Human ‘knockouts’ may reveal why some drugs fail

When scientists want to figure out what a specific gene does in mice, they knock it out. That can’t be done with humans, but some people are natural knockouts—born missing one or more genes. Now, a look at the DNA of 10,500 Pakistanis has found more than 1300 genes that are knocked out without causing obvious medical issues. The results may help confirm why a new heart disease drug flopped in clinical trials, and why another new drug should work just fine.

The study is the latest of several hunts for apparently healthy human knockouts that have included Iceland and the United Kingdom. “The Human Genome Project gave us a parts list of 18,000 genes, and this project is trying to understand what missing a part means in terms of biological consequences,” says heart disease geneticist Sekar Kathiresan of the Broad Institute in Cambridge, Massachusetts, who co-led the study.

In Pakistan, people often marry their first cousins. That raises the odds that a mother and father will both pass identical copies of a mutation in a specific gene to their children. (Unless the mutated gene is on a sex chromosome, both parental copies of a gene have to be disabled for a full knockout.) Kathiresan’s group sequenced the DNA of 10,503 Pakistanis who are participating in a long-term heart disease and diabetes study and found 1317 fully knocked-out genes. The team then looked for abnormalities in about 200 clinical blood biomarkers such as cholesterol.

Seven genes were disabled in at least two people and clearly matched up with some biomarker change, such as unusually low insulin levels, the team reports today in Nature . One codes for an enzyme called Lp-PLA2 that has been linked to arterial plaque. Because higher blood levels of Lp-PLA2 correlate with more heart attacks, drug companies have already spent billions of dollars on Lp-PLA2–blocking drugs. But Pakistanis who lacked one or both copies of the gene didn’t have a lower risk of heart disease, which adds to other genetics studies that may explain why these drugs failed in the clinic.

On the other hand, the study found strong support for another heart disease drug target, a protein called ApoC-III that limits the body’s ability to metabolize fats called triglycerides. Although Kathiresan’s team has studied people missing one copy of the APCO3 gene, “we've been looking for the past 4 years for humans who completely lack it.” They had found none in the United States and Europe, he says, but in Pakistan, his group identified a whole family where both parents and all nine of their children lack the APCO3 gene.

When the family members drank a fat-laden milkshake, their blood fat levels barely rose, suggesting they have little artery-clogging fat in their bodies and should be protected against heart attacks. The family also seemed perfectly healthy, so ApoC-III–blocking drugs now in clinical testing should be safe, Kathiresan predicts. The drugs could eventually join another heart disease–preventing drug that came out of the discovery of a healthy woman missing a gene called PCSK9.

The Pakistani study is the first in which researchers tested some of the knockouts they had found to learn more about their health, says human geneticist David Van Heel of Queen Mary University of London, who last year published a smaller knockout study of British-Pakistanis. Because these individuals are so rare, “we really all need to keep going to sequence more and more people,” he says. About 200,000 Pakistanis would be enough to find knockouts of about 8700 genes, Kathiresan’s team estimates. (Some of these genes are essential to early development, however, so a human knockout would never be born.)

Kathiresan and others is now calling for a Human Knockout Project that would pool all the data coming out of these projects and other large population genetics studies in a single database. Co-author Daniel MacArthur of the Broad Institute will soon release a prototype containing knocked-out genes from a larger collection of human genomes called ExAC. Eventually the plan is to make it possible for academic researchers—and drug companies—to reach out to the leaders of the original study so they can contact an individual knockout from the database and bring the person into a clinic for more testing.