With $191 million in startup capital, the genomics startup will draw on existing genetic databases to create personalized medicine therapies for chronic diseases
Why do some people get sick while others do not? That’s what genetic researchers at Maze Therapeutics want to find out. They have developed a new approach to using tools such as CRISPR gene editing to identify and manipulate proteins in genetic code that may be the key to providing personalized protection against specific diseases.
If viable, the results of Maze’s research could mean the development of specific drugs designed to mimic genetic code in a way that is uniquely therapeutic to specific patients. This also would create the need for clinical laboratories to sequence and analyze patients’ DNA to determine whether a patient would be a candidate for any new therapies that come from this line of research.
Based in San Francisco, Maze Therapeutics (Maze) is studying modifier genes—genes that affect the phenotype or physical properties of other genes—and attempting to create drugs that replicate them, reported MIT Technology Review. Maze believes that genetic modifiers could afford a “natural form of protection” against disease.
“If you have a disease-causing gene, and I have the disease-causing gene, why is it that you may be healthy and I may be sick? Are there other genes that come into play that provide a protective effect? Is there a drugging strategy to recover normal phenotype and recover from the illness?” Maze Chief Executive Officer Jason Coloma, PhD, asked in an interview with FierceBiotech.
In 2019, Maze received $191 million in financing from Third Rock Ventures, ARCH Venture Partners, and others, to find ways to translate their findings into personalized medicines, according to a news release. And with the availability of international public genetic databases and CRISPR gene editing, now may be good timing.
“This was the perfect time to get into this space with the tools that were being developed and the amount of data that has been accumulated on the human genetic side,” Charles Homcy, MD, Third Rock Ventures Partner and Maze Scientific Founder, told Forbes, which noted that Maze is tapping existing population-wide genetic databases and large-scale studies, including the United Kingdom’s Biobank and Finland’s Finngen.
To help find genetic modifier drug targets, Maze is accessing CRISPR gene editing capabilities. Jonathan Weissman, PhD, Maze Scientific Founder and Professor of Cellular Molecular Pharmacology at University of California, San Francisco (UCSF), told MIT Technology Review: “You take a cell with a disease-causing gene and then see if you can turn it back to normal. We can do 100,000 experiments at once because each cell is its own experiment.”
“At Maze, we are focused on expanding our understanding of the natural disease protection provided by genetic modifiers through an integrated approach that combines studying natural human genetic variation across the globe and conducting large-scale experiments of gene perturbations,” Charles Homcy, MD (above), Founder and interim CEO of Maze and a partner at Third Rock Ventures, said in a news release. “Through our integrated approach, we believe we will create novel medicines based around those modifiers to treat a number of diseases.” (Photo copyright: Forbes.)
Using CRISPR to Identify the Cause of Disease
One drug research program reportedly progressing at Maze involves developing gene therapy for the neurogenerative disease amyotrophic lateral sclerosis (ALS). The program borrows from previous research conducted by Aaron Gitler, PhD, Professor of Genetics at Stanford University and Maze co-founder, which used CRISPR to find genetic modifiers of ALS. The scientists found that when they removed the protein coding gene TMX2 (Thioredoxin Related Transmembrane Protein 2), the toxicity of proteins building the disease was reduced, reported Chemical and Engineering News.
“We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells,” Gitler and colleagues wrote in Nature Genetics. “Together, our results demonstrate the promise of using CRISPR-Cas9 screens in defining the mechanisms of neurodegenerative diseases.”
“We have the flexibility to think differently. We like to
think of ourselves as part of this new breed of biotech companies,” Coloma told
FierceBiotech.
It’s an exciting time. Clinical laboratories can look
forward to new precision medicine diagnostic tests to detect disease and
monitor the effects of patient therapies. And the research initiatives by Maze
and other genetic companies represent a new approach in the use of genetic code
to create specific drug therapies targeted at specific diseases that work best
for specific patients.
The companion diagnostics that may come from this research would
be a boon to anatomic pathology.
These “off-target” genetic alterations demonstrate that certain CRISPR base editors need further refinement in a research finding of interest to pathologists
Could CRISPR
DNA-editing technology unintentionally effect RNA as well? A new study conducted
at Massachusetts General Hospital
(MGH) suggests that it can. Clinical
laboratories doing genetic testing will want to understand why this
research implies that refinements to CRISPR may be needed for it to be accurate
in therapeutic applications.
For years, a huge value of CRISPR (Clustered Regularly
Interspaced Short Palindromic Repeats) base editors have been their ability to
edit genes or convert a specific DNA base without breaking the DNA. Now, the MGH
scientists have discovered that certain CRISPR base editors may extend beyond
the targeted DNA and perform unwanted edits to RNA, according to a news release.
“Most investigation of off-target base editing has focused
on DNA, but we have found that this technology can induce large numbers of RNA
alterations as well. This surprising finding suggests the need to look at more
than just genetic alterations when considering unintended off-target effects of
base editors in cells,” J. Keith Joung, MD,
PhD, MGH Pathologist and Professor of Pathology at Harvard Medical School, stated in the news release.
The MGH scientists published their study in Nature.
How the MGH Researchers
Found Off-Target Effects on RNA
The researchers had set their sights on developing a base
editor that targets cytosine,
according to the study.
“Previous studies of cytosine base editor specifically have
identified off-target DNA edits in human cells. Here, we show that a cytosine
base editor with rat APOBEC1
[rAPOBEC1] enzyme can cause extensive transcriptome-wide RNA
cytosine deamination in
human cells,” the scientists wrote in Nature.
According to the news
release, when the researchers put base editors into human liver and kidney cells,
they found their technology induced efficient edits at the target DNA site.
However, they also discovered tens of thousands of cytosine-to-uracil edits in the cells. They
found that deaminases, an enzyme that acts as a catalyst, which they used in
their base editor to change DNA, also altered the RNA in the cells, Science reported.
“Base editors are still incredibly powerful tools. This is just another parameter we need to understand,” J. Keith Joung, MD, PhD (above), MGH Pathologist and Professor of Pathology at Harvard Medical School, told Science. (Photo copyright: Massachusetts General Hospital.)
The researchers developed a way to reduce the unwanted RNA
edits, while maintaining the targeted DNA effects. They came up with cytosine
base editor variants, which they dubbed SElective Curbing of Unwanted RNA
Editing (SECURE).
“We engineered two cytosine base editor variants bearing
rAPOBEC1 mutations that substantially decreased the number of RNA edits in
human cells,” the researchers wrote in their study.
However, they also
called for changes to how base editors are used. “For research applications,
scientists using base editors will need to account for potential RNA off-target
effects in their experiments,” the MGH news release notes. “For therapeutic
applications, our results further argue for limiting the duration of base-editor
expression to the shortest length of time possible and the importance of
minimizing and accounting for potential impacts of these effects in safety
assessments.”
Other Studies Explore CRISPR
Other studies published earlier this year on mice and on rice also suggested
that “modified CRISPR-Cas9 technology will need to be further refined before it
can safely be used for research and therapeutic applications,” The Scientist reported.
Clinical laboratory leaders and pathologists recognize
CRISPR technology is changing the way research is done for diagnosing disease
as well as guiding treatment. Dark Daily has reported on key
CRISPR developments over many years.
And now, though the MGH study may appear to be a set-back
for CRISPR, it also may propel further research into possible therapeutic
applications of CRISPR base editing. It’s a development worth watching.
Researchers at UC Berkley developed new ways to use CRISPR as a genetic “search engine” in addition to a cut and paste tool
Clinical pathology laboratory professionals have long been aware of the potential diagnostic properties related to CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology. Now, new tests using the gene-editing tool show that potential is being realized.
One example involves using CRISPR to detect diseases in Nigeria, where a Lassa fever epidemic has already led to the death of 69 people this year alone. According the journal Nature, this diagnostic test “relies on CRISPR’s ability to hunt down genetic snippets—in this case, RNA from the Lassa virus—that it has been programmed to find. If the approach is successful, it could help to catch a wide range of viral infections early, so that treatments can be more effective and health workers can curb the spread of infection.”
Researchers in Honduras and California are working on similar projects to develop diagnostic tests for dengue fever, Zika, and the strains of human papillomavirus (HPV) that lead to cancer. There’s also a CRISPR-based Ebola test pending in the Democratic Republic of Congo.
These new genetic tests, which may be as simple as at-home
pregnancy tests to use, could save many lives throughout the world. They will
give medical laboratories new tools for diagnosing disease and guiding
therapeutic decisions.
Shift in How
Researchers View CRISPR
“We really think of CRISPR fundamentally as a kind of search engine for biology—like Google for biology—rather than [a kind of] word processing tool, although it’s really good at that too,” Trevor Martin, PhD, co-founder and CEO of Mammoth Biosciences, told CRISPR Cuts, a Synthego CRISPR podcast.
Professor of Biochemistry and Molecular Biology, and Li Ka
Shing Chancellor’s Professor in Biomedical and Health.
Martin’s statement represents a shift in how researchers are thinking about CRISPR. At first, CRISPR was seen as a tool for cutting and pasting genetic material. Scientists could tell it to find a target DNA sequence, make a cut, and paste in something different. However, by thinking of the tool as a search engine, CRISPR’s tremendous diagnostic potential becomes apparent.
“This is a very exciting direction for the CRISPR field to
go in,” Doudna told Nature.
Martin told CRISPR
Cuts that diagnostics is “fundamentally a search problem,” adding, “Now you
can program [CRISPR] to find something, and then tell you that result.”
Doudna notes in Technology Networks that, “Mammoth’s technology exemplifies some of the most urgent, impactful, and untapped potential in the CRISPR space.”
Fehintola Ajogbasile (above), a graduate student at the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria, uses a CRISPR diagnostic test to look for Lassa virus in a blood sample. Similar clinical pathology laboratory tests are becoming available in the US as well. (Photo and caption copyright: Nature/Amy Maxmen.)
Investors See
Economic Benefits of CRISPR
The potential financial and economic impact of simple-to-use CRISPR-based diagnostic tools is considerable. Technology Networks notes that the diagnostics market is estimated at $45 billion, and that venture capital firms Mayfield, First Trust Mid Cap Core AlphaDEX Fund (NASDAQ:FNX), and 8VC have all invested in Mammoth Biosciences.
Although the diagnostics market is huge, a critical aspect
of the Lassa fever diagnostic test the Nigerian researchers are developing is
that it will be as accurate as conventional clinical laboratory testing
methods, but much simpler and less expensive.
Dhamari Naidoo, a technical officer at the World Health Organization (WHO) told Nature that researchers often fail to think about the fact that new technology must be affordable for use in low-income countries.
About a dozen diagnostic tests for Ebola have been
developed, according to Naidoo, but only two have been used recently in the
Democratic Republic of Congo, where the virus is resurging, due to economic
concerns. To be useful, medical laboratory tests in low-income countries must
be affordable to license and distribute, and critically, the manufacturers must
identify a market large enough to motivate them to make and distribute such
diagnostic tests.
Future Directions for
CRISPR and Clinical Pathology
Researchers first discovered what would come to be known as CRISPR in the early 1990s. However, it wasn’t until 2012 – 2013 that scientists used CRISPR and Cas9 for genome editing, a Broad Institute CRISPR timeline notes.
Now, researchers around the world are finding innovative
ways to employ the technology of CRISPR to detect disease in some of the most
remote, challenging areas where diseases such as Lassa fever, Zika, and dengue
fever among others, have devastated the populations, as Dark Daily has previously reported.
What’s next for clinical and pathology laboratories and
CRISPR? We’ll let you know.
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.
“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.
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.
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.
Three innovative technologies utilizing CRISPR-Cas13, Cas12a, and Cas9 demonstrate how CRISPR might be used for more than gene editing, while highlighting potential to develop new diagnostics for both the medical laboratory and point-of-care (POC) testing markets
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is in the news again! The remarkable genetic-editing technology is at the core of several important developments in clinical laboratory and anatomic pathology diagnostics, which Dark Daily has covered in detail for years.
Now, scientists at three universities are investigating ways to expand CRISPR’s use. They are using CRISPR to develop new diagnostic tests, or to enhance the sensitivity of existing DNA tests.
One such advancement improves the sensitivity of SHERLOCK (Specific High Sensitivity Reporter unLOCKing), a CRISPR-based diagnostic tool developed by a team at MIT. The new development harnesses the DNA slicing traits of CRISPR to adapt it as a multifunctional tool capable of acting as a biosensor. This has resulted in a paper-strip test, much like a pregnancy test, that can that can “display test results for a single genetic signature,” according to MIT News.
Such a medical laboratory test would be highly useful during pandemics and in rural environments that lack critical resources, such as electricity and clean water.
One Hundred Times More Sensitive Medical Laboratory Tests!
MIT News highlighted the high specificity and ease-of-use of their system in detecting Zika and Dengue viruses simultaneously. However, researchers stated that the system can target any genetic sequence. “With the original SHERLOCK, we were detecting a single molecule in a microliter, but now we can achieve 100-fold greater sensitivity … That’s especially important for applications like detecting cell-free tumor DNA in blood samples, where the concentration of your target might be extremely low,” noted Abudayyeh.
“The [CRISPR] technology demonstrates potential for many healthcare applications, including diagnosing infections in patients and detecting mutations that confer drug resistance or cause cancer,” stated senior authorFeng Zhang, PhD. Zhang, shown above in the MIT lab named after him, is a Core Institute Member of the Broad Institute, Associate Professor in the departments of Brain and Cognitive Sciences and Biological Engineering at MIT, and a pioneer in the development of CRISPR gene-editing tools. (Photo copyright: MIT.)
Creating a Cellular “Black Box” using CRISPR
Another unique use of CRISPR technology involved researchers David Liu, PhD, and Weixin Tang, PhD, of Harvard University and Howard Hughes Medical Institute (HHMI). Working in the Feng Zhang laboratory at the Broad Institute, they developed a sort of “data recorder” that records events as CRISPR-Cas9 is used to remove portions of a cell’s DNA.
They published the results of their development of CRISPR-mediated analog multi-event recording apparatus (CAMERA) systems, in Science. The story was also covered by STAT.
“The order of stimuli can be recorded through an overlapping guide RNA design and memories can be erased and re-recorded over multiple cycles,” the researchers noted. “CAMERA systems serve as ‘cell data recorders’ that write a history of endogenous or exogenous signaling events into permanent DNA sequence modifications in living cells.”
This creates a system much like the “black box” recorders in aircraft. However, using Cas9, data is recorded at the cellular level. “There are a lot of questions in cell biology where you’d like to know a cell’s history,” Liu told STAT.
While researchers acknowledge that any medical applications are in the far future, the technology holds the potential to capture and replay activity on the cellular level—a potentially powerful tool for oncologists, pathologists, and other medical specialists.
Using CRISPR to Detect Viruses and Infectious Diseases
Another recently developed technology—DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR)—shows even greater promise for utility to anatomic pathology groups and clinical laboratories.
Also recently debuted in Science, the DETECTR system is a product of Jennifer Doudna, PhD, and a team of researchers at the University of California Berkeley and HHMI. It uses CRISPR-Cas12a’s indiscriminate single-stranded DNA cleaving as a biosensor to detect different human papillomaviruses (HPVs). Once detected, it signals to indicate the presence of HPV in human cells.
Despite the current focus on HPVs, the researchers told Gizmodo they believe the same methods could identify other viral or bacterial infections, detect cancer biomarkers, and uncover chromosomal abnormalities.
Future Impact on Clinical Laboratories of CRISPR-based Diagnostics
Each of these new methods highlights the abilities of CRISPR both as a data generation tool and a biosensor. While still in the research phases, they offer yet another possibility of improving efficiency, targeting specific diseases and pathogens, and creating new assays and diagnostics to expand medical laboratory testing menus and power the precision medicine treatments of the future.
As CRISPR-based diagnostics mature, medical laboratory directors might find that new capabilities and assays featuring these technologies offer new avenues for remaining competitive and maintaining margins.
However, as SHERLOCK demonstrates, it also highlights the push for tests that produce results with high-specificity, but which do not require specialized medical laboratory training and expensive hardware to read. Similar approaches could power the next generation of POC tests, which certainly would affect the volume, and therefore the revenue, of independent clinical laboratories and hospital/health system core laboratories.
