Mitochondrial DNA in Day 3 embryo culture medium is a novel, non-invasive biomarker of blastocyst potential and implantation outcome

Mitochondrial DNA quantity as a biomarker for blastocyst implantation potential

Of all the factors currently available for the evaluation of embryonic potential, chromosomal status appears to be the most definitive. The debate around this hotly contested issue does not focus on the question of whether aneuploidy is detrimental to development, but on whether current preimplantation genetic testing for aneuploidy methods are capable of accurately determining whether an embryo is chromosomally normal, aneuploid or a mixture of normal and abnormal cells (i.e., mosaic). Despite the importance of aneuploidy, it is clear that this is only one factor amongst many of relevance to embryo viability, as evidenced by the fact that even the transfer of a chromosomally normal embryo cannot guarantee a pregnancy. Mounting evidence supports the hypothesis that blastocysts having unusually high levels of mitochondrial DNA detected in the trophectoderm have greatly reduced implantation potential, but there remain significant areas where further validation is necessary and where our understanding is currently inadequate. This should provide fertile ground for future research and is likely to yield some fascinating insights in the coming years.

Presence of embryonic DNA in culture medium

Preimplantation genetic diagnosis (PGD) has successfully assisted couples with genetic diseases to conceive healthy babies during the past decades. However, biopsy of the blastomere has potential lesion to the embryos which commonly results in abortion. Thus, a noninvasive PGD is needed. In the past, the presence of genetic materials in maternal plasma or serum has triggered a great innovation of noninvasive prenatal diagnosis. Nevertheless, it is not clear whether embryonic DNA is also present in embryonic culture medium. Here, a rapid-boiling method has been used to harvest DNA from the medium or the discarded embryos, following Polymerase Chain Reaction (PCR) was applied to detect the dissociative DNA by amplifying SRY gene (Y-chromosome). For the first time, the Y sequences were detected in the medium which were used to culture embryo for above 3 days. None of the positive signal was examined in Day 1 and Day 2 embryonic culture medium. Our findings suggest that the Y chromosome fragments from the embryo may release into its culture medium. If validated in a larger cohort, detection of SRY gene may prove to be a useful method to screen Y-linked genetic disease. More importantly, detecting the free DNA in the embryonic culture medium may represent a novel strategy for noninvasive PGD.

The role of the mtDNA set point in differentiation, development and tumorigenesis

Mitochondrial DNA replication is critical for maintaining mtDNA copy number to generate sufficient cellular energy that is required for development and for functional cells. In early development, mtDNA copy number is strictly regulated at different stages, and, as a result, the establishment of the mtDNA set point is required for sequential cell lineage commitment. The failure to establish the mtDNA set point results in incomplete differentiation or embryonic arrest. The regulation of mtDNA copy number during differentiation is closely associated with cellular gene expression, especially with the pluripotency network, and DNA methylation profiles. The findings from cancer research highlight the relationship between mitochondrial function, mtDNA copy number and DNA methylation in regulating differentiation. DNA methylation at exon 2 of DNA polymerase gamma subunit A (POLGA) has been shown to be a key factor, which can be modulated to change the mtDNA copy number and cell fate of differentiating and tumour cells. The present review combines multi-disciplinary data from mitochondria, development, epigenetics and tumorigenesis, which could provide novel insights for further research, especially for developmental disorders and cancers.

Non-invasive pre-implantation aneuploidy screening and diagnosis of beta thalassemia IVSII654 mutation using spent embryo culture medium

BACKGROUND

Cell-free nuclear DNA has been isolated from spent embryo culture medium. Whether this small amount of DNA can be amplified at the whole genome level and the concordance rate of karyotypes and specific alleles between biopsied cells and media has not been evaluated.

METHODS

Seven couples were recruited, 88 donated embryos and their corresponding media were collected for whole genome amplification (WGA). The efficiency of WGA, the concordance of chromosome status, and the HBB gene IVSII654 allele between biopsied cells and media were investigated.

RESULTS

After WGA, the DNA detection rate was 90.90% with a mean concentration of 26.15 ng/μl. The full chromosome concordance rate between biopsied cells and medium was 64.52%, and it increased to 90.00% for diploid blastocyst samples. Analysis of the mutated IVSII654 locus and SNP linkage verified that the DNA present in the medium originated from embryonic cells.

CONCLUSION

We confirmed that nuclear DNA is present in spent culture medium and that the majority of this DNA can be amplified for subsequent analysis. Our results showed that non-invasive embryo genetic testing at the chromosomal-level using medium can concordant to the biopsied cells, but it needs further optimized before use in clinical applications. KEY MESSAGES The aggressive biopsy step during PGD/PGS procedure would have a negative effect on the future development of the embryo. Cell-free nuclear DNA has been observed in spent embryo culture medium, which holds promise for the development of non-invasive PGD/PGS approaches. The presence of DNA in medium, its efficiency for WGA, and the concordance between chromosome status and the HBB gene IVSII654 allele as diagnosed from biopsied cells or medium were investigated. Non-invasive embryo genetic testing at the chromosomal-level and allele site using medium can concordant to the biopsied cells, but it needs further optimized before use in clinical applications.

The embryonic stress response to in vitro culture: insight from genomic analysis

Recent genomic studies have shed light on the impact of in vitro culture (IVC) on embryonic homeostasis and the differential gene expression profiles associated with lower developmental competence. Consistently, the embryonic stress responses to IVC conditions correlate with transcriptomic changes in pathways related to energetic metabolism, extracellular matrix remodelling and inflammatory signalling. These changes appear to result from a developmental adaptation that enhances a Warburg-like effect known to occur naturally during blastulation. First discovered in cancer cells, the Warburg effect (increased glycolysis under aerobic conditions) is thought to result from mitochondrial dysfunction. In the case of IVC embryos, culture conditions may interfere with mitochondrial maturation and oxidative phosphorylation, forcing cells to rely on glycolysis in order to maintain energetic homeostasis. While beneficial in the short term, such adaptations may lead to epigenetic changes with potential long-term effects on implantation, foetal growth and post-natal health. We conclude that lessening the detrimental effects of IVC on mitochondrial activity would lead to significantly improved embryo quality.

Characterizing nuclear and mitochondrial DNA in spent embryo culture media: genetic contamination identified

OBJECTIVE

To characterize nuclear and mitochondrial DNA (mtDNA) in spent culture media from normally developing blastocysts to determine whether it could be used for noninvasive genetic assessment.

DESIGN

Prospective embryo cohort study.

SETTING

Academic center and private in vitro fertilization (IVF) clinic.

PATIENT(S)

Seventy patients undergoing intracytoplasmic sperm injection (ICSI) and 227 blastocysts.

INTERVENTION(S)

Culture media assessment, artificial blastocoele fluid collapse and DNA analysis using digital polymerase chain reaction (dPCR), long-range PCR, quantitative PCR (qPCR), and DNA fingerprinting.

MAIN OUTCOME MEASURE(S)

Presence of nuclear and mtDNA in three different commercial culture media from Vitrolife and Irvine Scientific, spent embryo media assessment at the cleavage and blastocyst stages of development, and analysis of the internal media controls for each patient that had been exposed to identical conditions as embryo media but did not come into contact with embryos.

RESULT(S)

Higher levels of nuclear and mtDNA were observed in the culture media that had been exposed to embryos compared with the internal media controls. Nuclear DNA (∼4 copies) and mtDNA (∼600 copies) could be detected in spent media, and the levels increased at the blastocyst stage. No increase in DNA was detected after artificial blastocoele fluid collapse. Mixed sex chromosome DNA was detected. This originated from contamination in the culture media and from maternal (cumulus) cells. Due to the limited amount of template, the presence of embryonic nuclear DNA could not be confirmed by DNA fingerprinting analysis.

CONCLUSION(S)

Currently DNA from culture media cannot be used for genetic assessment because embryo-associated structures release DNA into the culture medium and the DNA is of mixed origin.

Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization

Preimplantation genetic screening (PGS) is widely used to select in vitro-fertilized embryos free of chromosomal abnormalities and to improve the clinical outcome of in vitro fertilization (IVF). A disadvantage of PGS is that it requires biopsy of the preimplantation human embryo, which can limit the clinical applicability of PGS due to the invasiveness and complexity of the process. Here, we present and validate a noninvasive chromosome screening (NICS) method based on sequencing the genomic DNA secreted into the culture medium from the human blastocyst. By using multiple annealing and looping-based amplification cycles (MALBAC) for whole-genome amplification (WGA), we performed next-generation sequencing (NGS) on the spent culture medium used to culture human blastocysts (n = 42) and obtained the ploidy information of all 24 chromosomes. We validated these results by comparing each with their corresponding whole donated embryo and obtained a high correlation for identification of chromosomal abnormalities (sensitivity, 0.882, and specificity, 0.840). With this validated NICS method, we performed chromosome screening on IVF embryos from seven couples with balanced translocation, azoospermia, or recurrent pregnancy loss. Six of them achieved successful clinical pregnancies, and five have already achieved healthy live births thus far. The NICS method avoids the need for embryo biopsy and therefore substantially increases the safety of its use. The method has the potential of much wider chromosome screening applicability in clinical IVF, due to its high accuracy and noninvasiveness.

Raman-based noninvasive metabolic profile evaluation of in vitro bovine embryos

The timing of the first embryonic cell divisions may predict the ability of an embryo to establish pregnancy. Similarly, metabolic profiles may be markers of embryonic viability. However, in bovine, data about the metabolomics profile of these embryos are still not available. In the present work, we describe Raman-based metabolomic profiles of culture media of bovine embryos with different developmental kinetics (fast x slow) throughout the in vitro culture. The principal component analysis enabled us to classify embryos with different developmental kinetics since they presented specific spectroscopic profiles for each evaluated time point. We noticed that bands at 1076  cm(−1) (lipids), 1300  cm(−1) (Amide III), and 2719  cm(−1) (DNA nitrogen bases) gave the most relevant spectral features, enabling the separation between fast and slow groups. Bands at 1001  cm(−1) (phenylalanine) and 2892  cm(−1) (methylene group of the polymethylene chain) presented specific patterns related to embryonic stage and can be considered as biomarkers of embryonic development by Raman spectroscopy. The culture media analysis by Raman spectroscopy proved to be a simple and sensitive technique that can be applied with high efficiency to characterize the profiles of in vitro produced bovine embryos with different development kinetics and different stages of development.

Nuclear and mitochondrial DNA in blastocoele fluid and embryo culture medium: evidence and potential clinical use

The ability to screen embryos for aneuploidy or inherited disorders in a minimally invasive manner may represent a major advancement for the future of embryo viability assessment. Recent studies have demonstrated that both blastocoele fluid and embryo culture medium contain genetic material, which can be isolated and subjected to downstream genetic analysis. The blastocoele fluid may represent an alternative source of nuclear DNA for aneuploidy testing, although the degree to which the isolated genetic material is solely representative of the developing embryo is currently unclear. In addition to nuclear DNA, mitochondrial DNA (mtDNA) can be detected in the embryo culture medium. Currently, the origin of this nuclear and mtDNA has not been fully evaluated and there are several potential sources of contamination that may contribute to the genetic material detected in the culture medium. There is however evidence that the mtDNA content of the culture medium is related to embryo fragmentation levels and its presence is predictive of blastulation, indicating that embryo development may influence the levels of genetic material detected. If the levels of genetic material are strongly related to aspects of embryo quality, then this may be a novel biomarker of embryo viability. If the genetic material does have an embryo origin, the mechanisms by which DNA may be released into the blastocoele fluid and embryo culture medium are unknown, although apoptosis may play a role. While the presence of this genetic material is an exciting discovery, the DNA in the blastocoele fluid and embryo culture medium appears to be of low yield and integrity, which makes it challenging to study. Further research aimed at assessing the methodologies used for both isolating and analysing this genetic material, as well as tracing its origin, are needed in order to evaluate its potential for clinical use. Should such methodologies prove to be routinely successful and the DNA recovered demonstrated to be embryonic in origin, then they may be used in a minimally invasive and less technical methodology for genetic analysis and embryo viability assessment than those currently available.

The relationship between mitochondrial DNA haplotype and the reproductive capacity of domestic pigs (Sus scrofa domesticus)

Background

The maternally inherited mitochondrial genome encodes key proteins of the electron transfer chain, which produces the vast majority of cellular ATP. Mitochondrial DNA (mtDNA) present in the mature oocyte acts as a template for all mtDNA that is replicated during development to meet the specific energy requirements of each tissue. Individuals that share a maternal lineage cluster into groupings known as mtDNA haplotypes. MtDNA haplotypes confer advantages and disadvantages to an organism and this affects its phenotype. In livestock, certain mtDNA haplotypes are associated with improved milk and meat quality, whilst, other species, mtDNA haplotypes have shown increased longevity, growth and susceptibility to diseases. In this work, we have set out to determine whether mtDNA haplotypes influence reproductive capacity. This has been undertaken using a pig model.

Results

To determine the genetic diversity of domestic pigs in Australia, we have sequenced the D-loop region of 368 pigs, and identified five mtDNA haplotypes (A to E). To assess reproductive capacity, we compared oocyte maturation, fertilization and development to blastocyst, and found that there were significant differences for maturation and fertilization amongst the haplotypes. We then determined that haplotypes C, D and E produced significantly larger litters. When we assessed the conversion of developmentally competent oocytes and their subsequent developmental stages to offspring, we found that haplotypes A and B had the lowest reproductive efficiencies. Amongst the mtDNA haplotypes, the number of mtDNA variants harbored at >25 % correlated with oocyte quality. MtDNA copy number for developmentally competent oocytes positively correlated with the level of the 16383delC variant. This variant is located in the conserved sequence box II, which is a regulatory region for mtDNA transcription and replication.

Conclusions

We have identified five mtDNA haplotypes in Australian domestic pigs indicating that genetic diversity is restricted. We have also shown that there are differences in reproductive capacity amongst the mtDNA haplotypes. We conclude that mtDNA haplotypes affect pig reproductive capacity and can be used as a marker to complement current selection methods to identify productive pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0375-4) contains supplementary material, which is available to authorized users.

Segregation of Naturally Occurring Mitochondrial DNA Variants in a Mini-Pig Model

The maternally inherited mitochondrial genome (mtDNA) is present in multimeric form within cells and harbors sequence variants (heteroplasmy). While a single mtDNA variant at high load can cause disease, naturally occurring variants likely persist at low levels across generations of healthy populations. To determine how naturally occurring variants are segregated and transmitted, we generated a mini-pig model, which originates from the same maternal ancestor. Following next-generation sequencing, we identified a series of low-level mtDNA variants in blood samples from the female founder and her daughters. Four variants, ranging from 3% to 20%, were selected for validation by high-resolution melting analysis in 12 tissues from 31 animals across three generations. All four variants were maintained in the offspring, but variant load fluctuated significantly across the generations in several tissues, with sex-specific differences in heart and liver. Moreover, variant load was persistently reduced in high-respiratory organs (heart, brain, diaphragm, and muscle), which correlated significantly with higher mtDNA copy number. However, oocytes showed increased heterogeneity in variant load, which correlated with increased mtDNA copy number during in vitro maturation. Altogether, these outcomes show that naturally occurring mtDNA variants segregate and are maintained in a tissue-specific manner across generations. This segregation likely involves the maintenance of selective mtDNA variants during organogenesis, which can be differentially regulated in oocytes and preimplantation embryos during maturation.

Extracellular embryo genomic DNA and its potential for genotyping applications

Background:

Preimplantation genetic diagnosis (PGD) currently relies on biopsy of one or few embryo cells. Our aim was to evaluate the embryo extracellular matrices (spent medium and blastocoele fluid) as source of DNA for embryo genotyping.

Results/methodology:

We first evaluated the amplifiability and the amount of genomic DNA in spent embryo culture media from day 3 (n = 32) and day 5/6 (n = 54). Secondly, we evaluated the possibility to genotype the MTHFR polymorphism C677T from media at day 5/6 (n = 8) and blastocoele fluids (n = 9) by direct sequencing. The C677T polymorphism detection rate was 62.5 and 44.4% in medium and fluid, respectively.

Conclusion:

A noninvasive approach for embryo genotyping was possible, but still with limitations due to low detection rate and possible allele dropout.

PGD currently relies on biopsy of embryo cells, which could imply some risk of embryo damage. Since embryo DNA was retrieved both in blastocoele cavity and culture medium, we evaluated if this extracellular DNA could be useful to obtain medical-related genetic information from the embryo. First, we used multicopy genes to verify amplifiability and amount of DNA in medium, then we amplified and sequenced one gene fragment containing a polymorphism of medical importance in a subset of samples. The polymorphism detection rate was not yet high enough to warrant clinical application but we demonstrated that this approach was possible.

Pre-implantation genetic diagnosis and screening: now and the future

Since 1989, the year of the first pre-implantation genetic diagnosis (PGD), many developments occurred both in assisted reproduction techniques and in molecular tools. While PGD is a well-established and documented application, pre-implantation genetic screening (PGS) for the detection of aneuploid embryos is still debated due to the presence of mosaicism in the embryo, but especially to the knowledge of the limits that label an embryo as healthy or as appropriate to the life. The aim of this review is to present the state-of-the-art in the field of PGD and PGS, illustrating its benefits and limitations, along with biopsy techniques and the use of new high-throughput technologies.

Cell-free DNA in Human Follicular Microenvironment: New Prognostic Biomarker to Predict in vitro Fertilization Outcomes

Cell-free DNA (cfDNA) fragments, detected in blood and in other biological fluids, are released from apoptotic and/or necrotic cells. CfDNA is currently used as biomarker for the detection of many diseases such as some cancers and gynecological and obstetrics disorders. In this study, we investigated if cfDNA levels in follicular fluid (FF) samples from in vitro fertilization (IVF) patients, could be related to their ovarian reserve status, controlled ovarian stimulation (COS) protocols and IVF outcomes. Therefore, 117 FF samples were collected from women (n = 117) undergoing IVF/Intra-cytoplasmic sperm injection (ICSI) procedure and cfDNA concentration was quantified by ALU-quantitative PCR. We found that cfDNA level was significantly higher in FF samples from patients with ovarian reserve disorders (low functional ovarian reserve or polycystic ovary syndrome) than from patients with normal ovarian reserve (2.7 ± 2.7 ng/μl versus 1.7 ± 2.3 ng/μl, respectively, p = 0.03). Likewise, FF cfDNA levels were significant more elevated in women who received long ovarian stimulation (> 10 days) or high total dose of gonadotropins (≥ 3000 IU/l) than in women who received short stimulation duration (7–10 days) or total dose of gonadotropins < 3000 IU/l (2.4 ± 2.8 ng/μl versus 1.5 ± 1.9 ng/μl, p = 0.008; 2.2 ± 2.3 ng/μl versus 1.5 ± 2.1 ng/μl, p = 0.01, respectively). Finally, FF cfDNA level was an independent and significant predictive factor for pregnancy outcome (adjusted odds ratio = 0.69 [0.5; 0.96], p = 0.03). In multivariate analysis, the Receiving Operator Curve (ROC) analysis showed that the performance of FF cfDNA in predicting clinical pregnancy reached 0.73 [0.66–0.87] with 88% specificity and 60% sensitivity. CfDNA might constitute a promising biomarker of follicular micro-environment quality which could be used to predict IVF prognosis and to enhance female infertility management.