Analysis of DNA Methylation Patterns in Single Blastocysts by Pyrosequencing®

Insights into the autoimmune aspect of premature ovarian insufficiency

Premature ovarian insufficiency (POI) refers to a continuum of decreasing ovarian function in women before the age of 40. To date, the cause of POI in the majority of cases remain unresolved. Many cases has been linked to genetic, toxic, infections, enzymatic and iatrogenic causes. A key function of the immune system is to identify and differentiate "self" and "non self" i.e. tolerance. Loss of self-tolerance results in an immune response against self-tissues and thus autoimmunity. Various investigations have highlighted the role of autoimmunity and its pertinence to POI. Several potential immune antigenic targets in the ovary have been reported to be involved in autoantibody induced autoimmune attack. The presence of lymphocytic oöphorits in ovarian samples of patients with POI provides histopathological evidence of autoimmune ovarian involvement. Finally, POI is strongly associated with other autoimmune conditions including for instance Addison disease, autoimmune polyglandular syndrome (APS) -1, APS-4, hypothyroidism, and diabetes mellitus among other autoimmune diseases. Taken together, these lines of evidence provide strong basis that support the role of autoimmunity as a potential cause of disease etiopathogenesis. Continuing research is increasingly providing more insight into the complex disease process. The aim of this review is to summarize the current literature related to the autoimmune nature of POI.

Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®

Many protocols for gene-specific DNA methylation analysis are either labor intensive, not quantitative and/or limited to the measurement of the methylation status of only one or very few CpG positions. Pyrosequencing is a real-time sequencing technology that overcomes these limitations. After bisulfite modification of genomic DNA, a region of interest is amplified by PCR with one of the two primers being biotinylated. The PCR generated template is rendered single-stranded and a pyrosequencing primer is annealed to analyze quantitatively cytosine methylation. In comparative studies, pyrosequencing has been shown to be among the most accurate and reproducible technologies for locus-specific DNA methylation analyses and has become a widely used tool for the validation of DNA methylation changes identified in genome-wide studies as well as for locus-specific analyses with clinical impact such as methylation analysis of the MGMT promoter. Advantages of the Pyrosequencing technology are the ease of its implementation, the high quality and the quantitative nature of the results, and its ability to identify differentially methylated positions in close proximity.

Inheritance of epigenetic dysregulation from male factor infertility has a direct impact on reproductive potential

OBJECTIVE

To evaluate the epigenetic consequence on the methylome and subsequent transcriptome in euploid blastocysts of male-factor (MF) infertility patients.

DESIGN

Methylome and transcriptome analysis on individual oligoasthenoteratozoospermia (OAT [MF]) blastocysts.

SETTING

Infertility clinic.

PATIENT(S)

Clinical data from 128 couples presenting with OAT (MF) and 118 maternal age-matched control (no MF) subjects undergoing infertility treatment from 2010 to 2014, along with 72 surplus cryopreserved blastocysts donated from 33 couples with their informed consents.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Methyl Maxi-Seq (Zymo Research) was used to determine genome-wide DNA methylation, and small cell number RNA-Seq was used to examine the global transcriptome. Validation experiments were performed with the use of pyrosequencing or quantitative real-time polymerase chain reaction. Statistical analysis used Student t test, analysis of variance in R, Fisher exact test, and pairwise fixed reallocation randomization test where appropriate, with significance at P<.05.

RESULT(S)

Clinical pregnancy rates were similar between OAT (MF) patients and control (no MF) subjects after euploid embryo transfer. However, the miscarriage rate for OAT (MF) patients was significantly higher (14.7% vs. 2.2%; P<.05). Methylome and transcriptome analyses of individual blastocysts revealed significant alterations in 1,111 CpG sites and 469 transcripts, respectively (P<.05). Pathway analysis elucidated genes involved in "regulation of cellular metabolic process" as universally affected. Validation of the genome-wide approaches was performed for SBF1 and SLC6A9 (P<.05).

CONCLUSION(S)

Methylation and transcription aberrations in individual OAT (MF) blastocysts illustrate an epigenetic consequence of MF infertility on embryogenesis, significantly altering key developmental genes and affecting embryonic competence. This epigenetic dysregulation provides an explanation for the reduced reproductive potential in OAT (MF) patients despite euploid blastocyst transfers.

An epigenetic association of malformations, adverse reproductive outcomes, and fetal origins hypothesis related effects

VACTERL, the prototype for associated congenital anomalies, also has connections with functional issues such as pregnancy losses, prematurity, growth delays, perinatal difficulties, and parental subfertility. This segues into a broader association with similar connections even in the absence of malformations. DNA methylation disturbances in the ovum are a likely cause, with epigenetic links to individual components and to folate effects before conception, explaining diverse fetal and placental findings and providing a link to fetal origin hypothesis-related effects. The association encompasses the following: (1) Pre- and periconceptual effects, with frequent fertility issues and occasional imprinting disorders. (2) Early malformations. (3) Adverse pregnancy outcomes (APOs), as above. (4) Developmental destabilization that resolves soon after birth. This potentiates other causes of association findings, introducing multiple confounders. (5) Long-term fetal origins hypothesis-related risks. The other findings are exceptional when the same malformations have Mendelian origins, supporting a distinct pathogenesis. Expressions are facilitated by one-carbon metabolic issues, maternal and fetal stress, and decreased embryo size. This may be one of the commonest causes of adverse reproductive outcomes, but multifactorial findings, variable onsets and phenotypes, and interactions with multiple confounders make recognition difficult. This association supports VACTERL as a continuum that includes isolated malformations, extends the fetal origins hypothesis, explains adverse effects linked to maternal obesity, and suggests possible interventions.

Transcriptomics analysis and human preimplantation development

The study of oocyte and preimplantation embryo biology has been regarded with great curiosity throughout scientific history, but it is not until the development of robust methods for in vitro observation and manipulation of animal gametes that developmental biology has flourished as a discipline. By far the biggest technical challenge in studying transcription in oocytes and early embryo has been the necessity of developing techniques that retain a high level of accuracy when starting from small amount of material. The objective of this narrative review is to summarize the knowledge gained about the embryonic preimplantation period in the human species from transcriptomics experiments, and to discuss technical limitations and solutions to the study of transcriptomics in these samples.

SIGNIFICANCE

In this review we identify key critical issues in performing transcriptomics experiments during the human preimplantation period, and identifying possible ways to overcome them. This, combined with a description of clinical perspectives and the definition of future avenues for research will provide useful for future research.