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Delivery system can make RNA vaccines more powerful

Delivery system can make RNA vaccines more powerful

Vaccines made from RNA hold great potential as a way to treat cancer or prevent a variety of infectious diseases. Many biotech companies are now working on such vaccines, and a few have gone into clinical trials.

One of the challenges to creating RNA vaccines is making sure that the RNA gets into the right immune cells and produces enough of the encoded protein. Additionally, the vaccine must stimulate a strong enough response that the immune system can wipe out the relevant bacteria, viruses, or cancer cells when they are subsequently encountered.

MIT chemical engineers have now developed a new series of lipid nanoparticles to deliver such vaccines. They showed that the particles trigger efficient production of the protein encoded by the RNA, and they also behave like an “adjuvant,” further boosting the vaccine effectiveness. In a study of mice, they used this RNA vaccine to successfully inhibit the growth of melanoma tumors.

“One of the key discoveries of this paper is that you can build RNA delivery lipids that can also activate the immune system in important ways,” says Daniel Anderson, an associate professor in MIT’s Department of Chemical Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science.

Anderson is the senior author of the study, which appears in the Sept. 30 issue of Nature Biotechnology. The lead authors of the study are former postdocs Lei Miao and Linxian Li and former research associate Yuxuan Huang. Other MIT authors include Derfogail Delcassian, Jasdave Chahal, Jinsong Han, Yunhua Shi, Kaitlyn Sadtler, Wenting Gao, Jiaqi Lin, Joshua C. Doloff, and Robert Langer, the David H. Koch Institute Professor at MIT and a member of the Koch Institute.

Vaccine boost

Most traditional vaccines are made from proteins produced by infectious microbes, or from weakened forms of the microbes themselves. In recent years, scientists have explored the idea of making vaccines using DNA that encodes microbial proteins. However, these vaccines, which have not been approved for use in humans, have so far failed to produce strong enough immune responses.

RNA is an attractive alternative to DNA in vaccines because unlike DNA, which has to reach the cell nucleus to become functional, RNA can be translated into protein as soon as it gets into the cell cytoplasm. It can also be adapted to target many different diseases.

“Another advantage of these vaccines is that we can quickly change the target disease,” he says. “We can make vaccines to different diseases very quickly just by tinkering with the RNA sequence.”

For an RNA vaccine to be effective, it needs to enter a type of immune cell called an antigen-presenting cell. These cells then produce the protein encoded by the vaccine and display it on their surfaces, attracting and activating T cells and other immune cells.

Anderson’s lab has previously developed lipid nanoparticles for delivering RNA and DNA for a variety of applications. These lipid particles form tiny droplets that protect RNA molecules and carry them to their destinations. The researchers’ usual approach is to generate libraries of hundreds or thousands of candidate particles with varying chemical features, then screen them for the ones that work the best.

“In one day, we can synthesize over 1,000 lipid materials with multiple different structures,” Miao says. “Once we had that very large library, we could screen the molecules and see which type of structures help RNA get delivered to the antigen-presenting cells.”

They discovered that nanoparticles with a certain chemical feature — a cyclic structure at one end of the particle — are able to turn on an immune signaling pathway called stimulator of interferon genes (STING). Once this pathway is activated, the cells produce interferon and other cytokines that provoke T cells to leap into action.

“Broad applications”

The researchers tested the particles in two different mouse models of melanoma. First, they used mice with tumors engineered to produce ovalbumin, a protein found in egg whites. The researchers designed an RNA vaccine to target ovalbumin, which is not normally found in tumors, and showed that the vaccine stopped tumor growth and significantly prolonged survival.

Then, the researchers created a vaccine that targets a protein naturally produced by melanoma tumors, known as Trp2. This vaccine also stimulated a strong immune response that slowed tumor growth and improved survival rates in the mice.

Anderson says he plans to pursue further development of RNA cancer vaccines as well as vaccines that target infectious diseases such as HIV, malaria, or Ebola.

“We think there could be broad applications for this,” he says. “A particularly exciting area to think about is diseases where there are currently no vaccines.”

Materials provided by Massachusetts Institute of Technology

crispr gene art

Scientists create new CRISPR model that allows to edit several genes at once

We have seen several uses of CRISPR gene editing such as accurate cutting and pasting of specific genes in DNA. Scientists have now developed a technique which makes it possible to edit several hundreds of genes at once. This would be very beneficial to the scientists who can reprogram cells in a larger and complex manner thus assisting in the study of genetic disorders. 

CRISPR could mostly edit one gene at a time. As per the latest study, the new technique can hit 25 targets within genes at once. Biochemist Randall Platt, ETH Zurich said that this technique makes it possible to modify entire gene networks in one step which was not even thought in the past. The work has been published in the journal Nature Methods. 

The key to this process is a plasmid, a stabilised RNA structure that can hold and process several RNA molecules. These act as address labels for targeting gene sites. Along with the RNA molecules the plasmid also carries Cas9 enzyme which performs the main cutting and binding job. Cas9 has been mainly used although here Cas12a is used which improves the accuracy of CRISPR editing. Researchers were able to insert this plasmid into human cells in the laboratory. Hence it enables scientists to make gene editing at scale. It can be quite tiring to make a single change at one time as proteins, genes act in complex manners. Operations such as increasing and decreasing the gene activities can be done with greater precision. 

However, this also means that we would be moving in uncharted territories as we do not know the effects of this simultaneous change in the body of the organism. There might be secondary changes which are not expected thus increasing the risk of gene editing. 

Researchers mention that direct repeat sequences and pacers which possess the complementary sequences could create secondary RNA structures which can affect the maturation of the CRISPR RNAs present in the cells. As a result of which, it is essential to consider the complementary regions in pre-CRISPR RNA so as to improve the maturation of CRISPR RNA. Research overcoming these limitations would create several applications for genome engineering. 

CRISPR has been already used in eliminating genes responsible for diseases and killing the superbugs. There is a whole range of applications awaiting as researchers now have better toolkit at their disposal. Therefore this technique creates a platform in which different types of investigation related to genetic programs affecting the cell behaviour can be carried out. 

Journal Reference: Nature Methods

gene editing artist

Chinese scientists create safer alternative to CRISPR which avoids ethical concerns

A team of Chinese researchers have created an efficient and very safe technology for editing RNA that could avoid the side effects to a great extent and also the ethical concerns which came from the previous technologies of gene-editing. The study has been published in the journal Nature Biotechnology

This feat comes after half a year when Chinese researcher He Jiankui claimed that he had made the world’s first gene-edited twins who are immune to HIV. This announcement caused a whirlwind of condemnation all over the world. Many Chinese and international researchers condemned it as any application of gene editing was unethical if used on human embryos for reproductive purposes. He used the technology of CRISPR-Cas9, that was adapted from a genome editing system which occurred naturally in bacteria. The Cas9 enzyme, a protein that plays a very important role in the immunological defence of specific bacteria against the DNA viruses would be introduced for cutting the DNA of the viruses in the human body. 

Wei Wensheng, a leading researcher of the technology and also a biologist at the Peking University said that this technology essentially depends on the delivery of chemically modified guide RNAs or exogenous proteins that may lead to a delivery barrier.

Zhou Zhuo, another research team member said that on the contrary, the latest technology known as Leveraging Endogenous ADAR for Programmable Editing of RNA or LEAPER uses the native proteins and hence does not alter the DNA in a direct manner. Because of these factors, it would not bring any heritable changes and is safe. It uses engineered RNA’s for recruiting native enzymes to change certain adenosine to inosine. Zhou also stated that experiments conducted at a cellular level in the last two years showed that LEAPER is capable of achieving editing efficiencies up to 80 percent. He further mentioned that the team is now conducting tests on rats. Hence we have to wait to understand if it is suitable for use in human beings.

LEAPER is active in a very broad spectrum of cell types which includes several human primary cell types. It can also restore the deficient cells of patients having Hurler syndrome without evoking any kind of innate immune responses. Being a single-molecule system, LEAPER ensures highly precise and efficient RNA editing with large scale applications for basic research and therapy. 

Journal Reference: Nature Biotechnology


Using human genome, scientists build CRISPR for RNA to open pathways for medicine

Less than a decade ago, biology underwent one of those once-in-a-generation events that shakes up a scientific field, when the discovery of gene editing technology called CRISPR/Cas-9 made it possible to precisely alter the sequence of DNA in a living being.

But while DNA may be the raw blueprints for life, RNA is the architect—translating those ideas into reality for the cell through proteins and regulation. While CRISPR systems that target RNA have recently been discovered, none offers a single clear solution.

A group of scientists from the University of Chicago has announced a breakthrough method to alter RNA—and instead of using a protein from bacteria, like CRISPR, the new system is built out of parts from the human genome. Announced June 20 in Cell, the discovery could open new pathways for treating diseases or injuries by temporarily altering how the genetic template is carried out in the cell.

“People had delayed targeting RNA for a long time because it’s so complex in how it works,” said study author Bryan Dickinson, an associate professor of chemistry at UChicago. “But I think now we’re realizing that complexity is an opportunity to figure out how to exploit and change those pathways. In principle, you could make even more dramatic changes to the cell than with DNA, and now we finally have the tools to do so.”

Even as DNA-targeting CRISPR methods begin their initial clinical trials in humans, scientists have become increasingly interested in equivalent systems for RNA. An RNA-targeting method that can safely be applied to humans would be a valuable complement to CRISPR, Dickinson said.

“If you imagine the universe of diseases that CRISPR is going to correct, it’ll be really important ones, but only those that are based off of one single mutation in your DNA,” said Dickinson, whose work tries to create functional molecules that lead to biological breakthroughs. “There are many more diseases out there with multiple causes in the cell, which may be much more difficult to understand—and there will also be those where the risks associated with changing someone’s DNA permanently are just too high.”

Because the effects of RNA alteration are temporary rather than permanent, an RNA-CRISPR is inherently less risky, because doctors can simply stop the treatment if there are intolerable side effects. It could also be used for things like briefly boosting a person’s system to accelerate wound healing: “We know what to do for that—you would encourage processes for cell growth and proliferation,” Dickinson said. “But those are the same things that cause cancer, so you could never do that at the DNA level.”

But translating these microbial systems into therapeutics is going to be challenging, he said. “RNA-targeting drugs need to be continually administered, so the foreign nature of CRISPR/Cas systems it going to create an immune backlash when applied to humans.”

This presents key roadblocks for natural CRISPR systems, which Dickinson’s team realized it had an opportunity to correct by reengineering the whole system from scratch.

“In principle, you could make even more dramatic changes to the cell than with DNA, and now we finally have the tools to do so.”

—Assoc. Prof. Bryan Dickinson on targeting RNA

Because it’s a very large protein, CRISPR is generally too big to use the most common delivery system to insert genetic material into cells—“phages,” which originate from tiny viruses. This is a problem, especially if you need to deliver them continually. More critically, because CRISPR comes from a microbe, there are significant concerns about the human immune system reacting to it.

Instead, the team broke down CRISPR into its components based on what each part does, and looked for human versions of those proteins that did equivalent tasks. Then they cobbled those together into a cohesive whole—which is smaller than CRISPR, and made out of human material.

“Although there’s still a lot of work to do, the crazy thing is it actually works,” Dickinson said.

Their system succeeded in altering RNA in tests in the lab. The scientists plan to improve the system at a few points where the performance is not as good as CRISPR, they said, but they’re encouraged by the early results.

“As we learn more, you could imagine targeting multiple RNAs in different ways, and doing more complex reprogramming of the cell at the RNA level,” Dickinson said. “It’s a really exciting field right now.”

The first author was graduate student Simone Rauch; other co-authors were visiting scholar Michael Srienc, postdoctoral fellow Huiqing Zhou, high school student Emily He and graduate student Zijie Zhang.

The scientists are working with the Polsky Center for Entrepreneurship and Innovation at the University of Chicago to advance this discovery.

Materials provided by University of Chicago

Representation of dna body strand

Researchers find evidence of DNA and RNA even before life on Earth

Scientists have found a piece of strong evidence that both DNA and RNA might have been formed from the same precursor molecules even before the evolution of life on Earth. The research published in Nature Chemistry shows that the first living beings on our planet might have had both RNA and DNA like all other cellular-based life forms. This is in contrast to the current understanding that the earliest life forms only possessed RNA and DNA was formed with the evolution of life. This is commonly known as the RNA World Hypothesis. After this new finding, scientists should not fully rely on the RNA World Hypothesis for carrying out investigations on the origin of life on Earth.

RNA and DNA are chemically quite similar but chemists have not been able to show how one could have been converted to the other in earliest stages of our planet without the help of enzymes which are produced by the organisms. Because of this reason, researchers have always concluded that RNA is the basic component of the earliest life forms. RNA can store genetic information like DNA and also store catalyse biochemical reactions like protein enzymes. Hence it could have performed the basic biological functions in the earliest forms of life.

Ramanarayanan Krishnamurthy, a chemistry professor at Scripps Research along with his colleagues found a compound which was present in pre-biotic Earth and performed the essential task of linking RNA blocks to larger RNA strands and could have done the same for proteins and DNA.

Scientists have identified a compound named thiouridine which was likely to be present on Earth before the formation of life and it could have been a chemical precursor to the nucleoside blocks of the early RNA. It was found that by means of few chemical reactions this compound could be transformed to deoxyadenosine, a basic building block of DNA. They could also convert thiouridine to deoxyribose which is very closely related to deoxyadenosine.

These findings are a strong indicator that both RNA and DNA developed together and were present in the earliest life forms. Scientists have also suggested that both RNA and DNA might have been combined to form the first genes.  Although no such organism has occurred naturally but a  paper by Scripps Research described an engineered bacteria which can survive with genes formed by a combination of RNA and DNA.

Irrespective of the ways in which life formed, both RNA and DNA with their respective strengths and weaknesses would have arranged themselves into a proper division of labour as evident in the cells today.