Mechanisms Of Cell Reprogramming Research Articles

Dynamics of cell-type transition mediated by epigenetic modifications

Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of the probability landscape to develop into distinct cell types. However, how adult stem cells achieve a delicate balance between self-renewal and differentiation remains unclear. We propose that random inheritance of epigenetic states plays a pivotal role in stem cell differentiation and present a hybrid model of stem cell differentiation induced by epigenetic modifications. Our comprehensive model integrates gene regulation networks, epigenetic state inheritance, and cell regeneration, encompassing multi-scale dynamics ranging from transcription regulation to cell population. Through model simulations, we demonstrate that random inheritance of epigenetic states during cell divisions can spontaneously induce cell differentiation, dedifferentiation, and transdifferentiation. Furthermore, we investigate the influences of interfering with epigenetic modifications and introducing additional transcription factors on the probabilities of dedifferentiation and transdifferentiation, revealing the underlying mechanism of cell reprogramming. This in silico model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming and offers a promising path to enhance the field of regenerative medicine.

Exogenous OCT4 and SOX2 Contribution to In Vitro Reprogramming in Cattle.

Mechanisms of cell reprogramming by pluripotency-related transcription factors or nuclear transfer seem to be mediated by similar pathways, and the study of the contribution of OCT4 and SOX2 in both processes may help elucidate the mechanisms responsible for pluripotency. Bovine fibroblasts expressing exogenous OCT4 or SOX2, or both, were analyzed regarding the expression of pluripotency factors and imprinted genes H19 and IGF2R, and used for in vitro reprogramming. The expression of the H19 gene was increased in the control sorted group, and putative iPSC-like cells were obtained when cells were not submitted to cell sorting. When sorted cells expressing OCT4, SOX2, or none (control) were used as donor cells for somatic cell nuclear transfer, fusion rates were 60.0% vs. 64.95% and 70.53% vs. 67.24% for SOX2 vs. control and OCT4 vs. control groups, respectively; cleavage rates were 66.66% vs. 81.68% and 86.47% vs. 85.18%, respectively; blastocyst rates were 33.05% vs. 44.15% and 52.06% vs. 44.78%, respectively. These results show that the production of embryos by NT resulted in similar rates of in vitro developmental competence compared to control cells regardless of different profiles of pluripotency-related gene expression presented by donor cells; however, induced reprogramming was compromised after cell sorting.

Long noncoding RNAs in induced pluripotent stem cells and their differentiation.

The breakthrough technology for reprogramming somatic cells into induced pluripotent stem cells (iPSCs) has created a new path for science and medicine. The iPSC technology provides a powerful tool for elucidating the mechanisms of cellular differentiation and cell fate decision as well as to study targets and pathways relevant to pathological processes. As they can be generated from any person, iPSCs are a promising resource for regenerative medicine potentiating the possibility to discover new drugs in a high-throughput screening format and treat diseases through personalized cell therapy-based strategies. However, the reprogramming process is complex, and its regulation needs fine tuning. The regulatory mechanisms of cell reprogramming and differentiation are still not elucidated, but significant results show that multiple long noncoding RNAs (lncRNAs) play essential roles. In this mini-review, we discuss the latest research on lncRNAs in iPSC stemness, neuronal, and cardiac differentiation.

Exploring the mechanisms of cell reprogramming and transdifferentiation via intercellular communication.

In the past years, the mechanisms of cell reprogramming and transdifferentiation via the way of gene regulation, stochastic fluctuations, or chemical induction to realize cell type transitions from the perspectives of single cells were explored. In multicellular organisms, intercellular communication plays crucial roles in cell fate decisions. However, the importance of intercellular communication to the processes of cell reprogramming and transdifferentiation is often neglected. In this paper, the mechanisms of cell reprogramming and transdifferentiation by intercellular communication are investigated. A two-gene circuit with mutual inhibition and self-activation as a basic model is selected. Then, a coupling mechanism via intercellular communication by introducing a specific signaling molecule into the gene circuit is considered. Finally, the influence of coupling intensity on the dynamics of the coupled system of two cells is analyzed. Moreover, when the coupling intensity changes with respect to the cell number in a discrete way, the effects of coupling intensity on cell reprogramming and transdifferentiation are discussed. Some theoretical analysis of stability and bifurcation of the systems are also given. Our research shows that cells can realize cell reprogramming and transdifferentiation via intercellular interaction at opportune coupling intensity. These results not only further enrich previous studies but also are beneficial to understand the mechanisms of cell reprogramming and transdifferentiation via intercellular communication in the growth and development of multicellular organisms.

Infectious Agents as Stimuli of Trained Innate Immunity.

The discoveries made over the past few years have modified the current immunological paradigm. It turns out that innate immunity cells can mount some kind of immunological memory, similar to that observed in the acquired immunity and corresponding to the defense mechanisms of lower organisms, which increases their resistance to reinfection. This phenomenon is termed trained innate immunity. It is based on epigenetic changes in innate immune cells (monocytes/macrophages, NK cells) after their stimulation with various infectious or non-infectious agents. Many infectious stimuli, including bacterial or fungal cells and their components (LPS, β-glucan, chitin) as well as viruses or even parasites are considered potent inducers of innate immune memory. Epigenetic cell reprogramming occurring at the heart of the phenomenon may provide a useful basis for designing novel prophylactic and therapeutic strategies to prevent and protect against multiple diseases. In this article, we present the current state of art on trained innate immunity occurring as a result of infectious agent induction. Additionally, we discuss the mechanisms of cell reprogramming and the implications for immune response stimulation/manipulation.

Artificial acceleration of mammalian cell reprogramming by bacterial proteins.

The molecular mechanisms of cell reprogramming and differentiation involve various signaling factors. Small molecule compounds have been identified to artificially influence these factors through interacting cellular proteins. Although such small molecule compounds are useful to enhance reprogramming and differentiation and to show the mechanisms that underlie these events, the screening usually requires a large number of compounds to identify only a very small number of hits (e.g., one hit among several tens of thousands of compounds). Here, we show a proof of concept that xenospecific gene products can affect the efficiency of cell reprogramming to pluripotency. Thirty genes specific for the bacterium Wolbachia pipientis were forcibly expressed individually along with reprogramming factors (Oct4, Sox2, Klf4 and c-Myc) that can generate induced pluripotent stem cells in mammalian cells, and eight were found to affect the reprogramming efficiency either positively or negatively (hit rate 26.7%). Mechanistic analysis suggested one of these proteins interacted with cytoskeleton to promote reprogramming. Our results raise the possibility that xenospecific gene products provide an alternative way to study the regulatory mechanism of cell identity.

Probability, odds and random chance: the difficult task of modulating the epigenetic profile of cloned embryos

Since the beginning of modern embryology, scientists have wondered about how a small number of totipotent embryonic cells can become an individual with a wide variety of organs and tissues with distinct functions. Also, the idea of generating a cloned animal using a nucleus from a donor cell is not recent. However, it has taken years of research to achieve this goal, especially regarding mechanisms of cell reprogramming required to return a differentiated cell to totipotency. Cloning by somatic cell nuclear transfer (SCNT) has been a valuable tool to understand epigenetic mechanisms related to cellular reprogramming. However, cloning efficiency is still low, with a low percentage of embryos resulting in healthy animals. The high attrition rate is associated with incomplete or abnormal epigenetic reprogramming, such that many cloned embryos have DNA methylation patterns different than controls, resulting in faulty gene expression and subsequent developmental failures. Attempts to improve genome reprogramming by modulation of oocyte quality and/or somatic cell plasticity, thereby increasing cloning efficiency and preventing detrimental effects on development, have proven ineffective. The recent development of DNA editing techniques may facilitate an improved understanding of cellular reprogramming and the role of DNA methylation in development. These novel tools may lead to new means to modulate epigenetic programming and inheritance, and hold great promise to assist in epigenetic remodeling of the donor nucleus. Such strategies are likely to improve the odds for successful cloning.

Helicobacter pylori as a crucial factor in intestinal metaplasia development of gastric mucosa

<p class="BodyText1"><em>Helicobacter pylori</em> (<em>H. pylori</em>) is detected on the surface of gastric epithelium and in goblet cells, predominantly in patients with chronic atrophic gastritis and incomplete intestinal metaplasia (IM). <em>H. pylori</em> infection persistence leads to the formation of gastrointestinal phenotype of IM. <em>H. pylori</em> can be considered as an etiological factor of IM. It inhibits the expression of SOX2 in gastric epithelial cells, hence activating transcription factor CDX2 as a counterpart to <em>MUC5AC</em> gene inhibition and <em>MUC2</em> gene induction. Thus, in metaplastic cells, programming differentiation after intestinal phenotype will develop. The role of <em>H. pylori</em> in the origin of intestinal metaplasia of gastric mucosa was defined in this study to elucidate the probable mechanism of cell reprogramming. The activation of CDX2, with simultaneous inactivation and decreased number of genes (<em>e.g.</em>, <em>SHH</em>, <em>SOX2</em>, and <em>RUNX3</em>) responsible for gastric differentiation, was identified to cause the appearance of IM. </p>

Short Communication Forced expression of OCT4 influences the expression of pluripotent genes in human mesenchymal stem cells and fibroblasts

Genetic reprogramming of adult cells to generate induced pluripotent stem (iPS) cells is a new and important step in sidestepping some of the ethical issues and risks involved in the use of embryonic stem cells. iPS cells can be generated by introduction of transcription factors, such as OCT4, SOX2, KLF4, and CMYC. iPS cells resemble embryonic stem cells in their properties and differentiation potential. The mechanisms that lead to induced pluripotency and the effect of each transcription factor are not completely understood. We performed a critical evaluation of the effect of overexpressing OCT4 in mesenchymal stem cells and fibroblasts and found that OCT4 can activate the expression of other stemness genes, such as SOX2, NANOG, CMYC, FOXD3, KLF4, and βCATENIN, which are not normally or are very weakly expressed in mesenchymal stem cells. Transient expression of OCT4 was also performed to evaluate whether these genes are affected by its overexpression in the first 48 h. Transfected fibroblast cells expressed around 275-fold more OCT4 than non-transfected cells. In transient expression, in which cells were analyzed after 48 h, we detected only the up-regulation of FOXD3, SOX2, and KLF4 genes, suggesting that these genes are the earlier targets of OCT4 in this cellular type. We conclude that forced expression of OCT4 can alter cell status and activate the pluripotent network. Knowledge gained through study of these systems may help us to understand the kinetics and mechanism of cell reprogramming.

New views and new tools for complex diseases

The non-transmittable chronic diseases such as cancer, cardiovascular, metabolic and neurodegeneration diseases already become the major threats to the mankind. All of these chronic diseases are recognized as complex diseases, which involve in multiple genetic factors, environment factors and the interaction of these two kinds of the factors, and the complicated molecular networks consisting of huge number of the genes and proteins. Therefore, it is clear that the conventional experimental biology that focuses on individual gene or protein is not enough to reveal the molecular mechanisms of complex diseases. The collection of six papers in this issue deliver new views to understand the molecular mechanisms of the initiation and progression of the complex diseases, and might provide new powerful tools to fight these diseases. Conventional way often labels particular genes as ‘oncogene’ or ‘tumor suppressor gene’ for their tumorigenic potential. Wu’s group revealed that a famous tumor suppressor gene p53 activated by 5-aza-2 ′ -deoxycytidine (ZdCyd) resulted in high protumorigenicity of mouse P19 embryonic carcinoma cells that are growing in suspension condition, whereas the ZdCyd-induced p53 activation resulted in suppression of tumorigenic potential of P19 EC cells growing on adherent condition. Based on their developed computational method, the authors revealed two different p53-dominant gene-regulatory networks of ZdCyd-treated P19 EC cells at adherent and non-adherent growth conditions, respectively. This study implies that changing cellular contexts of mammalian cells from adherent to non-adherent growth conditions rewires p53-regulating networks that could convert the tumor suppression to tumor-promoting activity. In addition, Auberger’s group reported that Imatinib, an inhibitor of a chimeric tyrosine kinase BCR-ABL, as the leading compound to treat chronic myelogenous leukemia (CML), presented various inhibitory effects on different CML cells. They also found that the variation in the drug effects was derived from different molecular contexts in the CML subpopulations. Regenerative medicine is an important way to treat the chronic diseases such as heart disease, diabetes and Alzheimer’s disease. Stem cells and the related molecular mechanisms of cell reprogramming have been recognized as potential tools for regenerative medicine. Asuelime and Shi reviewed the recent progress on cell-lineage reprogramming and its potential in regenerative medicine. Although the researchers have achieved significant progress, these authors conclude that more studies on this area need to be done before the technology based on lineage reprogramming is ready to the clinical practice. In addition, Kumar’s group in a letter reported that a transcription factor, zinc-finger transcription factor in cerebellum-3 (Zic3), combined with other three transcriptional factors, could induce the conversion of human fibroblasts to neuroprogenitorlike cells in a rapid way; and they suggest that this new approach to reprogramming cells could be a potential tool for screening chemical compounds against neural diseases. Diabetes is a typical age-dependent chronic disease. In this issue, Lammert’s group reported that the up-regulation of an antioxidant protein, DJ-1, in mouse and human islets during aging with non-diabetic conditions, whereas the expression of DJ-1 could be reduced in pancreatic islets of patients with type 2 diabetes mellitus (T2DM). Their further experimental data suggest that DJ-1 might serve as a novel drug target for T2DM. In another paper in this issue, Jia’s group showed that ficolin-3 as an innate immune protein presented a low serum level in the population with insulin-resistance based on a human cross-sectional study. The authors further proposed that serum ficolin-3 could be used as a biomarker for predicting the development of T2DM and even as a potential drugtarget for the treatment of T2DM. We hope that these papers will provide different angles from conventional views to understand the molecular mechanism of complex diseases and new potential tools against these diseases.

Cell Reprogramming, IPS Limitations, and Overcoming Strategies in Dental Bioengineering

The procurement of induced pluripotent stem cells, or IPS cells, from adult differentiated animal cells has the potential to revolutionize future medicine, where reprogrammed IPS cells may be used to repair disease-affected tissues on demand. The potential of IPS cell technology is tremendous, but it will be essential to improve the methodologies for IPS cell generation and to precisely evaluate each clone and subclone of IPS cells for their safety and efficacy. Additionally, the current state of knowledge on IPS cells advises that research on their regenerative properties is carried out in appropriate tissue and organ systems that permit a safe assessment of the long-term behavior of these reprogrammed cells. In the present paper, we discuss the mechanisms of cell reprogramming, current technical limitations of IPS cells for their use in human tissue engineering, and possibilities to overcome them in the particular case of dental regeneration.

Identification of an intermediate state as spermatogonial stem cells reprogram to multipotent cells.

The aim of this study was to understand the mechanisms that allow mSSC lines to be established from SSCs. Small, multilayer clumps of SSCs formed during two to four weeks of in vitro culture and were then transferred to MEF feeders. Small, round, monolayer colonies containing cells destined to convert to mSSCs, designated as intermediate state SSCs (iSSCs), first appeared after two to three passages. During an additional nine passages (47-54 days) under the same culture conditions, iSSCs slowly proliferated and maintained their morphology. Ultimately, a cell type with an ES-like morphology (mSSC) appeared from the iSSC colonies, and two mSSC cell lines were established. The mSSCs had a high proliferative potential in serum-free ES culture medium and have been successfully maintained since their first establishment (> 12 months). We also compared the specific characteristics of iSSCs with those of SSCs and mSSCs using immunocytochemistry, FACS, RT-PCR, DNA methylation, and miRNA analyses. The results suggest that iSSCs represent a morphologically distinct intermediate state with characteristic expression patterns of pluripotency-related genes and miRNAs that arise during the conversion of SSCs into mSSCs. Our results suggest that iSSCs could be a useful model for evaluating and understanding the initiation mechanisms of cell reprogramming.