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Study Finds 1,317 Knocked-out Genes in Sample From Pakistan

By Mahrukh Sarwar

The team discovers a unique family whose 11 members were missing a protein that naturally produces cholesterol; this puts them at a lower risk of heart disease.

Research published in the journal Nature has analyzed the DNA of 10,503 Pakistanis who were participating in a Pakistan Risk of Myocardial Infarction Study (PROMIS) and discovered 1,317 disabled or “knocked-out” genes.

People who are natural knockouts, that is, they were born missing one or more genes without any obvious medical problems are few and far between. Humans inherit two copies of every gene – one from the mother and one from the father. If one copy is damaged or inactivated, then the presence of the other fully functional copy may help alleviate most problems. However, if the parents are biologically related, then the chances of inheriting two inactivated copies are much higher. The person with two inactivated copies may not have the functioning protein at all and will be a natural knockout for that specific gene.

The high number of human knockouts found in the country is due to the cultural tradition of cousin marriages that is prevalent here. Search for human knockouts has also been conducted in other countries including Iceland and the United Kingdom.

In order to study what a particular gene does, scientists have traditionally made use of genetic engineering to breed mice with a mutation in that gene (as this type of experimentation is not possible with humans.) Once they have discovered what the gene does, it is possible to make new drugs that can either block a gene if it is harmful or enhance its positive functions if it turns out to be useful.

However, while such research is informative, evidence from studies in animal knockouts often does not hold for humans. This is explained by a substantial number of failures seen in recent clinical trials that tested new drugs for the prevention of coronary heart disease.

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“Studies in human knockouts can provide data regarding whether natural inhibition of a given pathway is useful or not,” says Dr. Danish Saleheen, lead author and principal investigator of the study published in Nature. This evidence could be translated to develop new drugs, and prioritize or deprioritize existing drug programs. 

Some knocked-out genes protect against disease. Absence of the gene ALOX5 protects against stress-induced memory deficits, synaptic dysfunction and tauopathy which can help prevent Alzheimer’s disease or lower its progression. The discovery of a human PCSK9 knockout who had astonishingly low levels of LDL cholesterol and up to 90% less chances of getting a heart attack has resulted in the development of a new class of drugs that could prevent heart disease.

The lead author of the study stands next to a man with an unusual genetic mutation that could lead to a new treatment for heart disease.

The Nature research study discovered that individuals without the gene APOC3 were protected against coronary heart disease. The protein Apo-CIII is encoded by the APOC3 gene and inhibits hepatic uptake of fats called triglycerides. The team was able to study a family of Pakistanis missing both copies of the APOC3 gene. The human knockouts were given an oral fat load in the form of a milkshake. When compared to other family members who had the gene, individuals with an absence of APOC3 didn’t get a significant post-prandial rise in their blood fat levels and were perfectly healthy. This showed the human knockouts had little artery-clogging fat in their body and had a considerably lower risk of getting a heart attack. So the research team was able to reason that ApoC-III–blocking drugs that are currently in clinical trials could be beneficial in preventing heart disease.

The team was only able to make this discovery after identifying an entire family of natural knockouts for APOC3 in Pakistan. They had been searching for the past four years for someone who was missing both copies of the gene but hadn’t found a single person in the United States and Europe. It was only in Pakistan that they were able to discover a family with both parents and nine children all of whom were missing the gene.

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This Pakistani research study is reportedly the first time where the knockouts found have been tested and their blood biomarkers like cholesterol have been studied to discover more about their health.

As part of this study, knockouts have been found that have not been seen anywhere else in the world. This includes knockouts for NRG4, A3GALT2 and CYP2F1 among others. In addition, the study found 734 genes where both copies were affected by predicted loss-of-function mutations (“double knock-outs”) which had never been described before.

“This cohort of individuals provides a great opportunity for further study and more extensive phenotyping,” says Dr. James Peters, Clinical Research Fellow at the British Heart Foundation. A particular strength of this study is that individuals with a specific mutation can be contacted and brought back for further detailed measurements, he adds. 

However, some geneticists caution that drugs made from this kind of genetic analysis might not be effective. In an article, geneticist Stephen Rich from the University of Virginia in Charlottesville says that inhibiting ApoC-III late in life may not mimic being born with an APOC3 mutation, which protects for a lifetime.

The research team is now calling for a “human knockout project” to make one complete database for all the information coming from new genetics studies. The project would make it possible to systematically conduct deep phenotyping studies on human knockouts and learn more about the natural deletion of those genes in humans. In the future, the team plans on testing the genomes of 200,000 participants from Pakistan to find knockouts of approximately 8,000 genes.

“Such studies provide unprecedented opportunities to understand the function of genes and provide important insights into the development of drugs,” says Dr. Saleheen.

This research study was the result of an international collaboration between scientists from Pakistan, the United Kingdom and the United States.

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  • P A Khan

    Amazing..

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