Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos

Evolutionary developmental biology (EVO-DEVO) tries to decode evolutionary constraints on the stages of embryonic development. Two models--the "funnel-like" model and the "hourglass" model--have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED) were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA). Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

Gene expression profile differences in embryos derived from prepubertal and adult Japanese Black cattle during in vitro development

The present study was carried out to compare the gene expression profiles of in vitro-generated embryos derived from adult and prepubertal Japanese Black cattle oocytes using GeneChip Bovine Genome Array (containing 24072 probe sets representing over 23000 transcripts). Microarray experiments were performed on populations of 8- to 16-cell stage embryos and blastocysts derived from adult (24-35 months old) versus prepubertal (9-10 months old) Japanese Black cattle oocytes matured and fertilised in vitro. In total, 591 (2.4%) and 490 (2.0%) genes were differentially expressed in prepubertal and adult bovine in 8- to 16-cell and blastocyst stage embryos, respectively. Out of these, 218 and 248 genes were upregulated, while 373 and 242 were downregulated in prepubertal and adult 8- to 16-cell and blastocysts stage embryos, respectively. Gene ontology classification regarding biological process, molecular functions and cellular component revealed diversity in transcript abundances between prepubertal and adult groups in both the distinct developmental stages. Quantitative reverse transcription-PCR validated the expression differences of some selected transcripts as identified by microarray analysis. To our knowledge, this is the first report indicating the significant number of genes differentially expression (>2-fold, P<0.01) in preimplantition embryos between adult and prepubertal Japanese Black cattle during in vitro development.

Embryonic gene expression profiling using microarray analysis

Microarray technology enables the interrogation of thousands of genes at one time and therefore a systems level of analysis. Recent advances in the amplification of RNA, genome sequencing and annotation, and the lower cost of developing microarrays or purchasing them commercially, have facilitated the analysis of single preimplantation embryos. The present review discusses the components of embryonic expression profiling and examines current research that has used microarrays to study the effects of in vitro production and nuclear transfer.

What can we learn from gene expression profiling of mouse oocytes?

Mammalian ooplasm supports the preimplantation development and reprograms the introduced nucleus transferred from a somatic cell to confer pluripotency in a cloning experiment. However, the underlying molecular mechanisms of oocyte competence remain unknown. Recent advances in microarray technologies have allowed gene expression profiling of such tiny specimens as oocytes and preimplantation embryos, generating a flood of information about gene expressions. So, what can we learn from it? Here, we review the initiative global gene expression studies of mouse and/or human oocytes, focusing on the lists of maternal transcripts and their expression patterns during oogenesis and preimplantation development. Especially, the genes expressed exclusively in oocytes should contribute to the uniqueness of oocyte competence, driving mammalian development systems of oocytes and preimplantation embryos. Furthermore, we discuss future directions for oocyte gene expression profiling, including discovering biomarkers of oocyte quality and exploiting the microarray data for ‘making oocytes’.

The quiet embryo hypothesis: molecular characteristics favoring viability

It has been proposed that the viability of early mammalian embryos is associated with a metabolism that is "quiet" rather than "active" (Leese HJ, 2002:BioEssays 24:845-849). The data on which this hypothesis was based were largely drawn from measurements on the depletion and appearance of amino acids from the culture medium. Data on the de novo synthesis of protein in in vivo- and in vitro-derived bovine embryos, as determined from the flux of radiolabeled methionine, have provided further support of the hypothesis and are interpreted to provide a new set of testable propositions that could illuminate the molecular basis of the quiet metabolism phenotype. The propositions are based on the premise that the extent of DNA damage, and the RNA and protein content of the immature oocyte, are key factors in determining whether the zygote progresses to the blastocyst stage. We propose that stochastic events and environmental stresses determine whether the condition of the genome, transcriptome, and proteome of the zygote will support development. Several molecular components are identified that may determine the viability of a zygote, and we speculate that the cellular response to unfavorable events or excessive DNA damage may be the premature activation of the embryonic genome and of apoptosis.

Application of DNA array technology to mammalian embryos

Early embryogenesis depends on a tightly choreographed succession of gene expression patterns which define normal development. Fertilization and the first zygotic cleavage involve major changes to paternal and maternal chromatin and translation of maternal RNAs which have been sequestered in the oocyte during oogenesis. At a critical species-specific point known as the major onset of embryonic expression, there is a dramatic increase in expression from the new diploid genome. The advent of array technology has, for the first time, made possible to determine the transcriptional profile of all approximately 20,000 mammalian genes during embryogenesis, although the small amount of mRNA in a single embryo necessitates either pooling large numbers of embryos or a global amplification procedure to give sufficient labeled RNA for analysis. Following array hybridization, various bioinformatic tools must be employed to determine the expression level for each gene, often based on multiple oligonucleotide probes and complex background estimation protocols. The grouped analysis of clusters of genes which represent specific biological pathways provides the key to understanding embryonic development, embryonic stem cell proliferation and the reprogramming of gene expression after somatic cloning. Arrays are being developed to address specific biological questions related to embryonic development including DNA methylation and microRNA expression. Array technology in its various facets is an important diagnostic tool for the early detection of developmental aberrations; for improving the safety of assisted reproduction technologies for man; and for improving the efficiency of producing cloned and/or transgenic farm animals. This review discusses current approaches and limitations of DNA microarray technology with emphasis on bovine embryos.

Gender effects on the incidence of aneuploidy in mammalian germ cells

Aneuploidy occurs in 0.3% of newborns, 4% of stillbirths, and more than 35% of all human spontaneous abortions. Human gametogenesis is uniquely and gender-specific susceptible to errors in chromosome segregation. Overall, between 1% and 4% of sperm and as many as 20% of human oocytes have been estimated by molecular cytogenetic analysis to be aneuploid. Maternal age remains the paramount aetiological factor associated with human aneuploidy. The majority of extra chromosomes in trisomic offspring appears to be of maternal origin resulting from nondisjunction of homologous chromosomes during the first meiotic division. Differences in the recombination patterns between male and female meiosis may partly account for the striking gender- and chromosome-specific differences in the genesis of human aneuploidy, especially in aged oocytes. Nondisjunction of entire chromosomes during meiosis I as well as premature separation of sister chromatids or homologues prior to meiotic anaphase can contribute to aneuploidy. During meiosis, checkpoints at meiotic prophase and the spindle checkpoint at M-phase can induce meiotic arrest and/or cell death in case of disturbances in pairing/recombination or spindle attachment of chromosomes. It has been suggested that gender differences in aneuploidy may result from more permissive checkpoints in females than males. Furthermore, age-related loss of chromosome cohesion in oocytes as a cause of aneuploidy may be female-specific. Comparative data about the susceptibility of human male and female germ cells to aneuploidy-causing chemicals is lacking. Increases of aneuploidy frequency in sperm have been shown after exposure to therapeutic drugs, occupational agents and lifestyle factors. Conversely, data on oocyte aneuploidy caused by exogenous agents is limited because of the small numbers of oocytes available for analysis combined with potential maternal age effects. The vast majority of animal studies on aneuploidy induction in germ cells represent cause and effect data. Specific studies designed to evaluate possible gender differences in induction of germ cell aneuploidy have not been found. However, the comparison of rodent data available from different laboratories suggests that oocytes are more sensitive than male germ cells when exposed to chemicals that effect the meiotic spindle. Only recently, in vitro experiments, analyses of transgenic animals and knockdown of expression of meiotic genes have started to address the molecular mechanisms underlying chromosome missegregation in mammalian germ cells whereby striking differences between genders could be shown. Such information is needed to clarify the extent and the mechanisms of gender effects, including possible differential susceptibility to environmental agents.

Global gene expression profiling of preimplantation embryos

Preimplantation development is marked by four major events: the transition of maternal transcripts to zygotic transcripts, compaction, the first lineage differentiation into inner cell mass and trophectoderm, and implantation. The scarcity of the materials of preimplantation embryos, both in size (diameter < 100 microm) and in quantity (only a few to tens of oocytes from each ovulation), has hampered molecular analysis of preimplantation embryos. Recent progress in RNA amplification methods and microarray platforms, including genes unique to preimplantation embryos, allow us to apply global gene expression profiling to the study of preimplantation embryos. Our gene expression profiling during preimplantation development revealed the distinctive patterns of maternal RNA degradation and embryonic gene activation, including two major transient waves of de novo transcription. The first wave corresponds to zygotic genome activation (ZGA). The second wave, mid-preimplantation gene activation (MGA), contributes dramatic morphological changes during late preimplantation development. Further expression profiling of embryos treated with inhibitors of transcription or translation revealed that the translation of maternal RNA is required for the initiation of ZGA, suggesting a cascade of gene activation from maternal RNA/protein sets to ZGA gene sets and thence to MGA gene sets. To date, several reports of microarray experiments using mouse and human preimplantation embryos have been published. The identification of a large number of genes and multiple signaling pathways involved at each developmental stage by such global gene expression profiling accelerates understanding of molecular mechanisms underlining totipotency/pluripotency and programs of early mammalian development.

Dynamics of global transcriptome in bovine matured oocytes and preimplantation embryos

Global activation of the embryonic genome is the most critical event in early mammalian development. After fertilization, a rich supply of maternal proteins and RNAs support development whereas a number of zygotic and embryonic genes are expressed in a stage-specific manner leading to embryonic genome activation (EGA). However, the identities of embryonic genes expressed and the mechanism(s) of EGA are poorly defined in the bovine. Using the Affymetrix bovine-specific DNA microarray as the biggest available array at present, we analyzed gene expression at two key stages of bovine development, matured oocytes (MII) and 8-cell-stage embryos, constituting the ultimate reservoir for life and a stage during which EGA takes place, respectively. Key genes in regulation of transcription, chromatin-structure cell adhesion, and signal transduction were up-regulated at the 8-cell stage as compared with 8-cell embryos treated with alpha-amanitin and MII. Genes controlling DNA methylation and metabolism were up-regulated in MII. These changes in gene expression, related to transcriptional machinery, chromatin structure, and the other cellular functions occurring during several cleavage stages, are expected to result in a unique chromatin structure capable of maintaining totipotency during embryogenesis and leading to differentiation during postimplantation development. Dramatic reprogramming of gene expression at the onset of development also has implications for cell plasticity in somatic cell nuclear transfer, genomic imprinting, and cancer.

Transcriptional Profiling of Pig Embryogenesis by Using a 15-K Member Unigene Set Specific for Pig Reproductive Tissues and Embryos1

Differential mRNA expression patterns were evaluated between germinal vesicle oocytes (pgvo), four-cell (p4civv), blastocyst (pblivv), and in vitro-produced four-cell (p4civp) and in vitro-produced blastocyst (pblivp) stage embryos to determine key transcripts responsible for early embryonic development in the pig. Five comparisons were made: pgvo to p4civv, p4civv to pblivv, pgvo to pblivv, p4civv to p4civp, and pblivv to pblivp. ANOVA (P < 0.05) was performed with the Benjamini and Hochberg false-discovery-rate multiple correction test on each comparison. A comparison of pgvo to p4civv, p4civv to pblivv, and pgvo to pblivv resulted in 3214, 1989, and 4528 differentially detected cDNAs, respectively. Real-time PCR analysis on seven transcripts showed an identical pattern of changes in expression as observed on the microarrays, while one transcript deviated at a single cell stage. There were 1409 and 1696 differentially detected cDNAs between the in vitro- and in vivo-produced embryos at the four-cell and blastocyst stages, respectively, without the Benjamini and Hochberg false-discovery-rate multiple correction test. Real-time polymerase chain reaction (PCR) analysis on four genes at the four-cell stage showed an identical pattern of gene expression as found on the microarrays. Real-time PCR analysis on four of five genes at the blastocyst stage showed an identical pattern of gene expression as found on the microarrays. Thus, only 1 of the 39 comparisons of the pattern of gene expression exhibited a major deviation between the microarray and the real-time PCR. These results illustrate the complex mechanisms involved in pig early embryonic development.

Molecular biology of preimplantation embryos: primer for philosophical discussions

This article is based on a presentation at the First International Conference on Ethics, Science and Moral Philosophy of Assisted Human Reproduction. The goal is to provide scientific background for the discussion of philosophic issues. Recent advances in the systematic molecular analysis of preimplantation embryos are summarized, including the molecular identification of nearly all genes involved in preimplantation development and their detailed expression patterns. Notwithstanding a quantum leap in molecular understanding of preimplantation embryos, molecular evidence seems to provide no decisive definition of a threshold for the beginning of human life during preimplantation development.

Whole-genome approaches for large-scale gene identification and expression analysis in mammalian preimplantation embryos

The elucidation, unravelling and understanding of the molecular basis of transcriptional control during preimplantion development is of utmost importance if we are to intervene and eliminate or reduce abnormalities associated with growth, disease and infertility by applying assisted reproduction. Importantly, these studies should enhance our knowledge of basic reproductive biology and its application to regenerative medicine and livestock production. A major obstacle impeding progress in these areas is the ability to successfully generate molecular portraits of preimplantation embryos from their minute amounts of RNA. The present review describes the various approaches whereby classical embryology fuses with molecular biology, high-throughput genomics and systems biology to address and solve questions related to early development in mammals.

Conserved and divergent paths that regulate self-renewal in mouse and human embryonic stem cells

The past few years have seen remarkable progress in our understanding of embryonic stem cell (ES cell) biology. The necessity of examining human ES cells in culture, coupled with the wealth of genomic data and the multiplicity of cell lines available, has enabled researchers to identify critical conserved pathways regulating self-renewal and identify markers that tightly correlate with the ES cell state. Comparison across species has suggested additional pathways likely to be important in long-term self-renewal of ES cells including heterochronic genes, microRNAs, genes involved in telomeric regulation, and polycomb repressors. In this review, we have discussed information on molecules known to be important in ES cell self-renewal or blastocyst development and highlighted known differences between mouse and human ES cells. We suggest that several additional pathways required for self-renewal remain to be discovered and these likely include genes involved in antisense regulation, microRNAs, as well as additional global repressive pathways and novel genes. We suggest that cross species comparisons using large-scale genomic analysis tools are likely to reveal conserved and divergent paths required for ES cell self-renewal and will allow us to derive ES lines from species and strains where this has been difficult.

Genome activation and developmental block in bovine embryos

The ultimate goal of in vitro embryo culture systems is to perfectly mimic the condition of oocyte maturation, fertilization and embryo development. These systems are far more complex than standard in vitro cell culture because of the various environments through which the gametes and embryos pass during in vivo development. Improvement of the medium and other culture conditions has allowed for full development of a percentage of the fertilized oocytes but the great majority of bovine zygotes stop developing within a few cell cycles after initiating cleavage. This developmental block arises in the bovine embryo at the eight-cell-stage and is likely correlated with the cytoplasmic quality of the oocyte. Oocytes harbor all mRNAs and proteins needed to reach the fourth or fifth cell cycle, however, embryos that fail to transcribe their own genome fail to further develop. In this article, we review some of the advances in developmental block knowledge and describe a possible role of active embryo transcription that drives incompetent embryos to block and death.

Human embryo implantation: current knowledge and clinical implications in assisted reproductive technology

A pregnancy rate of approximately 15% per cycle renders the process of human reproduction inefficient. The cycle-dependent expression of molecules involved in the embryo-endometrial dialogue has lead to the identification of a 'window of implantation'. This is the unique temporal and spatial expression of factors that allows the embryo to implant (via signalling, appositioning, attachment and invasion) in a specific time frame of 48 h, 7-10 days after ovulation. Integrin molecules, L-selectin ligands, mucin-1, heparin-binding epidermal growth factor and pinopodes are involved in appositioning and attachment. The embryo produces cytokines and growth factors [interleukins, prostaglandins, vascular endothelial growth factor (VEGF)] and receptors for endometrial signals (leukaemia inhibitory factor receptor, colony stimulating factor receptor, insulin-like growth factors and heparin binding epidermal growth factor receptor). The immune system plays an important role. Immunomodulatory factors such as glycodelin, inhibin and interleukin prevent a graft-versus-host reaction. Angiogenesis controlled by VEGF and prostaglandins is needed for formation of a receptive endometrium and a placenta. Identification of these factors has led to their use as markers of implantation that may identify defects causing subfertility. An ideal marker of implantation is sensitive and specific, and easy to obtain without disturbing implantation. Glycodelin and leukaemia inhibitory factor (serum) and integrins and pinopodes (biopsies) are promising candidates.