Missing Genes Point to Possible Drug Targets

Human knockout projectEvery person’s genetic blueprint, or genome, is unique because of variations that occasionally occur in our DNA sequences. Most of those are passed on to us from our parents. But not all variations are inherited—each of us carries 60 to 100 “new mutations” that happened for the first time in us. Some of those variations can knock out the function of a gene in ways that lead to disease or other serious health problems, particularly in people unlucky enough to have two malfunctioning copies of the same gene. Recently, scientists have begun to identify rare individuals who have loss-of-function variations that actually seem to improve their health—extraordinary discoveries that may help us understand how genes work as well as yield promising new drug targets that may benefit everyone.

In a study published in the journal Nature, a team partially funded by NIH sequenced all 18,000 protein-coding genes in more than 10,500 adults living in Pakistan [1]. After finding that more than 17 percent of the participants had at least one gene completely “knocked out,” researchers could set about analyzing what consequences—good, bad, or neutral—those loss-of-function variations had on their health and well-being.

Gene knockouts are expected to occur more frequently in certain countries, such as Pakistan, where people sometimes marry and have children with their first cousins. That makes it much more likely that a person carrying a loss-of-function gene variation will have inherited that same variation from both of their parents.

In the latest study, a team led by Sekar Kathiresan at the Broad Institute of Harvard and MIT, Boston, turned to the Pakistan Risk of Myocardial Infarction Study (PROMIS) in hopes of finding more gene knockouts. The PROMIS study serves as resource for researchers to study various aspects of heart disease, including its genetics. Nearly 40 percent of participants have parents who were cousins, while roughly the same number had married a cousin.

With the genomic sequencing data in hand, the researchers’ work was just beginning. They next analyzed the participants’ health histories, looking for associations between loss-of-function gene variations and about 200 disease or biochemical traits tracked as a part of the PROMIS study. These traits include cholesterol levels, various hormones levels, and whether a person has asthma or diabetes. Their analyses uncovered associations between 26 loss-of-function variations and at least one of the traits.

One of the most striking examples involves a gene called APOC3, known to code for a protein that acts as a “brake” on the clearance of dietary fat, or triglycerides, from the bloodstream. In 2014, Kathiresan and his colleagues published a paper showing people carrying one malfunctioning copy of APOC3 have lower triglycerides and a 40 percent lower risk of a heart attack [2]. The findings suggested that when the APOC3 brake was not working at normal levels, cholesterol and other lipids were removed from the bloodstream faster.

It was exciting news, suggesting that drugs targeting APOC3 might lower harmful triglycerides and offer protection against heart disease in people without that genetic advantage. But because researchers had yet to find a person with two malfunctioning copies of the APOC3 gene, there were concerns that reducing the ApoC3 protein further might prove harmful.

Kathiresan and his colleagues have now perhaps laid that fear to rest. In their new study, they found a Pakistani man who carried the APOC3 knockout and met some of his family members. Additional testing showed that his wife carried the same loss-of-function APOC3 gene as did their nine children! All appeared healthy and, with some further testing, the researchers found when these “human gene knockouts” consumed a high-fat meal, they cleared the fat from their bloodstream far better than family members with normal functioning APOC3 genes.

In another intriguing example, the researchers found that people without a working PLA2G7 gene, which is thought to influence the buildup of plaque in arteries, are not protected against cardiovascular disease. That finding might help to explain why costly efforts to produce a heart-healthy drug targeting the PLA2G7 protein recently ended in failure.

As promising as it may be, this collection of 1,300 or so human gene knockouts in Pakistan represents what is likely just the start of a rapidly growing area of scientific research and drug development. Ultimately, the hope is to enable researchers and drug developers to search a database, find a gene and a person with a corresponding knockout, and then conduct additional studies to figure out how that particular loss of the gene function affects human biology. One potential way to discover more of these unique individuals is NIH’s new All of Us Research Program, which will aim to enroll one million American volunteers in a long-term study that will ultimately include DNA sequencing.

References:

[1] Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Saleheen D et al. Nature. 2017 April 12 544: 235-239.

[2] Loss-of-function mutations in APOC3, triglycerides, and coronary disease.TG and HDL Working Group of the Exome Sequencing Project, National Heart, Lung, and Blood Institute. N Engl J Med. 2014 Jul 3;371(1):22-31.

Links:

The Pakistan Risk of Myocardial Infarction Study (Center for Non Communicable Diseases, Karachi, Pakistan)

Sekar Kathiresan (Massachusetts General Hospital, Boston)

All of Us Research Program (NIH)

NIH Support: National Human Genome Research Institute; National Heart, Lung, and Blood Institute

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