Comprehensive mitochondrial DNA analysis and IVF outcome

Abstract

Study question: Do mitochondrial DNA (mtDNA) copy number and heteroplasmy in human embryos affect the ongoing pregnancy rate?

Summary answer: Our study suggests that mtDNA copy number above a specific threshold is associated with the ongoing pregnancy rate.

What is known already: Mitochondria play a vital role in cell function. Recently, there has been increasing research on mtDNA as a biomarker of embryo implantation. Although reports showed that high levels of mtDNA in the blastocyst are associated with low implantation potential, other publications were unable to confirm this. Confounding factors may influence the mtDNA copy number in euploid embryos. On the other hand it has been speculated that both mtDNA heteroplasmy and copy number contribute to mitochondrial function. Next generation sequencing (NGS) allows us to study in depth mtDNA heteroplasmy and copy number simultaneously.

Study design size duration: A prospective non-selection study was performed. We included 159 blastocyst biopsies from 142 couples who attended our clinic for preimplantation genetic testing for aneuploidies (PGT-A), from January 2017 to December 2017. All embryos were biopsied on Day 5 or Day 6. The aneuploid testing was performed by NGS. All blastocysts were diagnosed as euploid non-mosaic and were transferred. The mtDNA analysis was performed once the embryo diagnosis was known.

Participants/materials setting methods: Sequencing reads mapping to the mtDNA genome were extracted from indexed bam files to identify copy number and heteroplasmy. The relative measure of mtDNA copy number was calculated by dividing the mtDNA reads by the nuclear DNA value to normalize for technical variants and the number of cells collected at the biopsy. All the results were subjected to a mathematical correction factor according to the embryo genome. Heteroplasmy was assigned by MitoSeek.

Main results and the role of chance: The mean average copy number and SD of mtDNA per genome was 0.0016 ± 0.0012. Regarding heteroplasmy, 40 embryos were heteroplasmy carriers (26.32%). MtDNA variants were detected in coding and non-coding regions and the highest number of variants in an embryo was eight. With respect to IVF outcome for mtDNA copy number analysis, we set a threshold of 0.003 for the following analysis. The vast majority of the embryos were below the threshold (142/159, 89.31%) and 17 embryos were classified as having higher mtDNA levels. We showed a reduction in ongoing pregnancy rate associated with elevated mtDNA copy number (42.96% versus 17.65%, P < 0.05). This result was independent of maternal age and day of the biopsy: these factors were included as confounding factors because mtDNA copy number was negatively correlated with female age (25 -30 y: 0.0017 ± 0.0011, 30 -35 y: 0.0012 ± 0.0007, 35 -40 y: 0.0016 ± 0.0009, over 40 y: 0.0024 + 0.0017, P < 0.05). Embryos biopsied on Day 5 were more likely to have higher quantities of mtDNA compared with those biopsied on Day 6 (0.0017 versus 0.0009, P < 0.001). According to IVF outcome and heteroplasmy, a lower ongoing pregnancy rate was reported for embryos that carried more than two variants. However, this did not reach statistical significance when we compared embryos with a number of variants lower or higher than two (39.15 versus 20.0, P = 0.188). Finally, a clear positive association between the mtDNA variants and copy number was reported when we compare embryos with or without heteroplasmy (0.0013 ± 0.0009 versus 0.0025 ± 0.0014, P < 0.001) and among different numbers of variants (0:0.0013 ± 0.0009, 1-2:0.0023 ± 0.0012, >2:0.0043 ± 0.0014, P < 0.05).

Limitations reasons for caution: A limitation may be the size of the sample and the high-throughput sequencing technology that might not have detected heteroplasmy levels below 2% which requires high sequence depth A clinical randomized trial comparing the clinical outcome after the transfer of embryos selected according to mtDNA levels or only by morphological evaluation will be necessary. More research into the impact of mtDNA heteroplasmy and copy number on IVF outcome is needed.

Wider implications of the findings: Our results demonstrate that embryos with elevated mtDNA copy number have a lower chance of producing an ongoing pregnancy. MtDNA copy number is higher in older women and is dependent upon the number of cell divisions that preceded biopsy. Moreover, our data suggest that mitochondrial activity could be a balance between functional capacity and relative mtDNA copy number.

Study funding/competing interests: There are no conflicts of interest or sources of funding to declare.

Trial registration number: Not applicable.

Keywords: PGT-A; heteroplasmy; implantation rate; mtDNA; ongoing pregnancy.

Figure 1

Association between mitochondrial DNA copy number and maternal and embryo factors. (A) mitochondrial DNA (mtDNA) and maternal factors, (B) mtDNA and embryo factors. PGT-A, preimplantation genetic testing for aneuploidies; RIF, recurrent implantation failure; RPL, recurrent pregnancy loss.

Figure 2

Distribution of mtDNA copy number in the trophoectoderm of human non-mosaic euploid embryos included in the study. The distribution of mtDNA quantity in the euploid blastocyst shows a positive asymmetry and a long kurtosis.

Figure 3

Receiver operating characteristic curve analysis to calculate the discriminative power of mtDNA to predict an ongoing pregnancy.

Figure 4

Association between mtDNA copy number and the presence of heteroplasmy and number of heteroplasmic sites.