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.
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
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
It has been regularly demonstrated in recent decades that human breath contains elements that could be incorporated into clinical laboratory tests, so the decision to use this “breath biopsy” test in a therapeutic drug trial will be closely watched
When a major pharma company pays attention to a breath test, implications for clinical laboratories are often forthcoming. Such may be the case with GlaxoSmithKline (GSK). The global healthcare company has selected Owlstone Medical’s Breath Biopsy technology for use in its Phase II clinical trial of danirixin (DNX), a respiratory drug under development by GSK for treatment of chronic obstructive pulmonary disease (COPD), an Owlstone Medical news release announced.
Anatomic pathologists and medical laboratory leaders will be intrigued by GSK’s integration of breath-based specimens in a clinical trial of a respiratory drug. The partners in the trial aim to analyze breath samples to better understand the drug’s treatment effects and to discover personalized medicine (AKA, precision medicine) opportunities.
GSK (NYSE:GSK), headquartered in the UK but with a large presence in the US, researches and develops pharmaceutical medicines, vaccines, and other consumer health products.
Owlstone Medical, a diagnostic company, is developing a breathalyzer for disease and says it is on a mission to save 100,000 lives and $1.5 billion in healthcare costs. Dark Daily previously reported on Owlstone Medical’s Breath Biopsy platform. The Cambridge, England-based company has raised significant funding ($23.5 million) and already garnered credible cancer trial collaborators including the UK’s National Health Service (NHS).
Now, Owlstone Medical has brought its breath analysis technology to bear on chronic disease outside of cancer diagnostics development. A pharmaporum article called Owlstone’s Medical’s work with GSK an “additional boost of confidence” in the company’s technology, as well as a means for revenue.
Billy Boyle, co-founder and Chief Executive Officer, Owlstone Medical (above), shown with the company’s ReCIVA Breath Sampler device. This will be used by GSK in its Phase II respiratory disease clinical trial of danirixin to “capture VOC biomarkers in breath samples.” (Photo copyright: Business Weekly UK.)
GSK Studying Future Treatments for Respiratory Diseases
COPD affects about 700 million people worldwide, an increase of about 65% since 1990, GSK pointed out. In September 2017, GSK presented respiratory disease data and its pipeline medications at the European Respiratory Society in Milan, Italy. Included was information on danirixin (an oral CXCR2 antagonist), which is part of the company’s focus on COPD disease modification, according to a GSK news release.
“Each of our studies sets the bar for our future research and innovation,” noted Neil Barnes, MA Cantab, FRCP, FCCP(Hon), Vice President, Global Franchise Medical Head, GSK Respiratory, in the GSK press release.
Clinical Trial Aimed at Identifying the ‘Right’ Patients
With Owlstone Medical’s breathalyzer, GSK plans to explore how volatile organic compounds (VOCs) can help identify patients who will benefit most from the company’s medications, as well as evaluate Danirixin’s effects. A critical element of personalized medicine.
“It’s part of our efforts to identify the right patient for the right treatment,” said Ruth Tal-Singer, PhD, GSK’s Vice President of Medicine Development Leader and Senior Fellow, Respiratory Research and Development, in the Owlstone Medical news release.
VOCs in breath will be captured in a non-invasive way from patients who wear Owlstone Medical’s ReCIVA Breath Sampler, which, according to Owlstone Medical, has CE-mark clearance, a certification noting conformity with European health and safety standards. The VOCs breath samples will then be sent to Owlstone Medical’s lab for high-sensitivity analysis.
“Non-invasive Breath Biopsy can establish a role in precision medicine applications such as patient stratification and monitoring treatment response,” said Billy Boyle, Owlstone Medical’s co-Founder and Chief Executive Officer.
VOC Biomarkers in Respiratory Disease
VOC profiles can be characteristic of COPD as well as other respiratory diseases including asthma, tuberculosis, and cystic fibrosis, reported Science/Business.
According to Owlstone Medical’s Website, VOCs are gaseous molecules produced by the human body’s metabolism that are suitable for Breath Biopsy. Their research suggests that exhaled breath reflects molecular processes responsible for chronic inflammation. Thus, VOCs captured through Breath Biopsy offer insight into respiratory disease biomarkers.
Breath also includes VOCs that originate from circulation, which can provide information on a patient’s response to medications.
How the Breath Biopsy Platform Works
Owlstone Medical’s platform relies on its patented Field Asymmetric Ion Mobility Spectrometry (FAIMS) technology, which “has the ability to rapidly monitor a broad range of VOC biomarkers from breath, urine and other bodily fluids with high sensitivity and selectivity,” according to the company’s website. During the process:
- Gases are exchanged between circulating blood and inhaled fresh air in the lungs;
- VOC biomarkers pass from the circulation system into the lungs along with oxygen, carbon dioxide, and other gases;
- Exhaled breath contains exiting biomarkers.
It takes about a minute for blood to flow around the body. So, a breath sample during that time makes possible collection and analysis of VOC biomarkers from any part of the body touched by the circulatory system.
The medical analysis is enabled by software in the Owlstone Medical lab, Boyle told the Cambridge Independent.
“There’s an analogy with blood prints—you get the blood and can look for different diseases, and we’ve developed core hardware and technology to analyze the breath sample,” he said.
Another Breath Sample Device
The ReCIVA Breath Sampler is not the only breathalyzer focused on multiple diseases. Dark Daily reported on research conducted by Technion, Israel’s Institute of Technology, into a breath analyzer that can detect up to 17 cancers, and inflammatory and neurological diseases.
But Owlstone Medical stands out due, in part, to its noteworthy partners: the UK’s National Health Service, as well as the:
And now the company can add collaboration with GSK to its progress. Though some question the reliability of breath tests as biomarkers in the areas of sensitivity and specificity required for cancer diagnosis, Owlstone Medical appears to have the wherewithal to handle those hurdles. It is a diagnostics company that many pathologists and medical laboratory professionals may find worth watching.
—Donna Marie Pocius
Owlstone Medical’s Breath Biopsy Platform Integrated into GSK’s Phase II Respiratory Disease Clinical Trial
GSK Utilizes Owlstone Disease Breathalyser for Key Clinical Trials
GSK Presents Respiratory Data from Pipeline to Clinical Practice at ERS
GSK Boosts Medtech First Owlstone with Use of Breath Biopsy in Respiratory Trial
Glaxo to Stratify COPD Trial Using Breath Biopsy Device
Billy Boyle of Owlstone Medical on the Inspiration Behind His Mission to Save 100,000 From Dying of Cancer
Owlstone Medical and UK’s NHS Study Whether Breath Contains Useful Biomarkers
Breath Based Biomarker Detection: Informing Drug Development and Future Treatment Regimes
Clinical Laboratories Could Soon Diagnose 17 Diseases with a Single Breath Analyzer Test from Israel’s Institute of Technology
Pathologists and clinical lab managers can help physicians more effectively select appropriate genetic tests and better interpret results to identify the most appropriate therapies for their patients
Clinical laboratories and pathology groups aren’t the only healthcare providers being scrutinized for cost cutting and workflow efficiencies. Physicians ordering genetic tests are now in the spotlight thanks to a study of genetic test misordering by one healthcare institution.
In her award-winning presentation, “Genetic Testing Costs and Compliance with Clinical Best Practices,” given at the 2016 annual clinical and scientific meeting of the American College of Obstetricians and Gynecologists (ACOG), Kathleen Ruzzo, MD, revealed some startling facts to the attendees. Ruzzo is an obstetrics and gynecology (OB-GYN) resident at the Naval Medical Center (NMC) in San Diego. She and a team of NMC researchers had reviewed all genetic tests ordered during a 3-month period. They found that more than one-third of the genetic tests examined were unnecessary and had led to more than $20,000 in additional healthcare expenditures. This got the attention of the ACOG, which awarded her 1st prize.
Critical Importance of Staying Informed on Genetic Tests
The researchers examined 114 charts that contained billing codes for genetic tests. They evaluated the charts for compliance with practice guidelines and completed a cost analysis of the tests. The tests were classified per GeneReviews guidelines and were labeled as:
- Misordered/Not Indicated;
- Misordered/False Reassurance; or
GeneReviews is an online database focusing on information, diagnosis, management, and counseling of single-gene disorders. It is published by the National Center for Biotechnology Information.
The researchers found that:
- 44 of the 114 charts examined (39%) were misordered based on the guidelines;
- 24 of the tests were labeled as misordered/not indicated;
- Eight tests were classified as misordered/false reassurance; and
- 12 tests were determined to be misordered/inadequate.
“We know there is an ever-expanding number of genetic tests available for clinicians to order, and there is more direct marketing to the patient,” stated Ruzzo in an Ob. Gyn. News article. “It can be difficult to stay on top of that as we have so many different clinical responsibilities.”
Kathleen Ruzzo, MD (above right) and Monica Lutgendorf, MD (above left) of the Naval Medical Center in San Diego, reviewed 114 genetic tests ordered during a three-month period. They discovered that 39% of the tests were misordered according to guidelines, costing a total of $75,000. (Photo copyright: Naval Medical Center.)
The actual testing was performed by Laboratory Corporation of America and occurred over a three-month period. The seven common genetic tests that were reviewed were tests for:
The cost analysis of the tests revealed that $20,000 could have been saved by following the GeneReviews guidelines. The total costs affiliated with the 114 tests reached $75,000. Potential savings were thus 26.6% of the total cost of the genetic tests involved in this study. In many clinical settings, if pathologists and medical laboratory managers could help physicians better utilize genetic tests while reducing the cost of such testing by almost 27%, that would be a major contribution. Plus, patients would be getting better care.
Ordering the Right Genetic Test Saves Money and Protects Patients
According to the National Institutes of Health (NIH), costs affiliated with genetic tests can range from less than $100 to more than $2,000 depending on the type and intricacy of the test. The NIH notes that many insurance companies will pay for genetic testing if ordered by a physician.
Ruzzo also shared that many of her cohorts were surprised at the results of the research.
“I think it opened a lot of people’s eyes … to be more meticulous about [genetic] testing and to ask for help when you need help,” she stated in the Ob. Gyn. News article. “Having trained individuals, reviewing genetic tests could save money in the healthcare system more broadly. We could also approve the appropriate testing for the patient.”
Ruzzo did admit there were limitations to the study; the researchers only looked at small amounts of tests for a short period and they did not concentrate on the consequences of the misordering to the patients.
Monica Lutgendorf, MD, Maternal Fetal Medicine Physician at the Naval Medical Center, was one of the coauthors of the paper. In the Ob. Gyn. News article, she described the findings as “a call to action in general for ob-gyns to get additional training and resources to handle the ever-expanding number of [genetic] tests.”
“I don’t think that this is unique to any specific institution. I think this is part of the new environment of practice that we’re in,” Lutgendorf concluded.
Due to the costs of genetic testing and the fact that so many physicians have not been able to keep up with all the latest advances in genetic medicine and testing, misordering will, most likely, continue to be a problem. Nevertheless, pathologists and clinical laboratory managers can serve a crucial role in helping physicians be more effective at selecting the correct genetic tests and assisting them in interpreting results to choose the most appropriate therapies for their patients.
Meanwhile, for those pathologists and medical laboratory professionals interested in developing effective utilization management programs for lab tests, Dark Daily is presenting a special webinar, titled, “Simple, Swift Approaches to Lab Test Utilization Management: Proven Ways for Your Clinical Laboratory to Use Data and Collaborations to Add Value.” It will take place on Thursday, June 29, 2017 at 1PM EDT.
For information about this high-value webinar and to register, use this link (or copy this URL and paste into your browser: https://ddaily.wpengine.com/webinar/simple-swift-approaches-to-lab-test-utilization-management-proven-ways-for-your-clinical-laboratory-to-use-data-and-collaborations-to-add-value.)
More Than One-Third of Genetic Tests Misordered, Study Finds
Genetic Tests Often Overused and Misinterpreted, Sometimes with Tragic Consequences
Webinar: Simple, Swift Approaches to Lab Test Utilization Management: Proven Ways for Your Clinical Laboratory to Use Data and Collaborations to Add Value
Research Awards Announced for ACOG 2017 Annual Meeting
Unnecessary Genetic Tests Wastes $500 Million Annually
Most insurers still determine coverage on a case-by-case basis, but two major payers now have coverage policies that are helpful to clinical labs that perform WES
Whole exome sequencing (WES) is not new for clinical pathologists, but it is becoming more common in a clinical setting as more physicians learn about its uses.
This is due to two reasons. First, researchers are identifying new ways to use whole exome sequencing to improve patient care. Second, the cost of whole genome sequencing continues to fall at a steady rate, making it ever more affordable to use in clinical settings.
As recently as 2009, WES was prohibitively expensive and there was little possibility that insurers would cover the cost of the test, as it was considered experimental. Now, however, evidence is mounting that it is an effective diagnostic tool. Therefore, more payers are announcing coverage for WES for an expanding number of diagnostic purposes. (more…)
A growing number of media stories claim medical lab companies that develop genetic screening assays oversell the accuracy of such tests and fail to educate parents and doctors about the risks of false positives and false negatives
In response to growing concerns by consumers about the accuracy of some proprietary genetic screening assays, several media outlets have begun reporting on this sector of the clinical laboratory industry.
What gives these news stories emotional punch is the fact that patients use these proprietary medical laboratory tests to make decisions that can be life-changing. In its story about these tests, the Boston Sunday Globe used the headline “Oversold prenatal tests spur some to choose abortions.” (more…)