Scientists from the Allen Institute and Seattle Children’s Research Institute have announced a breakthrough in the development of gene replacement therapies for Dravet syndrome, a rare form of epilepsy. According to details published in a Science Translational Medicine paper, mice treated with the new therapy survived and had alleviated symptoms and long-term recovery without toxicity and negative side effects. The paper is titled, “Interneuron-specific dual-AAV SCN1A gene replacement corrects epileptic phenotypes in mouse models of Dravet syndrome.”

Dravet syndrome is a severe and difficult to treat condition that is typically caused by a loss-of-function mutation in the SCN1A gene which encodes a sodium channel protein that is involved in brain cell signaling. This mutation leads to problems with interneurons, brain cells that help regulate brain activity. The disease, which is characterized by severe seizures and developmental delays, affects 1 in 15,700 children.

“People who take drugs for epilepsy often complain that the drugs are very impactful, they can slow down the seizures but it changes a lot about their brain,” said Boaz Levi, PhD, associate investigator at the Allen Institute and one of the lead scientists on the study. The goal of the new therapy was “to be very precise” and “just deliver the gene that’s missing.” The result is a treatment that is safer and more effective with significantly fewer side effects, he said.

To ensure that the genes were delivered to the precise location in the defective genes, the researchers used specialized enhancers, short stretches of DNA that act like switches to control when and where specific genes are turned on. They also had to solve the problem of delivering the gene. The conventional approach using adeno-associated viruses would not work for SCN1A because of the gene’s size. Their workaround was to split the gene into two parts and carry each half in separate AAVs. The halves are delivered to the same cells and fused together to make the final gene at their destination.

According to results reported in the paper, dual or single injections of the therapy, dubbed DLX2.0-SCN1A, into mice “did not result in increased mortality, weight loss, or gliosis as measured by immunohistochemistry.”

These results are promising for patients living with Dravet who would “have a severely impacted standard of living” without treatment, Levi said. “We are hopeful this sort of therapy could have a huge impact on families and that’s what’s exciting to me.”

An international team of scientists has—for the first time, they suggest—systematically analyzed somatic mutations in stomach lining tissue to unpick mutational processes, some of which can lead to cancer. The results from their newly reported study in addition uncovered hints of a potential new cause of stomach cancer that needs further research.

The researchers, including scientists at the Wellcome Sanger Institute, Broad Institute of MIT and Harvard, the University of Hong Kong, and collaborators, sequenced the whole genomes of normal stomach lining samples from people with and without gastric cancer. They discovered that cells with “driver” mutations in cancer genes occupy almost 10% of the gastric lining by age 60 years, and in addition reported the unusual finding that gastric cells in some, but not all, individuals carried three copies of certain chromosomes, hinting toward exposure to an unknown mutagen.

Tim Coorens, PhD, previously at the Wellcome Sanger Institute and now at the Broad Institute of MIT and Harvard, said, “By studying somatic mutations in normal tissues, which we acquire over our lifetimes, we can explore the earliest stages of cancer development. We found that despite constant exposure to acidic stomach contents, the stomach lining is protected. However, in those with gastric cancer, we see higher numbers of mutations in normal cells, resembling the earliest stages of stomach cancer.” The study, Coorens noted, “… adds to a mutation map of the gastrointestinal tract, including the esophagus, stomach, small intestine, and colon, to compare mutation rates and mutational processes across the body.”

The work will support researchers as they explore fundamental mutational processes and compare mutation rates across the body, with a view to further understanding the earliest stages of cancer development. Coorens is first author of the team’s published paper in Nature, titled, “The somatic mutation landscape of normal gastric epithelium,” in which the team concluded: “Our findings provide insights into intrinsic and extrinsic influences on somatic evolution in the gastric epithelium in healthy, precancerous and malignant states.”

Gastric—or stomach—cancer is the fifth most common cancer worldwide, with nearly one million new cases in 2022, the authors reported. It is the third leading cause of cancer-related deaths globally, with the highest number of cases in East Asia and South America.

“The epidemiology of gastric cancer indicates that many extrinsic factors, through exposures and chronic inflammation, influence somatic mutagenesis in the stomach,” they further stated. Factors that increase the risk of developing stomach cancer include being overweight, smoking, and infection with the bacterium, Helicobacter pylori, which can trigger inflammation and stomach ulcers. H. pylori infection causes around 40% of stomach cancers in the U.K.

The stomach acts as a reservoir at the first stage of processing food for digestion, and its contents are acidic. The layer of cells that line the stomach—the gastric epithelium—form gastric glands, or pits, and these contain the cells that can give rise to stomach cancer.

The cells in our body acquire genetic changes, known as somatic mutations, throughout our lifetime. “Over the course of a lifetime, cells in the human body acquire somatic mutations, thus generating genetic diversity and enabling natural selection in tissues,” the team noted. With new DNA sequencing technologies, researchers can now analyze these mutations in normal tissues and trace them back over time, providing insights into aging and the earliest stages of cancer development. “These mutation landscapes provide insights into somatic evolution in normal tissues during an individual’s lifetime and into the earliest stages of cancer development.”

The somatic mutation landscapes of normal epithelial cells lining the esophagus, small intestine, and large intestine have recently been characterized, the authors commented. For their newly reported study, Coorens and colleagues set out to investigate somatic mutations within the gastric epithelium to explore the transition between normal, age-related mutations, and those that go on to form stomach cancer.

The team carried out whole genome sequencing of 238 samples of normal, non-cancerous gastric gland tissue from the stomachs of 30 people from Hong Kong, the United States, and the U.K., of whom 18 had gastric cancer and 12 did not. With laser capture microdissection, they used a laser to precisely dissect individual cells, or glands, from the stomach lining samples for genome sequencing.

The researchers found that despite regular exposure to the acidic contents of the stomach, mutations in normal gastric glands were generated at a similar rate to most cells of the body. This suggests the cells in the gastric epithelium are protected against any toxic effects of the acidic stomach contents.

However, in people with gastric cancer, some of the glands from the normal, non-cancerous stomach lining showed changes under the microscope that resembled the early stages of transitioning to cancer. These normal glands had increased numbers of mutations, which may have contributed to initiating gastric cancer. In the cancerous tissue, the number of mutations was much higher, showing that gastric cancers massively accelerate mutations later during their development.

An unusual finding was that some of the stomach lining cells carried three copies (trisomy) of chromosomes 13, 18, and 20. This has not been seen in other tissues in previous studies, suggesting it is unique to the stomach. Trisomies were found multiple times in some of the individuals, but not present in others. “Remarkably, trisomies were concentrated in a subset of individuals and had often arisen independently and several times in the same individual,” the investigators wrote. This implies these individuals may have been exposed to an unknown, external mutagen. “Our data indicate that rather than a continuous age-associated increase of whole-chromosome duplications, these trisomies were generated at a specific time during the lifespan of each individual and possibly confined to specific regions of the stomach,” the scientists further pointed out.

Co-lead author Suet Yi Leung, MD, at the University of Hong Kong, said: “We discovered an unusual phenomenon, where some individuals had three copies of certain chromosomes—known as trisomy—whereas others did not. We’ve not seen this in any other tissue, and it hints toward an unknown, external mutagen that only some of these people may have been exposed to.”

The scientists also found that by the age of 60 years, “driver” mutations in cancer genes, many of which are known to be mutated in gastric cancer, occupy nearly 10% of the stomach lining. This proportion increases when patients experience severe chronic inflammation, a known risk factor for gastric cancer. “Chronic inflammation can lead to metaplasia, a remodeling of the gastric epithelium to resemble intestinal epithelium, which is thought of as a precursor to overt cancer,” the investigators noted.

As people age, increasing numbers of cells in many of their tissues acquire such driver mutations—genetic changes that directly contribute to the development of cancer. While most cells remain normal, this can lead to abnormal cell growth and division, and can result in cancerous tumors. “The prevalence of mutant clones increases with age to occupy roughly 8% of the gastric epithelial lining by age 60 years and is significantly increased by the presence of severe chronic inflammation,” the authors stated.

This finding points to the need for further research into the mechanism by which chronic inflammation increases the risk of gastric cancer. “Severe chronic inflammation was significantly associated with elevated numbers of driver mutations in gastric glands and overall proportions of mutant epithelium in this study, highlighting a role for chronic inflammation in molding the preneoplastic selection landscape, as also identified in inflammatory bowel,” the team further stated in their paper.

Co-lead author professor Sir Mike Stratton, FMedSci FRS, at the Wellcome Sanger Institute, commented, “Ten years ago, we knew very little about the fundamental processes of mutations that are occurring in our bodies. Now with advanced genome sequencing technologies, we can investigate somatic mutations in all cell types, across various normal tissues. This enables us to look back at the evolution of our cells over a lifetime, to understand the key mutational processes that can lead to cancer. At the Sanger Institute, we are leading the way in investigating the causes and consequences of somatic mutations, and exploring the possibility that somatic mutations may also contribute to diseases other than cancer.”

In an associated News & Views, Callum Oddy and Marnix Jansen, at UCL Cancer Institute, University College London, commented that the study reported by Coorens et al. offers a “… comprehensive analysis that reshapes understanding of how mutations accumulate in normal gastrointestinal tissues and how these changes could set the stage for cancer.” The findings, Oddy and Jansen suggest, “… underscore the value of considering the genetic and epigenetic landscape of normal tissues, not just malignant ones, when studying carcinogenesis.”

Researchers at the Martin Luther University Halle-Wittenberg (MLU) have developed RNA-based active agents that appear to reliably protect plants against cucumber mosaic virus (CMV), the most common virus in agriculture and horticulture. Developed to help fight the virus by directing the plant’s natural defenses in the right direction the new molecules, known as efficient double-stranded RNA (edsRNA), demonstrate a broad spectrum effect supporting the plant’s immune system in combating the virus. The team’s laboratory experiments found that 80–100% of treated plants survived CMV infection with a high viral load.

Research lead Sven-Erik Behrens, PhD, at the Institute of Biochemistry and Biotechnology at MLU, and colleagues, reported their findings in Nucleic Acids Research, in a paper titled, “A new level of RNA-based plant protection – dsRNAs designed from functionally characterized siRNAs highly effective against cucumber mosaic virus.” In their paper, the team concluded, “Overall, the results of this study significantly expand the potential for more efficient use of RNA in biological crop protection.”

Virus-induced plant diseases remain a major problem in agriculture that is “recently exacerbated by global trade and climate change,” the authors wrote. Pesticides represent the most common methods for controlling viral infections, but such agents may have non-specific effects on other organisms and can be harmful to humans. “Urgently needed alternative crop protection methods should not only be environmentally sustainable, but also specific, i.e., effective only against a specific target pathogen, and adaptable to the evolution of the pathogen,” the team noted. “RNA-mediated crop protection increasingly becomes a viable alternative to agrochemicals that threaten biodiversity and human health.”

Cucumber mosaic virus is a particularly devastating virus for crops. About 90 species of aphids transmit the virus, which affects more than 1,200 plant species, including numerous agricultural crops such as squash, cucumbers, cereals, and medicinal and aromatic plants. Infected plants are easily identified by a characteristic mosaic pattern on their leaves. Once infected, the plants fail to thrive and their fruits cannot be sold. There are currently no approved agents against CMV.

When a virus infects a plant it uses the plant’s cells as a host. The virus multiplies via its genetic material in the form of RNA molecules in the plant cells. Once injected, these foreign RNA molecules trigger an initial response from the plant’s immune system. Special enzyme scissors recognize and cut the viral RNA molecules. This process produces small interfering RNAs (siRNAs), which spread throughout the plant and trigger a second step of the immune response. The siRNA molecules bind to special protein complexes and guide them to the RNA molecules of the virus. Once there, the proteins begin to break down the harmful RNA molecules of the virus by converting them into harmless, degradable fragments.

“In general, this defense process is not very effective,” said Behrens. “A viral infection produces many different siRNA molecules, but only a few have a protective effect.” Through their newly reported work, the team developed a method to identify functionally effective siRNA molecules, termed esiRNAs, that are highly efficient in the process. “Using an in vitro screen that reliably identifies esiRNAs from siRNA pools, we identified esiRNAs against cucumber mosaic virus …,” the authors explained.

They were able to combine several of these esiRNA molecules into efficient double-stranded RNA molecules (edsRNAs) that could be applied to plants. These edsRNAs act as a package that, soon after entering the plant cells, is broken down into a large number of highly effective siRNA molecules that attack the virus at different sites which can significantly increase the protective effect. “RNA viruses such as the cucumber mosaic virus are dangerous because they can evolve rapidly,” Behrens said. “In addition, the genetic material of this virus is made up of three separate parts, which can get mixed up, further increasing the chance of new mutations. To achieve maximum protection against the virus, our active ingredients target different parts of the genome.”

The team conducted numerous laboratory experiments on the model plant Nicotania benthamiana and was able to show that edsRNA-based active agents reliably protected against cucumber mosaic virus. “The plants in our experiments were infected with a very high viral load: all of our untreated plants died,” reported Behrens. In contrast, 80–100% of the treated plants survived. “… optimal protection was achieved with newly designed multivalent ‘effective dsRNAs’ (edsRNAs), which contain the sequences of several esiRNAs and are preferentially processed into precisely these esiRNAs,” the authors stated. “The esiRNA components can attack one or more target RNAs at different sites, be active in different silencing complexes, and provide cross-protection against different viral variants—important properties for combating rapidly mutating pathogens such as CMV.”

The team has in addition optimized the process of screening for efficient siRNAs and can adapt the procedure to target new viral mutations within two to four weeks. “Time is an important factor: when a new virus variant emerges, we can very quickly modify the active agent accordingly,” Behrens said. The approach may also be applied to other pathogens and pests. “The success of our approach, eNA screen followed by edsRNA design from the identified esiRNAs, promises similar success for other plant pathogens, most of which have significantly less plasticity than CMV,” the authors stated.

Until now, the substances have been administered manually in the laboratory, either by injection or by rubbing them into the plant leaves. The team is working with pharmacist and drug delivery specialist Karsten Mäder, PhD, a professor at MLU to make the RNA-based substances more durable and easier to apply to plants. For example, they could be sprayed on.

At the same time, the researchers are planning field trials to test the RNA-based substances under real conditions. “It will now be important to further test and improve esiRNA and edsRNA actives in combination with suitable formulations in agricultural applications, i.e., greenhouse or field trials,” the investigators wrote in their report. They are also talking to companies about future industrial production. In addition, potential new crop protection products still have to go through an approval process, so it will be some time before a product to combat cucumber mosaic virus enters the market. “However, we are convinced that our approach is feasible. The first crop protection product with an RNA-based active ingredient was recently approved in the USA,” said Behrens.

Ori Biotech officials say the company has launched its Preferred Partner Network (PPN), bringing together academic medical centers (AMCs) and contract development and manufacturing organizations (CDMOs) to deliver best-in-class solutions to accelerate the development and commercialization of cell and gene therapies.

The founding members of the Ori Preferred Partner Network in the United States include Charles River Laboratories, CTMC (a joint venture between MD Anderson Cancer Center and Resilience), ElevateBio, Kincell, and other currently undisclosed partners.

PPN membership offers the opportunity to develop core expertise with the new IRO® platform to accelerate cell therapy product development, according to Jason C. Foster, CEO, Ori Biotech.

“By partnering with the top academic institutions and CDMOs globally, Ori is helping to deliver proven solutions that speed time to clinic, reduce comparability risk, and shorten development timelines,” continued Foster. “The PPN enhances the flexibility of therapy developers to choose both best-of-breed technologies and service providers to deliver on their program goals. End-to-end solution providers often try to lock developers in, restricting flexibility, which is the opposite of what we need at this critical juncture for the industry.”

IRO was designed to deliver flexible solutions by integrating with other best-in-breed upstream and downstream technologies providing a streamlined and closed workflow to achieve optimal clinical and commercial success, noted Foster, who added that recently announced technology partnerships, like with Fresenius Kabi, alongside the launch of the PPN, mark a significant step forward in Ori’s mission to enable widespread patient access to life-saving cell and gene therapies.

“Ori’s mission mirrors our own: expedite the delivery of life-saving therapies to patients,” said Matthew Hewitt, PhD, vice president, CTO, manufacturing business division, Charles River.

“CTMC provides comprehensive solutions to our academic and biotech partners, enabling seamless translation from concept to clinic,” explained Jason Bock, CEO, CTMC. “By integrating the automated capabilities of Ori Biotech’s IRO platform, we enhance our technology offerings, streamlining cell therapy manufacturing and accelerating the path to patients.”

“Through the Ori Preferred Partner Network, we are able to offer our partners the necessary technologies and service solutions to accelerate development, manufacturing, and their path to commercialization,” stated Michael Paglia, CTO, ElevateBio BaseCamp.

“As the cell therapy field matures, innovative technologies that simplify the manufacturing of these complex therapies and reduce the cost of goods will enable broad distribution of these life-saving medicines,” pointed out Bruce Thompson, PhD, CTO, Kincell Bio. “Kincell Bio is excited to partner with Ori Biotech on the launch of the IRO platform to help our partners and clients ensure their cell therapy products reach patients in need.”