VCU scientists used the technique to measure mutations associated with acute myeloid leukemia, potentially offering an attractive alternative to DNA sequencing
More accurate but less-costly cancer diagnostics are the Holy Grail of cancer research. Now, research scientists at Virginia Commonwealth University (VCU) say they have developed a clinical laboratory diagnostic technique that could be far cheaper and more capable than standard DNA sequencing in diagnosing some diseases. Their method combines digital polymerase chain reaction (dPCR) technology with high-speed atomic force microscopy (HS-AFM) to generate nanoscale-resolution images of DNA.
The technique allows the researchers to measure polymorphisms—variations in gene lengths—that are associated with many cancers and neurological diseases. The VCU scientists say the new technique costs less than $1 to scan each dPCR reaction.
“We chose to focus on FLT3 mutations because they are difficult to [diagnose], and the standard assay is limited in capability,” said physicist Jason Reed, PhD, Assistant Professor in the Virginia Commonwealth University Department of Physics, in a VCU press release.
Reed is an expert in nanotechnology as it relates to biology and medicine. He led a team that included other researchers in VCU’s physics department as well as physicians from VCU Massey Cancer Center and the Department of Internal Medicine at VCU School of Medicine.
“The technology needed to detect DNA sequence rearrangements is expensive and limited in availability, yet medicine increasingly relies on the information it provides to accurately diagnose and treat cancers and many other diseases,” said Jason Reed, PhD (above center, with Andrey Mikheikin, PhD, on left and Sean Koebley, PhD, on right), in a press release from Virginia Commonwealth University (VCU). “We’ve developed a system that combines a routine laboratory process with an inexpensive yet powerful atomic microscope that provides many benefits over standard DNA sequencing for this application, at a fraction of the cost.” (Photo copyright: Virginia Commonwealth University.)
Validating the Clinical Laboratory Test
The physicists worked with two VCU physicians—hematologist/oncologist Amir Toor, MD, and hematopathologist Alden Chesney, MD—to compare the imaging technique to the LeukoStrat CDx FLT3 Mutation Assay, which they described as the “current gold standard test” for diagnosing FLT3 gene mutations.
The researchers said their technique matched the results of the LeukoStrat test in diagnosing the mutations. But unlike that test, the new technique also can measure variant allele frequency (VAL). This “can show whether the mutation is inherited and allows the detection of mutations that could potentially be missed by the current test,” states the VCU press release.
“We plan to continue developing and testing this technology in other diseases involving DNA structural mutations,” Reed said. “We hope it can be a powerful and cost-effective tool for doctors around the world treating cancer and other devastating diseases driven by DNA mutations.”
“In our approach we first used digital PCR, in which a mixed sample is diluted to less than one target molecule per aliquot and the aliquots are amplified to yield homogeneous populations of amplicons,” he said. “Then, we deposited each population onto an atomically-flat partitioned surface.”
The VCU researchers “scanned each partition with high-speed atomic force microscopy, in which an extremely sharp tip is rastered across the surface, returning a 3D map of the surface with nanoscale resolution,” he said. “We wrote code that traced the length of each imaged DNA molecule, and the distribution of lengths was used to determine whether the aliquot was a wild type [unmutated] or variant.”
In Diagnostics World, Reed said the method “doesn’t really have any more complexity than a PCR assay itself. It can easily be done by most lab technicians.”
Earlier Research
A VCU press release from 2017 noted that Reed’s research team had developed technology that uses optical lasers (similar to those in a DVD player) to accelerate the scanning. The researchers previously published a study about the technique in Nature Communications, and a patent is currently pending.
“DNA sequencing is a powerful tool, but it is still quite expensive and has several technological and functional limitations that make it difficult to map large areas of the genome efficiently and accurately,” Reed said in the 2017 VCU press release. “Our approach bridges the gap between DNA sequencing and other physical mapping techniques that lack resolution. It can be used as a stand-alone method or it can complement DNA sequencing by reducing complexity and error when piecing together the small bits of genome analyzed during the sequencing process.”
Using CRISPR technology, the team also developed what they described as a “chemical barcoding solution,” placing markers on DNA molecules to identify genetic mutations.
New DNA Clinical Laboratory Testing?
Cancer diagnostics are constantly evolving and improving. It is not clear how long it will be before VCU’s new technique will reach clinical laboratories that perform DNA testing, if at all. But VCU’s new technique is intriguing, and should it prove viable for clinical diagnostic use it could revolutionize cancer diagnosis. It is a development worth watching.
The self-cleaning material has been proven to repel even the deadliest forms of antibiotic resistant (ABR) superbugs and viruses. This ultimate non-stick coating is a chemically treated form of transparent plastic wrap which can be adhered to surfaces prone to gathering germs, such as door handles, railings, and intravenous therapy (IV) stands.
“We developed the wrap to address the major threat that is posed by multi-drug resistant bacteria,” Leyla Soleymani, PhD, Associate Professor at McMaster University and one of the leaders of the study, told CNN. “Given the limited treatment options for these bugs, it is key to reduce their spread from one person to another.”
According to research published in the peer-reviewed Southern Medical Journal, “KPC-producing bacteria are a group of emerging highly drug-resistant Gram-negative bacilli causing infections associated with significant morbidity and mortality.”
Were those surfaces covered in this new bacterial-resistant
coating, life-threatening infections in hospital ICUs could be prevented.
Taking Inspiration from Nature
In designing their new anti-microbial wrap, McMaster researchers took their inspiration from natural lotus leaves, which are effectively water-resistant and self-cleaning thanks to microscopic wrinkles that repel external molecules. Substances that come in contact with surfaces covered in the new non-stick coating—such as a water, blood, or germs—simply bounce off. They do not adhere to the material.
The “shrink-wrap” is flexible, durable, and inexpensive to
manufacture. And, the researchers hope to locate a commercial partner to
develop useful applications for their discovery.
“We’re structurally tuning that plastic,” Soleymani told SciTechDaily. “This material gives us something that can be applied to all kinds of things.”
In the video above, Leyla Soleymani, PhD, Associate Professor at McMaster University, explains how “The new plastic surface—a treated form of conventional transparent wrap—can be shrink-wrapped onto door handles, railings, IV stands, and other surfaces that can be magnets for bacteria such as MRSA and C. difficile. This may be technology that has great value to clinical laboratories and microbiology laboratories. Click here to watch the video. (Image and video copyright: McMaster University/YouTube.)
Industries Outside of Healthcare Also Would Benefit
According to the US Centers for Disease Control and Prevention (CDC), at least 2.8 million people get an antibiotic-resistant infection in the US each year. More than 35,000 people die from these infections, making it one of the biggest health challenges of our time and a threat that needs to be eradicated. This innovative plastic coating could help alleviate these types of infections.
And it’s not just for healthcare. The researchers said the coating could be beneficial to the food industry as well. The plastic surface could help curtail the accidental transfer of bacteria, such as E. coli, Salmonella, and Listeria in food preparation and packaging, according to the published study.
“We can see this technology being used in all kinds of institutional and domestic settings,” Tohid Didar, PhD, Assistant Professor at McMaster University and co-author of the study, told SciTechDaily. “As the world confronts the crisis of anti-microbial resistance, we hope it will become an important part of the anti-bacterial toolbox.”
Clinical laboratories also are tasked with preventing the
transference of dangerous bacteria to patients and lab personnel. Constant
diligence in application of cleaning protocols is key. If this new anti-bacterial
shrink wrap becomes widely available, medical laboratory managers and
microbiologists will have a new tool to fight bacterial contamination.
Doctors may begin ordering FITs in greater numbers, increasing the demand on clinical laboratories to process these home tests
All clinical laboratory managers and pathologists know that timely screening for colon cancer is an effective way to detect cancer early, when it is easiest to treat. But, invasive diagnostic approaches such as colonoscopies are not popular with consumers. Now comes news of a large-scale study that indicates the non-invasive fecal immunochemical test (FIT) can be as effective as a colonoscopy when screening for colon cancer.
FITs performed annually may be as effective as colonoscopies at detecting colorectal cancer (CRC) for those at average risk of developing the disease. That’s the conclusion of a study conducted at the Regenstrief Institute, a private, non-profit research organization affiliated with the Indiana University School of Medicine in Indianapolis, Ind.
The researchers published their findings in the Annals of Internal Medicine (AIM), a journal published by the American College of Physicians (ACP). The team reviewed data from 31 previous studies. They then analyzed the test results from more than 120,000 average-risk patients who took a FIT and then had a colonoscopy. After comparing the results between the two tests, the researchers concluded that the FIT is a sufficient screening tool for colon cancer.
FIT is Easy, Safe, and Inexpensive
As a medical laboratory test, the FIT is low risk, non-invasive,
and inexpensive. In addition, the FIT can detect most cancers in the first
application, according to the Regenstrief Institute researchers. They recommend
that the FIT be performed on an annual basis for people at average risk for
getting colorectal cancers.
“This non-invasive test for colon cancer screening is available for average risk people,” Imperiale told NBC News. “They should discuss with their providers whether it is appropriate for them.”
FIT is performed in the privacy of the patient’s home. To
use the test, an individual collects a bowel specimen in a receptacle provided
in a FIT kit. They then send the specimen to a clinical laboratory for
evaluation. The FIT requires no special preparations and medicines and food do
not interfere with the test results.
Thomas Imperiale, MD (above), is a Lawrence Lumeng Professor of Gastroenterology and Hepatology at Indiana University School of Medicine, and a research scientist at the Regenstrief Institute. He led a study which concluded that FITs are as effective as colonoscopies at detecting cancer in average risk patient populations. Should these conclusions become widely accepted, doctors may begin ordering FITs in greater numbers, increasing the demand on clinical laboratories that process the tests. (Photo copyright: Indiana University School of Medicine.)
‘A Preventative Health Success Story’
The FIT can be calibrated to different sensitivities at the
lab when determining results. Imperiale and his team found that 95% of cancers
were detected when the FIT was set to a higher sensitivity, however, that
setting resulted in 10% false positives. At lower sensitivity the FIT produced
fewer false positives (5%), but also caught fewer cancers (75%). However, when
the FIT was performed every year, the cancer detection rate was similar at both
sensitivities over a two-year period.
“FIT is an excellent option for colon cancer screening only if it is performed consistently on a yearly basis,” Felice Schnoll-Sussman, MD, told NBC News. Sussman is a gastroenterologist and Professor of Clinical Medicine at Weill Cornell Medicine. “Colon cancer screening and its impact on decreasing rates of colon cancer is a preventative health success story, although we have a way to go to increase rates to our previous desired goal of 80% screened in the US by 2018.”
The FIT looks for hidden blood in the stool by detecting protein hemoglobin found in red blood cells. A normal result indicates that FIT did not detect any blood in the stool and the test should be repeated annually. If the FIT comes back positive for blood in the stool, other tests, such as a sigmoidoscopy or colonoscopy should be performed. Cancers in the colon may not always bleed and the FIT only detects blood from the lower intestines.
Patients are Skipping the Colonoscopy
Approximately 35% of individuals who should be receiving colonoscopies do not undergo the test, NBC News noted. The American Cancer Society (ACS) lists the top five reasons people don’t get screened for colorectal cancer are that they:
fear the test will be difficult or painful;
have no family history of the disease and feel
testing is unnecessary;
have no symptoms and think screening is only for
those with symptoms;
are concerned about the costs associated with
screening; and
they are concerned about the complexities of
taking the tests, including taking time off from work, transportation after the
procedure, and high out-of-pocket expenses.
“Colorectal cancer screening is one of the best opportunities to prevent cancer or diagnose it early, when it’s most treatable,” Richard Wender, MD, Chief Cancer Control Officer for the ACS stated in a press release. “Despite this compelling reason to be screened, many people either have never had a colorectal cancer screening test or are not up to date with screening.”
Colorectal cancer is the third most common cancer diagnosed in both men and women in the United States. The ACS estimates there will be 101,420 new cases of colon cancer and 44,180 new cases of rectal cancer diagnosed this year. The disease is expected to be responsible for approximately 51,020 deaths in 2019.
New cases of the disease have been steadily decreasing over
the past few decades in most age populations, primarily due to early screening.
However, the overall death rate among people younger than age 55 has increased
1% per year between 2007 and 2016. The ACS estimates there are now more than
one million colorectal cancer survivors living in the US.
The ACS recommends that average-risk individuals start
regular colorectal cancer screenings at age 45. The five-year survival rate for
colon cancer patients is 90% when there is no sign that the cancer has spread
outside the colon.
Clinical laboratory professionals may find it unpleasant to
test FIT specimens. Opening the specimen containers and extracting the samples
can be messy and malodorous. However, FITs are essential, critical tests that
can save many lives.
