In 2008, pediatric cardiologist Deepak Srivastava treated a newborn baby who suffered from acute heart failure and had to be put on life support. At the time, the Gladstone Institutes physician-researcher didn’t know what had caused the emergency. But when he found out that the baby’s parents had previously lost a child at 24 weeks into the pregnancy, Srivastava became suspicious that there was a genetic component to the disease.
In 2011, Srivastava and collaborators used whole-exome sequencing to search for genetic variants in Tatiana, by then three years old, and her parents. It turned out that Tatiana’s father had mutations in MYH7 and MKL2 (also known as MRTFB or myocardin related transcription factor B), genes important for heart and muscle development. Her mother, meanwhile, had a variant of the NKX2-5 gene, which encodes a cardiac-specific protein involved in regulating embryo development. Each mutation led to a single amino acid difference at the protein level.
The researchers examined the parents’ hearts and found that the father showed subtle signs of lowered heart function, while the mother was apparently unaffected by her mutation. The researchers also used whole-exome sequencing to scan the genomes of Tatiana’s older sister, Anna, and of tissue from the failed pregnancy that was sampled during an autopsy. They found that all three children had inherited all three genetic mutations—and, on further examination, that they all had similar heart problems. Each child’s left ventricle had failed to mature properly, and their hearts were thus unable to pump blood effectively.
The researchers decided to experimentally investigate whether the combination of the parents’ mutated genes might be responsible for the children’s symptoms. They used CRISPR technology to recreate the same genetic mutations in mice and found that, although animals with just one of the mutations had normal phenotypes, mice with all three mutations had heart pathology similar to the children’s (Science, 364:865-870, 2019). The team also created induced pluripotent stem cells from the parents and Tatiana, and differentiated them into beating heart cells in vitro. When compared with cells from the father or mother, cells derived from Tatiana’s tissue showed reduced adhesion to the cell-culture dish, along with lowered expression of adhesion-related genes and higher expression of genes associated with immature heart-cell stages.
It seems that the genetic mutation the children inherited from their mother acts as a modifier for the father’s mutations, says Srivastava. The NKX2-5 variant appears to have exacerbated the abnormal development caused by the father’s mutations, leading to a phenotype that is more severe in the children than in either of the parents.
The phenomenon of a handful of genes together determining a phenotype is known as oligogenic inheritance, and it’s not a new theory for disease mechanisms. Traditionally, “we’ve be able to understand human disease through [single gene] disorders that are relatively rare but easier to detect,” says Srivastava. Yet the fact that many genetic variants are not deterministic of disease “would suggest most disease is a combination of genes,” he tells The Scientist.
“What is important here is that they used different techniques to show that this is really oligogenic inheritance,” says muscle researcher Nyamkhishig Sambuughin of the Uniformed Services University of the Health Sciences who was not involved in the study. “It not only explains genetic mechanism, but it also explains disease mechanism, which I think will be very important,” as it could guide the development of therapeutics.
With advances in techniques such as gene editing, researchers will increasingly be able to focus on the functional effects of mutations in multiple genes, says Nicholas Katsanis, a geneticist at Lurie Children’s Hospital and Northwestern University who was also not involved in the work. “As more papers like this one come out, we’ll all come to accept the idea that you cannot explain a disease by a single allele of a gene.”
Picking apart multiple genes’ effects is challenging, however. With some diseases, the genes involved could number in the dozens or more. “We are not able to experimentally validate all possible candidates for such oligogenic inheritance patterns,” says Artem Kim, a geneticist and bioinformatician at Université de Rennes who did not take part in the work. Current bioinformatics approaches are able to identify genes that have strong effects on phenotype, says Kim, but struggle to detect those with subtle effects that are common in oligogenic disorders.
To test more combinations of gene variants, Srivastava and collaborators are now developing CRISPR-based single-cell technologies to help them assay hundreds of gene variants in thousands of cells. Ultimately, says Srivastava, identifying additional genetic modifiers like the mother’s variant in this study may be key to understanding and developing therapies for oligogenic diseases.