Doctoral defence: Yan Zhao "Unravelling the mechanisms of chromosomal instability during early embryogenesis"

On 5 March at 16:00 Yan Zhao will defend her doctoral thesis "Unravelling the mechanisms of chromosomal instability during early embryogenesis" for obtaining the degree of Doctor of Gene Technology.

Supervisors:
professor Ants Kurg, University of Tartu
professor Joris Vermeesch, KU Leuven
professor Thierry Voet, KU Leuven

Oponent:
Yan Zhao will defend her doctoral thesis in front of the KU Leuven (Belgium) examination committee, including two members from University of Tartu.

Abstract:
Chromosomal instability (CIN) is a hallmark of preimplantation embryos for mammals such as human and bovine. These chromosomal abnormalities are known to be selected against during development and cause embryo loss, spontaneous abortion, or lead to congenital abnormalities if compatible with live birth.

In the first project, we explored whether CIN observed in human preimplantation embryos also occurs in equine preimplantation embryos. We adapted the haplarithmisis algorithm to be compatible for equine analysis and uncovered frequent chromosomal abnormalities in equine preimplantation embryos, with higher chromosomal errors in arrested cleavage stage embryos compared to blastocysts, similar to findings in human and bovine. The method can be used to select equine embryos devoid of genetic errors and pathogenic variants, while carrying variants of interest. In addition to aneuploidies, whole-genome (WG) aberrations are also detected in preimplantation embryos. For example, triploidy involves the presence of an additional haploid set of chromosomes from one parent. Notably, we recently observed androgenetic, gynogenetic, and polyploid blastomeres coexisting within the same embryo.

In the second project, we explored the origin and developmental potential of these chimeric and mixoploid embryos. We confirmed that parental genomes segregate into distinct blastomeres during the first zygotic division, resulting in the co-occurrence of WG abnormal cells with normal diploid cells or other WG abnormal cells, a process we previously discovered and coined “heterogoneic division”. Stress responses in gene expression contribute to developmental impairment in WG abnormal cells, and their differing developmental fates can explain the formation of androgenotes, gynogenotes, triploidy, chimerism and mixoploidy observed later during development. We therefore recommend haplotype-based preimplantation genetic testing (PGT) for WG abnormalities to enhance baby-take home rates during IVF programs.

With the rapid development of long-read sequencing technology, we explored the performance of long-read whole-genome sequencing (lrWGS)-based comprehensive PGT in the third project. A benchmark study using the Genome in a Bottle (GIAB) Ashkenazi trio demonstrated the high performance of lrWGS data from single cells for variant calling and phasing. Testing lrWGS-based PGT on human embryos showed 100% consistency with array-based comprehensive PGT for single nucleotide variations (SNVs), indels, and aneuploidies, highlighting lrWGS-based PGT as a promising alternative to current methods.

The three projects within this PhD program introduced innovative approaches for embryo study and selection, significantly advancing our understanding of the origins and developmental impacts of chromosomal abnormalities in preimplantation mammalian embryos.