New CRISPR Systems Discovered, Enhancing Gene Editing Precision

What makes us unique? Different from most, yet similar to a few? What shapes our physical, behavioral, and even mental makeup? The answer lies in our genes.

Passed from parents to their offspring, genes contain the information that specifies physical and biological traits.

But that’s not all. Genes are also responsible for diseases. Faulty genes can cause all kinds of issues that can manifest as birth defects, chronic diseases, or developmental problems.

A highly advanced way of tackling this is through gene or genome editing, which allows scientists to make precise changes to the DNA. Gene editing involves adding, removing, or altering the genetic material at specific locations.

These specific, targeted changes to DNA can lead to alterations in physical traits or disease risk. 

This technology is not only used to treat genetic diseases by correcting faulty genes but also to develop new treatments and gain a deeper understanding of gene function. Additionally, it can enhance crops by making precise changes to their DNA. A well-known and widely used gene-editing technology is CRISPR-Cas9, which is based on a naturally occurring bacterial defense system.

CRISPR-Cas9 is derived from CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), a bacterial immune system that helps bacteria defend against viral infections by recognizing and destroying viral DNA. 

In this system, CRISPR acts as a genetic homing device, while Cas9, a protein, functions as molecular ‘scissors’ to cut DNA at specific sites. It is simpler, cheaper, and more precise than previous gene editing techniques. 

A method for genome editing based on CRISPR-Cas9 technology was actually awarded The Nobel Prize in Chemistry in 2020. It was the first time in history that a Nobel prize was awarded to two women.

CRISPR: Transforming Modern Biology with Gene Editing

CRISPR was first identified a few decades ago. In 1987, Yoshizumi Ishino and his team at Osaka University observed it in (E. coli) bacterial genomes. However, it wasn’t until the early 2000s that CRISPR’s role as bacterial immunity was identified.

In the last few years, this technology has advanced significantly and has been transforming modern biology.  

One instance of this is the use of CRISPR–Cas9 to modify human embryo cells, allowing genetic changes to be passed on to future generations. This has been widely disapproved of, with calls to ban inheritable genetic modifications.

Besides this, CRISPR–Cas9 and related technologies are also being successfully used to cure life-threatening diseases. 

In just the first three months of this year, several researchers have used CRISPR to achieve several breakthroughs.

Earlier this month, a team of scientists at Colossal Biosciences created ‘wooly mice'—mice with long fur similar to the extinct woolly mammoth. They did this by simultaneously editing seven genes linked to hair growth, color, and texture.

The team is working on several de-extinction projects, including thylacine and the dodo, with the mammoth being their flagship project. All these projects involve taking stem cells from a species closely related to the extinct one and then editing changes based on the deceased species’ genomes. For this, the researchers used variations of the CRISPR/Cas9 and CRISPR/Cas systems.

Last month, scientists at MIT’s McGovern Institute for Brain Research and the Broad Institute of MIT and Harvard discovered¹ an ancient RNA-guided system that can expand the genome editing toolbox and simplify the delivery of gene editing therapies.

These systems, called TIGR (Tandem Interspaced Guide RNA), can be reprogrammed to target any DNA sequence. They also have distinct functional modules that act on the targeted DNA. In addition to its modularity, TIGR is highly compact.

According to Feng Zhang, a Professor of Neuroscience at MIT, whose team previously adapted bacterial CRISPR systems into gene editing tools and found various programmable proteins:

“This is a very versatile RNA-guided system with a lot of diverse functionalities.” 

In their latest work, the team focused on a structural feature of the CRISPR-Cas9 protein that binds to the enzyme’s RNA guide. They have discovered over 20,000 different Tas proteins, experimented with dozens of them, and demonstrated that some could be programmed to make targeted cuts to DNA in human cells. They are now planning to develop TIGR-Tas systems into programmable tools.

Scientists are even exploring gene editing to correct trisomy at the cellular level. They recently successfully removed extra copies of chromosome 21 in Down syndrome cell lines using CRISPR-Cas9, restoring normal gene expression.

Down syndrome occurs when there’s an extra copy of chromosome 21. This condition affects about 1 in 700 live births, and while it is easily diagnosed early on, currently, no treatments exist for this.

But the latest breakthrough, which was achieved in lab-grown cells, was able to remove the extra chromosome from trisomy 21 cell lines, which were derived from both pluripotent stem cells and skin fibroblasts, leaving only one copy from each parent rather than two identical ones.

Though not ready for use in living organisms, it does suggest potential for application in neurons and glial cells.

In another instance, Chinese scientists have built a safer gene-editing system using deadly viruses like dengue fever to improve efficiency and safety. The system uses mRNA to avoid the risk of foreign DNA being left behind to create unwanted mutations.

According to the research team, the optimized mRNA delivery system “increases the flexibility and applicability of transgene-free genome editing in plants.”

So, gene-editing technology has revolutionized not only human biology but also agriculture by modifying plant DNA to enhance desirable traits like high yields.

Just this month, scientists from Johns Hopkins University and Cold Spring Harbor Laboratory discovered key genes that decide fruit size. These genes can be controlled with CRISPR, paving the way for larger and more flavorful produce.

The research is part of a broader initiative to map the complete genomes of 22 nightshade crops, including potatoes, eggplants, and tomatoes, to understand and enhance their genetic traits.

“Once you’ve done the gene editing, all it takes is one seed to start a revolution.”

– Co-lead author Michael Schatz, a geneticist at Johns Hopkins University

All these developments show just how far the technology has come, but it’s just the beginning. Researchers at Duke University and North Carolina State University have now discovered new CRISPR-Cas systems that further enhance the capabilities of existing gene-editing technologies.

Click here to learn all about CRISPR-Cas9. 

Advancing CRISPR: New Systems Boost Gene Editing Precision

Since CRISPR-Cas systems were first discovered in bacteria, numerous orthologs have been identified. Orthologs are genes evolved from a common ancestral gene through a speciation event. They are present in different species and potentially retain the same function.

At least six types and 33 subtypes of orthologs have been characterized, but despite this, type II systems are most widely used in biotechnology and biomedical research. These type II systems use Cas9 to cut DNA.

The ease of reprogramming Cas9 target sites has made it so popular and has ushered in a wave of potential genome editing therapeutics. 

However, despite the abundance of bacterial CRISPR-Cas9 systems, few are effective in human cells, limiting the CRISPR tech’s overall potential. 

This creates a need for additional Cas9 orthologs to expand the range of targetable DNA sequences. This will also help overcome delivery size limitations and improve the specificity and efficiency of CRISPR-Cas9 gene editing.

So, the researchers from Duke University and NC State University explored thousands of bacterial genomes for new CRISPR-Cas systems and discovered some that can be added to the gene editing toolbox.

The study, published in the Proceedings of the National Academy of Sciences (PNAS)² this month, effectively expands the technology’s impact on research, medicine, and biotechnology.

“It’s actually remarkable that the first CRISPR-Cas systems researchers used on human cells is still the one that works the best. We wanted to scour bacteria found in more obscure settings for different CRISPR systems that might have different abilities.”

– Charlie Gersbach, Professor of Biomedical Engineering at Duke

Among the newly discovered bacterial genomes, one particular system derived from bacteria, which is typically found in dairy cows, demonstrates promise for human health.

This orthogonal effector allows for complementary and flexible targeting of diverse genetic sequences for next-gen genome editing.

The system is also highly efficient, comparable to the widely used Streptococcus pyogenes CRISPR-Cas9. Streptococcus pyogenes is the bacterial species on which CRISPR-Cas9 and most subsequent research using CRISPR are built.

According to Rodolphe Barrangou, the Professor of Food, Bioprocessing and Nutrition Sciences at NC State:

“There is a lot more CRISPR-Cas system diversity in nature than people appreciate, and it can be very useful to mine for diverse effectors with functional potential as molecular machines.”

Several years before the paper on the technology received the Nobel Prize, Barrangou had characterized CRISPR as a defense system in bacteria used in dairy starter cultures, and since then, his laboratory has been exploring its diversity for probiotics, food manufacturing, editing tree genomes, and altering wood properties.

Barrangou said the following about the latest research:

“While some incumbent effectors like SpyCas9 have shown great potential in the clinic already, we need to expand the CRISPR toolbox for next-generation manipulation of the genome, transcriptome, and epigenome.” 

He has developed a program called “CRISPRdisco,” which identifies CRISPR-Cas systems within large databases of bacterial genomes. The program helped the researchers identify over 1000 different unexplored CRISPR systems.

The researchers cut those systems to just 50 candidates for Gersbach’s laboratory to engineer.

Upon testing these CRISPR systems in human cells for their abilities as gene activators, repressors, and genetic and epigenetic editors, four systems stood out for their individual successes.

One (SubCas9) was particularly remarkable for its versatility. This promising CRISPR component is found in the bacteria Streptococcus uberis, which is commonly found in dairy cows and is also used in some human probiotic products.

Researchers are excited about SubCas9 for a number of reasons. For starters, the new system's small size —smaller than the conventionally used Cas9 DNA molecular scalpel—allows for its easier delivery into human cells. 

Additionally, it can target unique gene sequences that are inaccessible to other systems, including the original counterpart. 

The typically used Cas9 works at genomic targets adjacent to the DNA sequence ‘GG,’ which is “a fairly common DNA sequence.” However, if a GG isn’t nearby, one needs an alternative, and the new system offers that by working at sites neighboring “AATA” or “AGTA” patterns.

“This system can give researchers flexibility for using different Cas9s when they need to be really precise with their target site selection.”

– Gabe Butterfield, the postdoc fellow in the Gersbach Lab

In addition, it is less likely to be recognized by the human immune system as S. uberis isn’t usually found in humans. This is unlike bacteria species, which are used to isolate the more common Cas9 proteins. 

So, if used in a therapeutic application, most people’s immune systems would not recognize SubCas9 from a previous natural exposure.

“Besides potential for therapeutic applications, we also appreciate that bacteria that have adapted to diverse habitats harbor effectors better suited for various kinds of hosts, with much potential for discovery of systems more suited for plants, livestock, and environmental applications.”

– Barrangou

In the next step, the researchers will look into SubCas9’s ability to bypass preexisting immunity as they expect. They are also testing incorporating it into a number of cell and gene therapies. The researchers may also get back to the massive bacterial metagenomic databases to find more CRISPR systems for investigation.

Overall, the latest advancements in CRISPR-Cas9 gene editing present a major breakthrough that can significantly improve gene therapy techniques, allowing for more precise and efficient treatments for genetic disorders, cancers, and other diseases. 

Given the rapid pace of CRISPR research, these new systems could be integrated into clinical applications within the next 3 to 5 years, pending further validation and regulatory approvals.​

Innovative Company

Editas Medicine, Inc. (EDIT -5.28%)

Editas Medicine is a leading genome editing company focused on developing CRISPR-based therapies to treat a range of serious diseases.

It is a clinical-stage genome editing company developing in vivo-administered gene-editing medicines, where the treatment is injected directly into the patient to edit cells inside their body. CEO Gilmore O’Neill, M.B., M.M.Sc earlier this month, while sharing business updates, said:

“Our objective and strategy to become a leader in in vivo gene editing accelerated in the fourth quarter after we achieved in vivo preclinical proof of concept ahead of schedule and shared positive preclinical in vivo data demonstrating the potential of our platform technology to achieve gene upregulation, or amplifying the expression of an existing protein to achieve clinically relevant levels that could potentially drive cures across tissues with a single dose.” 

As of writing, the shares of the $117 million market cap company are trading at $1.41, up 11.02% YTD. Its EPS (TTM) is -2.88, and the P/E (TTM) ratio is -0.48.

Earlier this month, the company reported its fourth quarter and full year 2024 financial results. The net loss was $45.4 million, or $0.55 per share, far bigger than the $18.9 million recorded in Q4 2023. 

Revenue decreased to $30.6 million, and research and development expenses increased to $48.6 million during this period.

At the end of 2024, the company had $269.9 million in cash, cash equivalents, and marketable securities, slightly better than its previous at the end of the previous quarter. As per the company’s announcement, it expects these funds, along with the retained portions of the payments payable under its license agreement with Vertex Pharmaceuticals, to fund both operating expenses and capital expenditures well into the Q2 of 2027.

For the full year 2024, the net loss was $237.1 million, or $2.88 per share, collaboration revenues decreased to $32.3 million, R&D expenses increased to $199.2 million, General and administrative expenses increased to $72 million, and restructuring charges were $12.2 million.

The company’s recent achievements include showing preclinical proof of concept (PoC) in humanized mice and non-human primates.

This CTO Linda C. Burkly, Ph.D., said exhibits the company's ability to “attain in vivo gene editing via gene upregulation to increase the level of a functioning protein to address diseases caused by loss of function or deleterious mutations.” She further shared the potential of the gene upregulation strategy across multiple tissues with the ‘plug ‘n play’ program.

Editas has also shared that it is on track to announce an in vivo development candidate for Hematopoietic Stem Cells and liver cells in mid-2025, and by year-end, it aims to share more preclinical in vivo HSC and liver data.

Amidst this, the company ended its reni-cel program to treat sickle cell disease (SCD) after its extensive search failed to get a commercial partner. With this move, the company began measures to save costs, under which it will reduce its headcount by 65%, around 180 jobs.

Latest on Editas Medicine, Inc.

Conclusion

Over the past decade, CRISPR-based technologies have revolutionized biotechnology by enabling genome editing. They have created diverse new opportunities for biomedical research, therapeutic genome, and epigenome editing. 

Current approaches, however, face limitations due to their disproportionate focus on a single Cas9 effector with select efficiency and constrained targeting specificity. 

The discovery of new CRISPR-Cas systems marks a major advancement in gene editing. By expanding the precision, efficiency, and versatility of current technologies, the latest study promises more targeted treatments for genetic disorders and improved agricultural outcomes. With researchers refining these systems, once they gain real-world adoption, the next generation of gene editing could unlock new frontiers in medicine and biotechnology!

Click here for a list of top CRISPR companies to invest in.