Chromosomal integrity of human preimplantation embryos at different days post fertilization

Mapping of long interspersed element-1 (L1) insertions by TIPseq provides information about sub chromosomal genetic variation in human embryos

PURPOSE

Retrotransposons play important roles during early development when they are transiently de-repressed during epigenetic reprogramming. Long interspersed element-1 (L1), the only autonomous retrotransposon in humans, comprises 17% of the human genome. We applied the Single Cell Transposon Insertion Profiling by Sequencing (scTIPseq) to characterize and map L1 insertions in human embryos.

METHODS

Sixteen cryopreserved, genetically tested, human blastocysts, were accessed from consenting couples undergoing IVF at NYU Langone Fertility Center. Additionally, four trios (father, mother, and embryos) were also evaluated. scTIPseq was applied to map L1 insertions in all samples, using L1 locations reported in the 1000 Genomes as controls.

RESULTS

Twenty-nine unknown and unique insertions were observed in the sixteen embryos. Most were intergenic; no insertions were located in exons or immediately upstream of genes. The location or number of unknown insertions did not differ between euploid and aneuploid embryos, suggesting they are not merely markers of aneuploidy. Rather, scTIPseq provides novel information about sub-chromosomal structural variation in human embryos. Trio analyses showed a parental origin of all L1 insertions in embryos.

CONCLUSION

Several studies have measured L1 expression at different stages of development in mice, but this study for the first time reports unknown insertions in human embryos that were inherited from one parent, confirming no de novo L1 insertions occurred in parental germline or during embryogenesis. Since one-third of euploid embryo transfers fail, future studies would be useful for understanding whether these sub-chromosomal genetic variants or de novo L1 insertions affect embryo developmental potential.

Blastocyst transfer after extended culture of cryopreserved cleavage embryos improves in vitro fertilization cycle outcomes

Cryopreserved blastocyst embryo transfer has been reported to result in better pregnancy outcomes than those by cleavage embryo transfer. Women who had previously failed in the cleavage-stage embryo transfer, underwent extended culture of their warmed cleavage embryos to the blastocyst stage, thereby improving cryopreserved embryo transfer (CET) outcomes, although the ability of embryos to reach the extended blastocyst as well as the value of the prolonged culture was limited. This study aimed to investigate the effectiveness of blastocyst transfer by extending the culture of vitrified-warmed cleavage embryos. CET cycles were collected from January 2018 to June 2020. Pregnancy outcomes were analyzed and compared between three groups: day 2 embryo transfer using cryopreserved embryos (D2 CET), blastocyst transfer (D5 CET), and extended culture vitrified day 2 embryo transfer (D2-5 CET). A total of 52.77% of vitrified-warmed cleavage embryos developed into blastocysts in D2-5 CET group. Although D2-5 CET had a lower number of transferred embryos and grade A embryos, the pregnancy outcomes were significantly better than those in D2 CET, with respect to hCG positivity, clinical pregnancy and implantation rates (59.62% vs. 24.64%, 46.15% vs. 21.71%, 27.18% vs. 9.09%, respectively, P < 0.05). There were no significant different outcomes between the D2-5 CET and D5 CET groups. This study demonstrated a way of achieving better pregnancy outcomes in 8CET cycles by means of extended culture to blastocysts in patients with vitrified cleavage embryo failure.

The Effect of Teratozoospermia on Sex Chromosomes in Human Embryos

Purpose

The aim of this study is to evaluate the effect of abnormal semen morphology on the frequency of sex chromosomal abnormalities in embryos obtained by ICSI, which represents the first to be studied in Egyptian population.

Methods

Forty-two couples suffering from male infertility due to teratozoospermia were divided into two groups: patients with severe and moderate teratozoospermia (group A and B, respectively). All involved couples were subjected to careful history taking and had a normal clinical examination and karyotype. Females were subjected to hormonal assays, pelvic ultrasound, hysterosalpingography and yielded normal results, while male partners were subjected to computerized semen analysis. Preimplantation genetic diagnosis was performed for all suitably developed embryos including embryo biopsy, fixation of biopsied cells and fluorescent in situ hybridization (FISH) analysis.

Results

Couples included in the two groups were found to be homogenous in terms of age of both partners and duration of infertility. Interpretation of FISH results was performed by evaluation of embryos’ chromosomal constitution as regards abnormalities in chromosomes X, Y and 18. Twenty-seven embryos (48.2%) were found chromosomally abnormal in group A, while only 14 embryos (25.0%) were found chromosomally abnormal in group B. Aneuploidies involved only sex chromosomes were tripled in group A embryos when compared to their frequency in group B embryos (26.8% and 8.3%, respectively) with statistically significant difference between the two groups (p=0.002). Monosomies were the most common type of aneuploidy and were significantly higher in group A (14.3%) when compared to group B (3.6%) (p=0.047). Embryos with mosaic abnormalities were more common in group A (12.5%) when compared to group B (3.6%), however not statistically significantly different (p= 0.162). A significant difference between the two studied groups as regards the total number of potentially viable chromosomal abnormalities detected and the potentially viable sex chromosomal aneuploidies detected (p<0.001 and p=0.002), respectively.

Conclusion

The cases with severe teratozoospermia undergoing ICSI treatment can display a higher rate of sex chromosome aneuploidies in their embryos (threefold) than cases with moderate teratozoospermia.

Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development

Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.

Improving the clinical outcomes by extended culture of day 3 embryos with low blastomere number to blastocyst stage following frozen-thawed embryo transfer

Purpose

This study aimed to investigate whether the extended culture of day 3 (D3) embryos with low blastomere number to blastocyst following frozen–thawed embryo transfer improved the clinical outcomes.

Methods

This was a retrospective study of clinical data of women undergoing in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) cycles in the Tangdu Hospital. The patients were divided into groups with 4–5, 6, 7–9 and > 9 cells based on the blastomere number of D3 embryos. The clinical outcomes were compared.

Results

In fresh transfer cycles, the implantation and clinical pregnancy rates significantly decreased, while the abortion rate significantly increased in the groups with 4–5 and 6 cells compared with those with 7–9 and > 9 cells. In frozen–thawed transfer cycles, the clinical pregnancy and implantation rates for a single blastocyst transfer cycle showed no significant differences in the groups with 4–5 and 6 cells compared with those with 7–9 and > 9 cells. However, the abortion rate was significantly higher in the group with 4–5 cells than in that with 7–9 and > 9 cells. In the double blastocyst transfer cycle, the clinical pregnancy rate showed no significant differences among the groups with 4–5, 6, and 7–9 cells.

Conclusion

The implantation and clinical pregnancy rates of D3 embryos with 6 cells significantly decreased; these embryos were not considered as high-quality embryos. Extended culture of D3 embryos with ≤ 6 blastomeres to blastocysts, particularly 6-cell embryos, resulted in a similar clinical pregnancy rate as that of blastocysts derived from D3 embryos with ≥ 7 blastomeres.

Developmental potential of clinically discarded human embryos and associated chromosomal analysis

Clinically discarded human embryos, which are generated from both normal and abnormal fertilizations, have the potential of developing into blastocysts. A total of 1,649 discarded human embryos, including zygotes containing normal (2PN) and abnormal (0PN, 1PN, 3PN and ≥4PN) pronuclei and prematurely cleaved embryos (2Cell), were collected for in vitro culture to investigate their developmental potential and chromosomal constitution using an SNP array-based chromosomal analysis. We found that blastocyst formation rates were 63.8% (for 2Cell embryos), 22.6% (2PN), 16.7% (0PN), 11.2% (3PN) and 3.6% (1PN). SNP array-based chromosomal analysis of the resultant blastocysts revealed that the percentages of normal chromosomes were 55.2% (2Cell), 60.7% (2PN), 44.4% (0PN) and 47.4% (0PN). Compared with clinical preimplantation genetic diagnosis (PGD) data generated with clinically acceptable embryos, results of the SNP array-based chromosome analysis on blastocysts from clinically discarded embryos showed similar values for the frequency of abnormal chromosome occurrence, aberrant signal classification and chromosomal distribution. The present study is perhaps the first systematic analysis of the developmental potential of clinically discarded embryos and provides a basis for future studies.

The Effect of Prolonged Culture of Chromosomally Abnormal Human Embryos on The Rate of Diploid Cells

Background

A decrease in aneuploidy rate following a prolonged co-culture of human blastocysts has been reported. As co-culture is not routinely used in assisted reproductive technology, the present study aimed to evaluate the effect of the prolonged single culture on the rate of diploid cells in human embryos with aneuploidies.

Materials and Methods

In this cohort study, we used fluorescence in situ hybridi- zation (FISH) to reanalyze surplus blastocysts undergoing preimplantation genetic diagnosis (PGD) on day 3 postfertilization. They were randomly studied on days 6 or 7 following fertilization.

Results

Of the 30 analyzed blastocysts, mosaicism was observed in 26(86.6%), while 2(6.7%) were diploid, and 2(6.7%) were triploid. Of those with mosaicism, 23(88.5%) were determined to be diploid-aneuploid and 3(11.5%) were aneuploid mosaic. The total frequency of embryos with more than 50% diploid cells was 33.3% that was lower on day 7 in comparison with the related value on day 6 (P<0.05); however, there were no differences when the embryos were classified according to maternal age, blastocyst developmental stage, total cell number on day 3, and embryo quality.

Conclusion

Although mosaicism is frequently observed in blastocysts, the prolonged single culture of blastocysts does not seem to increase the rate of normal cells.

Array comparative genomic hybridization analyses of all blastomeres of a cohort of embryos from young IVF patients revealed significant contribution of mitotic errors to embryo mosaicism at the cleavage stage

BACKGROUND

Embryos produced by in vitro fertilization (IVF) have a high level of aneuploidy, which is believed to be a major factor affecting the success of human assisted reproduction treatment. The aneuploidy rate of cleavage stage embryos based on 1-2 biopsied blastomeres has been well-reported, however, the true aneuploidy rate of whole embryos remain unclear because of embryo mosaicism. To study the prevalence of mosaicism in top quality IVF embryos, surplus embryos donated from young patients (aged 28-32) in the assisted reproduction program at Queen Mary Hospital, Hong Kong were used.

METHODS

Thirty-six good quality day 2 embryos were thawed. Out of the 135 blastomeres in these embryos, 121 (89.6%) survived thawing. Twelve of these embryos without lysed blastomeres and which cleaved to at least seven cells after a 24-h culture were dissembled into individual blastomeres, which were analysed by array comparative genomic hybridization and microsatellite marker analysis by fluorescent PCR.

RESULTS

Out of 12 day-3 embryos, 2 (16.7%) were normal, 3 (25%) were diploid/aneuploidy with <38% abnormality, 4 (33.3%) were diploid/aneuploidy mosaic with > =38% abnormality, and three (25%) were mosaic aneuploids. Conclusive chromosomal data were obtained from a high percentage of blastomeres (92.8%, 90/97). Microsatellite marker analysis performed on blastomeres in aneuploid embryos enabled us to reconstruct the chromosomal status of the blastomeres in each cleavage division. The results showed the occurrence of meiotic errors in 3 (25%) of the studied embryos. There were 16 mitotic errors (18.8%, 16/85) in the 85 mitotic divisions undertaken by the studied embryos. The observed mitotic errors were mainly contributed by endoreduplication (31.3%, 5/16), non-disjunction (25%, 4/16) and anaphase lagging (25%, 4/16). Chromosome breakages occurred in 6 divisions (7.1%, 6/85).

CONCLUSIONS

Mosaicism occurs in a high percentage of good-quality cleavage stage embryos and mitotic errors contribute significantly to the abnormality.

Oligonucleotide arrays vs. metaphase-comparative genomic hybridisation and BAC arrays for single-cell analysis: first applications to preimplantation genetic diagnosis for Robertsonian translocation carriers

Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.

CDK1 plays an important role in the maintenance of pluripotency and genomic stability in human pluripotent stem cells

Human embryonic stem cells (hESC) and induced pluripotent stem cells (hiPSC) are characterised by an unusual and tightly regulated cell cycle that has been shown to be important for the maintenance of a pluripotent phenotype. Cyclin-dependant kinase 1 (CDK1) is a key player in cell cycle regulation and particularly mitosis; however, its role has not been studied previously in hESC and hiPSC. To investigate the impacts of CDK1 downregulation, we performed RNA interference studies which in addition to expected mitotic deficiencies revealed a large range of additional phenotypes related to maintenance of pluripotency, ability to repair double strand breaks (DSBs) and commitment to apoptosis. Downregulation of CDK1 led to the loss of typical pluripotent stem cell morphology, downregulation of pluripotency markers and upregulation of a large number of differentiation markers. In addition, human pluripotent stem cells with reduced CDK1 expression accumulated a higher number of DSBs were unable to activate CHK2 expression and could not maintain G2/M arrest upon exposure to ionising radiation. CDK1 downregulation led to the accumulation of cells with abnormal numbers of mitotic organelles, multiple chromosomal abnormalities and polyploidy. Furthermore, such cells demonstrated an inability to execute apoptosis under normal culture conditions, despite a significant increase in the expression of active PARP1, resulting in tolerance and very likely further propagation of genomic instabilities and ensuing of differentiation process. On the contrary, apoptosis but not differentiation, was the preferred route for such cells when they were subjected to ionising radiation. Together these data suggest that CDK1 regulates multiple events in human pluripotent stem cells ranging from regulation of mitosis, G2/M checkpoint maintenance, execution of apoptosis, maintenance of pluripotency and genomic stability.

The clinical outcomes of day 3 4-cell embryos after extended in vitro culture

OBJECTIVE

To evaluate the development potential and clinical significance of day 3 4-cell embryos after extended in vitro culture.

METHODS

This study was a retrospective cohort study for patients with infertility treatment between January 2011 and July 2013. Patients undergoing blastocyst culture in controlled ovarian hyperstimulation cycles using surplus embryos were analyzed in the study. A total of 764 women undergoing blastocyst culture with 1,522 surplus 4-cell embryos on day 3 were analyzed. An additional 2,391 patients with embryos undergoing blastocyst culture during the same period with embryos having more blastomeres were chosen as control.

RESULTS

After extended culture, 253 embryos from 183 cycles in the study group which developed to blastocysts were frozen, and 118 embryos were warmed in subsequent frozen embryo transfer cycles. Implantation rates, clinical pregnancy rates (PRs) and ongoing PRs were 33.3 %, 38.4 % and 31.4 %, respectively, which were similar to those of the control group. The singleton birth weights of newborns using these blastocysts showed no significant difference to that seen in the control group.

CONCLUSION

Surplus 4-cell embryos on day 3 displayed lower blastulation rates. However, once a blastocyst is obtained, it has equivalent clinical outcomes. Embryos that are developmentally lagging on day 3 can be observed in extended culture to increase the cumulative chances of a successful pregnancy.

Detection of monogenic disorders and chromosome aberrations by preimplantation genetic diagnosis

This chapter highlights the methodologies of single cell genetic diagnosis along with the strengths and weaknesses of existing techniques.

Comparative genomic hybridization selection of blastocysts for repeated implantation failure treatment: a pilot study

The aim of this study is to determine if the use of preimplantation genetic screening (PGS) by array comparative genomic hybridization (array CGH) and transfer of a single euploid blastocyst in patients with repeated implantation failure (RIF) can improve clinical results. Three patient groups are compared: 43 couples with RIF for whom embryos were selected by array CGH (group RIF-PGS), 33 couples with the same history for whom array CGH was not performed (group RIF NO PGS), and 45 good prognosis infertile couples with array CGH selected embryos (group NO RIF PGS). A single euploid blastocyst was transferred in groups RIF-PGS and NO RIF PGS. Array CGH was not performed in group RIF NO PGS in which 1-2 blastocysts were transferred. One monoembryonic sac with heartbeat was found in 28 patients of group RIF PGS and 31 patients of group NO RIF PGS showing similar clinical pregnancy and implantation rates (68.3% and 70.5%, resp.). In contrast, an embryonic sac with heartbeat was only detected in 7 (21.2%) patients of group RIF NO PGS. In conclusion, PGS by array CGH with single euploid blastocyst transfer appears to be a successful strategy for patients with multiple failed IVF attempts.

Cell lines from morphologically abnormal discarded IVF embryos are typically euploid and unaccompanied by intrachromosomal aberrations

Routine IVF practices result in the discarding of a significant proportion of embryos due to their unsuitability for transfer or cryopreservation. The present study plated clinically unusable human blastocysts to derive cellular outgrowths for aneuploidy studies and genome-wide analysis of DNA copy number variations, and to evaluate their potential as a source for pluripotent stem cells. Just 79 cellular outgrowths were obtained from 1026 abnormal blastocysts (7.7%), reflecting their low developmental potential. Of these, 13 (16.5%) were karyotypically abnormal and included trisomies frequently detected in miscarriages, each of which was uniform (nonmosaic) and the result of meiotic nondisjunction. Evaluation of submicroscopic DNA gains and losses in 10 diploid cellular outgrowths did not identify increased rates of copy number variations. Five of these outgrowths were shown to express pluripotency markers and could be developed into cell lineages representative of the three germ layers. These data suggest that embryos with chromosomal abnormalities resist cell-line derivation, and mosaic aneuploidy produced from mitotic nondisjunction, common in preimplantation embryos, is likely to be diminished or lost under conditions of diploid cell competition. Furthermore, this work demonstrated that abnormal embryos discarded in IVF programmes can provide a valuable source for pluripotent stem cell lines. During IVF, a large proportion of embryos are clinically unsuitable due to abnormal development and these embryos only have a small chance of achieving a pregnancy. Here we used these abnormal embryos to create cell lines for genetic testing and to determine their potential as stem cells. Of the 1026 abnormal embryos used, 79 (7.7%) created cell lines, reflecting their low developmental potential. Of those, only 16.5% had chromosomal anomalies, a much lower number than expected. This included chromosome abnormalities frequently observed in miscarriages, all of which were found in each cell tested (nonmosaic) and originated from the egg or the sperm as opposed to cell division. In-depth testing of 10 normal cell lines for small DNA gains and losses did not reveal an increased frequency of mutations. Furthermore, five of the cell lines were examined for stem cell properties and found to exhibit the hallmark features of stem cells including their ability to make mature cells from different parts of the body. Our data suggest that embryos with abnormal chromosomes resist making cell lines and that abnormalities that arise during cell division are likely to be lost due to competition with normal cells. We also demonstrated that abnormal embryos usually discarded in IVF programmes can provide a valuable source for stem cell lines.