivated on top of MEFs, STO, and neonate and adult TSCs feeder layers for 30 days. The number and diameter of colonies and also the number of cells were evaluated during day 7, 15, 25, and 30 of culture. The mRNA expression of germ cells and somatic cells were analyzed.

Results

In our study, we observed a significant difference in the proliferation rates and colony size of SSCs among the groups, especially for MEFs (P<0.05). SSCs can proliferate on MEFS, but not on STO, neonate or adult TSCs. Using immunocytochemistry by KI67 the proliferative activities of SSC colonies on MEFs were confirmed. The results of Fluidigm real-time polymerase chain reaction (RT-PCR) showed a high expression of the germ cell genes the promyelocytic leukemia zinc finger protein (PLZF), deleted in azoospermia-like (DAZL), octamer-binding transcription factor 4 (OCT4), and DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 (DDX4 or VASA) in SSCs, and a low expression of these genes in the feeder layers. Furthermore, we observed a higher expression of vimentin and integrin-B1 in feeder layers than in SSCs (P<0.05).

Conclusion

Based on the optimal effect of MEFs for better colonization of SSCs, these feeder cells seem to be appropriate candidates for SSC cultures prior to transplantation. Therefore, it is suggested using these feeder cells for SSC cultivation.

Human embryonic stem cell cultivation: historical perspective and evolution of xeno-free culture systems

Human embryonic stem cells (hESC) have emerged as attractive candidates for cell-based therapies that are capable of restoring lost cell and tissue function. These unique cells are able to self-renew indefinitely and have the capacity to differentiate in to all three germ layers (ectoderm, endoderm and mesoderm). Harnessing the power of these pluripotent stem cells could potentially offer new therapeutic treatment options for a variety of medical conditions. Since the initial derivation of hESC lines in 1998, tremendous headway has been made in better understanding stem cell biology and culture requirements for maintenance of pluripotency. The approval of the first clinical trials of hESC cells for treatment of spinal cord injury and macular degeneration in 2010 marked the beginning of a new era in regenerative medicine. Yet it was clearly recognized that the clinical utility of hESC transplantation was still limited by several challenges. One of the most immediate issues has been the exposure of stem cells to animal pathogens, during hESC derivation and during in vitro propagation. Initial culture protocols used co-culture with inactivated mouse fibroblast feeder (MEF) or human feeder layers with fetal bovine serum or alternatively serum replacement proteins to support stem cell proliferation. Most hESC lines currently in use have been exposed to animal products, thus carrying the risk of xeno-transmitted infections and immune reaction. This mini review provides a historic perspective on human embryonic stem cell culture and the evolution of new culture models. We highlight the challenges and advances being made towards the development of xeno-free culture systems suitable for therapeutic applications.

Hypoxic culture maintains self-renewal and enhances embryoid body formation of human embryonic stem cells

Hypoxic environment is theoretically more physiological for the growth of human embryonic stem (hES) cells. It has been reported that hypoxic culture maintained better undifferentiation of hES cells, but the effects on differentiation are less well established. The hES cells were thus cultured and compared in hypoxia (2% oxygen [O2]) and normoxia (21% O2). The data showed that the undifferentiated state of hES cells was maintained more favorably in hypoxia during prolonged culture. Most tested genes belonging to FGF, TGF-beta/GMP, and Wnt signaling pathways were enriched in undifferentiated hES cells and downregulated upon differentiation, accompanied with differential expression of FGFR1, FGFR2, and FRAT2 between hypoxia and normoxia. Higher P-Smad2/3 level was identified in hypoxia, favoring the maintenance of hES cells in undifferentiation. Bisulfite sequencing showed similar imprinting status between different O2 tensions at H19 differentially methylated region (DMR) and KvDMR loci. Embryoid body formation was enhanced in hypoxia accompanied with suppressed Sox17, Desmin, Gata4, Brachyury, and Cdx2 expression. We concluded that hypoxia improved self-renewal of hES cells through modulation of major signaling pathways and was also more efficient for differentiation to embryoid bodies, though they might present with suppressed expression of some lineage-specific genes across all the three embryonic germ layers and trophectoderm.

A scalable approach for discovering conserved active subnetworks across species

Overlaying differential changes in gene expression on protein interaction networks has proven to be a useful approach to interpreting the cell's dynamic response to a changing environment. Despite successes in finding active subnetworks in the context of a single species, the idea of overlaying lists of differentially expressed genes on networks has not yet been extended to support the analysis of multiple species' interaction networks. To address this problem, we designed a scalable, cross-species network search algorithm, neXus (Network - cross(X)-species - Search), that discovers conserved, active subnetworks based on parallel differential expression studies in multiple species. Our approach leverages functional linkage networks, which provide more comprehensive coverage of functional relationships than physical interaction networks by combining heterogeneous types of genomic data. We applied our cross-species approach to identify conserved modules that are differentially active in stem cells relative to differentiated cells based on parallel gene expression studies and functional linkage networks from mouse and human. We find hundreds of conserved active subnetworks enriched for stem cell-associated functions such as cell cycle, DNA repair, and chromatin modification processes. Using a variation of this approach, we also find a number of species-specific networks, which likely reflect mechanisms of stem cell function that have diverged between mouse and human. We assess the statistical significance of the subnetworks by comparing them with subnetworks discovered on random permutations of the differential expression data. We also describe several case examples that illustrate the utility of comparative analysis of active subnetworks.

Microarrays are a powerful tool for discovering genes whose expression is associated with a particular biological process or phenotype. Differential expression analysis can often generate a list of several hundred or even thousands of significant genes. While these genes represent real expression differences, the large number of candidates can make the process of hypothesis generation for further experimental studies challenging. Use of complementary datasets such as protein-protein interactions can help filter such candidate lists to genes involved with the most relevant pathways. This approach has been applied successfully by many groups, but to date, no one has developed an approach for discovering active pathways or subnetworks that are conserved across multiple species. We propose an algorithm, neXus (Network – cross(X)-species – Search), for cross-species active subnetwork discovery given candidate gene lists from two species and weighted protein-protein interaction networks. We validate our approach on expression studies from human and mouse stem cells. We find many active subnetworks that are conserved across species relevant to stem cell biology as well as other subnetworks that show species-specific behavior. We show that these networks are not likely to have been discovered by chance and discuss several specific cases that reveal potentially novel stem cell biology.

Wip1-expressing feeder cells retain pluripotency of co-cultured mouse embryonic stem cells under leukemia inhibitory factor-deprivated condition

The optimization of in vitro culture conditions for embryonic stem cells (ESCs) is a matter of critical importance; a prompt supply of a sufficient population of cells that retain their pluripotency capabilities must be secured in order to make possible future cell therapies. Despite a number of reports asserting that a variety of cytokines, signaling ligands, and small molecules can help in maintaining the pluripotency of ESCs, mammalian feeder cells continue to be broadly accepted as the method of choice for ESC cultures. This appears to be because mammalian feeder cells seem to produce some as-yet-unidentified factor that makes them very effective as feeder cells. In this study, we investigated wild-type p53 inducible phosphatase (Wip1), the knockdown of which increases Wnt inhibitory factor-1 expression, in its feeder functions toward mouse embryonic stem cells, lowering the effect of Wnt, one of key signaling in maintaining stemness of ESCs. For this purpose, Wip1 was stably expressed in mouse embryonic fibroblast cell line (STO) using retro-viral gene delivery system and then the function as a feeder cell was monitored either with or without leukemia inhibitory factor (LIF) in culture medium. We demonstrated that mouse embryonic stem cells grown with Wip1 expressing STO showed higher alkaline phosphatase activity and sustained Oct-4 expression level even under LIF deprivation condition compared to both control and Wip1 phosphatase activity dead mutant expressing STO. These results imply that Wip1 phosphatase activity in feeder cells is important to retain pluripotency of mouse embryonic stem cells under LIF deprivation conditions. These results indicate that genetically engineered feeder cells such as Wip1 expressing cell lines, are alternative strategy for the optimization of maintenance and expansion of mouse embryonic stem cells.

Analysis of the factors that limit the ability of feeder cells to maintain the undifferentiated state of human embryonic stem cells

Human embryonic stem cell (hESC) culture is routinely performed using inactivated mouse embryonic fibroblasts (MEFs) as a feeder cell layer (FL). Although these cells maintain pluripotency of hESCs, the molecular basis for this is unknown. Objectives of this study were to determine whether timing between MEF inactivation and their use as a FL influenced hESC growth and differentiation, and to begin defining the mechanism(s) involved. hESCs were plated on MEFs prepared 1 (MEF-1), 4 (MEF-4), and 7 (MEF-7) days earlier. hESC colony morphology and Oct3/4 expression levels were evaluated to determine the influence of different FLs. Significant enhancement of hESC growth (self-renewal) was observed on MEF-1 compared with MEF-4 and/or MEF-7. Conditioned media (CM) collected from MEF-1 supported significantly better hESC growth in a FL-free system compared to MEF-7 CM. Effects of MEFs on hESC growth were not caused by differences in cell density or viability, although indications of apoptosis were observed in MEF-7. Scanning electron microscopy demonstrated that MEF-7 were morphologically distinct from MEF-1 and MEF-4. Microarray analysis identified 19 genes related to apoptosis with significantly different levels of expression between MEF-1 and MEF-7. Several differentially expressed RNAs had gene ontology classifications associated with extracellular matrix (ECM) structural constituents and growth factors. Because members of Wnt signaling pathway were identified in the array analysis, we examined the ability of the Wnt1 CM and secreted frizzled-related proteins to affect hESC growth and differentiation. The addition of Wnt1 CM to both MEF-1 and MEF-7 significantly increased the number of undifferentiated colonies, while the addition of Sfrps promoted differentiation. Together, these results suggest that microenvironment, ECM, and soluble factors expressed by MEF-1 are significantly better at maintaining self-renewal and pluripotency of hESCs. Our findings have important implications in the optimization of hESC culture when MEFs are used as FL or CM is used in FL-free culture.

Functional response to SDF1 alpha through over-expression of CXCR4 on adult subventricular zone progenitor cells

The chemokine receptor CXCR4 and its ligand, stromal cell derived factor-1 alpha (SDF1 alpha) regulate neuroblast migration towards the ischemic boundary after stroke. Using loss- and gain-function, we investigated the biological effect of CXCR4/SDF1 alpha on neural progenitor cells. Neural progenitor cells, from the subventricular zone (SVZ) of the adult rat, were transfected with rat CXCR4-pLEGFP-C1 and pSIREN-RetroQ-CXCR4-siRNA retroviral vectors. Migration assay analysis showed that inhibition of CXCR4 by siRNA significantly reduced cell migration compared to the empty vector, indicating that CXCR4 mediated neural progenitor cell motility. When neural progenitor cells were cultured in growth medium containing bFGF (20 ng/ml), over-expression of CXCR4 significantly reduced the cell proliferation as measured by the number of bromodeoxyuridine+ (BrdU+) cells (26.4%) compared with the number in the control group (54.0%). Addition of a high concentration of SDF1 alpha (500 ng/ml) into the progenitor cells with over-expression of CXCR4 reversed the cell proliferation back to the control levels (57.6%). Immunostaining analysis showed that neither over-expression nor inhibition of CXCR4 altered the population of neurons and astrocytes, when neural progenitor cells were cultured in differentiation medium. These in vitro results suggest that CXCR4/SDF1 alpha primarily regulates adult neural progenitor cell motility but not differentiation, while over-expression of CXCR4 in the absence of SDF1 alpha decreases neural progenitor cell proliferation.