Studying gene function through natural gene knockouts in humans

DATE: 04/03/16
By Vagheesh Narasimhan

Autozygous stretches

Autozygosity and rhLOF in 3,222 individuals. Count of number of individuals with mean number of rhLOF genotypes per individual. Credit Science DOI: /10.1126/science.aac8624

Some people are naturally missing a working copy of one of their genes.  Studying their genome sequences allows us to investigate what our genes do, and has shown us that only a small fraction of our genes are essential for human health.

We know that the human genome has approximately 20,000 genes which code for specific proteins. But what do each of these genes do? Classically, geneticists studied this by inactivating, or “knocking out”, the corresponding gene in mice or other model organisms. Then by observing any differences from normal behaviour or physiology in the mice, researchers tried to infer the probable function of the gene in humans. However learning what the gene does in mice doesn’t always translate to humans.

Perhaps surprisingly, such gene disrupting mutations or loss-of-function (LoF) variants, as they are called in scientific parlance, are found in every human genome sequenced. These mutations are mostly rare and therefore typically affect just one of the two copies we have of almost all genes, leaving the other copy intact. However some people have both the loss-of-function variant in both copies, leading to a knockout of the gene.

In this study, we sequenced over 3,000 healthy individuals from two research studies, the Born in Bradford Study and the UK Asian Diabetics Study.  These studies include a relatively high fraction of people whose parents are related. Such individuals have some portions of their genome that are identical, and so are more likely to carry loss-of-function mutations in both copies.  Approximately one in every four individuals that we sequenced carried rare, but naturally occurring gene knockouts.

By looking at electronic health records we showed that the individuals with gene knockouts were no more likely to visit their doctor than those with all genes intact, nor did they have higher prescription rates. We found over 20 people with knockouts of genes that were previously thought to have been causative for disease, without any sign of the expected disease. One such example was a knockout in the GJB2 gene which had been strongly associated with hearing loss, but the health records of the individual clearly showed normal audiometry (hearing).

This does not mean however that all such knockouts are so well tolerated.  We were able to estimate that we should have seen over 900 gene knockouts, rather than the 781 that we did see.  From this we could estimate that approximately 15% of genes when knocked out would have led to lethality or severe disease. A further consequence is that on average each of us is carrying a genetic burden of two severe recessive mutations, that is we have an average of two loss-of-function mutations which only affect one gene copy, but which if they affected both copies would lead to lethality or severe disease.

Most importantly, our study can be directly informative about novel gene function. We found a woman with a knockout in a gene, PRDM9, which has been extensively studied previously in experimental systems. This gene has been shown to play a central role in the initiation of genetic rearrangement (recombination) during reproduction in mammals, and loss of PRDM9 in mice leads to infertility. To our surprise, the woman with a knockout for this gene was a healthy mother of 3 children, clearly not infertile!

To investigate this further, we used a new experimental technique (single molecule phasing) to find the recombination sites in the genome of one of her children.  The results revealed that a normal number of recombination events had occurred in the mother, but that they were in different locations in the genome to those seen normally.  So in humans, unlike mice, PRDM9 is not needed for recombination, although it does direct where it normally happens.

This study demonstrates the promise of studying gene function directly in humans through naturally occurring knockout mutations in the genomes of healthy people, rather than studying gene function indirectly in model organisms. Sequencing more individuals will allow us to investigate the function of further genes, as well as separate better those mutations that cause disease from those that do not.

Vagheesh Narasimhan is a PhD student at the Wellcome Trust Sanger Institute, studying in Richard Durbin’s Computational Genomics group.

Reference:

Narasimhan et al. (2016) Health and population effects of rare gene knockouts in adult humans with related parents. Science.  DOI:  10.1126/science.aac8624 

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