Scientists at Duke University say they have connected rare and precise duplications and deletions in the human genome to their complex disease consequences by duplicating them in zebrafish. The findings are based on studies of five people missing a small fragment of their genome and suffering from a mysterious syndrome of craniofacial features, visual anomalies, and developmental delays, according to the researchers.
When those patient observations were coupled to analyses of the anatomical defects in genetically altered zebrafish embryos, the investigators were able to identify the contribution specific genes made to the pathology. They believe they have developed a new tool that can now be applied to unraveling many other complex and rare human genetic conditions.
The findings in the research article (“SCRIB and PUF60 Are Primary Drivers of the Multisystemic Phenotypes of the 8q23.4 Copy-Number Variant”) are broadly important for human genetic disorders because copy-number variants (CNVs), which are fragments of the genome that are either missing or existing in extra copies, are quite common. But their precise contribution to diseases has been difficult to determine because CNVs can affect the function of many genes simultaneously.
“Because a CNV can perturb many genes, it is difficult to know which of them is responsible,” said Nicholas Katsanis, Ph.D., a professor of cell biology who directs the Center for Human Disease Modeling and the Task Force for Neonatal Genomics at Duke.
Last year, Dr. Katsanis and his team found they could trace recurrent copy-number variants and dissect the consequences of each perturbed gene to particular features in patients. The new study goes one step further by showing that they can also do this in more challenging cases, when CNVs differ in size from one individual to the next. In this case, “each person has his or her own private deletion or duplication,” added Dr. Katsanis, with the potential to affect a different number of genes.
The researchers showed that partially overlapping microdeletions found in the human patients include a region that contains three genes. By manipulating those genes in zebrafish, first one at a time and then in combination, they were able to connect the genes to specific features of the human syndrome.
“Fine mapping localized a commonly deleted 78 kb region that contains three genes: SCRIB, NRBP2, and PUF60,” write the researchers in the American Journal of Human Genetics. “In vivo dissection of the CNV showed discrete contributions of the planar cell polarity effector SCRIB and the splicing factor PUF60 to the syndromic phenotype, and the combinatorial suppression of both genes exacerbated some, but not all, phenotypic components. Consistent with these findings, we identified an individual with microcephaly, short stature, intellectual disability, and heart defects with a de novo c.505C>T variant leading to a p.His169Tyr change in PUF60.”
In principle, the Duke group says they can now examine the role of copy-number variants in any human syndrome, so long as the condition is associated with features that are measurable in the fish.
“We will need to study lots of CNVs to find the edges of our capabilities,” explained Dr. Katsanis. “As we add this layer of dissection and interpretation, we will have prediction, diagnosis, and the beginnings of biological understanding.”