Haplotyping-based preimplantation genetic testing reveals parent-of-origin specific mechanisms of aneuploidy formation

Abstract

Chromosome instability is inherent to human IVF embryos, but the full spectrum and developmental fate of chromosome anomalies remain uncharacterized. Using haplotyping-based preimplantation genetic testing for monogenic diseases (PGT-M), we mapped the parental and mechanistic origin of common and rare genomic abnormalities in 2300 cleavage stage and 361 trophectoderm biopsies. We show that while single whole chromosome aneuploidy arises due to chromosome-specific meiotic errors in the oocyte, segmental imbalances predominantly affect paternal chromosomes, implicating sperm DNA damage in segmental aneuploidy formation. We also show that postzygotic aneuploidy affects multiple chromosomes across the genome and does not discriminate between parental homologs. In addition, 6% of cleavage stage embryos demonstrated signatures of tripolar cell division with excessive chromosome loss, however hypodiploid blastomeres can be excluded from further embryo development. This observation supports the selective-pressure hypothesis in embryos. Finally, considering that ploidy violations may constitute a significant proportion of non-viable embryos, using haplotyping-based approach to map these events might further improve IVF success rate.

Parental genomes segregate into distinct blastomeres during multipolar zygotic divisions leading to mixoploid and chimeric blastocysts

“…Single-cell genotyping and haplotyping has shown that chromosomal instability is extremely frequent during the first cleavages of human, bovine, and primate embryos. This instability is the cause of the high incidence of chromosomal aneuploidy and chromosomal mosaicism in cleavage-stage embryos and blastocysts [ 8 – 11 , 66 , 73 ]. To select for euploid embryos, which have a higher implantation and baby-take home rate as compared to aneuploid embryos, preimplantation genetic testing for aneuploidies (PGT-A) has become a standard procedure in many human IVF laboratories world-wide.…”

“…In human, the multipolar zygotic division has been associated with hypodiploid blastomeres and variants of the Polo-like kinase 4 (PLK4) gene [ 1 , 92 ]. Since PLK4 is a centrosome regulator, tripolar spindles generated by centrosomal dysfunction or dysregulation are thought to randomly segregate the diploid chromosome complement in hypodiploid blastomeres, which are characterized by excessive chromosomal losses rather than the segregation of whole parental genomes through heterogoneic division [ 1 , 2 , 73 ]. The majority of GW mosaic bovine embryos described here contain two different paternal haplotypes indicating the oocyte was fertilized by (at least) two sperm, pointing to polyspermic fertilization as a major trigger of multipolar and heterogoneic division of the zygote.…”

“…The development and clinical implementation of concurrent GW haplotyping and copy number profiling of single blastomeres during preimplantation genetic testing (PGT) [ 64 , 76 , 77 ] provides a screen of genome-wide error profiles in human embryos fertilized through ICSI. In a retrospective study, 2300 day-3 single blastomere biopsies derived from 2257 cleavage-stage embryos which reached the blastocyst stage were analyzed [ 73 ]. Embryo culture, biopsy, and biopsy processing for these embryos were performed under a standard clinical workflow for PGT at UZ Leuven, as previously described by [ 138 ].…”

Stem Cell-Based Trophoblast Models to Unravel the Genetic Causes of Human Miscarriages

“…Although extensive research into human aneuploidy has shed light on the mechanisms of its occurrence [ 186 , 187 ], and manifestations in early embryogenesis [ 185 , 188 , 189 ], currently, there is only a superficial understanding of its influence on the further development of the embryo. Which defects of embryogenesis result in the lethality of embryos bearing specific aneuploidies remains unknown.…”

“…The predominance of the meiotic origin of trisomy 16 in embryos [ 187 ], together with its adverse impact on early placental development, explain why it is one of the most frequently observed genetic abnormalities in spontaneous abortions up to 10 weeks of gestation [ 48 ], but is less commonly detected in noninvasive prenatal testing that is usually performed at week 12 [ 226 , 227 ]. The inappropriate trophoblast development observed in trisomy 16 embryos could potentially explain the intrauterine growth restriction and preeclampsia commonly observed in cases of CPM of trisomy 16 [ 228 ].…”