What happens when we ‘turn off’ a gene?

Heart defects are diagnosed in at least 1 in 180 births. That’s around 12 babies each day in the UK, with more diagnoses later in life.

Environmental influences such as excessive alcohol consumption can cause heart defects. But many are also the result of faulty genes that can be passed on from one generation to the next. Identifying the genes involved is key to understanding how to identify when a baby might be at risk and could also help us develop new ways to treat or prevent these heart defects. But with more than 20,000 genes in the human genome there are a mind-boggling number of possibilities.

Photographs of isolated mouse embryo hearts. On the left is a ‘normal’ heart — this mouse was not missing any genes. On the right, due to a missing gene, the heart has a defect called ‘Double Outlet Right Ventricle’. Here, the heart’s two major arteries (the pulmonary artery and the aorta) both connect to the right ventricle. In a normal heart the aorta connects to the left ventricle.

Dr Jenna Lane, from the DMDD (Deciphering the Mechanisms of Developmental Disorders) programme at the Francis Crick Institute, tells us about their unexpected impacts on hearts when looking at the what happens when we ‘turn off’ genes.

A screen of mouse embryos by the DMDD programme has identified a huge number of genes related to heart defects and other developmental abnormalities, and is now a potential goldmine of information on the genetic basis of heart conditions. Part of an open data initiative by the Wellcome Trust, the project has made all of its data available online, with a goal of helping to spark further research into heart defects and rare disease.

Inactivating genes to understand rare disease

The DMDD team studies mouse embryos that have been bred to have a single one of their 20,000 genes inactivated — a process that’s known as knocking out a gene. As each embryo grows, any abnormalities in the way it develops are likely to be due to the missing gene and this provides powerful information about the sort of birth defects that the gene could be linked to. Although we might look very different, mice and humans are thought to share around 98% of our genes, so the effects of a missing gene on a developing mouse can tell us a lot about what we might expect if the same faulty gene is found in humans.

2D images of mouse embryos taken through the chest and heart using High Resolution Episcopic Microscopy (HREM) at 14.5 days of gestation. The image on the left shows a ‘septal defect’ (red box) — a gap in the developing wall that separates the left and right chambers of the heart — in a mouse that is missing the gene Ssr2. The image on the right is a ‘normal’ heart with a complete septal wall.

We concentrate specifically on genes that, when knocked out, cause a mouse embryo to die before birth. On the face of it, studying these genes might not seem so important to people living with rare genetic diseases — these people have already survived past birth. But genes like these are a rich source of information about human genetic diseases. Many rare disease patients have mutations that act as genetic dimmer switches, increasing or decreasing a gene’s activity rather than turning it off. A particular gene may only be partially turned on (called a hypomorph mutation) or it may be turned on more than normal (known as a hypermorph mutation). If we are able to understand the effect of fully turning off a gene, we can then begin to infer what might happen to patients who have a hypomorph or hypermorph mutation.

By the end of the project, DMDD will have studied the effects of 250 different gene knockouts — it’s a huge opportunity to learn more about genetic causes of rare diseases in humans. And the biggest surprise in the results so far is the overwhelming prevalence of defects in the developing embryo hearts.

This image shows four mouse embryo hearts on a penny. The biggest is from a mouse just before birth, the smallest is from about halfway through gestation.

Identifying heart defects

So far the team have analysed more than 200 embryos, each with one of 42 different genes knocked out. But unexpectedly, more than 80% of the gene deletions resulted in heart defects. Using an imaging technique called High Resolution Episcopic Microscopy the embryos were reconstructed in incredible 3D detail and studied down to the level of individual nerves and blood vessels.

“Even though we know that heart defects are common, we were really surprised that they were caused by more than 80% of our gene deletions. The data is a potential goldmine of information about the genetic basis of many different types of heart condition.” Dr Tim Mohun, DMDD.

The most common defects were problems with the walls that separate the right and left chambers of the heart. But there were also many defects in the heart valves, the outflow vessels (which carry blood out of the heart to the body or the lungs) and in the structure of the heart itself.

Several of the gene knockouts result in developmental defects that mimic known human genetic disorders. For example knocking out the genes Psph or Psat1 causes a range of developmental defects that appear similar to Neu-Laxova syndrome, a serious condition that leads to miscarriage or neonatal death.

Tim Mohun added “We know that many rare genetic diseases cause problems with the heart as it develops. Having so much new data about heart defects is exciting, because there is the potential for us to learn more about rare disease.”
In this image, the developing embryo heart is less than 2mm across — about the same thickness as a matchstick — yet even the tiniest abnormality can be picked up.

The Placenta: a key to understanding the heart?

In the first study of its kind the placentas from a large collection of knockout embryos has also been analysed, and the results show an unexpected link between the placenta and the heart. Around a third of gene knockouts that cause placental abnormalities also cause a heart defect in the developing embryo. A more detailed statistical study of the data has shown that this is a genuine link.

Dr Myriam Hemberger of the Babraham Institute, who performed the work as part of the DMDD programme, said “It could be that the restricted nutrient supply or blood circulation defects caused by an abnormal placenta adversely affect heart development. It does suggest there is more we could learn about some rare heart conditions by studying the placenta.”

Initial analysis of the DMDD embryo and placenta data has shown it to be a rich resource for those studying rare disease and developmental disorders. But, unexpectedly, it may shed particular light onto the genetic basis of heart defects.

All data from the DMDD programme is freely available at dmdd.org.uk. For further information about the project please contact @dmdduk on Twitter.