NEW YORK (GenomeWeb) – A team led by researchers from the Wellcome Trust Sanger Institute identified early embryonic mutations, and used them to reconstruct developmental lineages of adult cells. They showed that cells at the two-cell stage of development do not contribute equally to tissue, organ, and blood development.
Mutations that occur during embryo development are fairly randomly distributed through the genome, and the vast majority of them will not affect the developing embryo. However, the formation of somatic mutations has been a longstanding puzzle for researchers, since it has proven to be nearly impossible to study directly.
The new study, published yesterday in Nature, focused in on percentages of variant allele fractions (VAFs) in an attempt to differentiate between mutation types. "Somatic mutations of early embryonic derivations can be distinguished from inherited polymorphisms as they will generally show lower [VAFs]," the researchers wrote.
First author Young Seok Ju, a researcher affiliated with the Wellcome Trust Sanger Institute and the Korea Advanced Institute of Science and Technology, added in a statement that this is the first study of its kind. "There are just a handful of mutations [that arise in very early human development], compared with millions of inherited genetic variations, and finding them allowed us to track what happened during embryogenesis," he said.
The researchers began by collecting 304 blood samples from patients participating as normal controls in the International Cancer Genome Consortium. They extracted DNA from white-blood cells and eliminated 25 samples for contamination. The remaining samples underwent whole-genome sequencing and were analyzed to detect early embryonic mutations. The researchers validated these findings with ultrahigh-depth targeted sequencing.
The team identified 605 somatic base substitutions with accurate VAF estimates, then eliminated some samples to prevent reflection of other conditions. After further analysis, the researchers identified 163 mosaic mutations. They also extracted genomic DNA from formalin-fixed, paraffin embedded lymph nodes and normal breast tissue to confirm that the identified early embryonic mutations were present in other types of somatic cells.
Based on their findings, the researchers used mutations from the first, second, and third divisions of the fertilized egg to calculate the number of adult cells that were produced from the two-cell stage. After running some cell models, they also determined that, based on the VAFs present in the cells, the first two cells contribute differently to whole body development.
"We determined the relative contribution of the first embryonic cells to the adult blood cell pool and found one dominant cell — that led to 70 percent of the blood cells — and one minor cell," Inigo Martincorena, co-author and researcher at the Sanger Institute, said. "We also sequenced normal lymph and breast cells, and the results suggested that the dominant cell also contributes to these other tissues at a similar level."
In addition to identifying mutations and reconstructing early cell division lineages, the researchers were also able to measure the rate of mutation in early human development in up to three generations of cell division. In previous studies, researchers had estimated that there was one mutation per cell division. However, the Sanger-led team actually measured three mutations for each cell doubling, in every daughter cell.
"This is a significant step forward in widening the range of biological insights that can be extracted using genome sequences and mutations," Michael Stratton, senior author and director of the Sanger Institute, said. "Essentially, the mutations are archaeological traces of embryonic development left in our adult tissues, so if we can find and interpret them, we can understand human embryology better. This is just one early insight into human development, with hopefully many more to come in the future."