RNA polymerase III transcription as a disease factor.

RNA polymerase (Pol) III is responsible for transcription of different noncoding genes in eukaryotic cells, whose RNA products have well-defined functions in translation and other biological processes for some, and functions that remain to be defined for others. For all of them, however, new functions are being described. For example, Pol III products have been reported to regulate certain proteins such as protein kinase R (PKR) by direct association, to constitute the source of very short RNAs with regulatory roles in gene expression, or to control microRNA levels by sequestration. Consistent with these many functions, deregulation of Pol III transcribed genes is associated with a large variety of human disorders. Here we review different human diseases that have been linked to defects in the Pol III transcription apparatus or to Pol III products imbalance and discuss the possible underlying mechanisms.

Transcriptional interference by RNA polymerase III affects expression of the Polr3e gene.

Overlapping gene arrangements can potentially contribute to gene expression regulation. A mammalian interspersed repeat (MIR) nested in antisense orientation within the first intron of the Polr3e gene, encoding an RNA polymerase III (Pol III) subunit, is conserved in mammals and highly occupied by Pol III. Using a fluorescence assay, CRISPR/Cas9-mediated deletion of the MIR in mouse embryonic stem cells, and chromatin immunoprecipitation assays, we show that the MIR affects Polr3e expression through transcriptional interference. Our study reveals a mechanism by which a Pol II gene can be regulated at the transcription elongation level by transcription of an embedded antisense Pol III gene.

Differential regulation of RNA polymerase III genes during liver regeneration.

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcription. Our results broadly define a class of genes close to H3K4me3 and Pol II peaks, whose Pol III occupancy is high and stable, and another class, distant from Pol II peaks, whose Pol III occupancy strongly increases after partial hepatectomy. Pol III regulation in the liver thus entails both highly expressed housekeeping genes and genes whose expression can adapt to increased demand.

Cell Immortality: In Vitro Effective Techniques to Achieve and Investigate Its Applications and Challenges.

Cells are very important to researchers due to their use in various biological studies in in vitro and in vivo settings. This importance stems from the short lifespan of most cells under laboratory conditions, which can pose significant challenges, such as the difficulties associated with extraction from the source tissue, ethical concerns about separating cells from human or animal models, limited cell passage ability, and variation in results due to differences in the source of the obtained cells, among other issues. In general, cells in laboratory conditions can divide into a limited number, known as the Hayflick limit, due to telomere erosion at the end of each cellular cycle. Given this problem, researchers require cell lines that do not enter the senescence phase after a limited number of divisions. This can allow for more stable studies over time, prevent the laborious work associated with cell separation and repeated cultivation, and save time and money in research projects. The aim of this review is to summarize the function and effect of immortalization techniques, various methods, their advantages and disadvantages, and ultimately the application of immortalization and cell line production in various research fields.

RNA-binding protein Rbm47 binds to Nanog in mouse embryonic stem cells.

Embryonic stem cells (ES cells) are pluripotent cells capable for self-renewal and to differentiate to all cell types. Finding the molecular mechanisms responsible for these unique characteristics of ES cells is important. RNA-binding proteins play important roles in post-transcriptional gene regulation by binding to specific mRNA targets. In this study, we investigated the targets of RNA-binding protein Rbm47 in mouse ES cells. Overexpression of HA epitope-tagged Rbm47 in mouse ES cells followed by RNA-binding protein immunoprecipitation, and then RT-PCR analysis of co-immunoprecipitated RNA showed that Rbm47 binds to Nanog transcript in mouse ES cells and doesn't bind to Sox2 and Oct4 transcripts in these cells. This finding can give rise to reveal molecular mechanisms underlying pluripotency and stemness of ES cells and will be necessary for efficient application of these cells in regenerative medicine and tissue engineering.

Cryopreserved clinical-grade human embryonic stem cell-derived dopaminergic progenitors function in Parkinson's disease models.

AIM: Parkinson's Disease (PD) is a common age-related neurodegenerative disorder with a rising prevalence. Human pluripotent stem cells have emerged as the most promising source of cells for midbrain dopaminergic (mDA) neuron replacement in PD. This study aimed to generate transplantable mDA progenitors for treatment of PD. MATERIALS AND METHODS: Here, we optimized and fine-tuned a differentiation protocol using a combination of small molecules and growth factors to induce mDA progenitors to comply with good manufacturing practice (GMP) guidelines based on our clinical-grade human embryonic stem cell (hESC) line. KEY FINDINGS: The resulting mDA progenitors demonstrated robust differentiation and functional properties in vitro. Moreover, cryopreserved mDA progenitors were transplanted into 6-hydroxydopamine-lesioned rats, leading to functional recovery. SIGNIFICANCE: We demonstrate that our optimized protocol using a clinical hESC line is suitable for generating clinical-grade mDA progenitors and provides the ground work for future translational applications.

A facile method to generate cerebral organoids from human pluripotent stem cells.

Human cerebral organoids (COs) are self-organizing three-dimensional (3D) neural structures that provide a human-specific platform to study the cellular and molecular processes that underlie different neurological events. The first step of CO generation from human pluripotent stem cells (hPSCs) is neural induction, which is an in vitro simulation of neural ectoderm development. Several signaling pathways cooperate during neural ectoderm development and in vitro differentiation of hPSCs toward neural cell lineages is also affected by them. In this study, we considered some of the known sources of these variable signaling cues arising from cell culture media components and sought to modulate their effects by applying a comprehensive combination of small molecules and growth factors for CO generation. Histological analysis demonstrated that these COs recapitulate the neural progenitor zone and early cortical layer organization, containing different types of neuronal and glial cells which was in accordance with single-nucleus transcriptome profiling results. Moreover, patch clamp and intracellular Ca2+ dynamic studies demonstrated that the COs behave as a functional neural network. Thus, this method serves as a facile protocol for generating hPSC-derived COs that faithfully mimic the features of their in vivo counterparts in the developing human brain. See also Figure 1(Fig. 1).

Correction to: Efficient Differentiation of Human Embryonic Stem Cells Toward Dopaminergic Neurons Using Recombinant LMX1A Factor.

The original version of this article was published without article note. The article note is given below.

Efficient differentiation of human embryonic stem cells toward dopaminergic neurons using recombinant LMX1A factor.

Direct differentiation of dopaminergic (DA) neurons from human pluripotent stem cells (hPSCs) in the absence of gene manipulation is the most desired alternative to clinical treatment of Parkinson disease. Protein transduction-based methods could be efficient, safe approaches to enhance direct differentiation of human embryonic stem cells (hESCs) to DA neurons. In the present study, we compared the differentiation efficiency of DA neurons from hESCs with and without the application of LIM homeobox transcription factor 1 alpha (LMX1A), a master regulatory protein in the development of the midbrain neurons and SHH proteins. The results obtained revealed that the treatment of hESCs with recombinant LMX1A (rLMX1A) protein along with dual SMAD inhibition led to higher expression of LMX1B, LMX1A, FOXA2, PITX3, EN1, and WNT1 effector endogenous genes and two-fold expression of PITX3. Moreover, the highest expression level of PITX3 and TH was observed when rLMX1A was added to the induction medium supplemented with SHH. To our best knowledge, this is the first report demonstrating the application of TAT-LMX1A recombinant protein to enhance hESC differentiation to DA as shown by the expression of DA specific makers. These findings pave the way for enhancing the differentiation of hESCs to DA neurons safely and efficiently without genetic modification.

ISL1 protein transduction promotes cardiomyocyte differentiation from human embryonic stem cells.

BACKGROUND: Human embryonic stem cells (hESCs) have the potential to provide an unlimited source of cardiomyocytes, which are invaluable resources for drug or toxicology screening, medical research, and cell therapy. Currently a number of obstacles exist such as the insufficient efficiency of differentiation protocols, which should be overcome before hESC-derived cardiomyocytes can be used for clinical applications. Although the differentiation efficiency can be improved by the genetic manipulation of hESCs to over-express cardiac-specific transcription factors, these differentiated cells are not safe enough to be applied in cell therapy. Protein transduction has been demonstrated as an alternative approach for increasing the efficiency of hESCs differentiation toward cardiomyocytes. METHODS: We present an efficient protocol for the differentiation of hESCs in suspension by direct introduction of a LIM homeodomain transcription factor, Islet1 (ISL1) recombinant protein into the cells. RESULTS: We found that the highest beating clusters were derived by continuous treatment of hESCs with 40 µg/ml recombinant ISL1 protein during days 1-8 after the initiation of differentiation. The treatment resulted in up to a 3-fold increase in the number of beating areas. In addition, the number of cells that expressed cardiac specific markers (cTnT, CONNEXIN 43, ACTININ, and GATA4) doubled. This protocol was also reproducible for another hESC line. CONCLUSIONS: This study has presented a new, efficient, and reproducible procedure for cardiomyocytes differentiation. Our results will pave the way for scaled up and controlled differentiation of hESCs to be used for biomedical applications in a bioreactor culture system.