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
Last week, The Dark Report was in San Diego and Houston to attend the annual meetings of the United States & Canadian Academy of Pathology (USCAP) and the Clinical Laboratory Management Association (CLMA). Time spent in the exhibit halls of both meetings spoke volumes about the changing trends in the laboratory profession.
First was the USCAP meeting, conducted in San Diego, California. This is a growing meeting and attracts more than 3,000 pathologists from countries around the world. One can hear many different languages spoken as one walks among the crowd between sessions. The exhibit hall of USCAP is also growing. It featured 245 exhibitors and represented a good cross section of companies selling instrument systems, consumables, and services to anatomic pathology laboratories.
Of particular note were two things seen in USCAP’s exhibition hall. First, there was an intriguing spread of companies offering digital solutions for anatomic pathology. Technology is advancing and, even if the current generation of products fall a bit short of the functionality desired by customers, it is clear that lots of money is being invested to advance all aspects of pathology informatics and digital imaging. Second, molecular pathology was definitely a major product sector at this exhibition. Whether it was the marketing of new diagnostic assays or companies offering services in molecular pathology, there was high interest in how molecular pathology could be used to provide higher quality diagnostic support to pathologists and their referring clinicians.
Following the USCAP meeting, I flew to Houston, Texas to catch the CLMA annual meeting. Just as laboratory consolidation in the hospital industry over the past decade has steadily concentrated laboratory management duties into the hands of fewer people, CLMA has seen a corresponding shift in the numbers of attendees and the composition of vendors in its exhibition hall. One obvious difference from past years is the lower profile of several in vitro diagnostic (IVD) companies at this year’s event. Yet, a survey of vendors throughout the exhibition hall indicated that the people passing through the exhibition were qualified buyers and their expectation was that new business would be result from their participation at the exhibition.
Just as at the USCAP exhibition hall, CLMA’s exhibitor line-up featured a growing number of software and informatics vendors compared to past years. I take this as a sign that laboratory directors and pathologists are taking active steps to use information technology to guide their management of laboratory operations and work flow. The range of middleware solutions and vendors on the exhibition floor would be a response by vendors to the demand for those functions by laboratory customers.
Another observation was gained from attendance at the annual meetings of USCAP and CLMA. There is plenty of optimism about the future of laboratory medicine among attendees and vendors at both events. Despite the rapid pace of change in healthcare and unfavorable reimbursement trends, pathologists and laboratory managers believe that new diagnostic tests and advances in laboratory medicine are giving them important new tools to help patients and their physicians.
Your traveling editor,
Send your comments and observations to Robert at email@example.com.
Today Dark Daily wants to introduce you to the emerging medical discipline of “multi-modality diagnosis.” Advances in genetics and molecular technologies are actively breaking down the traditional scope of practice for several medical specialists. At ground zero in this new area of medicine are pathology and radiology.
Multi-modality diagnosis can be defined in a simple manner. It is the use of several different types of clinical data-in an integrated fashion-to make a diagnosis. “Integration” is the key concept here, since physicians have always assembled information about the patient from several sources as they proceeded to evaluate the patient and make a diagnosis.
As doctors and researchers learn more about genetics and the role of DNA, RNA, and proteomics in various illnesses and ailments, there are huge increases in the volume of data now relevant in assessing the patient’s condition and determining the most accurate diagnosis. At the same time, medical specialties, particularly those of radiology and pathology, that formerly could work somewhat independently to evaluate the patient and provide the referring clinician with a report that was rather straightforward and simple, now face a new challenge. The expanding knowledge base of genetic and molecular information means that their evaluation of the patient needs to incorporate the findings of other medical specialists if the final assessment is to be accurate and useful to the referring clinician.
In other words, genetic medicine is the active catalyst that is already motivating different medical specialties to interact more closely to assess and diagnose certain types of diseases. At the forefront of this trend are progressive radiologists and pathologists-specifically those working with molecular imaging and molecular pathology. For example, in leading academic centers, it is growing ever more common for the neuropathologist and the neuroradiologist to review each other’s images before signing out their respective cases. In some laboratory settings, these two subspecialists are already developing a single, integrated report that goes to the referring physician.
Healthcare informatics is another channel of innovation propelling multi-modality diagnostics forward. Independent of pathology and radiology, there are informaticians pulling together disparate sets of patient data, then running this data through sophisticated software algorithms to develop diagnostic information that gives the patient’s physician new knowledge. Within the field of healthcare informatics, these innovators constantly describe their work as bringing together multiple modalities of data. Dark Daily readers should note that this effort is happening outside of the pathology and radiology specialties. It is an external trend to both professions.
Those interested in learning more about multi-modality diagnosis have two resources. In a recent issue of The Dark Report, a detailed intelligence briefing was published on this topic under the title “Multi-Modality Diagnosis Heading for Lab Medicine.” Dark Daily subscribers who would like a complementary copy of this intelligence briefing should contact Ron Martin at firstname.lastname@example.org.
The second resource for learning more about multi-modality diagnosis is the upcoming Molecular Summit on the Integration of In Vivo and In Vitro Diagnostics http://www.molecular-summit.com On February 10-11, 2009, national and world leaders in molecular imaging, molecular diagnostics, and integrated informatics will be leading strategic sessions and case studies on this subject. Location is the Sheraton Society Hill Hotel in Philadelphia, Pennsylvania.
Speakers from such organizations as Massachusetts General Hospital, Stanford University Medical Center, MD Anderson Medical Center, UCLA Medical Center, Siemens, and the Institute for Systems Biology will provide the latest innovations in the integration of in vivo and in vitro diagnostics. Last year’s Molecular Summit attracted 225 attendees, along with editors and reporters from 15 healthcare publications. This next Molecular Summit has compelling case studies of how molecular diagnostics, when integrated with molecular imaging and other data sets, is giving clinicians powerful new insights for making diagnoses, identifying appropriate therapies, and monitoring patient progress.
The full agenda and speaker line-up for this year’s Molecular Summit can be viewed here (or paste this URL into your browser: http://www.molecular-summit.com/agenda.htm )
Make your plans to join us at Molecular Summit 2009 to learn how your laboratory can benefit from multi-modality diagnostics.
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As healthcare becomes a global business, laboratory vendors from overseas are casting an envious eye on the market in the United States. After all, it is the world’s biggest and richest healthcare market, with more than $2 trillion in spending. Better yet, because healthcare in this country is organized around multiple payers and private providers, it provides competitive opportunities that don’t exist in many countries with single-payer health systems. (more…)