From intestine to muscle: nuclear reprogramming through defective cloned embryos

Restoring totipotency through epigenetic reprogramming

Epigenetic modifications are implicated in the maintenance and regulation of transcriptional memory by marking genes that were previously transcribed to facilitate transmission of these expression patterns through cell division. During germline specification and maintenance, extensive epigenetic modifications are acquired. Yet somehow at fertilization, the fusion of the highly differentiated sperm and egg results in formation of the totipotent zygote. This massive change in cell fate implies that the selective erasure and maintenance of epigenetic modifications at fertilization may be critical for the re-establishment of totipotency. In this review, we discuss recent studies that provide insight into the extensive epigenetic reprogramming that occurs around fertilization and the mechanisms that may be involved in the re-establishment of totipotency in the embryo.

Reprogramming of gene expression following nuclear transfer to the Xenopus oocyte

Transplantation of Xenopus laevis cell nucleus to enucleated Xenopus egg leads to the generation of cloned animal. This exemplifies the process of nuclear reprogramming by which the nucleus of a specialized cell is reset to an embryonic state from which it can generate all the cells of an organism. Using the precursor of the egg, the oocyte, it is also possible to reprogram somatic cell. The advantage of this approach is the direct reprogramming of gene expression in the absence of cell division. Using this strategy it is possible to investigate the mechanism leading to transcriptional reprogramming of somatic nuclei. By combining real time monitoring of chromatin protein exchange and gene expression analysis, we have observed that a simultaneous loss of somatic H1 linker histone and incorporation of the oocyte-specific linker histone B4 precede transcriptional reprogramming. The loss of H1 is not required for gene reprogramming. We have demonstrated both by antibody injection experiments and by dominant negative interference that the incorporation of B4 linker histone is required for pluripotency gene reactivation during nuclear reprogramming. We suggest that the binding of oocyte specific B4 linker histone to chromatin is a key primary event in the reprogramming of somatic nuclei transplanted to amphibian oocytes.

Efficiencies and mechanisms of nuclear reprogramming

The differentiated state of somatic cells is highly stable, but it can be experimentally reversed. The resulting cells can then be redirected into many different pathways. Nuclear reprogramming has been achieved by nuclear transfer to eggs, cell fusion, and overexpression of transcription factors. The mechanisms of nuclear reprogramming are not understood, but some insight into them is provided by comparing the efficiencies of different reprogramming strategies. Here, we compare these efficiencies by describing the frequency and rapidity with which reprogramming is induced and by the proportion of cells and level of expression in which reprogramming is achieved. We comment on the mechanisms that lead to successful somatic-cell reprogramming and on those that resist in helping to maintain the differentiated state of somatic cells.

Characterization of somatic cell nuclear reprogramming by oocytes in which a linker histone is required for pluripotency gene reactivation

When transplanted into Xenopus oocytes, the nuclei of mammalian somatic cells are reprogrammed to express stem cell genes such as Oct4, Nanog, and Sox2. We now describe an experimental system in which the pluripotency genes Sox2 and Oct4 are repressed in retinoic acid-treated ES cells but are reprogrammed up to 100% within 24 h by injection of nuclei into the germinal vesicle (GV) of growing Xenopus oocytes. The isolation of GVs in nonaqueous medium allows the reprogramming of individual injected nuclei to be seen in real time. Analysis using fluorescence recovery after photobleaching shows that nuclear transfer is associated with an increase in linker histone mobility. A simultaneous loss of somatic H1 linker histone and incorporation of the oocyte-specific linker histone B4 precede transcriptional reprogramming. The loss of H1 is not required for gene reprogramming. We demonstrate both by antibody injection experiments and by dominant negative interference that the incorporation of B4 linker histone is required for pluripotency gene reactivation during nuclear reprogramming. We suggest that the binding of oocyte-specific B4 linker histone to chromatin is a key primary event in the reprogramming of somatic nuclei transplanted to amphibian oocytes.

Hypocellularity and absence of compaction as criteria for embryonic death

BACKGROUND

A precise definition of death is important for the appropriate application of medical resources and the harvesting of tissues for transplantation. For developed humans, life is considered to end when the criteria for brain death are met, but corresponding criteria are lacking for human embryos, and thus, we undertook a natural history study of embryonic death.

METHODS

De-identified records of the observations of human embryos in culture were analyzed retrospectively. The embryos were generated by in vitro fertilization for the purpose of reproduction. Cell number and morphology were recorded on embryonic days 2, 3, 5, and 6. Viable embryos (n = 248) were compared to nonviable embryos (n = 444) and the latter were analyzed in subgroups defined by cell number and morphology.

RESULTS

Many nonviable embryos (n = 142 out of 444) were hypocellular and lacked compaction on embryonic day 5 (ED5). All of these hypocellular embryos did not progress to compacted morula or normal blastocyst when observed further. No criteria could be discerned for the diagnosis of death on ED3.

CONCLUSIONS

Arrested development at the multicellular stage on ED5 indicates an irreversible loss of integrated organic function, and hence, the condition of death for the organism. Approximately a fifth of all embryos generated for in vitro fertilization--heretofore misclassified among the 'nonviable'--are in fact dead on ED5 by our criteria. We propose that the ethical framework currently used for obtaining essential organs from deceased persons for transplantation could be applied to the harvesting of live cells from dead human embryos for the creation of stem cells.

Framing the future: embryonic stem cells, ethics and the emerging era of developmental biology

Throughout the 20(th) century, advances in biology were accomplished largely through the study of biochemical parts apart from their place within the whole organism. This reductive and analytic approach, which has culminated in the sequencing of the human genome, has now led us back to the study of living beings. When applied to human biology, this inquiry re-opens the most fundamental questions concerning the moral meaning of developing life. The current conflict over ES (embryonic stem) cell research is just the first in a series of difficult controversies that will require us to clearly and precisely define the boundaries of humanity that we seek to defend. Through a careful consideration of the social, political, and scientific foundations of our current debate, we may discern the terms of a possible resolution that can sustain social consensus while opening avenues for scientific advance. Four such proposals were discussed in a May 2005 publication by the President's Council on Bioethics, entitled "Alternative Sources of Pluripotent Stem Cells." One of these methods, altered nuclear transfer, proposes to use the technology of somatic cell nuclear transfer (SCNT), but with a pre-emptive genetic or epigenetic alteration that precludes the integrated and coordinated organization essential for natural embryogenesis. The moral and scientific dimensions of this proposal are discussed as a way forward for embryonic stem cell research as well as a frame for further studies in developmental biology.

An obligatory caravanserai stop on the silk road to neural induction: Inhibition of BMP/GDF signaling

Work in Xenopus laevis produced the first molecular explanation for neural specification, the default model, where inactivation of the BMP pathway in ectodermal cells changes fates from epidermal to neural. This review covers the present status of our understanding of neural specification, with emphasis on Xenopus, but including relevant facts in other model systems. While recent experiments have increased the complexity of the molecular picture, they have also provided additional support for the default model and the central position of the BMP pathway. We conclude that synergy between accumulated knowledge and technical progress will maintain Xenopus at the forefront of research in neural development.

Origin and progress of nuclear transfer in nonmammalian animals

This chapter traces the origin and progress of nuclear transfer that later became the paradigm for cloning animals. Classic studies in cytology, embryology, or genetics spanning more than five centuries that led to nuclear transfers in unicellular animals and to those in oocytes of insects, fish and amphibians are reviewed. The impetus for the development of successful nuclear transfers in amphibian oocytes in 1952 was to determine whether or not differentiated somatic cell nuclei are developmentally equivalent to zygote nuclei. Experiments in amphibians demonstrated several important results: (1) specialized somatic cell nuclei are extensively multipotent; (2) fertile adult amphibians can be cloned from embryonic and larval nuclei; (3) serial cloning expands the number of clones; (4) transplanting nuclei into oocyte cytoplasm induces reprogramming of their gene function; and (5) amphibian cloning became the model for cloning mammals. Subsequent studies in mice, a more technically favorable species, revealed that specialized cell nuclei are equivalent to zygote nuclei.

Rescuing human embryonic stem cell research: the Blastocyst Transfer Method

Despite the therapeutic potential of human embryonic stem (HES) cells, many people believe that HES cell research should be banned. The reason is that the present method of extracting HES cells involves the destruction of the embryo, which for many is the beginning of a person. This paper examines a number of compromise solutions such as parthenogenesis, the use of defective embryos, genetically creating a "pseudo embryo" that can never form a placenta, and determining embryo death, and argues that none of these proposals are likely to satisfy embryoists, that is, those who regard the embryo as a person. This paper then proposes a method of extracting HES cells, what might be called the Blastocyst Transfer Method, that meets the ethical requirements of embryoists, and it considers some possible concerns regarding this method. It concludes by encouraging future HES cell research to investigate this method.

Epigenetic memory of active gene transcription is inherited through somatic cell nuclear transfer

The transplantation of somatic cell nuclei to enucleated eggs has shown that genes can be reprogrammed to an embryonic pattern of expression, thereby indicating a reversal of their epigenetic state. However, in Xenopus nuclear transfer experiments using both endoderm and neuroectoderm donor cells, we have observed substantial overexpression of donor cell type-specific genes, both spatially and temporally, in the wrong cell type in some nuclear transplant embryos. For example, more than half of the embryos prepared from transplanted neuroectoderm nuclei overexpressed the neuroectodermal marker gene Sox2 to an excessive level in their endoderm cells. Because, in Xenopus, there is no transcription for the first 12 cell cycles, some somatic cell nuclei must remember a developmentally activated gene state and transmit this to their mitotic progeny in the absence of the conditions that induced that state. We also find that donor cell-specific genes are transcribed at an earlier stage than normal in an inappropriate cell type. This phenomenon of epigenetic memory applies to genes that are transcribed in donor nuclei; it does not influence those genes that are competent to be transcribed in nuclear transplant embryo tissue, but were not actually transcribed in donor nuclei at the time of nuclear transfer. We conclude that an epigenetic memory is established in differentiating somatic cells and applies to genes that are in a transcriptionally active state.

Embryonic death and the creation of human embryonic stem cells

The creation of human embryonic stem cells through the destruction of a human embryo pits the value of a potential therapeutic tool against that of an early human life. This contest of values has resulted in a polarized debate that neglects areas of common interest and perspective. We suggest that a common ground for pursuing research on human embryonic stem cells can be found by reconsidering the death of the human embryo and by applying to this research the ethical norms of essential organ donation.

Nuclear reprogramming in mammalian somatic cell nuclear cloning

Nuclear cloning is still a developing technique used to create genetically identical animals by somatic cell nuclear transfer into unfertilized eggs. Despite an intensive effort in a number of laboratories, the success rate of obtaining viable offspring from this technique remains less than 5%. In the past few years many investigators reported the reprogramming of specific nuclear activities in cloned animals, such as genome-wide gene expression patterns, DNA methylation, genetic imprinting, histone modifications and telomere length regulation. The results highlight the tremendous difficulty the clones face to reprogram the original differentiation status of the donor nuclei. Nevertheless, nuclei prepared from terminally differentiated lymphocytes can overcome this barrier and produce apparently normal mice. Study of this striking nuclear reprogramming activity should significantly contribute to our understanding of cell differentiation in more physiological settings.

Exploitation of stem cell plasticity

For many years, adult haemopoietic stem cells (HSCs) have been considered 'plastic' in their proliferative and differentiation capacities. Recently, evidence that supports newer concepts of adult stem cell plasticity has been reported. In particular, stem cells from haemopoietic tissues seem to have 'extraordinary' abilities to generate or switch between haemopoietic and nonhaemopoietic lineages, exhibiting an unexpected degree of developmental or differentiation potential. The mechanisms by which cell fate reprogramming occurs are still poorly understood. Nevertheless, an increasing number of studies is challenging one of the main dogmas in biology, namely that mammalian cell differentiation follows established programmes in a hierarchical fashion, and once committed to a particular somatic cell lineage, cells do not change into another somatic lineage. The 'nonhierarchical', 'reversible' phenotype of stem cells in haemopoietic tissues, if it exists, would be an advantage that could be exploited in regenerative medicine. Here, we review the recent advances in HSC biology and discuss the general concepts of adult stem cell plasticity with respect to these cells and how these might be exploited clinically.

Pluripotency deficit in clones overcome by clone-clone aggregation: epigenetic complementation?

Abnormal gene expression patterns in somatic cell clones and their attrition in utero are commonly considered a consequence of errors in nuclear reprogramming. We observe that mouse clone blastocysts have less than half the normal cell number, and that higher cell number correlates with correct expression of Oct4, a gene essential for peri-implantation development and embryonic pluripotency. To increase the cell number, we aggregated genetically identical clones at the 4-cell stage. Clone-clone aggregates did not form more blastocysts, but the majority expressed Oct4 normally and had higher rates of fetal and postnatal development. Fertilized blastocysts with low cell numbers, induced by removal of two blastomeres at the 4-cell stage, did not exhibit abnormal Oct4 expression, indicating that improved gene expression and post-implantation development of clone-clone aggregates is not a consequence of increased cell number. Rather, we propose that complementation of non-cell-autonomous defects of genetically identical, but epigenetically different, embryos results in improved gene expression in clone-clone aggregates.

Nuclear reprogramming and stem cell creation

The transplantation of a somatic cell nucleus to an enucleated egg results in a major reprogramming of gene expression and switch in cell fate. We review the efficiency of nuclear reprogramming by nuclear transfer. The serial transplantation of nuclei from defective first-transfer embryos and the grafting of cells from such embryos to normal host embryos greatly increases the proportion of nuclei that can be seen to have been reprogrammed. We discuss possible reasons for the early failure of most nuclear transfers from differentiated cells and describe the potential value of growing oocytes, rather than unfertilized eggs, as a source of nuclear reprogramming molecules and for the eventual identification of these molecules. Nuclear transfer provides a possible route for the creation of stem cells from adult somatic cells.

The first half-century of nuclear transplantation

Fifty years after Briggs and King first succeeded in obtaining normal tadpoles from transplanted embryo nuclei in vertebrates, two general principles have emerged from work in amphibia and mammals. One is the conservation of the genome during cell differentiation. A small percentage of adult or differentiated cells have totipotent nuclei, and a much higher percentage of cells committed to one pathway of cell differentiation have multipotent nuclei. The other is the remarkable reprogramming capacity of cell, and especially egg, cytoplasm. The eventual identification of reprogramming molecules and mechanisms could facilitate a route toward cell replacement therapy in humans.

DNA methylation in animal development

Nuclear transfer experiments have demonstrated that epigenetic mechanisms operate to limit gene expression during animal development. In somatic cells, silenced genes are associated with defined chromatin states which are characterised by hypermethylation of DNA, hypoacetylation of histones and specific patterns of methylation at distinct residues of the N-terminal tails of histone H3 and H4. This review describes the role of the DNA methylation-mediated repression system (Dnmt1's, MeCPs and MBDs and associated chromatin remodelling activities) in animal development. DNA methylation is essential for normal vertebrate development but has distinct regulatory roles in non-mammalian and mammalian vertebrates. In mammals, DNA methylation has an additional role in regulating imprinting. This suggests that epigenetic regulation is plastic in its application and should be considered in a developmental context that may be species specific.

Epigenetic reprogramming in early mammalian development and following somatic nuclear transfer

Epigenetic modifications of the genome play a significant role in the elaboration of the genetic code as established at fertilisation. These modifications affect early growth and development through their influence on gene expression especially on imprinted genes. Genome-wide epigenetic reprogramming in germ cells is essential in order to reset the parent-of-origin specific marking of imprinted genes, but may have a more general role in the restoration of totipotency in the early embryo. In a similar way, on somatic nuclear cloning, a differentiated cell must become 'reprogrammed' restoring totipotency in order to undergo development. Here we discuss the dynamic epigenetic reprogramming that takes place during normal development and highlight those areas with relevance to somatic nuclear cloning and the possibility of improving the efficiency of this process. We propose the concept of 'epigenetic checkpoints' for normal progression of development and the loss of totipotency.

Mammalian epigenomics: reprogramming the genome for development and therapy

Epigenetic modifications of DNA and chromatin are important for genome function during development and in adults. DNA and chromatin modifications have central importance for genomic imprinting and other aspects of epigenetic control of gene expression. In somatic lineages, modifications are generally stably maintained and are characteristic of different specialized tissues. The mammalian genome undergoes major reprogramming of modification patterns in germ cells and in the early embryo. Some of the factors that are involved both in maintenance and in reprogramming, such as methyltransferases, are being identified. Epigenetic reprogramming is deficient in animal cloning, which is a major explanation for the inefficiency of the cloning procedure. Deficiencies in reprogramming are likely to underlie the occurrence of epimutations and of epigenetic inheritance. Environmental factors can alter epigenetic modifications and may thus have long-lasting effects on phenotype. Epigenomics methods are being developed to catalogue genome modifications under normal and pathological conditions. Epigenetic engineering is likely to play an important role in medicine in the future.

Nuclear transplantation: lessons from frogs and mice

Nuclear transplantation was developed 50 years ago in frogs to test whether nuclei from differentiated cells remain genetically equivalent to zygotic nuclei. Results from cloning experiments in frogs and mice indicate that nuclei gradually lose potency during development from embryonic to adult cells. However, even though adult mature lymphocytes were recently shown to remain genetically totipotent, no evidence exists to show that surviving clones originate from the nuclei of terminally differentiated cells. Thus, it is equally possible that many cloned animals are in fact derived from the nuclei of less differentiated adult cells such as adult stem cells. These cells might be more easily reprogrammed than terminally differentiated cells and may support development of a clone at a higher efficiency. Importantly, irrespective of the donor cell, clones display common abnormalities such as foetal and placental overgrowth. Indeed, gene expression analyses and extensive phenotypic characterisation of cloned animals suggest that most, if not all, clones suffer from at least subtle abnormalities.

Abnormal gene expression in cloned mice derived from embryonic stem cell and cumulus cell nuclei

To assess the extent of abnormal gene expression in clones, we assessed global gene expression by microarray analysis on RNA from the placentas and livers of neonatal cloned mice derived by nuclear transfer (NT) from both cultured embryonic stem cells and freshly isolated cumulus cells. Direct comparison of gene expression profiles of more than 10,000 genes showed that for both donor cell types approximately 4% of the expressed genes in the NT placentas differed dramatically in expression levels from those in controls and that the majority of abnormally expressed genes were common to both types of clones. Importantly, however, the expression of a smaller set of genes differed between the embryonic stem cell- and cumulus cell-derived clones. The livers of the cloned mice also showed abnormal gene expression, although to a lesser extent, and with a different set of affected genes, than seen in the placentas. Our results demonstrate frequent abnormal gene expression in clones, in which most expression abnormalities appear common to the NT procedure whereas others appear to reflect the particular donor nucleus.