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Improved prime editing system makes gene-sized edits in human cells at therapeutic levels

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Improved prime editing system makes gene-sized edits in human cells at therapeutic levels


Scientists at the Broad Institute of MIT and Harvard have improved a gene-editing technology that is now capable of inserting or substituting entire genes in the genome in human cells efficiently enough to be potentially useful for therapeutic applications.

The advance, from the lab of Broad core institute member David Liu, could one day help researchers develop a single gene therapy for diseases such as cystic fibrosis that are caused by one of hundreds or thousands of different mutations in a gene. Using this new approach, they would insert a healthy copy of the gene at its native location in the genome, rather than having to create a different gene therapy to correct each mutation using other gene-editing approaches that make smaller edits.

The new method uses a combination of prime editing, which can directly make a wide range of edits up to about 100 or 200 base pairs, and newly developed recombinase enzymes that efficiently insert large pieces of DNA thousands of base pairs in length at specific sites in the genome. This system, called eePASSIGE, can make gene-sized edits several times more efficiently than other similar methods, and is reported in Nature Biomedical Engineering.

“To our knowledge this is one of the first examples of programmable targeted gene integration in mammalian cells that satisfies the main criteria for potential therapeutic relevance,” said Liu, who is senior author of the study, the Richard Merkin Professor and director of the Merkin Institute of Transformative Technologies in Healthcare at the Broad, a professor at Harvard University and a Howard Hughes Medical Institute investigator. “At these efficiencies, we expect that many if not most loss-of-function genetic diseases could be ameliorated or rescued, if the efficiency we observe in cultured human cells can be translated into a clinical setting.”

Graduate student Smriti Pandey and postdoctoral researcher Daniel Gao, both in Liu’s group, were co-first authors on the study, which was also a collaboration with Mark Osborn’s group at the University of Minnesota and Elliot Chaikof’s group at the Beth Israel Deaconess Medical Center.

“This system offers promising opportunities for cell therapies where it can be used to precisely insert genes into cells outside of the body before administering them to patients to treat disease, among other applications,” Pandey said.

“It’s exciting to see the high efficiency and versatility of eePASSIGE, which could enable a new category of genomic medicines,” added Gao. “We also hope that it will be a tool that scientists from across the research community can use to study basic biological questions.”

Prime improvements

Many scientists have used prime editing to efficiently install changes to DNA that are up to dozens of base pairs in length, sufficient to correct the vast majority of known pathogenic mutations. But introducing entire healthy genes, often thousands of base pairs long, in their native location in the genome has been a long-standing goal of the gene-editing field. Not only could this potentially treat many patients regardless of which mutation they have in a disease-causing gene, but it would also preserve the surrounding DNA sequences, which would increase the likelihood that the newly installed gene is properly regulated, rather than expressed too much, too little, or at the wrong time.

In 2021, Liu’s lab reported a key step towards this goal and developed a prime editing approach called twinPE that installed recombinase “landing sites” in the genome, and then used natural recombinase enzymes such as Bxb1 to catalyze the insertion of new DNA into the prime edited target sites.

The biotech company Prime Medicine, co-founded by Liu, soon began using this technology, which they called PASSIGE (prime-editing-assisted site-specific integrase gene editing), to develop treatments for genetic diseases.

PASSIGE installs edits in only a modest fraction of cells, which is enough to treat some but probably not most genetic diseases that result from the loss of a functioning gene. So Liu’s team, in the new work reported today, set out to boost PASSIGE’s editing efficiency. They found that the recombinase enzyme Bxb1 was the culprit in limiting the efficiency of PASSIGE. They then used a tool previously developed by Liu’s group called PACE (phage-assisted continuous evolution) to rapidly evolve more efficient versions of Bxb1 in the lab.

The resulting newly evolved and engineered Bxb1 variant (eeBxb1) improved the eePASSIGE method to integrate an average of 30 percent of gene-sized cargo in mouse and human cells, four times more than the original technique and about 16 times more than another recently published method called PASTE.

“The eePASSIGE system provides a promising foundation for studies integrating healthy gene copies at sites of our choosing in cell and animal models of genetic diseases to treat loss-of-function disorders,” Liu said. “We hope this system will prove to be an important step towards realizing the benefits of targeted gene integration for patients.”

With this goal in mind, Liu’s team is now working on combining eePASSIGE with delivery systems such as engineered virus-like particles (eVLPs) that may overcome hurdles that have traditionally limited therapeutic delivery of gene editors in the body.



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New drug shows promise in clearing HIV from brain

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Improved prime editing system makes gene-sized edits in human cells at therapeutic levels


An experimental drug originally developed to treat cancer may help clear HIV from infected cells in the brain, according to a new Tulane University study.

For the first time, researchers at Tulane National Primate Research Center found that a cancer drug significantly reduced levels of SIV, the nonhuman primate equivalent of HIV, in the brain by targeting and depleting certain immune cells that harbor the virus.

Published in the journal Brain, this discovery marks a significant step toward eliminating HIV from hard-to-reach reservoirs where the virus evades otherwise effective treatment.

“This research is an important step in tackling brain-related issues caused by HIV, which still affect people even when they are on effective HIV medication,” said lead study author Woong-Ki Kim, PhD, associate director for research at Tulane National Primate Research Center. “By specifically targeting the infected cells in the brain, we may be able to clear the virus from these hidden areas, which has been a major challenge in HIV treatment.”

Antiretroviral therapy (ART) is an essential component of successful HIV treatment, maintaining the virus at undetectable levels in the blood and transforming HIV from a terminal illness into a manageable condition. However, ART does not completely eradicate HIV, necessitating lifelong treatment. The virus persists in “viral reservoirs” in the brain, liver, and lymph nodes, where it remains out of reach of ART.

The brain has been a particularly challenging area for treatment due to the blood-brain barrier — a protective membrane that shields it from harmful substances but also blocks treatments, allowing the virus to persist. In addition, cells in the brain known as macrophages are extremely long-lived, making them difficult to eradicate once they become infected.

Infection of macrophages is thought to contribute to neurocognitive dysfunction, experienced by nearly half of those living with HIV. Eradicating the virus from the brain is critical for comprehensive HIV treatment and could significantly improve the quality of life for those with HIV-related neurocognitive problems.

Researchers focused on macrophages, a type of white blood cell that harbors HIV in the brain. By using a small molecule inhibitor to block a receptor that increases in HIV-infected macrophages, the team successfully reduced the viral load in the brain. This approach essentially cleared the virus from brain tissue, providing a potential new treatment avenue for HIV.

The small molecule inhibitor used, BLZ945, has previously been studied for therapeutic use in amyotrophic lateral sclerosis (ALS) and brain cancer, but never before in the context of clearing HIV from the brain.

The study, which took place at the Tulane National Primate Research Center, utilized three groups to model human HIV infection and treatment: an untreated control group, and two groups treated with either a low or high dose of the small molecule inhibitor for 30 days. The high-dose treatment lead to a notable reduction in cells expressing HIV receptor sites, as well as a 95-99% decrease in viral DNA loads in the brain .

In addition to reducing viral loads, the treatment did not significantly impact microglia, the brain’s resident immune cells, which are essential for maintaining a healthy neuroimmune environment. It also did not show signs of liver toxicity at the doses tested.

The next step for the research team is to test this therapy in conjunction with ART to assess its efficacy in a combined treatment approach. This could pave the way for more comprehensive strategies to eradicate HIV from the body entirely.

This research was funded by the National Institutes of Health, including grants from the National Institute of Mental Health and the National Institute of Neurological Disorders and Stroke, and was supported with resources from the Tulane National Primate Research Center base grant of the National Institutes of Health, P51 OD011104.



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Chemical analyses find hidden elements from renaissance astronomer Tycho Brahe’s alchemy laboratory

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In the Middle Ages, alchemists were notoriously secretive and didn’t share their knowledge with others. Danish Tycho Brahe was no exception. Consequently, we don’t know precisely what he did in the alchemical laboratory located beneath his combined residence and observatory, Uraniborg, on the now Swedish island of Ven.

Only a few of his alchemical recipes have survived, and today, there are very few remnants of his laboratory. Uraniborg was demolished after his death in 1601, and the building materials were scattered for reuse.

However, during an excavation in 1988-1990, some pottery and glass shards were found in Uraniborg’s old garden. These shards were believed to originate from the basement’s alchemical laboratory. Five of these shards — four glass and one ceramic — have now undergone chemical analyses to determine which elements the original glass and ceramic containers came into contact with.

The chemical analyses were conducted by Professor Emeritus and expert in archaeometry, Kaare Lund Rasmussen from the Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark. Senior researcher and museum curator Poul Grinder-Hansen from the National Museum of Denmark oversaw the insertion of the analyses into historical context.

Enriched levels of trace elements were found on four of them, while one glass shard showed no specific enrichments. The study has been published in the journal Heritage Science.

“Most intriguing are the elements found in higher concentrations than expected — indicating enrichment and providing insight into the substances used in Tycho Brahe’s alchemical laboratory,” said Kaare Lund Rasmussen.

The enriched elements are nickel, copper, zinc, tin, antimony, tungsten, gold, mercury, and lead, and they have been found on either the inside or outside of the shards.

Most of them are not surprising for an alchemist’s laboratory. Gold and mercury were — at least among the upper echelons of society — commonly known and used against a wide range of diseases.

“But tungsten is very mysterious. Tungsten had not even been described at that time, so what should we infer from its presence on a shard from Tycho Brahe’s alchemy workshop?,” said Kaare Lund Rasmussen.

Tungsten was first described and produced in pure form more than 180 years later by the Swedish chemist Carl Wilhelm Scheele. Tungsten occurs naturally in certain minerals, and perhaps the element found its way to Tycho Brahe’s laboratory through one of these minerals. In the laboratory, the mineral might have undergone some processing that separated the tungsten, without Tycho Brahe ever realizing it.

However, there is also another possibility that Professor Kaare Lund Rasmussen emphasizes has no evidence whatsoever — but which could be plausible.

Already in the first half of the 1500s, the German mineralogist Georgius Agricola described something strange in tin ore from Saxony, which caused problems when he tried to smelt tin. Agricola called this strange substance in the tin ore “Wolfram” (German for Wolf’s froth, later renamed to tungsten in English).

“Maybe Tycho Brahe had heard about this and thus knew of tungsten’s existence. But this is not something we know or can say based on the analyses I have done. It is merely a possible theoretical explanation for why we find tungsten in the samples,” said Kaare Lund Rasmussen.

Tycho Brahe belonged to the branch of alchemists who, inspired by the German physician Paracelsus, tried to develop medicine for various diseases of the time: plague, syphilis, leprosy, fever, stomach aches, etc. But he distanced himself from the branch that tried to create gold from less valuable minerals and metals.

In line with the other medical alchemists of the time, he kept his recipes close to his chest and shared them only with a few selected individuals, such as his patron, Emperor Rudolph II, who allegedly received Tycho Brahe’s prescriptions for plague medicine.

We know that Tycho Brahe’s plague medicine was complicated to produce. It contained theriac, which was one of the standard remedies for almost everything at the time and could have up to 60 ingredients, including snake flesh and opium. It also contained copper or iron vitriol (sulphates), various oils, and herbs.

After various filtrations and distillations, the first of Brahe’s three recipes against plague was obtained. This could be made even more potent by adding tinctures of, for example, coral, sapphires, hyacinths, or potable gold.

“It may seem strange that Tycho Brahe was involved in both astronomy and alchemy, but when one understands his worldview, it makes sense. He believed that there were obvious connections between the heavenly bodies, earthly substances, and the body’s organs. Thus, the Sun, gold, and the heart were connected, and the same applied to the Moon, silver, and the brain; Jupiter, tin, and the liver; Venus, copper, and the kidneys; Saturn, lead, and the spleen; Mars, iron, and the gallbladder; and Mercury, mercury, and the lungs. Minerals and gemstones could also be linked to this system, so emeralds, for example, belonged to Mercury,” explained Poul Grinder-Hansen.

Kaare Lund Rasmussen has previously analyzed hair and bones from Tycho Brahe and found, among other elements, gold. This could indicate that Tycho Brahe himself had taken medicine that contained potable gold.



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Nitrogen emissions have a net cooling effect: But researchers warn against a climate solution

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Improved prime editing system makes gene-sized edits in human cells at therapeutic levels


An international team of researchers has found that nitrogen emissions from fertilisers and fossil fuels have a net cooling effect on the climate. But they warn increasing atmospheric nitrogen has further damaging effects on the environment, calling for an urgent reduction in greenhouse gas emissions to halt global warming.

Published today in Nature, the paper found that reactive nitrogen released in the environment through human activities cools the climate by minus 0.34 watts per square metre. While global warming would have advanced further without the input of human-generated nitrogen, the amount would not offset the level of greenhouse gasses heating the atmosphere.

The paper was led by the Max Planck Institute in Germany and included authors from the University of Sydney. It comes one day after new data from the European Union’s Copernicus Climate Change Service indicated that Sunday, 21 July was the hottest day recorded in recent history.

The net cooling effect occurs in four ways:

  • Short-lived nitrogen oxides produced by the combustion of fossil fuels pollute the atmosphere by forming fine suspended particles which shield sunlight, in turn cooling the climate;

  • ammonia (a nitrogen and hydrogen-based compound) released into the atmosphere from the application of manure and artificial fertilisers has a similar effect;

  • nitrogen applied to crops allows plants to grow more abundantly, absorbing more CO2 from the atmosphere, enabling a cooling effect;

  • nitrogen oxides also play a role in the breakdown of atmospheric methane, a potent greenhouse gas.

The researchers warned that increasing atmospheric nitrogen was not a solution for combatting climate change.

“Nitrogen fertilisers pollute water and nitrogen oxides from fossil fuels pollute the air. Therefore, increasing rates of nitrogen in the atmosphere to combat climate change is not an acceptable compromise, nor is it a solution,” said Professor Federico Maggi from the University of Sydney’s School of Civil Engineering.

Sönke Zaehle from the Max Planck Institute said: “This may sound like good news, but you have to bear in mind that nitrogen emissions have many harmful effects, for example on health, biodiversity and the ozone layer. The current findings, therefore, are no reason to gloss over the harmful effects, let alone see additional nitrogen input as a means of combatting global warming.”

Elemental nitrogen, which makes up around 78 percent of the air, is climate-neutral, but other reactive nitrogen compounds can have direct or indirect effects on the global climate — sometimes warming and at other times cooling. Nitrous oxide (N2O) is an almost 300 times more potent greenhouse gas than CO2. Other forms of nitrogen stimulate the formation of ozone in the troposphere, which is a potent greenhouse gas and enhances global warming.

Professor Maggi said the research was important as it helped the team gain an understanding of the net-effect of the distribution of nitrogen emissions from agriculture.

“This work is an extraordinary example of how complex interactions at planetary scales cannot be captured with simplistic assessment tools. It shows the importance of developing mathematical models that can show the emergence of nonlinear — or unproportional — effects across soil, land, and atmosphere,” he said.

“Even if it appears counter-intuitive, reactive nitrogen introduced in the environment, mostly as agricultural fertilisers, can reduce total warming. However, this is minor compared with the reduction in greenhouse gas emissions required to keep the planet within safe and just operational boundaries.

“New generation computational tools are helping drive new learnings in climate change science, but understanding is not enough — we must act with great urgency to reduce greenhouse gas emissions.”

Gaining a holistic understanding of the impacts of nitrogen

The scientists determined the overall impact of nitrogen from human sources by first analysing the quantities of the various nitrogen compounds that end up in soil, water and air.

They then fed this data into models that depict the global nitrogen cycle and the effects on the carbon cycle, for example the stimulation of plant growth and ultimately the CO2 and methane content of the atmosphere. From the results of these simulations, they used another atmospheric chemistry model to calculate the effect of man-made nitrogen emissions on radiative forcing, that is the radiant energy that hits one square metre of the Earth’s surface per unit of time.



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