Apr 18, 2018 | Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
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!
Co-lead authors Jonathan Gootenberg, PhD Candidate, Harvard University and Broad Institute; and Omar Abudayyeh, PhD and MD student, MIT, published their findings in Science. They used CRISPR Cas13 and Cas12a to chop up RNA in a sample and RNA-guided DNA binding to target genetic sequences. Presence of targeted sequences is then indicated using a paper-based testing strip like those used in consumer pregnancy 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 author Feng 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.)
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.
—Jon Stone
Related Information:
Multiplexed and Portable Nucleic Acid Detection Platform with Cas13, Cas12a, and Csm6
Rewritable Multi-Event Analog Recording in Bacterial and Mammalian Cells
CRISPR-Cas12a Target Binding Unleashes Indiscriminate Single-Stranded DNase Activity
Researchers Advance CRISPR-Based Tool for Diagnosing Disease
CRISPR Isn’t Just for Gene Editing Anymore
CRISPR’s Pioneers Find a Way to Use It as a Glowing Virus Detector
With New CRISPR Inventions, Its Pioneers Say, You Ain’t Seen Nothin’ Yet
New CRISPR Tools Can Detect Infections Like HPV, Dengue, and Zika
Breakthrough DNA Editing Tool May Help Pathologists Develop New Diagnostic Approaches to Identify and Treat the Underlying Causes of Diseases at the Genetic Level
CRISPR-Related Tool Set to Fundamentally Change Clinical Laboratory Diagnostics, Especially in Rural and Remote Locations
Harvard Researchers Demonstrate a New Method to Deliver Gene-editing Proteins into Cells: Possibly Creating a New Diagnostic Opportunity for Pathologists
Jun 14, 2017 | Digital Pathology, Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
New discoveries about the genetics of prostate cancer could lead to better tools for diagnosing the disease and selecting effective therapies based on each patient’s specific physiology
In recent decades, the biggest challenge for urologists, and for the pathologists who diagnosed the prostate tissue specimens they referred, has been how to accurately differentiate between non-aggressive prostate cancer, which can exist for decades with no apparent symptoms, and aggressive prostate cancer that kills quickly.
Thus, a research study that has identified unique genetic features within prostate cancer that can help determine if the cancer is aggressive or not, and whether certain drugs may be effective, is good news for men, for urologists, and for the clinical laboratories that will be called upon to perform testing.
These types of breakthroughs bring precision medicine ever closer to having viable tools for effective diagnosis of different types of cancer.
Genetic Fingerprints of Cancer Tumor Types
One such study into the genetic pathways of prostate cancer is bringing precision medicine ever-closer to the anatomic pathology laboratory. Researchers from the Princess Margaret Cancer Centre, which is associated with the University of Toronto Faculty of Medicine, have discovered that some tumors in prostate cancer have a genetic fingerprint that may indicate whether or not the disease will become more aggressive and less responsive to treatment.
Robert Bristow, MD, PhD, and Paul Boutros, PhD, conducted a study of nearly 500 Canadian men who had prostate cancer. Published in the journal Nature, the researchers examined the genetic sequences of those tumors, looking for differences between those that responded to surgery or radiation and those that did not.
In the video above, Dr. Robert Bristow, clinician-scientist at Princess Margaret Cancer Centre, discusses the findings of a key piece in the genetic puzzle that explains why men born with a BRCA2 mutation develop aggressive prostate cancer. (Caption and photo copyright: University Health Network/Princess Margaret Cancer Centre.)
According to a FierceBiotech article, approximately 30% of men who have a type of prostate cancer thought to be curable eventually develop an aggressive metastatic type of the disease. About half of the men who developed a metastatic form of cancer had mutations to three specific genes:
“This information gives us new precision about the treatment response of men with prostate cancer and important clues about how to better treat one set of men versus the other to improve cure rates overall,” stated Bristow in a University Health Network (UHN) press release.
In another study, researchers looked at 15 patients with BRCA2-inheritied prostate cancer and compared the genomic sequences of those tumors to a large group of sequences from tumors in less-aggressive cancer cases. According to a ScienceDaily news release, they found that only 2% of men with prostate cancer have the BRCA2-inherited type.
Knowing what type of cancer a man has could be critically important for clinicians tasked with prescribing the most efficient therapies.
“The pathways that we discovered to be abnormal in the localized BRCA2-associated cancers are usually only found in general population cancers when they become resistant to hormone therapy and spread through the body,” noted Bristow in the ScienceDaily release. If clinicians knew from diagnosis that the cancer is likely to become aggressive, they could choose a more appropriate therapy from the beginning of treatment.
Genetic Mutations Also Could Lead to Breast and Brain Cancer Treatments
BRCA mutations have also been implicated in breast, ovarian, and pancreatic cancers, among some other types. The knowledge that BRCA1 and BRACA2 mutations could indicate a more aggressive cancer is likely to spark investigation into whether poly ADP ribose polymerase (PARP) inhibitors could be used as an effective therapy.
PARP inhibitors are increasingly of interest to scientists. In addition to being used to treat some BRCA1/BRCA2-implicated cancers, two recent studies show that it could be effective in treating brain cancer with low-grade gliomas that involve a mutation to the gene isocitrate dehydrogenase (IDH), according to an article published by the National Cancer Institute and the National Institutes of Health (NIH).
Researchers of the study published in the journal Clinical Cancer Research investigated how PARP inhibitors impact DNA repair in gliomas.
Researchers of the study published in the journal Science Translational Medicine stated that they “demonstrate mutant IDH1-dependent PARP inhibitor sensitivity in a range of clinically relevant models, including primary patient-derived glioma cells in culture and genetically matched tumor xenografts in vivo.”
According to the UHN press release, the next step in using the knowledge that BRCA1 and BRCA2 may indicate a more aggressive prostate cancer is for researchers to create a diagnostic tool that can be used to determine what type of prostate cancer a man has. They expect the process to take several years. “This work really gives us a map to what is going on inside a prostate cancer cell, and will become the scaffold on which precision therapy will be built,” Boutros stated in a Prostate Cancer Canada news release.
Unlocking Knowledge That Leads to Accurate Diagnoses and Treatments
Research that furthers precision medicine and allows clinicians to choose the most appropriate treatment for individuals shows how quickly scientists are applying new discoveries. Every new understanding of metabolic pathways that leads to a new diagnostic tool gives clinicians and the patients they treat more information about the best therapies to select.
For the anatomic pathology profession, this shows how ongoing research into the genetic makeup of prostate cancer is unlocking knowledge about the genetic and metabolic pathways involved in this type of cancer. Not only does this help in diagnosis, but it can guide the selection of appropriate therapies.
On the wider picture, the research at the Princess Margaret Cancer Centre is one more example of how scientists are rapidly applying new knowledge about molecular and genetic processes in the human body to identify new ways to more accurately diagnose disease and select therapies.
—Dava Stewart
Related Information:
Genomic Hallmarks of Localized, Non-Indolent Prostate Cancer
Newly Discovered Genetic Fingerprint for Prostate Cancer Promises to Personalize Treatment
Prostate Cancer Team Cracks Genetic Code to Show Why Inherited Disease Can Turn Lethal
PARP Inhibitors May Be Effective in Brain, Other Caners with IDH Mutations
Chemosensitivity of IDH1-Mutated Gliomas Due to an Impairment in PARP1-Mediated DNA Repair
2-Hydroxyglutarate Produced by Neomorphic IDH Mutations Suppresses Homologous Recombination and Induces PARP Inhibitor Sensitivity
Prostate Cancer Researchers Find Genetic Fingerprint Identifying How, When Disease Spreads
Scientists Identify DNA Signature Linked to Prostate Cancer Severity
Sep 14, 2016 | Compliance, Legal, and Malpractice, Laboratory News, Laboratory Pathology, Laboratory Testing
Two new studies show patients are being increasingly burdened with a greater share of healthcare costs, which requires providers, including medical labs, to collect more money from patients at time of service
Although wage increases remain stagnant, consumers now pay a steadily increasing share of their healthcare costs. That’s because of rising deductibles, co-insurance, and other out-of-pocket costs. Not only will this cost-sharing trend continue to stretch patients’ budgets, it also will apply more pressure on clinical laboratories and pathology groups to increase price transparency for patients.
A recent study at the University of Michigan (UM), published in the Journal of the American Medical Association (JAMA), highlighted the growth in out-of-pocket insurance costs for hospitalized patients. For the average consumer with private health insurance, costs rose from $738 in 2009 to $1,013 in 2013—a 37% increase. During that same 4-year period, overall healthcare spending grew at 2.9% per year and health insurance premiums went up 5.1% annually.
Two types of health insurance plan charges were responsible for the biggest change in out-of-pocket spending: deductibles and co-insurance. During the same period, deductibles rose by 86%! Co-insurance costs increased 33% over the same period. Co-payments (a flat fee) were used in fewer hospitalizations. (more…)
Jun 8, 2016 | Digital Pathology, Instruments & Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing
U.S. Patent and Trademark Office will hold hearings to determine whether University of California Berkeley, or Broad Institute of Harvard and MIT, should receive patents for new genomic engineering technique
In the race to master gene-editing in ways that will advance genetic medicine and patient care, one of the hottest technologies is CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. But now a patent fight has the potential to complicate how pathologists and other scientists use this exciting technology.
This dispute over the CRISPR patent—a tool that has been hailed as one of the biggest biotech breakthroughs of the decade—will likely be settled in the coming months by the United States Patent and Trademark Office (USPTO).
The USPTO will be reviewing key patents awarded for what is called CRISPR/Cas9. The technology is already generating novel therapies for diseases, which should create new opportunities for pathologists and medical laboratories. (more…)
Nov 13, 2015 | Laboratory Instruments & Laboratory Equipment, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Lab-on-a-chip technology could reduce the time needed to identify infection-causing bacteria and for physicians to prescribe correct antibiotics
Pathology groups and medical laboratories may see their role in the patient-care process grow if researchers succeed in developing culture-independent diagnostic tools that quickly identify bacterial infections as well as pinpoint the antibiotics needed to treat them.
In the battle against antibiotic-resistant infections (AKA “super bugs”) the National Institutes of Health (NIH) is funding nine research projects aimed at thwarting the growing problem of life-threatening infections that no longer are controlled or killed by today’s arsenal of drugs.
Common Practices in Hospitals Leading to Super Bugs
Currently, when infections are suspected in hospitals or other settings where illness can quickly spread, samples are sent to a central medical laboratory where it may take up to three days to determine what germ is causing the infection. Because of that delay, physicians often prescribe broad-spectrum antibiotics based on a patient’s symptoms rather than lab test results, a practice that can lead to the growth of antibiotic-resistant microbes. (more…)
