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Research Consortium Identifies 188 New CRISPR Gene-Editing Systems, Some More Accurate than CRISPR

New gene-editing systems could provide markedly improved accuracy for DNA and RNA editing leading to new precision medicine tools and genetic therapies

In what may turn out to be a significant development in genetic engineering, researchers from three institutions have identified nearly 200 new systems that can be used for editing genes. It is believed that a number of these new systems can provide comparable or better accuracy when compared to CRISPER (Clustered Regularly Interspaced Short Palindromic Repeats), currently the most-used gene editing method.

CRISPR-Cas9 has been the standard tool for CRISPR gene editing and genetic engineering. However, publication of these new research findings are expected to give scientists better, more precise tools to edit genes. In turn, these developments could lead to new clinical laboratory tests and precision medicine therapies for patients with inherited genetic diseases.

Researchers from Broad Institute, Massachusetts Institute of Technology (MIT), and the federal National Institutes of Health (NIH) have uncovered 188 new CRISPR systems “in their native habitat of bacteria” with some showing superior editing capabilities, New Atlas reported.

“Best known as a powerful gene-editing tool, CRISPR actually comes from an inbuilt defense system found in bacteria and simple microbes called archaea. CRISPR systems include pairs of ‘molecular scissors’ called Cas enzymes, which allow microbes to cut up the DNA of viruses that attack them. CRISPR technology takes advantage of these scissors to cut genes out of DNA and paste new genes in,” according to Live Science.

In its article, New Atlas noted that the researchers looked to bacteria because “In nature, CRISPR is a self-defense tool used by bacteria.” They developed an algorithm—called FLSHclust—to conduct “a deep dive into three databases of bacteria, found in environments as diverse as Antarctic lakes, breweries, and dog saliva.”

The research team published their findings in the journal Science titled, “Uncovering the Functional Diversity of Rare CRISPR-Cas Systems with Deep Terascale Clustering.”

In their paper, the researchers wrote, “We developed fast locality-sensitive hashing–based clustering (FLSHclust), a parallelized, deep clustering algorithm with linearithmic scaling based on locality-sensitive hashing. FLSHclust approaches MMseqs2, a gold-standard quadratic-scaling algorithm, in clustering performance. We applied FLSHclust in a sensitive CRISPR discovery pipeline and identified 188 previously unreported CRISPR-associated systems, including many rare systems.”

“In lab tests [the newfound CRISPR systems] demonstrated a range of functions, and fell into both known and brand new categories,” New Atlas reported.

Soumya Kannan, PhD

“Some of these microbial systems were exclusively found in water from coal mines,” Soumya Kannan, PhD (above), a Graduate Fellow at MIT’s Zhang Lab and co-first author of the study, told New Atlas. “If someone hadn’t been interested in that, we may never have seen those systems.” These new gene-editing systems could lead to new clinical laboratory genetic tests and therapeutics for chronic diseases. (Photo copyright: MIT McGovern Institute.)

Deeper Look at Advancement                    

The CRISPR-Cas9 made a terrific impact when it was announced in 2012, earning a Nobel Prize in Chemistry.

Though CRISPR-Cas9 brought huge benefits to genetic research, the team noted in their Science paper that “existing methods for sequence mining lag behind the exponentially growing databases that now contain billions of proteins, which restricts the discovery of rare protein families and associations.

“We sought to comprehensively enumerate CRISPR-linked gene modules in all existing publicly available sequencing data,” the scientist continued. “Recently, several previously unknown biochemical activities have been linked to programmable nucleic acid recognition by CRISPR systems, including transposition and protease activity. We reasoned that many more diverse enzymatic activities may be associated with CRISPR systems, many of which could be of low abundance in existing [gene] sequence databases.”

Among the previously unknown gene-editing systems the researchers found were some belonging to the Type 1 CRISPR systems class. These “have longer guide RNA sequences than Cas9. They can be directed to their targets more precisely, reducing the risk of off-target edits—one of the main problems with CRISPR gene editing,” New Atlas reported.

“The authors also identified a CRISPR-Cas enzyme, Cas14, which cuts RNA precisely. These discoveries may help to further improve DNA- and RNA-editing technologies, with wide-ranging applications in medicine and biotechnology,” the Science paper noted.

Testing also showed these systems were able to edit human cells, meaning “their size should allow them to be delivered in the same packages currently used for CRISPR-Cas9,” New Atlas added.

Another newfound gene-editing system demonstrated “collateral activity, breaking down nucleic acids after binding to the target, New Atlas reported. SHERLOCK, a tool used to diagnose single samples of RNA or DNA to diagnose disease, previously utilized this system.

Additionally, New Atlas noted, “a type VII system was found to target RNA, which could unlock a range of new tools through RNA editing. Others could be adapted to record when certain genes are expressed, or as sensors for activity in cells.”

Looking Ahead

The strides in science from the CRISPR-Cas9 give a hint at what can come from the new discovery. “Not only does this study greatly expand the field of possible gene editing tools, but it shows that exploring microbial ecosystems in obscure environments could pay off with potential human benefits,” New Atlas noted.

“This study introduces FLSHclust as a tool to cluster millions of sequences quickly and efficiently, with broad applications in mining large sequence databases. The CRISPR-linked systems that we discovered represent an untapped trove of diverse biochemical activities linked to RNA-guided mechanisms, with great potential for development as biotechnologies,” the researchers wrote in Science.

How these newfound gene-editing tools and the new FLSHclust algorithm will eventually lead to new clinical laboratory tests and precision medicine diagnostics is not yet clear. But the discoveries will certainly improve DNA/RNA editing, and that may eventually lead to new clinical and biomedical applications.

—Kristin Althea O’Connor

Related Information:

Algorithm Identifies 188 New CRISPR Gene-Editing Systems

188 New Types of CRISPR Revealed by Algorithm

FLSHclust, a New Algorithm, Reveals Rare and Previously Unknown CRISPR-Cas Systems

Uncovering the Functional Diversity of Rare CRISPR-Cas Systems with Deep Terascale Clustering

Questions and Answers about CRISPR

Annotation and Classification of CRISPR-Cas Systems

SHERLOCK: Nucleic Acid Detection with CRISPR Nucleases

University of Maryland Scientists Develop CRISPR-Act 3.0, a New CRISPR Technology for Multiplex Gene Activation in Plants

CRISPR-Act 3.0 could significantly increase crop yields and plant diversity worldwide and help fight against global hunger and climate change

Clinical laboratory professionals and pathologists who read Dark Daily are highly aware of CRISPR gene editing technology. We’ve covered the topic in multiple ebriefings over many years. But how many know there’s a version of CRISPR specifically designed for editing and activating plant genes?

Scientists at the University of Maryland (UMD) developed a new version of CRISPRa (CRISPR Activation) for plants which they claim has four to six times the activation capacity of currently available CRISPRa systems and can activate up to seven genes at once. They call their new and improved CRISPRa technology “CRISPR-Act 3.0.”

According to a paper published in the journal Nature Plants, titled, “CRISPR-Act3.0 for Highly Efficient Multiplexed Gene Activation in Plants,” the UMD researchers developed “a highly robust CRISPRa system working in rice, Arabidopsis (rockcress), and tomato, CRISPR-Act 3.0, through systematically exploring different effector recruitment strategies and various transcription activators based on deactivated Streptococcus pyogenes Cas9 (dSpCas9).

Yiping Qi, PhD

“While my lab has produced systems for simultaneous gene editing [multiplexed editing] before, editing is mostly about generating loss of function to improve the crop,” said Yiping Qi, PhD (above), one of the authors of the UMD study, in a new release. “But if you think about it,” he added, “that strategy is finite, because there aren’t endless genes that you can turn off and actually still gain something valuable. Logically, it is a very limited way to engineer and breed better traits, whereas the plant may have already evolved to have different pathways, defense mechanisms, and traits that just need a boost.” (Photo copyright: University of Maryland.)

CRISPR-Act 3.0 Increases Function of Multiple Genes Simultaneously

The UMD researchers successfully applied CRISPR-Act 3.0 technology to activate many types of genes in plants, including the ability to expedite the breeding process via faster flowering. They hope that activating genes in plants to improve functionality will result in better plants and crops.

“Through activation, you can really uplift pathways or enhance existing capacity, even achieve a novel function. Instead of shutting things down, you can take advantage of the functionality already there in the genome and enhance what you know is useful,” said Yiping Qi, PhD, associate professor, Department of Plant Science and Landscape Architecture at the University of Maryland, in a UMD new release.

The scientists also noted that there may be other advantages to this type of multiplexed activation of genes.

“Having a much more streamlined process for multiplexed activation can provide significant breakthroughs. For example, we look forward to using this technology to screen the genome more effectively and efficiently for genes that can help in the fight against climate change and global hunger,” Qi added. “We can design, tailor, and track gene activation with this new system on a larger scale to screen for genes of importance, and that will be very enabling for discovery and translational science in plants.” 

The researchers hope this technology can have a major impact on the efficiency of crop and food production. 

“This type of technology helps increase crop yield and sustainably feed a growing population in a changing world,” Qi said. “I am very pleased to continue to expand the impacts of CRISPR technologies.”

Feeding the World’s Hungry with CRISPR

CRISPR is a robust tool used for editing genomes that typically operates as “molecular scissors” to cut DNA. CRISPR-Act 3.0, however, uses deactivated CRISPR-Cas9 which can only bind and not cut. This allows the system to work on the activation of proteins for designated genes of interest by binding to certain segments of DNA. The UMD researchers believe there is significant potential for expanding the multiplexed activation further, which could alter and improve genome engineering. 

“People always talk about how individuals have potential if you can nurture and promote their natural talents,” Qi said in the UMD news release. “This technology is exciting to me because we are promoting the same thing in plants—how can you promote their potential to help plants do more with their natural capabilities? That is what multiplexed gene activation can do, and it gives us so many new opportunities for crop breeding and enhancement.”

CRISPR is being developed and enhanced in many research settings, and knowledge of how to best use the gene editing technology is rapidly advancing. Though more research on CRISPR-Act 3.0 is needed to ensure its reliability, it’s exciting to consider the potential of gene activation for massively increasing crop yield worldwide.

Not to mention how new CRISPR technologies continue to drive innovations in clinical laboratory diagnostics and precision medicine treatments. 

JP Schlingman

Related Information:

UMD Associate Professor Introduces New CRISPR 3.0 System for Highly Efficient Gene Activation in Plants

CRISPR–Act3.0 for Highly Efficient Multiplexed Gene Activation in Plants

Another Milestone for CRISPR-Cas9 Technology: First Trial Data for Treatment Delivered Intravenously

New Understanding of CRISPR-Cas9-Guided Base Editors Could Trigger Development of Gene-Editing Tools Targeting Diseases and New Types of Clinical Laboratory Tests

Another Milestone for CRISPR-Cas9 Technology: First Trial Data for Treatment Delivered Intravenously

Unlike most other CRISPR/Cas-9 therapies that are ex vivo treatments in which cells are modified outside the body, this study was successful with an in vivo treatment

Use of CRISPR-Cas9 gene editing technology for therapeutic purposes can be a boon for clinical laboratories. Not only is this application a step forward in the march toward precision medicine, but it can give clinical labs the essential role of sequencing a patient’s DNA to help the referring physician identify how CRISPR-Cas9 can be used to edit the patient’s DNA to treat specific health conditions.

Most pathologists and medical lab managers know that CRISPR-Cas9 gene editing technology has been touted as one of the most significant advances in the development of therapies for inherited genetic diseases and other conditions. Now, a pair of biotech companies have announced a milestone for CRISPR-Cas9 with early clinical data involving a treatment delivered intravenously (in vivo).

The therapy, NTLA-2001, was developed by Intellia Therapeutics (NASDAQ:NTLA) and Regeneron Pharmaceuticals (NASDAQ:REGN) for treatment of hereditary ATTR (transthyretin) amyloidosis, a rare and sometimes fatal liver disease.  

As with other therapies, determining which patients are suitable candidates for specific treatments is key to the therapy’s success. Therefore, clinical laboratories will play a critical role in identifying those patients who would most likely benefit from a CRISPR-delivered therapy.

Such is the goal of precision medicine. As methods are refined that can correct unwelcome genetic mutations in a patient, the need to do genetic testing to identify and diagnose whether a patient has a specific gene mutation associated with a specific disease will increase.

The researchers published data from a Phase 1 clinical trial of NTLA-2001 in the New England Journal of Medicine (NEJM), titled, “CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis.” They also presented their findings at the Peripheral Nerve Society (PNS) Annual Meeting.

What is NTLA-2001 and Why Is It Important?

Cleveland Clinic describes ATTR amyloidosis as a “protein misfolding disorder” involving transthyretin (TTR), a protein made in the liver. The disease leads to deposits of the protein in the heart, nerves, or other organs.

According to Intellia and Regeneron, NTLA-2001 is designed to inactivate the gene that produces the protein.

The interim clinical trial data indicated that one 0.3 mg per kilogram dose of the therapy reduced serum TTR by an average of 87% at day 28. A smaller dose of 0.1 mg per kilogram reduced TTR by an average of 52%. The researchers reported “few adverse events” in the six study patients, “and those that did occur were mild in grade.”

Current treatments, the companies stated, must be administered regularly and typically reduce TTR by about 80%.

“These are the first ever clinical data suggesting that we can precisely edit target cells within the body to treat genetic disease with a single intravenous infusion of CRISPR,” said Intellia President and CEO John Leonard, MD, in a press release. “The interim results support our belief that NTLA-2001 has the potential to halt and reverse the devastating complications of ATTR amyloidosis with a single dose.”

He added that “solving the challenge of targeted delivery of CRISPR-Cas9 to the liver, as we have with NTLA-2001, also unlocks the door to treating a wide array of other genetic diseases with our modular platform, and we intend to move quickly to advance and expand our pipeline.”

Daniel Anderson, PhD

“It’s an important moment for the field,” MIT biomedical engineer Daniel Anderson, PhD (above), told Nature. Anderson is Professor, Chemical Engineering and Institute for Medical Engineering and Science at the Koch Institute for Integrative Cancer Research at MIT. “It’s a whole new era of medicine,” he added. Advances in the use of CRISPR-Cas9 for therapeutic purposes will create the need for clinical laboratories to sequence patients’ DNA to help physicians determine the best uses for a CRISPR-Cas9 treatment protocol. (Photo copyright: Massachusetts Institute of Technology.)

In Part 2 of the Phase 1 trial, Intellia plans to evaluate the new therapy at higher doses. After the trial is complete, “the company plans to move to pivotal studies for both polyneuropathy and cardiomyopathy manifestations of ATTR amyloidosis,” the press release states.

Previous clinical trials reported results for ex vivo treatments in which cells were removed from the body, modified with CRISPR-Cas9 techniques, and then reinfused. “But to be able to edit genes directly in the body would open the door to treating a wider range of diseases,” Nature reported.

How CRISPR-Cas9 Works

On its website, CRISPR Therapeutics, a company co-founded by Emmanuelle Charpentier, PhD, a director at the Max Planck Institute for Infection Biology in Berlin, and inventor of CRISPR-Cas9 gene editing, explained that the technology “edits genes by precisely cutting DNA and then letting natural DNA repair processes take over.” It can remove fragments of DNA responsible for causing diseases, as well as repairing damaged genes or inserting new ones.

The therapies have two components: Cas9, an enzyme that cuts the DNA, and Guide RNA (gRNA), which specifies where the DNA should be cut.

Charpentier and biochemist Jennifer Doudna, PhD, Nobel Laureate, Professor of Chemistry, Professor of Biochemistry and Molecular Biology, and Li Ka Shing Chancellor’s Professor in Biomedical and Health at the University of California Berkeley, received the 2020 Nobel Prize in Chemistry for their work on CRISPR-Cas9, STAT reported.

It is important to pathologists and medical laboratory managers to understand that multiple technologies are being advanced and improved at a remarkable pace. That includes the technologies of next-generation sequencing, use of gene-editing tools like CRISPR-Cas9, and advances in artificial intelligence, machine learning, and neural networks.

At some future point, it can be expected that these technologies will be combined and integrated in a way that allows clinical laboratories to make very early and accurate diagnoses of many health conditions.

—Stephen Beale

Related Information

Intellia and Regeneron Announce Landmark Clinical Data Showing Deep Reduction in Disease-Causing Protein After Single Infusion of NTLA-2001, an Investigational CRISPR Therapy for Transthyretin (ATTR) Amyloidosis

CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis

Landmark CRISPR Trial Shows Promise Against Deadly Disease

CRISPR Milestone Pushes Gene Editing Toward Its Promise

CRISPR Clinical Trials: A 2021 Update

CRISPR Gene Therapy: Applications, Limitations, and Implications for the Future

Diseases CRISPR Could Cure: Latest Updates on Research Studies and Human Trials

Faster, Better, Cheaper: The Rise of CRISPR in Disease Detection

The Potential of CRISPR-Based Diagnostic Assays and Treatment Approaches Against COVID-19

Two Female CRISPR Scientists Make History, Winning Nobel Prize in Chemistry for Genome-Editing Discovery

CRISPR-Cas9 DNA Editing Possibly Linked to Cancer, But CRISPR-Cas13d RNA Editing Could Offer New Avenues for Treatment

CRISPR-Cas9 connection to cancer prompts research to investigate different approaches to gene editing

Dark Daily has covered CRISPR-Cas9 many times in previous e-briefings. Since its discovery, CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, has been at the root of astonishing breakthroughs in genetic research. It appears to fulfill precision medicine goals for patients with conditions caused by genetic mutations and has anatomic pathologists, along with the entire scientific world, abuzz with the possibilities such a tool could bring to diagnostic medicine.

All of this research has contributed to a deeper understanding of how cells function. However, as is often the case with new technologies, unforeseen and problematic questions also have arisen.

CRISPR-Cas9 Connection to Cancer

Research conducted at the Wellcome Sanger Institute in the United Kingdom (UK) and published in Nature Biotechnology, examined potential damage caused by CRISPR-Cas9 editing.

“Here we report significant on-target mutagenesis, such as large deletions and more complex genomic rearrangements at the targeted sites in mouse embryonic stem cells, mouse hematopoietic progenitors, and a human differentiated cell line,” wrote the authors in their introduction.

Another study, this one conducted by biomedical researches at Cambridge, Mass., and published in Nature, describes possible toxicity caused by Cas9.

“Our results indicate that Cas9 toxicity creates an obstacle to the high-throughput use of CRISPR-Cas9 for genome engineering and screening in hPSCs [human pluripotent stem cells]. Moreover, as hPSCs can acquire P53 mutations, cell replacement therapies using CRISPR-Cas9-enginereed hPSCs should proceed with caution, and such engineered hPSCs should be monitored for P53 function.”

Essentially what both groups of researchers found is that CRISPR-Cas9 cuts through the double helix of DNA, which the cell responds to as it would any injury. A gene called p53 then directs a cellular “first-aid kit” to the “injury” site that either initiates self-destruction of the cell or repairs the DNA.

Therefore, in some instances, CRISPR-Cas9 is inefficient because the repaired cells continue to function. And, the repair process involves the p53 gene. P53 mutations have been implicated in ovarian, colorectal, lung, pancreatic, stomach, liver, and breast cancers.

Though important, some experts are downplaying the significance of the findings.

Erik Sontheimer, PhD (above), Professor, RNA Therapeutics Institute, at the University of Massachusetts Medical School, told Scientific American that the two studies are important, but not show-stoppers. “This is something that bears paying attention to, but I don’t think it’s a deal-breaker,” he said. (Photo copyright: University of Massachusetts.)

“It’s something we need to pay attention to, especially as CRISPR expands to more diseases. We need to do the work and make sure edited cells returned to patients don’t become cancerous,” Sam Kulkarni, PhD, CEO of CRISPR Therapeutics, told Scientific American.

Both studies are preliminary. The implications, however, is in how genes that have become corrupted are used.

“It is unclear if the findings translate into cells actually used in clinical studies,” Bernhard Schmierer, PhD, co-author of a paper titled, “CRISPR-Cas9 Genome Editing Induces a p53-mediated DNA Damage Response,” told Scientific American.

Nevertheless, the cancer-cat is out of the bag.

Targeting RNA Instead of DNA with CRISPR-Cas13d

A team from the Salk Institute may have found a solution. They are investigating a different enzyme—Cas13d—which, in conjunction with CRISPR would target RNA rather than DNA. “DNA is constant, but what’s always changing are the RNA messages that are copied from the DNA. Being able to modulate those messages by directly controlling the RNA has important implications for influencing a cell’s fate,” Silvana Konermann, PhD, a Howard Hughes Medical Institute (HHMI) Hanna Gray Fellow and member of the research team at Salk, said in a news release.

The Salk team published their findings in the journal Cell. The paper describes how “scientists from the Salk Institute are reporting for the first time the detailed molecular structure of CRISPR-Cas13d, a promising enzyme for emerging RNA-editing technology. They were able to visualize the enzyme thanks to cryo-electron microscopy (cryo-EM), a cutting-edge technology that enables researchers to capture the structure of complex molecules in unprecedented detail.”

The researchers think that CRISPR-Cas13d may be a way to make the process of gene editing more effective and allow for new strategies to emerge. Much like how CRISPR-Cas9 led to research into recording a cell’s history and to tools like SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing), a new diagnostic tool that works with CRISPR and changed clinical laboratory diagnostics in a foundational way.

Dark Daily reported on this breakthrough last year. (See, “CRISPR-Related Tool Set to Fundamentally Change Clinical Laboratory Diagnostics, Especially in Rural and Remote Locations,” August 4, 2017.)

Each discovery will lead to more branches of inquiry and, hopefully, someday it will be possible to cure conditions like sickle cell anemia, dementia, and cystic fibrosis. Given the high expectations that CRISPR and related technologies can eventually be used to treat patients, pathologists and medical laboratory professionals will want to stay informed about future developments.

—Dava Stewart

Related Information:

Repair of Double-Strand Breaks Induced by CRISPR-Cas9 Leads to Large Deletions and Complex Rearrangements

P53 Inhibits CRISPR-Cas9 Engineering in Human Pluripotent Stem Cells

CRISPR-Edited Cells Linked to Cancer Risk in 2 Studies

CRISPR-Cas9 Genome Editing Induces a p53-Mediated DNA Damage Response

Decoding the Structure of an RNA-Based CRISPR System

Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d

CRISPR Timeline

What Are Genome Editing and CRISPR-Cas9?

Federal Court Sides with Broad in CRISPR Patent Dispute

Top Biologists Call for Moratorium on Use of CRISPR Gene Editing Tool for Clinical Purposes Because of Concerns about Unresolved Ethical Issues

CRISPR-Related Tool Set to Fundamentally Change Clinical Laboratory Diagnostics, Especially in Rural and Remote Locations

Researchers at Several Top Universities Unveil CRISPR-Based Diagnostics That Show Great Promise for Clinical Laboratories

Harvard Medical School Researchers Use CRISPR Technology to Insert Images into the DNA of Bacteria

Technology allows retrievable information to be recorded directly into the genomes of living bacteria, but will this technology have value in clinical laboratory testing?

Researchers at Harvard Medical School have successfully used CRISPR technology to encode an image and a short film into the Deoxyribonucleic acid (DNA) of bacteria. Their goal is to develop a way to record and store retrievable information in the genomes of living bacteria. A story in the Harvard Gazette described the new technology as a sort of “biological hard drive.”

It remains to be seen how this technology might impact medical laboratories and pathology groups. Nevertheless, their accomplishment is another example of how CRISPR technology is leading to new insights and capabilities that will advance genetic medicine and genetic testing.

The researchers published their study in the journal Science, a publication of the American Association for the Advancement of Science (AAAS).

Recording Complex Biological Events in the Genomes of Bacteria

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are DNA sequences containing short, repetitive base sequences found in the genomes of bacteria and other micro-organisms that can facilitate the modification of genes within organisms. The term CRISPR also can refer to the whole CRISPR-Cas9 system, which can be programmed to pinpoint certain areas of genetic code and to modify DNA at exact locations.

Led by George Church, PhD, faculty member and Professor of Genetics at Harvard Medical School, the team of researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University in Cambridge, Mass., constructed a molecular recorder based on CRISPR that enables cells to obtain DNA information and produce a memory in the genome of bacteria. With it, they inserted a GIF image and a five-frame movie into the bacteria’s DNA.

“As promising as this was, we did not know what would happen when we tried to track about 100 sequences at once, or if it would work at all,” noted Seth Shipman, PhD, Postdoctoral Fellow, and one of the authors of the study in the Harvard Gazette story. “This was critical since we are aiming to use this system to record complex biological events as our ultimate goal.”

Translating Digital Information into DNA Code

The team transferred an image of a human hand and five frames of a movie of a running horse onto nucleotides to imbed data into the genomes of bacteria. This produced a code relating to the pixels of each image. CRISPR was then used to insert genetic code into the DNA of Escherichia coli (E-coli) bacteria. The researchers discovered that CRISPR did have the ability to encode complex information into living cells.

“The information is not contained in a single cell, so each individual cell may only see certain bits or pieces of the movie. So, what we had to do was reconstruct the whole movie from the different pieces,” stated Shipman in a BBC News article. “Maybe a single cell saw a few pixels from frame one and a few pixels from frame four … so we had to look at the relation of all those pieces of information in the genomes of these living cells and say, ‘Can we reconstruct the entire movie over time?’”

The team used an image of a digitized human hand because it embodies the type of intricate data they wish to use in future experiments. A movie also was used because it has a timing component, which could prove to be beneficial in understanding how a cell and its environment may change over time. The researchers chose one of the first motion pictures ever recorded—moving images of a galloping horse by Eadweard Muybridge, a British photographer and inventor from the late 19th century.

“We designed strategies that essentially translate the digital information contained in each pixel of an image or frame, as well as the frame number, into a DNA code that, with additional sequences, is incorporated into spacers. Each frame thus becomes a collection of spacers,” Shipman explained in the Harvard Gazette story. “We then provided spacer collections for consecutive frames chronologically to a population of bacteria which, using Cas1/Cas2 activity, added them to the CRISPR arrays in their genomes. And after retrieving all arrays again from the bacterial population by DNA sequencing, we finally were able to reconstruct all frames of the galloping horse movie and the order they appeared in.”

In the video above, Wyss Institute and Harvard Medical School researchers George Church, PhD, and Seth Shipman, PhD, explain how they engineered a new CRISPR system-based technology that enables the chronological recording of digital information, like that representing still and moving images, in living bacteria. Click on the image above to view the video. It is still too early to determine how this technology may be useful to pathologists and clinical laboratory scientists. (Caption and video copyright: Wyss Institute at Harvard University.)

“In this study, we show that two proteins of the CRISPR system, Cas1 and Cas2, that we have engineered into a molecular recording tool, together with new understanding of the sequence requirements for optimal spacers, enables a significantly scaled-up potential for acquiring memories and depositing them in the genome as information that can be provided by researchers from the outside, or that, in the future, could be formed from the cells natural experiences,” stated Church in the Harvard Gazette story. “Harnessed further, this approach could present a way to cue different types of living cells in their natural tissue environments into recording the formative changes they are undergoing into a synthetically created memory hotspot in their genomes.”

Encoding Information into Cells for Clinical Laboratory Testing and Therapy

The team plans to focus on creating molecular recording devices for other cell types and on enhancing their current CRISPR recorder to memorize biological information.

“One day, we may be able to follow all the developmental decisions that a differentiating neuron is taking from an early stem cell to a highly-specialized type of cell in the brain, leading to a better understanding of how basic biological and developmental processes are choreographed,” stated Shipman in the Harvard Gazette story. Ultimately, the approach could lead to better methods for generating cells for regenerative therapy, disease modeling, drug testing, and clinical laboratory testing.

According to Shipman in the BBC News article, these cells could “encode information about what’s going on in the cell and what’s going on in the cell environment by writing that information into their own genome.”

This field of research is still new and its full potential is not yet understood. However, if this capability can be developed, there could be opportunities for pathologists and molecular chemists to develop methods for in vivo monitoring of a patient’s cell function. These methods could prove to be an unexpected new way for clinical laboratories to add value and become more engaged with the clinical care team.

—JP Schlingman

Related Information:

New CRISPR Technology Takes Cells to the Movies

Molecular Recordings by Directed CRISPR Spacer Acquisition

GIF and Image Written into the DNA of Bacteria

Pro and Con: Should Gene Editing be Performed on Human Embryos?

CRISPR Gene Editing Can Cause Hundreds of Unintended Mutations

Intellia Therapeutics Announces Patent for CRISPR/Cas Genome Editing in China

Everything You Need to Know about CRISPR, the New Tool that Edits DNA

Breakthrough DNA Editor Born of Bacteria

Patent Dispute over CRISPR Gene-Editing Technology May Determine Who Will Be

Top Biologists Call for Moratorium on Use of CRISPR Gene Editing Tool for Clinical Purposes Because of Concerns about Unresolved Ethical Issues

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