Stem cells: a lesson from dedifferentiation

Genome-wide discovery of DNA variants in cucumber somaclonal lines

The emergence of somaclonal variability in in vitro cultures is undesirable during micropropagation, but this phenomenon may be a source of genetic variability sought by breeders. The main factors that affect the appearance of variability are known, but the exact mechanism has not yet been determined. In this paper, we used next-generation sequencing and comparative genomics to study changes in the genomes of cucumber lines resulting from in vitro regeneration and somaclonal mutation in comparison to a reference, the highly inbred B10 line. The total number of obtained polymorphisms differed between the three somaclonal lines S1, S2 and S3, with 8369, 7591 and 44510, respectively. Polymorphisms occurred most frequently in non-coding regions and were mainly SNPs. High-impact changes accounted for 1%-3% of all polymorphisms and most often caused an open reading frame shift. Functional analysis of genes affected by high impact variants showed that they were related to transport, biosynthetic processes, nucleotide-containing compounds and cellular protein modification processes. The obtained results indicated significant factors affecting somaclonal variability and the appearance of changes in the genome, and demonstrated a lack of dependence between phenotype and the number of genomic polymorphisms.

Senescence Meets Dedifferentiation

Senescence represents the final stage of leaf development but is often induced prematurely following exposure to biotic and abiotic stresses. Leaf senescence is manifested by color change from green to yellow (due to chlorophyll degradation) or to red (due to de novo synthesis of anthocyanins coupled with chlorophyll degradation) and frequently culminates in programmed death of leaves. However, the breakdown of chlorophyll and macromolecules such as proteins and RNAs that occurs during leaf senescence does not necessarily represent a one-way road to death but rather a reversible process whereby senescing leaves can, under certain conditions, re-green and regain their photosynthetic capacity. This phenomenon essentially distinguishes senescence from programmed cell death, leading researchers to hypothesize that changes occurring during senescence might represent a process of trans-differentiation, that is the conversion of one cell type to another. In this review, we highlight attributes common to senescence and dedifferentiation including chromatin structure and activation of transposable elements and provide further support to the notion that senescence is not merely a deterioration process leading to death but rather a unique developmental state resembling dedifferentiation.

Stress induces cell dedifferentiation in plants

Accumulating evidence lends support to the proposal that a major theme in plant responses to stresses is dedifferentiation, whereby mature cells acquire stem cell features (e.g. open chromatin conformation) prior to acquisition of a new cell fate. In this review, we discuss data addressing plant cell plasticity and provide evidence linking stress, dedifferentiation and a switch in cell fate. We emphasize the epigenetic modifications associated with stress-induced global changes in chromatin structure and conclude with the implications for genetic variation and for induced pluripotent stem cells in animals. It appears that stress is perceived as a signal that directs plant cells to undergo reprogramming (dedifferentiation) as a means for adaptation and in preparation for a stimulus-based acquisition of a new cell fate. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.

Stress cycles in stem cells/iPSCs development: implications for tissue repair

Stem cells have become a major topic, both publicly and scientifically, owing to their potential to cure diseases and repair damaged tissues. Particular attention has been given to the so-called "induced pluripotent stem cells" (iPSCs) in which somatic cells are induced by the expression of transcription factor encoding transgenes-a methodology first established by Takahashi and Yamanaka (Cell 126:663-676, 2006)-to acquire pluripotent state. This methodology has captured researchers' imagination as a potential procedure to obtain patient-specific therapies while also solving both the problem of transplant rejection and the ethical concerns often raised regarding the use of embryonic stem cells in regenerative medicine. The study of the biology of stem cells/iPSCs, in recent years, has uncovered some fundamental weaknesses that undermine their potential use in transplantation therapies.

Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids

BACKGROUND

Genetic and epigenetic alterations can be invoked by plant tissue culture, which may result in heritable changes in phenotypes, a phenomenon collectively termed somaclonal variation. Although extensive studies have been conducted on the molecular nature and spectrum of tissue culture-induced genomic alterations, the issue of whether and to what extent distinct plant genotypes, e.g., pure-lines, hybrids and polyploids, may respond differentially to the tissue culture condition remains poorly understood.

RESULTS

We investigated tissue culture-induced genetic and epigenetic alterations in a set of rice genotypes including two pure-lines (different subspecies), a pair of reciprocal F1 hybrids parented by the two pure-lines, and a pair of reciprocal tetraploids resulted from the hybrids. Using two molecular markers, amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP), both genetic and DNA methylation alterations were detected in calli and regenerants from all six genotypes, but genetic alteration is more prominent than epigenetic alteration. While significant genotypic difference was observed in frequencies of both types of alterations, only genetic alteration showed distinctive features among the three types of genomes, with one hybrid (N/9) being exceptionally labile. Surprisingly, difference in genetic alteration frequencies between the pair of reciprocal F1 hybrids is much greater than that between the two pure-line subspecies. Difference also exists in the pair of reciprocal tetraploids, but is to a less extent than that between the hybrids. The steady-state transcript abundance of genes involved in DNA repair and DNA methylation was significantly altered in both calli and regenerants, and some of which were correlated with the genetic and/or epigenetic alterations.

CONCLUSIONS

Our results, based on molecular marker analysis of ca. 1,000 genomic loci, document that genetic alteration is the major cause of somaclonal variation in rice, which is concomitant with epigenetic alterations. Perturbed expression by tissue culture of a set of 41 genes encoding for enzymes involved in DNA repair and DNA methylation is associated with both genetic and epigenetic alterations. There exist fundamental differences among distinct genotypes, pure-lines, hybrids and tetraploids, in propensities of generating both genetic and epigenetic alterations under the tissue culture condition. Parent-of-origin has a conspicuous effect on the alteration frequencies.

Dramatic genotypic difference in, and effect of genetic crossing on, tissue culture-induced mobility of retrotransposon Tos17 in rice

KEY MESSAGE : We show for the first time that intraspecific crossing may impact mobility of the prominent endogenous retrotransposon Tos17 under tissue culture conditions in rice. Tos17, an endogenous copia retrotransposon of rice, is transpositionally active in tissue culture. To study whether there exists fundamental genotypic difference in the tissue culture-induced mobility of Tos17, and if so, whether the difference is under genetic and/or epigenetic control, we conducted this investigation. We show that dramatic difference in tissue culture-induced Tos17 mobility exists among different rice pure-line cultivars sharing the same maternal parent: of the three lines studied that harbor Tos17, two showed mobilization of Tos17, which accrued in proportion to subculture duration, while the third line showed total quiescence (immobility) of the element and the fourth line did not contain the element. In reciprocal F1 hybrids between Tos17-mobile and -immobile (or absence) parental lines, immobility was dominant over mobility. In reciprocal F1 hybrids between both Tos17-mobile parental lines, an additive or synergistic effect on mobility of the element was noticed. In both types of reciprocal F1 hybrids, clear difference in the extent of Tos17 mobility was noted between crossing directions. Given that all lines share the same maternal parent, this observation indicates the existence of epigenetic parent-of-origin effect. We conclude that the tissue culture-induced mobility of Tos17 in rice is under complex genetic and epigenetic control, which can be either enhanced or repressed by intraspecific genetic crossing.

Transcriptome of protoplasts reprogrammed into stem cells in Physcomitrella patens

Background

Differentiated plant cells can retain the capacity to be reprogrammed into pluripotent stem cells during regeneration. This capacity is associated with both cell cycle reactivation and acquisition of specific cellular characters. However, the molecular mechanisms underlying the reprogramming of protoplasts into stem cells remain largely unknown. Protoplasts of the moss Physcomitrella patens easily regenerate into protonema and therefore provide an ideal system to explore how differentiated cells can be reprogrammed to produce stem cells.

Principal findings

We obtained genome-wide digital gene expression tag profiles within the first three days of P. patens protoplast reprogramming. At four time-points during protoplast reprogramming, the transcript levels of 4827 genes changed more than four-fold and their expression correlated with the reprogramming phase. Gene ontology (GO) and pathway enrichment analysis of differentially expressed genes (DEGs) identified a set of significantly enriched GO terms and pathways, most of which were associated with photosynthesis, protein synthesis and stress responses. DEGs were grouped into six clusters that showed specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes identified a number of key candidate genes and pathways in early stages of protoplast reprogramming, which provided important clues to reveal the molecular mechanisms responsible for protoplast reprogramming.

Conclusions

We identified genes that show highly dynamic changes in expression during protoplast reprogramming into stem cells in P. patens. These genes are potential targets for further functional characterization and should be valuable for exploration of the mechanisms of stem cell reprogramming. In particular, our data provides evidence that protoplasts of P. patens are an ideal model system for elucidation of the molecular mechanisms underlying differentiated plant cell reprogramming.

The stem cell state in plant development and in response to stress

Stem cells are commonly defined by their developmental capabilities, namely, self-renewal and multitype differentiation, yet the biology of stem cells and their inherent features both in plants and animals are only beginning to be elucidated. In this review article we highlight the stem cell state in plants with reference to animals and the plastic nature of plant somatic cells often referred to as totipotency as well as the essence of cellular dedifferentiation. Based on recent published data, we illustrate the picture of stem cells with emphasis on their open chromatin conformation. We discuss the process of dedifferentiation and highlight its transient nature, its distinction from re-entry into the cell cycle and its activation following exposure to stress. We also discuss the potential hazard that can be brought about by stress-induced dedifferentiation and its major impact on the genome, which can undergo stochastic, abnormal reorganization leading to genetic variation by means of DNA transposition and/or DNA recombination.

DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling

Plants have a profound capacity to regenerate organs from differentiated somatic tissues, based on which propagating plants in vitro was made possible. Beside its use in biotechnology, in vitro shoot regeneration is also an important system to study de novo organogenesis. Phytohormones and transcription factor WUSCHEL (WUS) play critical roles in this process but whether and how epigenetic modifications are involved is unknown. Here, we report that epigenetic marks of DNA methylation and histone modifications regulate de novo shoot regeneration of Arabidopsis through modulating WUS expression and auxin signaling. First, functional loss of key epigenetic genes—including METHYLTRANSFERASE1 (MET1) encoding for DNA methyltransferase, KRYPTONITE (KYP) for the histone 3 lysine 9 (H3K9) methyltransferase, JMJ14 for the histone 3 lysine 4 (H3K4) demethylase, and HAC1 for the histone acetyltransferase—resulted in altered WUS expression and developmental rates of regenerated shoots in vitro. Second, we showed that regulatory regions of WUS were developmentally regulated by both DNA methylation and histone modifications through bisulfite sequencing and chromatin immunoprecipitation. Third, DNA methylation in the regulatory regions of WUS was lost in the met1 mutant, thus leading to increased WUS expression and its localization. Fourth, we did a genome-wide transcriptional analysis and found out that some of differentially expressed genes between wild type and met1 were involved in signal transduction of the phytohormone auxin. We verified that the increased expression of AUXIN RESPONSE FACTOR3 (ARF3) in met1 indeed was due to DNA demethylation, suggesting DNA methylation regulates de novo shoot regeneration by modulating auxin signaling. We propose that DNA methylation and histone modifications regulate de novo shoot regeneration by modulating WUS expression and auxin signaling. The study demonstrates that, although molecular components involved in organogenesis are divergently evolved in plants and animals, epigenetic modifications play an evolutionarily convergent role in this process.

Plants have a strong ability to generate organs from differentiated somatic tissues. Due to this feature, shoot regeneration in vitro has been used as an important way for producing whole plants in agriculture and biotechnology. Phytohormones and the transcription factor WUSCHEL (WUS) are essential for reprogramming during de novo shoot regeneration. Epigenetic modifications are also critical for mammalian cell differentiation and organogenesis. Here, we show that epigenetic modifications mediate the de novo shoot regeneration in Arabidopsis. Mutations of key epigenetic genes resulted in altered WUS expression and developmental rates of regenerated shoots in vitro. Bisulfite sequencing and chromatin immunoprecipitation revealed that the regulatory regions of WUS were developmentally regulated by both DNA methylation and histone modifications. By transcriptome analysis, we identified that some differentially expressed genes between wild type and met1 are involved in signal transduction of the phytohormone auxin. Our results suggest that DNA methylation and histone modifications regulate de novo shoot regeneration by modulating WUS expression and auxin signaling. The study demonstrates that, although molecular components involved in organogenesis are divergently evolved in plants and animals, epigenetic modifications play an evolutionarily convergent role during de novo organogenesis.

[Heterochromatin, a plastic component in the nucleus of Arabidopsis thaliana cells]

The cytogenetic observation of the nucleus of Arabidopsis thaliana, a plant member of the brassicaceae family, reveals a simple organization of the nuclear content. Indeed, the nuclear volume is occupied by two distinct and easily distinguishable forms of chromatin: a large fraction of relatively decondensed and transcriptionnally active euchromatin surrounds about ten conspicuous regions, the chromocenters, which contain most repeated and highly condensed heterochromatic sequences. Remarkably, during the development of A. thaliana or when the plant is exposed to certain environmental variations, dramatic changes in the appearance, the size or the presence of the chromocenters occur. A number of cytogenetic studies have not only characterized the genomic sequences accommodated in the chromocenters, but have also established the dynamics of their assembly and disruption. Moreover, various endogenous and exogenous factors involved in the presence and the size of chromocenters were recently identified. Taken together, these studies carried out in A. thaliana suggest that heterochromatin is a truly "malleable" fraction of the genome whose dynamic organization is not controlled only by epigenetic marks and whose importance in nuclear function goes beyond merely grouping together non-coding genomic sequences.

Hormonal and cell division analyses in Watsonia lepida seedlings

The regeneration ability, cell division activity, auxin and cytokinin content of seedling regions and hypocotyl subsections of Watsonia lepida were studied. A total of 21 different cytokinins or conjugates were found in seedlings, with the highest cytokinin content in meristematic regions (root and shoot apical meristems). The greatest contribution to the cytokinin pool came from the biologically inactive cZRMP, suggesting that significant de novo synthesis was occurring. Five different auxins or conjugates were detected, being concentrated largely in the shoot apical meristem and leaves, IAA being the most abundant. Analysis of hypocotyl subsections (C1-C4) revealed that cell division was highest in subsection C2, although regeneration in vitro was significantly lower than in subsection C1. Anatomically, subsection C1 contains the apical meristem, and hence has meristematic cells that are developmentally plastic. In contrast, subsection C2 has cells that have recently exited the meristem and are differentiating. Despite high rates of cell division, cells in subsection C2 appear no longer able to respond to cues that promote proliferation in vitro. Auxin and cytokinin analyses of these subsections were conducted. Possibly, a lower overall cytokinin content, and in particular the free-base cytokinins, could account for this observed difference.

The Arabidopsis cell division cycle

Plant cells have evolved a complex circuitry to regulate cell division. In many aspects, the plant cell cycle follows a basic strategy similar to other eukaryotes. However, several key issues are unique to plant cells. In this chapter, both the conserved and unique cellular and molecular properties of the plant cell cycle are reviewed. In addition to division of individual cells, the specific characteristic of plant organogenesis and development make that cell proliferation control is of primary importance during development. Therefore, special attention should be given to consider plant cell division control in a developmental context. Proper organogenesis depends on the formation of different cell types. In plants, many of the processes leading to cell differentiation rely on the occurrence of a different cycle, termed the endoreplication cycle, whereby cells undergo repeated full genome duplication events in the absence of mitosis and increase their ploidy. Recent findings are focusing on the relevance of changes in chromatin organization for a correct cell cycle progression and, conversely, in the relevance of a correct functioning of chromatin remodelling complexes to prevent alterations in both the cell cycle and the endocycle.

The involvement of reactive oxygen species (ROS) in the cell cycle activation (G(0)-to-G(1) transition) of plant cells

Reactive oxygen species (ROS) are involved in various cellular processes in plants. Among those, resistance to abiotic stress, defence mechanisms and cell expansion have been intensively studied during the last years. We recently demonstrated that ROS, in concert with auxin, have a role in cell cycle activation of differentiated leaf cells.1 In this addendum we provide further evidence to show that oxidative stress/ROS accelerate auxin-mediated cell cycle entry (G(0)-to-G(1)) and may have a positive effect on the plant cell cycle machinery. A generalized model for concentration-dependent synergistic effect of auxin and ROS on differentiated plant cells is also shown.

Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells

Maintaining and acquiring the pluripotent cell state in plants is critical to tissue regeneration and vegetative multiplication. Histone-based epigenetic mechanisms are important for regulating this undifferentiated state. Here we report the use of genetic and pharmacological experimental approaches to show that Arabidopsis cell suspensions and calluses specifically repress some genes as a result of promoter DNA hypermethylation. We found that promoters of the MAPK12, GSTU10 and BXL1 genes become hypermethylated in callus cells and that hypermethylation also affects the TTG1, GSTF5, SUVH8, fimbrin and CCD7 genes in cell suspensions. Promoter hypermethylation in undifferentiated cells was associated with histone hypoacetylation and primarily occurred at CpG sites. Accordingly, we found that the process specifically depends on MET1 and DRM2 methyltransferases, as demonstrated with DNA methyltransferase mutants. Our results suggest that promoter DNA methylation may be another important epigenetic mechanism for the establishment and/or maintenance of the undifferentiated state in plant cells.

In vivo bioluminescence imaging study to monitor ectopic bone formation by luciferase gene marked mesenchymal stem cells

Mesenchymal stem cells (MSCs) represent a powerful tool for applications in regenerative medicine. In this study, we used in vivo bioluminescence imaging to noninvasively investigate the fate and the contribution to bone formation of adult MSCs in tissue engineered constructs. Goat MSCs expressing GFP-luciferase were seeded on ceramic scaffolds and implanted subcutaneously in immune-deficient mice. The constructs were monitored weekly with bioluminescence imaging and were retrieved after 7 weeks to quantify bone formation by histomorphometry. With increasing amounts of seeded MSCs (from 0 to 1 x 10(6) MSC/scaffold), a cell-dose related increase in bioluminescence was observed at all time points, correlating with increased bone formation at 7 weeks. To investigate the relevance of MSC proliferation to bone deposition, cell-seeded scaffolds were irradiated. The irradiated cells were functional with respect to oxygen consumption but no increase in bioluminescence was observed in vivo, and only minimal bone was produced. Proliferating MSCs are likely required for initiation of bone formation in tissue engineered constructs in vivo. Bioluminescence is a useful tool to monitor cellular responses and predict bone formation in vivo.

Human mesenchymal stem cell transformation is associated with a mesenchymal-epithelial transition

Carcinomas are widely thought to derive from epithelial cells with malignant progression often associated with an epithelial-mesenchymal transition (EMT). We have characterized tumors generated by spontaneously transformed human mesenchymal cells (TMC) previously obtained in our laboratory. Immunohistopathological analyses identified these tumors as poorly differentiated carcinomas, suggesting that a mesenchymal-epithelial transition (MET) was involved in the generation of TMC. This was corroborated by microarray and protein expression analysis that showed that almost all mesenchymal-related genes were severely repressed in these TMC. Interestingly, TMC also expressed embryonic antigens and were able to integrate into developing blastocysts with no signs of tumor formation, suggesting a dedifferentiation process was associated with the mesenchymal stem cell (MSC) transformation. These findings support the hypothesis that some carcinomas are derived from mesenchymal rather than from epithelial precursors.

A proteome study of the proliferation of culturedMedicago truncatula protoplasts

A proteome study of the first five days of Medicago truncatula protoplast cultures was done to investigate molecular changes taking place during protoplast proliferation. A total of 1556 protein spots were analysed, of which 886 protein spots showed significant (p<0.005) changes in abundance at some time during the first five days of protoplast culture. Of the 886 significantly changing protein spots, 89 proteins were identified by MALDI-TOF MS. The majority of the identified proteins were part of four main cellular processes that may be involved in protoplast proliferation: energy metabolism, defence or stress response, secondary metabolism and protein synthesis and folding. The accumulation pattern of these proteins indicates extensive changes in the energy metabolism of the cells, accompanied by the activation of stress response pathways and modifications of the cell wall. In addition, seven PR10-like (pathogenesis related) proteins were identified. The accumulation pattern of these seven PR10-like proteins suggests that they could have a developmental role during protoplast proliferation.

Influence of hormones on osteogenic differentiation processes of mesenchymal stem cells

Bone development, regeneration and maintenance are governed by osteogenic differentiation processes from mesenchymal stem cells through to mature bone cells, which are directed by local growth and differentiation factors and modulated strongly by hormones. Mesenchymal stem cells develop from both mesoderm and neural crest and can give rise to development, regeneration and maintenance of mesenchymal tissues, such as bone, cartilage, muscle, tendons and discs. There are only limited data regarding the effects of hormones on early events, such as regulation of stemness and maintenance of the mesenchymal stem cell pool. Hormones, such as estrogens, vitamin D-hormone and parathyroid hormone, besides others, are important modulators of osteogenic differentiation processes and bone formation, starting off with fate decision and the development of osteogenic offspring from mesenchymal stem cells, which end up in osteoblasts and osteocytes. Hormones are involved in fetal bone development and regeneration and, in childhood, adolescence and adulthood, they control adaptive needs for growth and reproduction, nutrition, physical power and crisis adaptation. As in other tissues, aging in mesenchymal stem cells and their osteogenic offspring is accompanied by the accumulation of genomic and proteomic damage caused by oxidative burden and insufficient repair. Failsafe programs, such as apoptosis and cellular senescence avoid tumorigenesis. Hormones can influence the pace of such events, thus supporting the quality of tissue regeneration in aging organisms in vivo; for example, by delaying osteoporosis development. The potential for hormones in systemic therapeutic strategies is well appreciated and some concepts are approved for clinical use already. Their potential for cell-based therapeutic strategies for tissue regeneration is probably underestimated and could enhance the quality of tissue-engineering constructs for transplantation and the concept of in situ-guided tissue regeneration.

Cell Cycle Regulation in Plant Development

Cell cycle regulation is of pivotal importance for plant growth and development. Although plant cell division shares basic mechanisms with all eukaryotes, plants have evolved novel molecules orchestrating the cell cycle. Some regulatory proteins, such as cyclins and inhibitors of cyclin-dependent kinases, are particularly numerous in plants, possibly reflecting the remarkable ability of plants to modulate their postembryonic development. Many plant cells also can continue DNA replication in the absence of mitosis, a process known as endoreduplication, causing polyploidy. Here, we review the molecular mechanisms that regulate cell division and endoreduplication and we discuss our understanding, albeit very limited, on how the cell cycle is integrated with plant development.