Global Gene Expression Profiling of Individual Human Oocytes and Embryos Demonstrates Heterogeneity in Early Development Lisa Shaw 1,2,3.¤a , Sharon F. Sneddon 1,2,3.¤b , Leo Zeef 3 , Susan J. Kimber 3 , Daniel R. Brison 1,2 * 1 Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom, 2 Department of Reproductive Medicine, Old St Mary’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom, 3 Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom Abstract Early development in humans is characterised by low and variable embryonic viability, reflected in low fecundity and high rates of miscarriage, relative to other mammals. Data from assisted reproduction programmes provides additional evidence that this is largely mediated at the level of embryonic competence and is highly heterogeneous among embryos. Understanding the basis of this heterogeneity has important implications in a number of areas including: the regulation of early human development, disorders of pregnancy, assisted reproduction programmes, the long term health of children which may be programmed in early development, and the molecular basis of pluripotency in human stem cell populations. We have therefore investigated global gene expression profiles using polyAPCR amplification and microarray technology applied to individual human oocytes and 4-cell and blastocyst stage embryos. In order to explore the basis of any variability in detail, each developmental stage is replicated in triplicate. Our data show that although transcript profiles are highly stage-specific, within each stage they are relatively variable. We describe expression of a number of gene families and pathways including apoptosis, cell cycle and amino acid metabolism, which are variably expressed and may be reflective of embryonic developmental competence. Overall, our data suggest that heterogeneity in human embryo developmental competence is reflected in global transcript profiles, and that the vast majority of existing human embryo gene expression data based on pooled oocytes and embryos need to be reinterpreted. Citation: Shaw L, Sneddon SF, Zeef L, Kimber SJ, Brison DR (2013) Global Gene Expression Profiling of Individual Human Oocytes and Embryos Demonstrates Heterogeneity in Early Development. PLoS ONE 8(5): e64192. doi:10.1371/journal.pone.0064192 Editor: Austin John Cooney, Baylor College of Medicine, United States of America Received January 30, 2013; Accepted April 10, 2013; Published May 22, 2013 Copyright: ß 2013 Shaw et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was funded by Cancer Research UK www.cancerresearchuk.org (grant reference C19686/A6233). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: Daniel.Brison@manchester.ac.uk ¤a Current address: School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, United Kingdom ¤b Current address: School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom . These authors contributed equally to this work. Introduction Development of the human embryo begins at fertilisation with fusion and reprogramming of the gamete pronuclei, followed by a series of cleavage stages and activation of the embryonic genome [1,2,3]. After embryonic genome activation (EGA) and cleavage compaction occurs, the blastocyst forms giving rise to the first differentiated tissues, the trophectoderm and inner cell mass [4]. Although early human development shares many features with other species, there are also some notable differences particularly in the timing of embryonic genome activation (EGA) which has been shown to occur at the two-cell stage in the mouse, four-cell stage in the pig and eight-to sixteen- cell stage in the sheep, cow and rabbit (for a comprehensive review see Telford et al [5]. In the human, EGA was thought to occur at the four-cell stage [1,4,6], however, Vassena et al, [3] has shown EGA may occur in the human embryo as early as the two-cell stage. Our current understanding of this phase of development is limited, and little is known about the molecular mechanisms that control the developmental programme which occurs following fertilisation. This lack of knowledge is a major concern as there is increasing evidence that the genetic and epigenetic blueprint for development is laid down at the preimplantation stage. In this period, parental genomes are reconfigured and the new embryonic genome is activated, methylation imprints are re-established, and the earliest stages of foetal development occur. Data from animal models and human assisted reproduction technologies (ART) has established beyond doubt that this sensitive period is highly vulnerable to perturbation [7]. In ART, the lack of basic understanding of regulators of human embryo viability and health is hampering efforts to select and transfer a single embryo, reducing success rates, increasing risk to offspring, and continuing to expose women to the increased risk of multiple pregnancy from multiple embryo transfer. The inability to characterise normal human embryonic development also has implications for the safety and efficacy of human embryonic stem cell (hESC) technologies, especially with the recent development of these towards clinical therapies. Major aspects of health and disease in adult life are now also widely recognised to originate as early as the preimplantation embryonic PLOS ONE | www.plosone.org 1 May 2013 | Volume 8 | Issue 5 | e64192